Echini

@misc{agassiz1872revision,
    author = "Agassiz, Alexander",
    title = "Revision of the Echini / by Alexander Agassiz",
    year = "1872",
    url = "https://doi.org/10.5962/bhl.title.40080",
    doi = "10.5962/bhl.title.40080",
    openalex = "W2479287064"
}

@article{crossref1873revision,
    title = "Revision of the Echini Illustrated Catalogue of the Museum of Comparative Zoology at Harvard College. No. Vii. Revision of the Echini. Alexander Agassiz",
    year = "1873",
    journal = "The American Naturalist",
    url = "https://doi.org/10.1086/271121",
    doi = "10.1086/271121",
    number = "4",
    openalex = "W4236833109",
    pages = "224-226",
    volume = "7"
}

@article{crossref1874revision,
    title = "Revision of the Echini. Alexander Agassiz",
    year = "1874",
    journal = "The American Naturalist",
    url = "https://doi.org/10.1086/271299",
    doi = "10.1086/271299",
    number = "4",
    openalex = "W4236861180",
    pages = "215-215",
    volume = "8"
}

This unassuming looking little volume is the single most influential scientific work of the 19th century. Darwin’s first publication of his theory of evolution was written for non-specialists and it attracted widespread and immediate interest. Darwin was an eminent scientist; his findings were taken seriously and the evidence he presented generated scientific, philosophical, and religious discussion. Within two decades there was general scientific agreement that evolution, with a branching pattern of common descent, had occurred, but scientists were slow to give natural selection the significance that Darwin thought appropriate. With the development of the modern evolutionary synthesis in the 1930s and 1940s, Darwin's concept of evolutionary adaptation through natural selection became central to modern evolutionary theory, and it has now become the unifying concept of the life sciences.

@article{doi101093nqs9viii207495b,
    title = "The Origin of Species by Means of Natural Selection",
    year = "1901",
    journal = "Notes and Queries",
    abstract = "This unassuming looking little volume is the single most influential scientific work of the 19th century. Darwin’s first publication of his theory of evolution was written for non-specialists and it attracted widespread and immediate interest. Darwin was an eminent scientist; his findings were taken seriously and the evidence he presented generated scientific, philosophical, and religious discussion. Within two decades there was general scientific agreement that evolution, with a branching pattern of common descent, had occurred, but scientists were slow to give natural selection the significance that Darwin thought appropriate. With the development of the modern evolutionary synthesis in the 1930s and 1940s, Darwin's concept of evolutionary adaptation through natural selection became central to modern evolutionary theory, and it has now become the unifying concept of the life sciences.",
    url = "https://doi.org/10.1093/nq/s9-viii.207.495b",
    doi = "10.1093/nq/s9-viii.207.495b",
    openalex = "W4243601689"
}

@book{doi105962bhltitle4630,
    author = "Jackson, Robert T.",
    title = "Phylogeny of the Echini, with a revision of Palaeozoic species",
    year = "1912",
    journal = "Memoirs read before the Boston Society of Natural History",
    url = "https://doi.org/10.5962/bhl.title.4630",
    doi = "10.5962/bhl.title.4630",
    openalex = "W658384462"
}

@misc{jackson1912phylogeny,
    author = "Jackson, Robert Tracy",
    title = "Phylogeny of the Echini, with a revision of Palaezoic species",
    year = "1912",
    url = "https://doi.org/10.5962/bhl.title.28491",
    doi = "10.5962/bhl.title.28491",
    openalex = "W4206354819"
}

@misc{jackson1912phylogeny1,
    author = "Jackson, R. T",
    title = "Phylogeny of the echini, with a revision of the Paleozoic species",
    year = "1912",
    howpublished = "Boston Society of Natural History, Memoirs, v. 7, p. 1-491",
    note = "talkorigins\_source = {true}; raw\_reference = {Jackson, R. T., 1912, Phylogeny of the echini, with a revision of the Paleozoic species: Boston Society of Natural History, Memoirs, v. 7, p. 1-491.}"
}

Crinoids are marine invertebrates of unsurpassed variety of form and complexity of skeletal organization. They range from Early Ordovician time to the present, but their development in kinds and numbers culminated during the Paleozoic.

@incollection{doi101130spe46p1,
    author = "Moore, Raymond C. and Laudon, L. R.",
    title = "Evolution and Classification of Paleozoic Crinoids",
    year = "1943",
    booktitle = "Geological Society of America Special Papers",
    abstract = "Crinoids are marine invertebrates of unsurpassed variety of form and complexity of skeletal organization. They range from Early Ordovician time to the present, but their development in kinds and numbers culminated during the Paleozoic.",
    url = "https://doi.org/10.1130/spe46-p1",
    doi = "10.1130/spe46-p1",
    openalex = "W2339692250"
}

@misc{sando1965revision,
    author = "Sando, W.J.",
    title = "Revision of some Paleozoic coral species from the Western United States",
    year = "1965",
    booktitle = "Professional Paper",
    url = "https://doi.org/10.3133/pp503e",
    doi = "10.3133/pp503e",
    openalex = "W950288184"
}

@article{doi101007bf01796042,
    author = "Fitch, Walter M. and Farris, James S.",
    title = "Evolutionary trees with minimum nucleotide replacements from amino acid sequences",
    year = "1974",
    journal = "Journal of Molecular Evolution",
    url = "https://doi.org/10.1007/bf01796042",
    doi = "10.1007/bf01796042",
    openalex = "W2024977466"
}

Many evolutionary trends are described in the post-Paleozoic echinoids and their functional advantages are discussed. In the ambulacra, the compound plate first appeared in the Late Triassic, becoming more pronounced during the Mesozoic, and reaching its zenith in the Cenozoic. Compounding enabled the echinoid to have more numerous tubefeet, strengthened the test, and increased the size of the ambulacral tubercles and spines. These larger spines provided greater protection from predators and faster locomotion. Petals first appeared in the Middle Jurassic and were developed for more efficient respiration. The first depressed petals occurred in the Late Jurassic, and by Late Cretaceous many echinoids had depressed petals culminating in deep petals in the Cenozoic. These depressions channeled water over the respiratory tubefeet, increased the width of the ambulacra and their tubefeet, and enabled these tubefeet to be protected from predators by the arching of spines over them. An anterior groove is slightly developed by the Middle Jurassic, distinct in the Cretaceous, and deepest in the Cenozoic. This groove provided a passage for food, and shelter for the large penicillate tubefeet. Phyllodes first occur in the Lower Jurassic in both the regular and irregular echinoids. During the Mesozoic the number of pores in the phyllodes in the irregular echinoids was reduced, and in most species one pore was eliminated of a porepair. The phyllodes provided a large number of feeding tubefeet near the peristome. In the apical system of the irregular echinoids, the periproct broke out during the Lower Jurassic. Its movement posteriorly served to separate the echinoid's excrement from its feeding and respiratory areas. The number of genital plates was reduced to a single plate in the cassiduloids by the Late Cretaceous, but this reduction occurred later in the holasteroids and spatangoids; many species living today have more than one genital plate. The Triassic and Early Jurassic echinoids were small; but during the latter part of the Jurassic, larger species occur, particularly among the irregulars and echinothurioids. All the Triassic echinoids except one were circular in marginal outline, but during the Jurassic the test in many irregulars became elongate enabling the echinoid to develop unidirectional movement. The flattening of the test permitted the echinoid to cover its test more easily, making the animal less conspicuous, less affected by wave motion, and placing more of the food-gathering tubefeet in contact with the seafloor. The Triassic lantern had grooved teeth and a shallow foramen, but by the Lower Jurassic some lanterns had a deeper foramen magnum. By the Middle Jurassic keeled teeth are present, and by the Late Cretaceous some lanterns have joined epiphyses. These changes permitted the lantern to be more mobile and strengthened the teeth and epiphyses. The lantern supports in all Triassic echinoids are outgrowths of interambulacral plates, but in the Lower Jurassic many species have ambulacral supports. By the Middle Jurassic these supports are joined together in some species to form an arch. These changes also increased the mobility and power of movement of the lantern. Gill notches first appeared in the Lower Jurassic (Hettangian) and were well developed by the Toarcian. The tubercles and their spines were large in the Triassic and gradually decreased in size in some species through the Mesozoic. This reduction enabled these echinoids with smaller spines to cover their tests with sediment. The rate of introduction of new plates was low in the Triassic, increasing during the Jurassic. This increase was mainly in the ambulacra and served to increase the number of tubefeet. Among the holasteroids-spatangoids some of the ventral interambulacral plates increased in size relative to adjacent plates during the Mesozoic and Cenozoic forming the labrum and plastron. These changes permitted the development of the “heart-shaped” test, and an anterior shift of the peristome. Diversity of echinoids increased since the Triassic with the development of different kinds of echinoids able to inhabit many varied habitats. All Triassic echinoids lived on top of the substrate, but in the Jurassic irregular echinoids began to burrow in the sediment. They increased in number of species during the Mesozoic and now are more numerous in species than the regular echinoids. The difference between Jurassic and Triassic species is not as abrupt as formerly thought, and all Jurassic echinoids are considered to have had a cidaroid ancestor.

@article{doi101017s0022336000061321,
    author = "Kier, Porter M.",
    title = "Evolutionary Trends and Their Functional Significance in the Post-Paleozoic Echinoids",
    year = "1974",
    journal = "Journal of Paleontology",
    abstract = "Many evolutionary trends are described in the post-Paleozoic echinoids and their functional advantages are discussed. In the ambulacra, the compound plate first appeared in the Late Triassic, becoming more pronounced during the Mesozoic, and reaching its zenith in the Cenozoic. Compounding enabled the echinoid to have more numerous tubefeet, strengthened the test, and increased the size of the ambulacral tubercles and spines. These larger spines provided greater protection from predators and faster locomotion. Petals first appeared in the Middle Jurassic and were developed for more efficient respiration. The first depressed petals occurred in the Late Jurassic, and by Late Cretaceous many echinoids had depressed petals culminating in deep petals in the Cenozoic. These depressions channeled water over the respiratory tubefeet, increased the width of the ambulacra and their tubefeet, and enabled these tubefeet to be protected from predators by the arching of spines over them. An anterior groove is slightly developed by the Middle Jurassic, distinct in the Cretaceous, and deepest in the Cenozoic. This groove provided a passage for food, and shelter for the large penicillate tubefeet. Phyllodes first occur in the Lower Jurassic in both the regular and irregular echinoids. During the Mesozoic the number of pores in the phyllodes in the irregular echinoids was reduced, and in most species one pore was eliminated of a porepair. The phyllodes provided a large number of feeding tubefeet near the peristome. In the apical system of the irregular echinoids, the periproct broke out during the Lower Jurassic. Its movement posteriorly served to separate the echinoid's excrement from its feeding and respiratory areas. The number of genital plates was reduced to a single plate in the cassiduloids by the Late Cretaceous, but this reduction occurred later in the holasteroids and spatangoids; many species living today have more than one genital plate. The Triassic and Early Jurassic echinoids were small; but during the latter part of the Jurassic, larger species occur, particularly among the irregulars and echinothurioids. All the Triassic echinoids except one were circular in marginal outline, but during the Jurassic the test in many irregulars became elongate enabling the echinoid to develop unidirectional movement. The flattening of the test permitted the echinoid to cover its test more easily, making the animal less conspicuous, less affected by wave motion, and placing more of the food-gathering tubefeet in contact with the seafloor. The Triassic lantern had grooved teeth and a shallow foramen, but by the Lower Jurassic some lanterns had a deeper foramen magnum. By the Middle Jurassic keeled teeth are present, and by the Late Cretaceous some lanterns have joined epiphyses. These changes permitted the lantern to be more mobile and strengthened the teeth and epiphyses. The lantern supports in all Triassic echinoids are outgrowths of interambulacral plates, but in the Lower Jurassic many species have ambulacral supports. By the Middle Jurassic these supports are joined together in some species to form an arch. These changes also increased the mobility and power of movement of the lantern. Gill notches first appeared in the Lower Jurassic (Hettangian) and were well developed by the Toarcian. The tubercles and their spines were large in the Triassic and gradually decreased in size in some species through the Mesozoic. This reduction enabled these echinoids with smaller spines to cover their tests with sediment. The rate of introduction of new plates was low in the Triassic, increasing during the Jurassic. This increase was mainly in the ambulacra and served to increase the number of tubefeet. Among the holasteroids-spatangoids some of the ventral interambulacral plates increased in size relative to adjacent plates during the Mesozoic and Cenozoic forming the labrum and plastron. These changes permitted the development of the “heart-shaped” test, and an anterior shift of the peristome. Diversity of echinoids increased since the Triassic with the development of different kinds of echinoids able to inhabit many varied habitats. All Triassic echinoids lived on top of the substrate, but in the Jurassic irregular echinoids began to burrow in the sediment. They increased in number of species during the Mesozoic and now are more numerous in species than the regular echinoids. The difference between Jurassic and Triassic species is not as abrupt as formerly thought, and all Jurassic echinoids are considered to have had a cidaroid ancestor.",
    url = "https://doi.org/10.1017/s0022336000061321",
    doi = "10.1017/s0022336000061321",
    openalex = "W2947356994",
    references = "doi101017s0025315400017574, doi101098rstb19590007, doi101126science17740541065, doi105962bhltitle11376, doi105962bhltitle30642, doi105962bhltitle4630, doi105962bhltitle54256, openalexw137635259, openalexw1522518756, openalexw2603113571"
}

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.

@article{doi105281zenodo16046014,
    author = "Smith, Andrew B.",
    title = "Implications of lantern morphology for the phylogeny of post-Palaeozoic echinoids",
    year = "1981",
    journal = "Biodiversity Heritage Library (Smithsonian Institution)",
    abstract = "(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.",
    url = "https://doi.org/10.5281/zenodo.16046014",
    doi = "10.5281/zenodo.16046014",
    openalex = "W2951959006"
}

Summary 1. Living echinoderms are characterized by an extensive water vascular system developed from the larval left hydrocoel, a complex, multi‐plated endoskeleton with stereom structure, and pentamery. Fossil evidence shows that stereom evolved before pentamery, but both were acquired during the Lower Cambrian. 2. Cladistic analysis of Lower Cambrian genera reveals very few characters in common between carpoids and true echinoderms, and that the split between them was the first fundamental evolutionary dichotomy within the Dexiothetica. 3. Helicoplacoids are stem group echinoderms with spiral plating and three ambulacra arranged radially around a lateral mouth. They are the most primitive echinoderms and the first to show a radial arrangement of the water vascular and ambulacral systems. Unlike later echinoderms, their skeleton shows no dorsal/ventral (aboral/oral) differentiation. They were probably sedentary suspension feeders. 4. Camptostroma is the most primitive known pentaradiate echinoderm and, in our view, possibly a common ancestor of all living groups. It had a short conical dorsal (aboral) surface with imbricate plating, a ridged lateral wall and a slightly domed ventral (oral) surface with five curved ambulacra in a 2‐1‐2 arrangement inherited from the triradiate pattern of the helicoplacoids. Interambulacral areas bore epispires and the CD interambulacrum contained the anus, hydropore and/or gonopore. All parts of the theca had plates in at least two layers. 5. All other echinoderms belong to one of two monophyletic subphyla, the Pelmatozoa and the Eleutherozoa. 6. Stromatocystites is the earliest known eleutherozoan and differs from Camptostroma in having a test with only one layer of plates and having lost the dorsal elongation. In Stromatocystites the dorsal surface is flat and the plating tesselate. Stromatocystites was an unattached, low‐level suspension feeder. 7. The lepidocystoids are the earliest known pelmatozoans. They differ from Camptostroma in having an attached dorsal stalk which retained the primitive imbricate plating, and by developing erect feeding structures along the ambulacra. In Kinzercystis, the ambulacra are confined to the thecal surface and erect, biserial brachioles arise alternately on either side. Lepidocystis has a similar arrangement except that, the distal part of each ambulacrum extends beyond the edge of the theca as a free arm. 8. Pelmatozoans diverged more or less immediately into crinoids, with multiple free arms composed of uniserial plates, and cystoids sensu lato, which retained brachioles. Gogia (Lower to Middle Cambrian) is the most primitive known cystoid and differs from Kinzercystis principally in having all plating tesselate, while Echmatocrinus (Middle Cambrian) is the most primitive known crinoid and differs from Lepidocystis in lacking brachioles and in having more than five free arms with uniserial plates. 9. Post Lower Cambrian differentiation of pelmatozoan groups proceeded rapidly, exploiting the primitive suspension‐feeding mode of life. Maximum morphological diversity was reached in the Ordovician, but thereafter crinoids progressively displaced cystoid groups and reached their peak diversity during the Carboniferous. The eleutherozoans were slower to diversify, but by the Arenig the earliest ‘sea‐stars’ (in reality, advanced members of the eleutherozoan stem group) had reversed their living orientation and had begun to exploit a deposit‐feeding mode of life. These in turn led to the ophiuroids, echinoids and holothuroids. 10. The basic echinoderm ambulacrum was already present in the helicoplacoids. It had biserial, alternate flooring plates and complexly plated sheets of cover plates on either side. The radial water vessel lay in the floor of the ambulacrum, external to the body cavity, and gave rise ventrally to short, lateral branches (fore‐runners of tube feet) that were used to open the cover plate sheets, and dorsally was connected to internal compensation sacs which acted as fluid reservoirs (and were preadapted for a role in gaseous exchange). Plating on the cover plate sheets was organized and reflected the positions of the lateral branches from the radial water vessel. In Camptostroma, the cover plate sheets had biserially aligned rows of cover plates associated with the lateral branches. 11. Brachioles arose by extension of the lateral branches of the radial water vessel and associated serially aligned cover plates found in Camptostroma. They bear a single alternate series of cover plates. In Lepidocystis the ambulacra extended beyond the edge of the oral surface as true arms. Brachial plates of arms are homologues of primary ambulacral flooring plates, and arms bear multiple series of cover plates. Uniserial ambulacral plating is a derived condition and evolved independently in crinoids, paracrinoids and isorophid edrioasteroids. Pinnules in crinoids arose independently in inadunates and camerates by a progressively more unequal branching of the arms. Thus all parts of the subvective system in crinoids are internally homologous, whereas in cystoids, brachioles and arms (or ambulacra) are not homologous structures. 12. The position of the hydropore is the best reference point in orientating echinoderms. Carpenter's system of identifying ambulacra by letters, arranged clock‐wise in oral view with the A ambulacrum opposite the hydropore, is consistent in all echinoderm classes. In all Lower Cambrian pentaradiate echinoderms the anus, gonopore and hydropore lie in the CD interambulacrum and this is accepted as the primitive arrangement. In helicoplacoids we tentatively suggest that the A ambulacrum spiralled down from the mouth while the two ambulacra that spiralled up represent the B + C and D + E ambulacra combined. 13. The pelmatozoan stem arose from a polyplated stalk, via a meric stem to a true column with holomeric (single piece) columnals. This happened independently in the crinoids and the cystoids. 14. Our analysis of echinoderm phylogeny leads us to recommend the following changes to the higher level classification of echinoderms: The phylum Echinodermata includes only those groups with radial symmetry superimposed upon a fundamental larval asymmetry. It has a stem group that contains the triradiate helicoplacoids and a crown group to which all other (pentaradiate) echinoderms belong. The crown group contains two monophyletic subphyla, the Pelmatozoa and the Eleutherozoa, and the Pelmatozoa contains two superclasses, the Crinoidea which are extant and the Cystoidea, which are extinct.

@article{doi101111j1469185x1984tb00411x,
    author = "Paul, C. R. C. and Smith, A. B.",
    title = "THE EARLY RADIATION AND PHYLOGENY OF ECHINODERMS",
    year = "1984",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Summary 1. Living echinoderms are characterized by an extensive water vascular system developed from the larval left hydrocoel, a complex, multi‐plated endoskeleton with stereom structure, and pentamery. Fossil evidence shows that stereom evolved before pentamery, but both were acquired during the Lower Cambrian. 2. Cladistic analysis of Lower Cambrian genera reveals very few characters in common between carpoids and true echinoderms, and that the split between them was the first fundamental evolutionary dichotomy within the Dexiothetica. 3. Helicoplacoids are stem group echinoderms with spiral plating and three ambulacra arranged radially around a lateral mouth. They are the most primitive echinoderms and the first to show a radial arrangement of the water vascular and ambulacral systems. Unlike later echinoderms, their skeleton shows no dorsal/ventral (aboral/oral) differentiation. They were probably sedentary suspension feeders. 4. Camptostroma is the most primitive known pentaradiate echinoderm and, in our view, possibly a common ancestor of all living groups. It had a short conical dorsal (aboral) surface with imbricate plating, a ridged lateral wall and a slightly domed ventral (oral) surface with five curved ambulacra in a 2‐1‐2 arrangement inherited from the triradiate pattern of the helicoplacoids. Interambulacral areas bore epispires and the CD interambulacrum contained the anus, hydropore and/or gonopore. All parts of the theca had plates in at least two layers. 5. All other echinoderms belong to one of two monophyletic subphyla, the Pelmatozoa and the Eleutherozoa. 6. Stromatocystites is the earliest known eleutherozoan and differs from Camptostroma in having a test with only one layer of plates and having lost the dorsal elongation. In Stromatocystites the dorsal surface is flat and the plating tesselate. Stromatocystites was an unattached, low‐level suspension feeder. 7. The lepidocystoids are the earliest known pelmatozoans. They differ from Camptostroma in having an attached dorsal stalk which retained the primitive imbricate plating, and by developing erect feeding structures along the ambulacra. In Kinzercystis, the ambulacra are confined to the thecal surface and erect, biserial brachioles arise alternately on either side. Lepidocystis has a similar arrangement except that, the distal part of each ambulacrum extends beyond the edge of the theca as a free arm. 8. Pelmatozoans diverged more or less immediately into crinoids, with multiple free arms composed of uniserial plates, and cystoids sensu lato, which retained brachioles. Gogia (Lower to Middle Cambrian) is the most primitive known cystoid and differs from Kinzercystis principally in having all plating tesselate, while Echmatocrinus (Middle Cambrian) is the most primitive known crinoid and differs from Lepidocystis in lacking brachioles and in having more than five free arms with uniserial plates. 9. Post Lower Cambrian differentiation of pelmatozoan groups proceeded rapidly, exploiting the primitive suspension‐feeding mode of life. Maximum morphological diversity was reached in the Ordovician, but thereafter crinoids progressively displaced cystoid groups and reached their peak diversity during the Carboniferous. The eleutherozoans were slower to diversify, but by the Arenig the earliest ‘sea‐stars’ (in reality, advanced members of the eleutherozoan stem group) had reversed their living orientation and had begun to exploit a deposit‐feeding mode of life. These in turn led to the ophiuroids, echinoids and holothuroids. 10. The basic echinoderm ambulacrum was already present in the helicoplacoids. It had biserial, alternate flooring plates and complexly plated sheets of cover plates on either side. The radial water vessel lay in the floor of the ambulacrum, external to the body cavity, and gave rise ventrally to short, lateral branches (fore‐runners of tube feet) that were used to open the cover plate sheets, and dorsally was connected to internal compensation sacs which acted as fluid reservoirs (and were preadapted for a role in gaseous exchange). Plating on the cover plate sheets was organized and reflected the positions of the lateral branches from the radial water vessel. In Camptostroma, the cover plate sheets had biserially aligned rows of cover plates associated with the lateral branches. 11. Brachioles arose by extension of the lateral branches of the radial water vessel and associated serially aligned cover plates found in Camptostroma. They bear a single alternate series of cover plates. In Lepidocystis the ambulacra extended beyond the edge of the oral surface as true arms. Brachial plates of arms are homologues of primary ambulacral flooring plates, and arms bear multiple series of cover plates. Uniserial ambulacral plating is a derived condition and evolved independently in crinoids, paracrinoids and isorophid edrioasteroids. Pinnules in crinoids arose independently in inadunates and camerates by a progressively more unequal branching of the arms. Thus all parts of the subvective system in crinoids are internally homologous, whereas in cystoids, brachioles and arms (or ambulacra) are not homologous structures. 12. The position of the hydropore is the best reference point in orientating echinoderms. Carpenter's system of identifying ambulacra by letters, arranged clock‐wise in oral view with the A ambulacrum opposite the hydropore, is consistent in all echinoderm classes. In all Lower Cambrian pentaradiate echinoderms the anus, gonopore and hydropore lie in the CD interambulacrum and this is accepted as the primitive arrangement. In helicoplacoids we tentatively suggest that the A ambulacrum spiralled down from the mouth while the two ambulacra that spiralled up represent the B + C and D + E ambulacra combined. 13. The pelmatozoan stem arose from a polyplated stalk, via a meric stem to a true column with holomeric (single piece) columnals. This happened independently in the crinoids and the cystoids. 14. Our analysis of echinoderm phylogeny leads us to recommend the following changes to the higher level classification of echinoderms: The phylum Echinodermata includes only those groups with radial symmetry superimposed upon a fundamental larval asymmetry. It has a stem group that contains the triradiate helicoplacoids and a crown group to which all other (pentaradiate) echinoderms belong. The crown group contains two monophyletic subphyla, the Pelmatozoa and the Eleutherozoa, and the Pelmatozoa contains two superclasses, the Crinoidea which are extant and the Cystoidea, which are extinct.",
    url = "https://doi.org/10.1111/j.1469-185x.1984.tb00411.x",
    doi = "10.1111/j.1469-185x.1984.tb00411.x",
    openalex = "W2111237039",
    references = "doi101007bf03160383, doi101007bf03190413, doi1010160012825280900641, doi101098rstb19630010, doi101111j1469185x1979tb00845x, doi101126science1403568820, doi101146annurevea03050175000455, doi103133ofr81743, doi105281zenodo16118842, doi105962bhltitle66379, openalexw3034464084, openalexw3157064287"
}

Comparative studies of the relationship between two phenotypes, or between a phenotype and an environment, are frequently carried out by invalid statistical methods. Most regression, correlation, and contingency table methods, including nonparametric methods, assume that the points are drawn independently from a common distribution. When species are taken from a branching phylogeny, they are manifestly nonindependent. Use of a statistical method that assumes independence will cause overstatement of the significance in hypothesis tests. Some illustrative examples of these phenomena have been given, and limitations of previous proposals of ways to correct for the nonindependence have been discussed. A method of correcting for the phylogeny has been proposed. It requires that we know both the tree topology and the branch lengths, and that we be willing to allow the characters to be modeled by Brownian motion on a linear scale. Given these conditions, the phylogeny specifies a set of contrasts among species, contrasts that are statistically independent and can be used in regression or correlation studies. The considerable barriers to making practical use of this technique have been discussed.

@article{doi101086284325,
    author = "Felsenstein, Joseph",
    title = "Phylogenies and the Comparative Method",
    year = "1985",
    journal = "The American Naturalist",
    abstract = "Comparative studies of the relationship between two phenotypes, or between a phenotype and an environment, are frequently carried out by invalid statistical methods. Most regression, correlation, and contingency table methods, including nonparametric methods, assume that the points are drawn independently from a common distribution. When species are taken from a branching phylogeny, they are manifestly nonindependent. Use of a statistical method that assumes independence will cause overstatement of the significance in hypothesis tests. Some illustrative examples of these phenomena have been given, and limitations of previous proposals of ways to correct for the nonindependence have been discussed. A method of correcting for the phylogeny has been proposed. It requires that we know both the tree topology and the branch lengths, and that we be willing to allow the characters to be modeled by Brownian motion on a linear scale. Given these conditions, the phylogeny specifies a set of contrasts among species, contrasts that are statistically independent and can be used in regression or correlation studies. The considerable barriers to making practical use of this technique have been discussed.",
    url = "https://doi.org/10.1086/284325",
    doi = "10.1086/284325",
    openalex = "W2013410948",
    references = "doi101007bf01734359, doi101038290699a0, doi101038293057a0, doi101093sysbio274401, doi101111j155856461981tb04991x, doi101126science1864167892, doi101126science6407108, doi101146annureves14110183001525, openalexw191281502, openalexw3045142570"
}

A revised classification and phylogeny at the family level and above are presented for post-Palaeozoic sea stars. Monophyly of the group is established by a character suite taken from the ambulacral column that thus far has been recognized in only one Palaeozoic genus. Compared to earlier studies, character selection here placed relatively greater emphasis on morphology and arrangement of ossicles and ossicular systems. Functional implications of many features are surveyed. Thirty-four families, three extinct, are recognized and a number of older familial concepts are suppressed; the extinct Trichasteropsidae is proposed. Superfamilies are recognized for the Valvatida. Eight orders, including the new, extinct Trichasteropsida, and three superorders are recognized. No living sea star is primitive in the sense of being close to ancestral sea stars and other echinoderm groups; the Paxillosida, which commonly has been considered primitive, is here considered specialized.

@article{doi10108000222938700771141,
    author = "Blake, Daniel B.",
    title = "A classification and phylogeny of post-Palaeozoic sea stars (Asteroidea: Echinodermata)",
    year = "1987",
    journal = "Journal of Natural History",
    abstract = "A revised classification and phylogeny at the family level and above are presented for post-Palaeozoic sea stars. Monophyly of the group is established by a character suite taken from the ambulacral column that thus far has been recognized in only one Palaeozoic genus. Compared to earlier studies, character selection here placed relatively greater emphasis on morphology and arrangement of ossicles and ossicular systems. Functional implications of many features are surveyed. Thirty-four families, three extinct, are recognized and a number of older familial concepts are suppressed; the extinct Trichasteropsidae is proposed. Superfamilies are recognized for the Valvatida. Eight orders, including the new, extinct Trichasteropsida, and three superorders are recognized. No living sea star is primitive in the sense of being close to ancestral sea stars and other echinoderm groups; the Paxillosida, which commonly has been considered primitive, is here considered specialized.",
    url = "https://doi.org/10.1080/00222938700771141",
    doi = "10.1080/00222938700771141",
    openalex = "W2038881251",
    references = "doi1010160031018268900989, doi103998mpub9690664"
}

Abstract- Several prominent cladists have questioned the importance of fossils in phylogenctic inference, and it is becoming increasingly popular to simply fit extinct forms, if they are considered at all, to a cladogram of Recent taxa. Gardiner's (1982) and Løvtrup's (1985) study of amniote phylogeny exemplifies this differential treatment, and we focused on that group of organisms to test the proposition that fossils cannot overturn a theory of relationships based only on the Recent biota. Our parsimony analysis of amniote phylogeny, special knowledge contributed by fossils being scrupulously avoided, led to the following best fitting classification, which is similar to the novel hypothesis Gardiner published: (lepidosaurs (turtles (mammals (birds, crocodiles)))). However, adding fossils resulted in a markedly different most parsimonious cladogram of the extant taxa: (mammals (turtles (lepidosaurs (birds, crocodiles)))). That classification is like the traditional hypothesis, and it provides a better fit to the stratigraphic record. To isolate the extinct taxa responsible for the latter classification, the data were successively partitioned with each phylogenetic analysis, and we concluded that: (1) the ingroup, not the outgroup, fossils were important; (2) synapsid, not reptile, fossils were pivotal; (3) certain synapsid fossils, not the earliest or latest, were responsible. The critical nature of the synapsid fossils seemed to lie in the particular combination of primitive and derived character slates they exhibited. Classifying those fossils, along with mammals, as the sister group to the lineage consisting of birds and crocodiles resulted in a relatively poor fit to data; one involving a 2-4 fold increase in evolutionary reversals! Thus, the importance of the critical fossils, collectively or individually, seems to reside in their relative primitive-ness, and the simplest explanation for their more conservative nature is that they have had less time to evolve. While fossils may be important in phylogenetic inference only under certain conditions, there is no compelling reason to prejudge their contribution. We urge systematists to evaluate fairly all of the available evidence.

@article{doi101111j109600311988tb00514x,
    author = "Gauthier, Jacques and Kluge, Arnold G. and Rowe, Timothy",
    title = "AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS",
    year = "1988",
    journal = "Cladistics",
    abstract = "Abstract- Several prominent cladists have questioned the importance of fossils in phylogenctic inference, and it is becoming increasingly popular to simply fit extinct forms, if they are considered at all, to a cladogram of Recent taxa. Gardiner's (1982) and Løvtrup's (1985) study of amniote phylogeny exemplifies this differential treatment, and we focused on that group of organisms to test the proposition that fossils cannot overturn a theory of relationships based only on the Recent biota. Our parsimony analysis of amniote phylogeny, special knowledge contributed by fossils being scrupulously avoided, led to the following best fitting classification, which is similar to the novel hypothesis Gardiner published: (lepidosaurs (turtles (mammals (birds, crocodiles)))). However, adding fossils resulted in a markedly different most parsimonious cladogram of the extant taxa: (mammals (turtles (lepidosaurs (birds, crocodiles)))). That classification is like the traditional hypothesis, and it provides a better fit to the stratigraphic record. To isolate the extinct taxa responsible for the latter classification, the data were successively partitioned with each phylogenetic analysis, and we concluded that: (1) the ingroup, not the outgroup, fossils were important; (2) synapsid, not reptile, fossils were pivotal; (3) certain synapsid fossils, not the earliest or latest, were responsible. The critical nature of the synapsid fossils seemed to lie in the particular combination of primitive and derived character slates they exhibited. Classifying those fossils, along with mammals, as the sister group to the lineage consisting of birds and crocodiles resulted in a relatively poor fit to data; one involving a 2-4 fold increase in evolutionary reversals! Thus, the importance of the critical fossils, collectively or individually, seems to reside in their relative primitive-ness, and the simplest explanation for their more conservative nature is that they have had less time to evolve. While fossils may be important in phylogenetic inference only under certain conditions, there is no compelling reason to prejudge their contribution. We urge systematists to evaluate fairly all of the available evidence.",
    url = "https://doi.org/10.1111/j.1096-0031.1988.tb00514.x",
    doi = "10.1111/j.1096-0031.1988.tb00514.x",
    openalex = "W1978557909",
    references = "crossref1943the, currie1985cranial, doi101001jama194302840160064031, doi1010079781468488517, doi101007978146848851721, doi101016002555648290027x, doi1010160169534789901626, doi101016b9781483198279500198, doi101016b9781483231426500124, doi101017cbo9780511693281002, doi101038142004a0, doi10108002724634198810011708, doi101086628623, doi101093sysbio1811, doi101093sysbio33183, doi1010970000505319311100000026, doi101098rstb19830079, doi101111j109636421977tb01031x, doi101111j109636421985tb01796x, doi101146annureven10010165000525, doi1023071005355, doi1023071220820, doi1023071292217, doi1023071441916, doi1023072412407, doi1023072412685, doi1023072413134, doi1023072413259, doi1023072413454, doi1023072485224, doi105281zenodo16171435, doi10560219780801847806, doi105962bhltitle6408, doi105962bhltitle82144, openalexw1534787790, openalexw1534857865, openalexw2954279587, openalexw2983381470, openalexw3146596760, openalexw3184837389, openalexw575222456, roaf1943the"
}

Part 1 Phylum characteristics: how to characterize the echinodermata - some implications of the sister-group relationship between echinoderms and chordates the meaning of developmental asymmetry for echinoderm evolution - a new interpretation. Part 2 Class relationships: molecular analysis of distant phylogenetic relationships in echinoderms collagen biochemistry and the phylogeny of echinoderms larvae, phylogeny and von Baer's law the phylogenetic relationship of holothurians - a cladistic analysis of the extant echinoderm classes fossil evidence for the relationship of extant echinoderm classes and their times of divergence. Part 3 Molecules and relationships: DNA evolution and echinoderm systematics DNA - DNA hybridization, the fossil record, phylogenetic reconstruction and the evolution of the clypeasteroid echinoids phylogenetic implications of genome rearrangement and sequence evolution in echinoderm mitochondrial DNA what molecular biology tells us about the genomic programme for development. Part 4 Ontogeny and phylogney: heterochrony and the evolution of echinoids roles of allometry and ecology in echinoid evolution a biomechanical approach to the ontogeny and phylogeny of echinoids experimental embryology as a tool for studying the evolution of echinoderm life histories. Part 5 Fossils and evolution: the phylogeny of the cystoids the evolutionary palaeoecology of the Blaistoidea the early evolution of the Crinoidea ontogeny and phylogeny of disparid crinoids the evolution of feeding structures in Palaeozoic crinoids the phylogeny of post-Palaeozoic crinoids. Part 6 Evolutionary biology: the ultrastructure of the tube foot epidermal cells and secretions - their relationship to the duo-glandular hypothesis and the phylogeny of the echinoderm classes crystallographic axes of echinoid genital plates reflect larval form - some phylogenetic implications mutable collagenous tissues and their significance for echinoderm palaeontology and phylogeny origins of the deep-sea hoasteroid fauna feeding and respiratory strategies in stylophora.

@book{openalexw635257420,
    author = "Paul, C. R. C. and Smith, Andrew B.",
    title = "Echinoderm phylogeny and evolutionary biology",
    year = "1988",
    abstract = "Part 1 Phylum characteristics: how to characterize the echinodermata - some implications of the sister-group relationship between echinoderms and chordates the meaning of developmental asymmetry for echinoderm evolution - a new interpretation. Part 2 Class relationships: molecular analysis of distant phylogenetic relationships in echinoderms collagen biochemistry and the phylogeny of echinoderms larvae, phylogeny and von Baer's law the phylogenetic relationship of holothurians - a cladistic analysis of the extant echinoderm classes fossil evidence for the relationship of extant echinoderm classes and their times of divergence. Part 3 Molecules and relationships: DNA evolution and echinoderm systematics DNA - DNA hybridization, the fossil record, phylogenetic reconstruction and the evolution of the clypeasteroid echinoids phylogenetic implications of genome rearrangement and sequence evolution in echinoderm mitochondrial DNA what molecular biology tells us about the genomic programme for development. Part 4 Ontogeny and phylogney: heterochrony and the evolution of echinoids roles of allometry and ecology in echinoid evolution a biomechanical approach to the ontogeny and phylogeny of echinoids experimental embryology as a tool for studying the evolution of echinoderm life histories. Part 5 Fossils and evolution: the phylogeny of the cystoids the evolutionary palaeoecology of the Blaistoidea the early evolution of the Crinoidea ontogeny and phylogeny of disparid crinoids the evolution of feeding structures in Palaeozoic crinoids the phylogeny of post-Palaeozoic crinoids. Part 6 Evolutionary biology: the ultrastructure of the tube foot epidermal cells and secretions - their relationship to the duo-glandular hypothesis and the phylogeny of the echinoderm classes crystallographic axes of echinoid genital plates reflect larval form - some phylogenetic implications mutable collagenous tissues and their significance for echinoderm palaeontology and phylogeny origins of the deep-sea hoasteroid fauna feeding and respiratory strategies in stylophora.",
    openalex = "W635257420"
}

Late Osagean to Meramecian Platycrinites and Eucladocrinus from Illinois, Iowa, and Missouri are redescribed and redefined from study of type material. Three of the oldest species were incorrectly synonymized with P. sarae, and this correction leads to a realignment of species systematics within Platycrinites. Accordingly, six species of Platycrinites and one species of Eucladocrinus are considered valid in the Keokuk Limestone through St. Louis Limestone of the stratotype area. Valid species include Platycrinites saffordi (Hall), P. sarae (Hall), P. georgii (Hall), P. pumilus (Hall), P. brevinodus (Hall), P. niotensis (Meek and Worthen), and Eucladocrinus millebrachiatus Wahsmuth and Springer. Nomenclatoral changes include the following: 1) P. sarae is redescribed and all junior synonyms are removed; 2) P. georgii is a valid senior synonym of P. bonoensis (White), P. aeternalis (Miller), P. boonvillensis (Miller), and P. cauducus; 3) P. pentagonus (Miller) is a junior synonym of P. niotensis; 4) P. pumilus is a valid senior synonym of P. prattenanus (Meek and Worthen), and P. monroensis (Worthen); 5) P. bloomfieldensis (Miller) is designated as a nomen dubium; and 6) Eucladocrinus millebrachiatus immaturus is a junior synonym of E. millebrachiatus. The evoluton of new species in Platycrinites was by a combination of cladogenesis and possibly anagenesis. Platycrinites sarae evolved from P. saffordi possibly through anagenesis, P. pumilus evolved from P. niotensis through cladogenesis, and P. hemisphaericus evolved through cladogenesis from P. brevinodus, although P. hemisphaericus does not occur in the geographic area of this study.

@article{doi101017s0022336000018977,
    author = "Ausich, William I. and Kammer, Thomas",
    title = "Systematics and phylogeny of the late Osagean and Meramecian crinoids Platycrinites and Eucladocrinus from the Mississippian stratotype region",
    year = "1990",
    journal = "Journal of Paleontology",
    abstract = "Late Osagean to Meramecian Platycrinites and Eucladocrinus from Illinois, Iowa, and Missouri are redescribed and redefined from study of type material. Three of the oldest species were incorrectly synonymized with P. sarae, and this correction leads to a realignment of species systematics within Platycrinites. Accordingly, six species of Platycrinites and one species of Eucladocrinus are considered valid in the Keokuk Limestone through St. Louis Limestone of the stratotype area. Valid species include Platycrinites saffordi (Hall), P. sarae (Hall), P. georgii (Hall), P. pumilus (Hall), P. brevinodus (Hall), P. niotensis (Meek and Worthen), and Eucladocrinus millebrachiatus Wahsmuth and Springer. Nomenclatoral changes include the following: 1) P. sarae is redescribed and all junior synonyms are removed; 2) P. georgii is a valid senior synonym of P. bonoensis (White), P. aeternalis (Miller), P. boonvillensis (Miller), and P. cauducus; 3) P. pentagonus (Miller) is a junior synonym of P. niotensis; 4) P. pumilus is a valid senior synonym of P. prattenanus (Meek and Worthen), and P. monroensis (Worthen); 5) P. bloomfieldensis (Miller) is designated as a nomen dubium; and 6) Eucladocrinus millebrachiatus immaturus is a junior synonym of E. millebrachiatus. The evoluton of new species in Platycrinites was by a combination of cladogenesis and possibly anagenesis. Platycrinites sarae evolved from P. saffordi possibly through anagenesis, P. pumilus evolved from P. niotensis through cladogenesis, and P. hemisphaericus evolved through cladogenesis from P. brevinodus, although P. hemisphaericus does not occur in the geographic area of this study.",
    url = "https://doi.org/10.1017/s0022336000018977",
    doi = "10.1017/s0022336000018977",
    openalex = "W2383024533",
    references = "doi101130spe46p1"
}

Journal Article Phylogeny as a Central Principle in Taxonomy: Phylogenetic Definitions of Taxon Names Get access Kevin de Queiroz, Kevin de Queiroz Department of Herpetology, California Academy of SciencesGolden Gate Park, San Francisco, California 94118 Search for other works by this author on: Oxford Academic PubMed Google Scholar Jacques Gauthier Jacques Gauthier Department of Herpetology, California Academy of SciencesGolden Gate Park, San Francisco, California 94118 Search for other works by this author on: Oxford Academic PubMed Google Scholar Systematic Biology, Volume 39, Issue 4, December 1990, Pages 307–322, https://doi.org/10.2307/2992353 Published: 01 December 1990 Article history Received: 13 February 1990 Accepted: 25 June 1990 Published: 01 December 1990

@article{doi1023072992353,
    author = "de Queiroz, Kevin and Gauthier, Jacques",
    title = "Phylogeny as a Central Principle in Taxonomy: Phylogenetic Definitions of Taxon Names",
    year = "1990",
    journal = "Systematic Zoology",
    abstract = "Journal Article Phylogeny as a Central Principle in Taxonomy: Phylogenetic Definitions of Taxon Names Get access Kevin de Queiroz, Kevin de Queiroz Department of Herpetology, California Academy of SciencesGolden Gate Park, San Francisco, California 94118 Search for other works by this author on: Oxford Academic PubMed Google Scholar Jacques Gauthier Jacques Gauthier Department of Herpetology, California Academy of SciencesGolden Gate Park, San Francisco, California 94118 Search for other works by this author on: Oxford Academic PubMed Google Scholar Systematic Biology, Volume 39, Issue 4, December 1990, Pages 307–322, https://doi.org/10.2307/2992353 Published: 01 December 1990 Article history Received: 13 February 1990 Accepted: 25 June 1990 Published: 01 December 1990",
    url = "https://doi.org/10.2307/2992353",
    doi = "10.2307/2992353",
    openalex = "W2004477458",
    references = "doi10108002724634198810011708, doi101086288811, doi1023071793007, doi1023072412685, doi1023072412744, doi1023072806339, doi1023072992272, doi1023073243026, doi105281zenodo16171435, openalexw2065464699, openalexw78510971"
}

Several metrics, including average difference among species, range of occupied morphological space, and number of character-state combinations, are used to investigate morphological diversification in Paleozoic crinoids. Despite several phases of taxonomic diversification, the maximal level of disparity reached in the Ordovician remained essentially unsurpassed. Although new regions in morphological space were occupied after the Devonian, these were not as extensive as those that had been evacuated prior to the Carboniferous. This discordance between extensive total morphological change and limited net change further supports previous arguments for the importance of morphological constraints in crinoid evolution. Major changes in the occupation of morphological space correspond with changes in taxonomic diversity within certain higher taxa. The extent to which advanced cladids (Poteriocrinina) appear to expand into new morphological space is exaggerated by the large number of very similar species in this group. If fewer species are sampled, by considering only those forms that differ from each other by at least some prescribed amount, poteriocrines appear to be less extreme morphologically. In contrast, other groups that seem to occupy unique regions in morphological space continue to do so even if fewer of them are sampled. Major crinoid clades—Camerata and Cladida+Flexibilia—do not show the same evolutionary pattern as Crinoidea, but instead exhibit a more gradual diversification of morphology. This observation provides additional support for the existence of qualitative differences among taxa of different rank.

@article{doi101017s0094837300013300,
    author = "Foote, Mike",
    title = "Morphological diversification of Paleozoic crinoids",
    year = "1995",
    journal = "Paleobiology",
    abstract = "Several metrics, including average difference among species, range of occupied morphological space, and number of character-state combinations, are used to investigate morphological diversification in Paleozoic crinoids. Despite several phases of taxonomic diversification, the maximal level of disparity reached in the Ordovician remained essentially unsurpassed. Although new regions in morphological space were occupied after the Devonian, these were not as extensive as those that had been evacuated prior to the Carboniferous. This discordance between extensive total morphological change and limited net change further supports previous arguments for the importance of morphological constraints in crinoid evolution. Major changes in the occupation of morphological space correspond with changes in taxonomic diversity within certain higher taxa. The extent to which advanced cladids (Poteriocrinina) appear to expand into new morphological space is exaggerated by the large number of very similar species in this group. If fewer species are sampled, by considering only those forms that differ from each other by at least some prescribed amount, poteriocrines appear to be less extreme morphologically. In contrast, other groups that seem to occupy unique regions in morphological space continue to do so even if fewer of them are sampled. Major crinoid clades—Camerata and Cladida+Flexibilia—do not show the same evolutionary pattern as Crinoidea, but instead exhibit a more gradual diversification of morphology. This observation provides additional support for the existence of qualitative differences among taxa of different rank.",
    url = "https://doi.org/10.1017/s0094837300013300",
    doi = "10.1017/s0094837300013300",
    openalex = "W1934468248",
    references = "doi101130spe46p1"
}

Phylogenetic relationships of higher taxa of echinoids have been investigated using a 163 character morphological data base and molecular sequences from large and small subunit (LSU and SSU) ribosomal RNA (rRNA) genes. The complete SSU rRNA gene has been sequenced for 21 taxa, with representatives from nine of the 14 extant orders of Echinoidea. Partial LSU sequences, representing the first 400 base pairs (b.p.) from the 5' end were also sequenced for three taxa to complement an existing data base of ten taxa. The two molecular sequences provided a total of 371 variable sites, of which 143 were phylogenetically informative (compared to 145 phylogenetically informative sites from morphological data). Morphological, LSU and SSU data have been analysed separately and together. Morphological and SSU sequence data generate topologies that are not significantly in conflict (under Templeton's test), but the strong signal pairing arbaciids with clypeasteroids in the LSU derived tree marks the LSU sequence data as anomalous for this taxon. A 'total evidence' approach derived a tree very similar in topology to that derived from morphological data. Rooted on the stem group echinoid Archaeocidaris, our total evidence tree suggested relationships of higher taxa as follows: Cidaroida (Phormosomatidae (Echinothuriidae (Diadematidae ((Spatangoida (Clypeasteroida, Cassiduloida)) ((Calycina, Arbacioida) (Stomopneustidae (Glyphocidaridae (Temnopleuridae (Echinometridae (Echinidae, Stronglyocentridae)))))))))). Phylogenetic analyses run both with and without key fossil taxa yielded slightly different topologies. It is important to include fossil taxa in a phylogenetic analysis where there are long stem-group branches or where the crown group is highly derived.

@article{doi101098rstb19950023,
    author = "Littlewood, D. Timothy J. and Smith, Andrew",
    title = "A combined morphological and molecular phylogeny for sea urchins (Echinoidea: Echinodermata)",
    year = "1995",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "Phylogenetic relationships of higher taxa of echinoids have been investigated using a 163 character morphological data base and molecular sequences from large and small subunit (LSU and SSU) ribosomal RNA (rRNA) genes. The complete SSU rRNA gene has been sequenced for 21 taxa, with representatives from nine of the 14 extant orders of Echinoidea. Partial LSU sequences, representing the first 400 base pairs (b.p.) from the 5' end were also sequenced for three taxa to complement an existing data base of ten taxa. The two molecular sequences provided a total of 371 variable sites, of which 143 were phylogenetically informative (compared to 145 phylogenetically informative sites from morphological data). Morphological, LSU and SSU data have been analysed separately and together. Morphological and SSU sequence data generate topologies that are not significantly in conflict (under Templeton's test), but the strong signal pairing arbaciids with clypeasteroids in the LSU derived tree marks the LSU sequence data as anomalous for this taxon. A 'total evidence' approach derived a tree very similar in topology to that derived from morphological data. Rooted on the stem group echinoid Archaeocidaris, our total evidence tree suggested relationships of higher taxa as follows: Cidaroida (Phormosomatidae (Echinothuriidae (Diadematidae ((Spatangoida (Clypeasteroida, Cassiduloida)) ((Calycina, Arbacioida) (Stomopneustidae (Glyphocidaridae (Temnopleuridae (Echinometridae (Echinidae, Stronglyocentridae)))))))))). Phylogenetic analyses run both with and without key fossil taxa yielded slightly different topologies. It is important to include fossil taxa in a phylogenetic analysis where there are long stem-group branches or where the crown group is highly derived.",
    url = "https://doi.org/10.1098/rstb.1995.0023",
    doi = "10.1098/rstb.1995.0023",
    openalex = "W2037668986",
    references = "doi105281zenodo16046014"
}

This paper presents an estimate of the phylogeny of all 203 species of primate. The composite tree is derived by applying a parsimony algorithm to over a hundred previous estimates, and is well resolved, containing 160 nodes. The ages of over half the clades in the tree have been estimated from information in the literature. Bootstrapping has been used to indicate the degree of certainty associated with each clade. The tree will be a useful framework for comparative biologists and shows which areas of primate phylogeny are still only sketchily known.

@article{doi101098rstb19950078,
    author = "Purvis, Andy",
    title = "A composite estimate of primate phylogeny",
    year = "1995",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "This paper presents an estimate of the phylogeny of all 203 species of primate. The composite tree is derived by applying a parsimony algorithm to over a hundred previous estimates, and is well resolved, containing 160 nodes. The ages of over half the clades in the tree have been estimated from information in the literature. Bootstrapping has been used to indicate the degree of certainty associated with each clade. The tree will be a useful framework for comparative biologists and shows which areas of primate phylogeny are still only sketchily known.",
    url = "https://doi.org/10.1098/rstb.1995.0078",
    doi = "10.1098/rstb.1995.0078",
    openalex = "W2081030047",
    references = "doi101016002555648290027x, openalexw638862129"
}

SEAVIEW and PHYLO_WIN are two graphic tools for X Windows-Unix computers dedicated to sequence alignment and molecular phylogenetics. SEAVIEW is a sequence alignment editor allowing manual or automatic alignment through an interface with CLUSTALW program. Alignment of large sequences with extensive length differences is made easier by a dot-plot-based routine. The PHYLO_WIN program allows phylogenetic tree building according to most usual methods (neighbor joining with numerous distance estimates, maximum parsimony, maximum likelihood), and a bootstrap analysis with any of them. Reconstructed trees can be drawn, edited, printed, stored, evaluated according to numerous criteria. Taxonomic species groups and sets of conserved regions can be defined by mouse and stored into sequence files, thus avoiding multiple data files. Both tools are entirely mouse driven. On-line help makes them easy to use. They are freely available by anonymous ftp at biom3.univ-lyon1.fr/pub/ mol_phylogeny or http:@acnuc.univ-lyon1.fr/, or by e-mail to galtier@biomserv.univ-lyon1.fr.

@article{doi101093bioinformatics126543,
    author = "Galtier, Nicolas and Gouy, Manolo and Gautier, Christian",
    title = "SEAVIEW and PHYLO\_WIN: two graphic tools for sequence alignment and molecular phylogeny",
    year = "1996",
    journal = "Computer applications in the biosciences",
    abstract = "SEAVIEW and PHYLO\_WIN are two graphic tools for X Windows-Unix computers dedicated to sequence alignment and molecular phylogenetics. SEAVIEW is a sequence alignment editor allowing manual or automatic alignment through an interface with CLUSTALW program. Alignment of large sequences with extensive length differences is made easier by a dot-plot-based routine. The PHYLO\_WIN program allows phylogenetic tree building according to most usual methods (neighbor joining with numerous distance estimates, maximum parsimony, maximum likelihood), and a bootstrap analysis with any of them. Reconstructed trees can be drawn, edited, printed, stored, evaluated according to numerous criteria. Taxonomic species groups and sets of conserved regions can be defined by mouse and stored into sequence files, thus avoiding multiple data files. Both tools are entirely mouse driven. On-line help makes them easy to use. They are freely available by anonymous ftp at biom3.univ-lyon1.fr/pub/ mol\_phylogeny or http:@acnuc.univ-lyon1.fr/, or by e-mail to galtier@biomserv.univ-lyon1.fr.",
    url = "https://doi.org/10.1093/bioinformatics/12.6.543",
    doi = "10.1093/bioinformatics/12.6.543",
    openalex = "W2149160071",
    references = "doi101007978140206754912413, doi101007bf02407308, doi101093oxfordjournalsmolbeva040343"
}

@article{doi101007bf00987959,
    author = "Oxelman, Bengt and Lid�n, Magnus and Berglund, Daniel",
    title = "Chloroplastrps16 intron phylogeny of the tribeSileneae (Caryophyllaceae)",
    year = "1997",
    journal = "Plant Systematics and Evolution",
    url = "https://doi.org/10.1007/bf00987959",
    doi = "10.1007/bf00987959",
    openalex = "W30417703",
    references = "doi101111j109600311989tb00573x, openalexw638862129"
}

A stepwise approach is employed to determine the phylogeny of the initial crinoid radiation during the Arenig and Llanvirn series of the Ordovician. Parsimony-based character analysis is completed first on Arenig crinoids and then for Arenig and Llanvirn crinoids combined. The topology from well-resolved trees of this early crinoid radiation indicates that the Crinoidea should be subdivided into six subclasses. A new subclass and new order, Aethocrinea and Aethocrinida, respectively, are proposed for crinoids with four circlets of plates in the aboral cup: lintels, infrabasals, basals, and radials. This aboral cup construction is best displayed by Aethocrinus, one of the oldest known crinoids (?Tremadoc-Arenig). However, this primitive aboral cup construction is also present in two Llanvirn crinoids, Perittocrinus and Tetracionocrinus. The Aethocrinea was a small, short-lived radiation of crinoids with this design that was different from those of other crinoids. Two families in the Aethocrinida are the Aethocrinidae, which includes Aethocrinus, and the Perittocrinidae, which includes Perittocrinus and Tetracionocrinus. In addition to the Aethocrinea, the following crinoid subclasses are recognized based on character analyses of these earliest crinoids: Cladida, Camerata, Disparida, Flexibilia, and Articulata.

@article{doi101017s0022336000024276,
    author = "Ausich, William I.",
    title = "Early phylogeny and subclass division of the Crinoidea (Phylum Echinodermata)",
    year = "1998",
    journal = "Journal of Paleontology",
    abstract = "A stepwise approach is employed to determine the phylogeny of the initial crinoid radiation during the Arenig and Llanvirn series of the Ordovician. Parsimony-based character analysis is completed first on Arenig crinoids and then for Arenig and Llanvirn crinoids combined. The topology from well-resolved trees of this early crinoid radiation indicates that the Crinoidea should be subdivided into six subclasses. A new subclass and new order, Aethocrinea and Aethocrinida, respectively, are proposed for crinoids with four circlets of plates in the aboral cup: lintels, infrabasals, basals, and radials. This aboral cup construction is best displayed by Aethocrinus, one of the oldest known crinoids (?Tremadoc-Arenig). However, this primitive aboral cup construction is also present in two Llanvirn crinoids, Perittocrinus and Tetracionocrinus. The Aethocrinea was a small, short-lived radiation of crinoids with this design that was different from those of other crinoids. Two families in the Aethocrinida are the Aethocrinidae, which includes Aethocrinus, and the Perittocrinidae, which includes Perittocrinus and Tetracionocrinus. In addition to the Aethocrinea, the following crinoid subclasses are recognized based on character analyses of these earliest crinoids: Cladida, Camerata, Disparida, Flexibilia, and Articulata.",
    url = "https://doi.org/10.1017/s0022336000024276",
    doi = "10.1017/s0022336000024276",
    openalex = "W2367231388",
    references = "doi101130spe46p1"
}

@article{doi101023a1001761008817,
    author = "Kurtzman, Cletus P. and Robnett, Christie J.",
    title = "Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences",
    year = "1998",
    journal = "Antonie van Leeuwenhoek",
    url = "https://doi.org/10.1023/a:1001761008817",
    doi = "10.1023/a:1001761008817",
    openalex = "W1868830645",
    references = "doi101007978140206754912413, doi101093sysbio422182, doi1023072992540"
}

▪ Abstract The Siluro-Devonian primary radiation of land biotas is the terrestrial equivalent of the much-debated Cambrian “explosion” of marine faunas. Both show the hallmarks of novelty radiations (phenotypic diversity increases much more rapidly than species diversity across an ecologically undersaturated and thus low-competition landscape), and both ended with the formation of evolutionary and ecological frameworks analogous to those of modern ecosystems. Profound improvements in understanding early land plant evolution reflect recent liberations from several research constraints: Cladistic techniques plus DNA sequence data from extant relatives have prompted revolutionary reinterpretations of land plant phylogeny, and thus of systematics and character-state acquisition patterns. Biomechanical and physiological experimental techniques developed for extant plants have been extrapolated to fossil species, with interpretations both aided and complicated by the recent knowledge that global landmass positions, currents, climates, and atmospheric compositions have been profoundly variable (and thus nonuniformitarian) through the Phanerozoic. Combining phylogenetic and paleoecological data offers potential insights into the identity and function of key innovations, though current evidence suggests the importance of accumulating within lineages a critical mass of phenotypic character. Challenges to further progress include the lack of sequence data and paucity of phenotypic features among the early land plant clades, and a fossil record still inadequate to date accurately certain crucial evolutionary and ecological events.

@article{doi101146annurevecolsys291263,
    author = "Bateman, Richard M. and Crane, Peter R. and DiMichele, William A. and Kenrick, Paul and Rowe, Nick and Speck, Thomas and Stein, William E.",
    title = "EARLY EVOLUTION OF LAND PLANTS: Phylogeny, Physiology, and Ecology of the Primary Terrestrial Radiation",
    year = "1998",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "▪ Abstract The Siluro-Devonian primary radiation of land biotas is the terrestrial equivalent of the much-debated Cambrian “explosion” of marine faunas. Both show the hallmarks of novelty radiations (phenotypic diversity increases much more rapidly than species diversity across an ecologically undersaturated and thus low-competition landscape), and both ended with the formation of evolutionary and ecological frameworks analogous to those of modern ecosystems. Profound improvements in understanding early land plant evolution reflect recent liberations from several research constraints: Cladistic techniques plus DNA sequence data from extant relatives have prompted revolutionary reinterpretations of land plant phylogeny, and thus of systematics and character-state acquisition patterns. Biomechanical and physiological experimental techniques developed for extant plants have been extrapolated to fossil species, with interpretations both aided and complicated by the recent knowledge that global landmass positions, currents, climates, and atmospheric compositions have been profoundly variable (and thus nonuniformitarian) through the Phanerozoic. Combining phylogenetic and paleoecological data offers potential insights into the identity and function of key innovations, though current evidence suggests the importance of accumulating within lineages a critical mass of phenotypic character. Challenges to further progress include the lack of sequence data and paucity of phenotypic features among the early land plant clades, and a fossil record still inadequate to date accurately certain crucial evolutionary and ecological events.",
    url = "https://doi.org/10.1146/annurev.ecolsys.29.1.263",
    doi = "10.1146/annurev.ecolsys.29.1.263",
    openalex = "W2167760809",
    references = "doi101017s0031819100009189, doi101017s009483730001280x, doi1023073515409"
}

Abstract The pattern of differential species longevities among five Osagean–Meramecian crinoid clades is analyzed for its evolutionary significance. Differences in mean species longevity between clades may have resulted from species sorting based on eurytopy (niche breadth). In order to test the relationship between longevity and eurytopy it was first necessary to recognize generalists (eurytopes) vs. specialists (stenotopes) objectively. Three different approaches were used: (1) the “Eurytopy Index” (EI), which is a measure of mean number of facies per species; (2) analysis of crinoid functional morphology; and (3) use of canonical discriminant analysis to analyze species distributions between facies in order to separate generalists from specialists. Mean species longevity for each clade was evaluated by four different approaches: (1) rarefaction was used to control for differences in sample size, including both species richness and number of occurrences, between clades; (2) potential facies control of species longevity was evaluated by a bootstrap that compared the observed data to a null model where species longevity was limited only by the actual occurrences of each species known facies through time; (3) uniformity of clade species richness through time was evaluated by the “Index of Uniformity for Species Richness” based on the standard deviation of clade species richness across the time intervals; and (4) potential species range truncations were evaluated by a biostratigraphic gap analysis based on the binomial distribution. The general order of increasing longevity and eurytopy is (from least to most): flexibles, advanced cladids, camerates, disparids, and primitive cladids. In general the pinnulate crinoids (advanced cladids and camerates) were specialists with lower mean species longevity, and the non-pinnulate crinoids (disparids and primitive cladids) were generalists with higher mean species longevity. Pinnulate crinoids were specialized for feeding in high-energy currents and, thus, were limited in their facies distribution and presumably more extinction-prone. The non-pinnulates could feed in both low- and high-energy currents and, thus, were less limited in their facies distribution and presumably less extinction-prone. The flexibles were the exception in that they were non-pinnulate but had the lowest mean species longevity, apparently because they were specialized for deeper-water clastic environments. On average, generalist clades have mean species longevities that at a minimum are up to 45% (≈1.0 ± 0.7 m.y.) longer than specialist clades. However, greater mean species longevity did not necessarily confer long-term advantages to a clade. The specialist advanced cladids became the dominant crinoid clade of the late Paleozoic and gave rise to the articulate crinoids of the post-Paleozoic. This may have resulted from the more rapid species turnover of stenotopes creating adaptive evolutionary novelties for their clade. Alternatively, it could simply be the result of stochastic processes. The finer subdivision of niche space by specialists has led previous workers to predict that specialist clades should have higher species richness than generalist clades. The present study supports this prediction.

@article{doi1016660094837319980240155esodsl23co2,
    author = "Kammer, Thomas and Baumiller, Tomasz K. and Ausich, William I.",
    title = "Evolutionary significance of differential species longevity in Osagean–Meramecian (Mississippian) crinoid clades",
    year = "1998",
    journal = "Paleobiology",
    abstract = "Abstract The pattern of differential species longevities among five Osagean–Meramecian crinoid clades is analyzed for its evolutionary significance. Differences in mean species longevity between clades may have resulted from species sorting based on eurytopy (niche breadth). In order to test the relationship between longevity and eurytopy it was first necessary to recognize generalists (eurytopes) vs. specialists (stenotopes) objectively. Three different approaches were used: (1) the “Eurytopy Index” (EI), which is a measure of mean number of facies per species; (2) analysis of crinoid functional morphology; and (3) use of canonical discriminant analysis to analyze species distributions between facies in order to separate generalists from specialists. Mean species longevity for each clade was evaluated by four different approaches: (1) rarefaction was used to control for differences in sample size, including both species richness and number of occurrences, between clades; (2) potential facies control of species longevity was evaluated by a bootstrap that compared the observed data to a null model where species longevity was limited only by the actual occurrences of each species known facies through time; (3) uniformity of clade species richness through time was evaluated by the “Index of Uniformity for Species Richness” based on the standard deviation of clade species richness across the time intervals; and (4) potential species range truncations were evaluated by a biostratigraphic gap analysis based on the binomial distribution. The general order of increasing longevity and eurytopy is (from least to most): flexibles, advanced cladids, camerates, disparids, and primitive cladids. In general the pinnulate crinoids (advanced cladids and camerates) were specialists with lower mean species longevity, and the non-pinnulate crinoids (disparids and primitive cladids) were generalists with higher mean species longevity. Pinnulate crinoids were specialized for feeding in high-energy currents and, thus, were limited in their facies distribution and presumably more extinction-prone. The non-pinnulates could feed in both low- and high-energy currents and, thus, were less limited in their facies distribution and presumably less extinction-prone. The flexibles were the exception in that they were non-pinnulate but had the lowest mean species longevity, apparently because they were specialized for deeper-water clastic environments. On average, generalist clades have mean species longevities that at a minimum are up to 45\% (≈1.0 ± 0.7 m.y.) longer than specialist clades. However, greater mean species longevity did not necessarily confer long-term advantages to a clade. The specialist advanced cladids became the dominant crinoid clade of the late Paleozoic and gave rise to the articulate crinoids of the post-Paleozoic. This may have resulted from the more rapid species turnover of stenotopes creating adaptive evolutionary novelties for their clade. Alternatively, it could simply be the result of stochastic processes. The finer subdivision of niche space by specialists has led previous workers to predict that specialist clades should have higher species richness than generalist clades. The present study supports this prediction.",
    url = "https://doi.org/10.1666/0094-8373(1998)024[0155:esodsl]2.3.co;2",
    doi = "10.1666/0094-8373(1998)024[0155:esodsl]2.3.co;2",
    openalex = "W2167883380",
    references = "doi101130spe46p1"
}

The Paleozoic and post-Paleozoic radiations of crinoids present an opportunity to explore genomic and ecological explanations for patterns of morphologic diversification. Analysis of discrete-character data that cover the principal features of the crinoid skeleton shows that both Paleozoic and post-Paleozoic increases in morphological disparity were abrupt; this is consistent with rapid exploitation of open ecological opportunities in both cases. For the post-Paleozoic, this result is sensitive to some aspects of data analysis and sampling, so it cannot be regarded as unequivocal. The deceleration in morphological diversification within each radiation is consistent with an observed decline in rates of taxonomic origination as well as with the attainment of functional or structural limits. Despite these similarities in the two radiations, Paleozoic crinoids exploited a wider range of morphological designs than did their post-Paleozoic successors. Post-Paleozoic crinoids exploited a wide range of ecological strategies despite being stereotyped in many aspects of form. This difference between the radiations is consistent with an increase in the rigidity of genetic and developmental systems. The range of post-Paleozoic designs is not in essence a subset of the Paleozoic spectrum. The two radiations resulted in morphological distributions that are largely nonoverlapping, perhaps reflecting a different range of ecological strategies.

@article{doi101017s0094837300020236,
    author = "Foote, Mike",
    title = "Morphological Diversity In The Evolutionary Radiation Of Paleozoic and Post-Paleozoic Crinoids",
    year = "1999",
    journal = "Paleobiology",
    abstract = "The Paleozoic and post-Paleozoic radiations of crinoids present an opportunity to explore genomic and ecological explanations for patterns of morphologic diversification. Analysis of discrete-character data that cover the principal features of the crinoid skeleton shows that both Paleozoic and post-Paleozoic increases in morphological disparity were abrupt; this is consistent with rapid exploitation of open ecological opportunities in both cases. For the post-Paleozoic, this result is sensitive to some aspects of data analysis and sampling, so it cannot be regarded as unequivocal. The deceleration in morphological diversification within each radiation is consistent with an observed decline in rates of taxonomic origination as well as with the attainment of functional or structural limits. Despite these similarities in the two radiations, Paleozoic crinoids exploited a wider range of morphological designs than did their post-Paleozoic successors. Post-Paleozoic crinoids exploited a wide range of ecological strategies despite being stereotyped in many aspects of form. This difference between the radiations is consistent with an increase in the rigidity of genetic and developmental systems. The range of post-Paleozoic designs is not in essence a subset of the Paleozoic spectrum. The two radiations resulted in morphological distributions that are largely nonoverlapping, perhaps reflecting a different range of ecological strategies.",
    url = "https://doi.org/10.1017/s0094837300020236",
    doi = "10.1017/s0094837300020236",
    openalex = "W4249583477",
    references = "doi101111j150239311977tb00628x"
}

A phylogeny describes the hierarchical pattern of descent of some group of species from a common ancestor. If information is available on the character states of the contemporary species, thepossibility is raised of using that information in combination with the phylogeny to reconstruct the historical events of evolution. These reconstructions can be used to retrieve a picture of theworld as the species evolved alongwhatwould become the branches of the phylogeny. This, in turn, provides a way to test hypotheses about evolution and adaptation. Methods based on the principle of parsimony reconstruct the ancestral character states to minimize the number of historical character changes required to produce the diversity observed among the contemporary species (seeMaddison et al., 1984, for a general account). An alternative to parsimony approaches makes use of the principle of maximum likelihood. Maximum likelihood solutions make the observed data most likely given somemodel of the process under investigation (see Edwards, 1972). In a phylogenetic context this means reconstructing the ancestral character states to make the character states observed among the contemporary species most probable, given some statistical model of the way evolution proceeds. Maximum likelihood solutions may or may not be the mostparsimonious solution. I restrict myself here to using maximum likelihood models to infer ancestral character states for binary discrete characters, that is, for characters that can adopt only two states, although the generalization to more than two states requires no new concepts.My approach to reconstructing ancestral states makes use of a Markov model of binary character evolution on phylogenies (Pagel, 1994). Sanderson (1993) describes a related model for investigating rates of gains and losses of characters for which the ancestral states are assumed to be known. Schluter (1995), Yang et al. (1995), and Koshi and Goldstein (1996) derive methods that are similar to the procedures I will describe here. However, Yang et al. (1995) and Koshi and Goldstein (1996) use what I shall term “global” methods for estimating ancestral characters, I argue for a “local” approach on grounds that the global method does not produce a maximum-likelihood estimate of the hypothesis of interest. Schluter (1995) reported global and local estimators in his investigation of artiodactyl ribonucleases, and Schluter et al. (1997) reported global estimators. In several recent papers, Schluter (1995; Schluter et al., 1997) called attention to the usefulness of reconstructing ancestral character states for testing ideas about adaptation and evolution, and much of what I say here owes its inspiration to these investigations. Mooers and Schluter (1999) now provide important additional examples of how maximum likelihood methods can return both more information about ancestral character states thanparsimony approaches, as well as information that is at odds with parsimony reconstructions. I intend this article to act as a primer to thosewhoare interested in usingmaximumlikelihood methods but who may not be familiar with the mathematics of the approach. Accordingly, I begin with the simplest case of estimating the ancestral state of two species.

@article{doi101080106351599260184,
    author = "Pagel, Mark",
    title = "The Maximum Likelihood Approach to Reconstructing Ancestral Character States of Discrete Characters on Phylogenies",
    year = "1999",
    journal = "Systematic Biology",
    abstract = "A phylogeny describes the hierarchical pattern of descent of some group of species from a common ancestor. If information is available on the character states of the contemporary species, thepossibility is raised of using that information in combination with the phylogeny to reconstruct the historical events of evolution. These reconstructions can be used to retrieve a picture of theworld as the species evolved alongwhatwould become the branches of the phylogeny. This, in turn, provides a way to test hypotheses about evolution and adaptation. Methods based on the principle of parsimony reconstruct the ancestral character states to minimize the number of historical character changes required to produce the diversity observed among the contemporary species (seeMaddison et al., 1984, for a general account). An alternative to parsimony approaches makes use of the principle of maximum likelihood. Maximum likelihood solutions make the observed data most likely given somemodel of the process under investigation (see Edwards, 1972). In a phylogenetic context this means reconstructing the ancestral character states to make the character states observed among the contemporary species most probable, given some statistical model of the way evolution proceeds. Maximum likelihood solutions may or may not be the mostparsimonious solution. I restrict myself here to using maximum likelihood models to infer ancestral character states for binary discrete characters, that is, for characters that can adopt only two states, although the generalization to more than two states requires no new concepts.My approach to reconstructing ancestral states makes use of a Markov model of binary character evolution on phylogenies (Pagel, 1994). Sanderson (1993) describes a related model for investigating rates of gains and losses of characters for which the ancestral states are assumed to be known. Schluter (1995), Yang et al. (1995), and Koshi and Goldstein (1996) derive methods that are similar to the procedures I will describe here. However, Yang et al. (1995) and Koshi and Goldstein (1996) use what I shall term “global” methods for estimating ancestral characters, I argue for a “local” approach on grounds that the global method does not produce a maximum-likelihood estimate of the hypothesis of interest. Schluter (1995) reported global and local estimators in his investigation of artiodactyl ribonucleases, and Schluter et al. (1997) reported global estimators. In several recent papers, Schluter (1995; Schluter et al., 1997) called attention to the usefulness of reconstructing ancestral character states for testing ideas about adaptation and evolution, and much of what I say here owes its inspiration to these investigations. Mooers and Schluter (1999) now provide important additional examples of how maximum likelihood methods can return both more information about ancestral character states thanparsimony approaches, as well as information that is at odds with parsimony reconstructions. I intend this article to act as a primer to thosewhoare interested in usingmaximumlikelihood methods but who may not be familiar with the mathematics of the approach. Accordingly, I begin with the simplest case of estimating the ancestral state of two species.",
    url = "https://doi.org/10.1080/106351599260184",
    doi = "10.1080/106351599260184",
    openalex = "W2114075279",
    references = "doi101093sysbio33183, doi101111j146364091997tb00423x, doi1023072413134"
}

The Paleozoic and post-Paleozoic radiations of crinoids present an opportunity to explore genomic and ecological explanations for patterns of morphologic diversification. Analysis of discrete-character data that cover the principal features of the crinoid skeleton shows that both Paleozoic and post-Paleozoic increases in morphological disparity were abrupt; this is consistent with rapid exploitation of open ecological opportunities in both cases. For the post-Paleozoic, this result is sensitive to some aspects of data analysis and sampling, so it cannot be regarded as unequivocal. The deceleration in morphological diversification within each radiation is consistent with an observed decline in rates of taxonomic origination as well as with the attainment of functional or structural limits. Despite these similarities in the two radiations, Paleozoic crinoids exploited a wider range of morphological designs than did their post-Paleozoic successors. Post-Paleozoic crinoids exploited a wide range of ecological strategies despite being stereotyped in many aspects of form. This difference between the radiations is consistent with an increase in the rigidity of genetic and developmental systems. The range of post-Paleozoic designs is not in essence a subset of the Paleozoic spectrum. The two radiations resulted in morphological distributions that are largely nonoverlapping, perhaps reflecting a different range of ecological strategies.

@article{doi101666009483731999251mditer20co2,
    author = "Foote, Mike",
    title = "Morphological Diversity In The Evolutionary Radiation Of Paleozoic and Post-Paleozoic Crinoids",
    year = "1999",
    journal = "Paleobiology",
    abstract = "The Paleozoic and post-Paleozoic radiations of crinoids present an opportunity to explore genomic and ecological explanations for patterns of morphologic diversification. Analysis of discrete-character data that cover the principal features of the crinoid skeleton shows that both Paleozoic and post-Paleozoic increases in morphological disparity were abrupt; this is consistent with rapid exploitation of open ecological opportunities in both cases. For the post-Paleozoic, this result is sensitive to some aspects of data analysis and sampling, so it cannot be regarded as unequivocal. The deceleration in morphological diversification within each radiation is consistent with an observed decline in rates of taxonomic origination as well as with the attainment of functional or structural limits. Despite these similarities in the two radiations, Paleozoic crinoids exploited a wider range of morphological designs than did their post-Paleozoic successors. Post-Paleozoic crinoids exploited a wide range of ecological strategies despite being stereotyped in many aspects of form. This difference between the radiations is consistent with an increase in the rigidity of genetic and developmental systems. The range of post-Paleozoic designs is not in essence a subset of the Paleozoic spectrum. The two radiations resulted in morphological distributions that are largely nonoverlapping, perhaps reflecting a different range of ecological strategies.",
    url = "https://doi.org/10.1666/0094-8373(1999)25[1:mditer]2.0.co;2",
    doi = "10.1666/0094-8373(1999)25[1:mditer]2.0.co;2",
    openalex = "W2177267176",
    references = "doi101007bf03190413, doi101017s0094837300003778, doi101017s0094837300012306, doi101017s009483730001263x, doi101038361219a0, doi101093biomet5334325, doi101126science2064415217, doi101126science21545391501, doi10113719781611970319, doi101146annurevecolsys281129, doi105962bhltitle66379"
}

Evolutionary biologists have adopted simple likelihood models for purposes of estimating ancestral states and evaluating character independence on specified phylogenies; however, for purposes of estimating phylogenies by using discrete morphological data, maximum parsimony remains the only option. This paper explores the possibility of using standard, well-behaved Markov models for estimating morphological phylogenies (including branch lengths) under the likelihood criterion. An important modification of standard Markov models involves making the likelihood conditional on characters being variable, because constant characters are absent in morphological data sets. Without this modification, branch lengths are often overestimated, resulting in potentially serious biases in tree topology selection. Several new avenues of research are opened by an explicitly model-based approach to phylogenetic analysis of discrete morphological data, including combined-data likelihood analyses (morphology + sequence data), likelihood ratio tests, and Bayesian analyses.

@article{doi101080106351501753462876,
    author = "Lewis, Paul O.",
    title = "A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data",
    year = "2001",
    journal = "Systematic Biology",
    abstract = "Evolutionary biologists have adopted simple likelihood models for purposes of estimating ancestral states and evaluating character independence on specified phylogenies; however, for purposes of estimating phylogenies by using discrete morphological data, maximum parsimony remains the only option. This paper explores the possibility of using standard, well-behaved Markov models for estimating morphological phylogenies (including branch lengths) under the likelihood criterion. An important modification of standard Markov models involves making the likelihood conditional on characters being variable, because constant characters are absent in morphological data sets. Without this modification, branch lengths are often overestimated, resulting in potentially serious biases in tree topology selection. Several new avenues of research are opened by an explicitly model-based approach to phylogenetic analysis of discrete morphological data, including combined-data likelihood analyses (morphology + sequence data), likelihood ratio tests, and Bayesian analyses.",
    url = "https://doi.org/10.1080/106351501753462876",
    doi = "10.1080/106351501753462876",
    openalex = "W2122082385",
    references = "doi101007bf00160154, doi101007bf01734359, doi101007bf02101694, doi101007bf02338839, doi101016b9781483232119500097, doi101093oxfordjournalsmolbeva025811, doi101093oxfordjournalsmolbeva026160, doi101098rspb19940006, doi1012019781003456285, openalexw2994240441"
}

MacClade is a computer program, with accompanying manual, that provides theory and tools for the graphic and interactive analysis of molecular and morphological data, phylogeny, and character evolution. Systematists and other evolutionary biologists can use its flexible tools to analyse phylogeny and character evolution, yet its ease of use allows beginning students to grasp phylogenetic principles in an interactive environment.

@article{doi105860choice392183,
    title = "MacClade 4.0: analysis of phylogeny and character evolution",
    year = "2001",
    journal = "Choice Reviews Online",
    abstract = "MacClade is a computer program, with accompanying manual, that provides theory and tools for the graphic and interactive analysis of molecular and morphological data, phylogeny, and character evolution. Systematists and other evolutionary biologists can use its flexible tools to analyse phylogeny and character evolution, yet its ease of use allows beginning students to grasp phylogenetic principles in an interactive environment.",
    url = "https://doi.org/10.5860/choice.39-2183",
    doi = "10.5860/choice.39-2183",
    openalex = "W1522592213"
}

▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community phylogenetic structure underlie the recent progress in these areas. We highlight the potential for community ecologists to benefit from phylogenetic knowledge and suggest several avenues for future research.

@article{doi101146annurevecolsys33010802150448,
    author = "Webb, Campbell O. and Ackerly, David D. and McPeek, Mark A. and Donoghue, Michael J.",
    title = "Phylogenies and Community Ecology",
    year = "2002",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community phylogenetic structure underlie the recent progress in these areas. We highlight the potential for community ecologists to benefit from phylogenetic knowledge and suggest several avenues for future research.",
    url = "https://doi.org/10.1146/annurev.ecolsys.33.010802.150448",
    doi = "10.1146/annurev.ecolsys.33.010802.150448",
    openalex = "W2109628725",
    references = "doi10100797814615696881, doi101007978303487527124, doi101007bf02806171, doi101016s0169534701021619, doi101038363342a0, doi10108010292389509380518, doi101086282106, doi101086282505, doi101086284325, doi101086285258, doi101086285357, doi101086627905, doi101093oso97801985052350010001, doi101093oso97801985464120010001, doi101093oxfordjournalsmolbeva003974, doi101093oxfordjournalsmolbeva025892, doi101098rstb19950125, doi101111j001438202001tb00826x, doi101111j109583122001tb01368x, doi101126science20343871299, doi101126science2354785167, doi101126science2785338692, doi101126science27953592115, doi101126science28554311265, doi101146annurevecolsys311343, doi1015159781400881376, doi1023071446122, doi1023071939377, doi1023072412182, doi1023072413039, doi1023072485224, doi1023073071998, doi1023073544421, doi1023075503, doi102307jctv1nzfgj7, doi105860choice295104, doi105860choice375647, doi105860choice392183, openalexw2273605253, openalexw3035987306"
}

Homology is at the foundation of comparative studies in biology at all levels from genes to phenotypes. Homology is similarity because of common descent and ancestry, homoplasy is similarity arrived at via independent evolution. However, given that there is but one tree of life, all organisms, and therefore all features of organisms, share some degree of relationship and similarity one to another. That sharing may be similarity or even identity of structure and the sharing of a most recent common ancestor--as in the homology of the arms of humans and apes--or it may reflect some (often small) degree of similarity, such as that between the wings of insects and the wings of birds, groups whose shared ancestor lies deep within the evolutionary history of the Metazoa. It may reflect sharing of entire developmental pathways, partial sharing, or divergent pathways. This review compares features classified as homologous with the classes of features normally grouped as homoplastic, the latter being convergence, parallelism, reversals, rudiments, vestiges, and atavisms. On the one hand, developmental mechanisms may be conserved, even when a complete structure does not form (rudiments, vestiges), or when a structure appears only in some individuals (atavisms). On the other hand, different developmental mechanisms can produce similar (homologous) features. Joint examination of nearness of relationship and degree of shared development reveals a continuum within an expanded category of homology, extending from homology --> reversals --> rudiments --> vestiges --> atavisms --> parallelism, with convergence as the only class of homoplasy, an idea that turns out to be surprisingly old. This realignment provides a glimmer of a way to bridge phylogenetic and developmental approaches to homology and homoplasy, a bridge that should provide a key pillar for evolutionary developmental biology (evo-devo). It will not, and in a practical sense cannot, alter how homoplastic features are identified in phylogenetic analyses. But seeing rudiments, reversals, vestiges, atavisms and parallelism as closer to homology than to homoplasy should guide us toward searching for the common elements underlying the formation of the phenotype (what some have called the deep homology of genetic and/or cellular mechanisms), rather than discussing features in terms of shared or independent evolution.

@article{doi101017s1464793102006097,
    author = "Hall, Brian K.",
    title = "Descent with modification: the unity underlying homology and homoplasy as seen through an analysis of development and evolution",
    year = "2003",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Homology is at the foundation of comparative studies in biology at all levels from genes to phenotypes. Homology is similarity because of common descent and ancestry, homoplasy is similarity arrived at via independent evolution. However, given that there is but one tree of life, all organisms, and therefore all features of organisms, share some degree of relationship and similarity one to another. That sharing may be similarity or even identity of structure and the sharing of a most recent common ancestor--as in the homology of the arms of humans and apes--or it may reflect some (often small) degree of similarity, such as that between the wings of insects and the wings of birds, groups whose shared ancestor lies deep within the evolutionary history of the Metazoa. It may reflect sharing of entire developmental pathways, partial sharing, or divergent pathways. This review compares features classified as homologous with the classes of features normally grouped as homoplastic, the latter being convergence, parallelism, reversals, rudiments, vestiges, and atavisms. On the one hand, developmental mechanisms may be conserved, even when a complete structure does not form (rudiments, vestiges), or when a structure appears only in some individuals (atavisms). On the other hand, different developmental mechanisms can produce similar (homologous) features. Joint examination of nearness of relationship and degree of shared development reveals a continuum within an expanded category of homology, extending from homology --> reversals --> rudiments --> vestiges --> atavisms --> parallelism, with convergence as the only class of homoplasy, an idea that turns out to be surprisingly old. This realignment provides a glimmer of a way to bridge phylogenetic and developmental approaches to homology and homoplasy, a bridge that should provide a key pillar for evolutionary developmental biology (evo-devo). It will not, and in a practical sense cannot, alter how homoplastic features are identified in phylogenetic analyses. But seeing rudiments, reversals, vestiges, atavisms and parallelism as closer to homology than to homoplasy should guide us toward searching for the common elements underlying the formation of the phenotype (what some have called the deep homology of genetic and/or cellular mechanisms), rather than discussing features in terms of shared or independent evolution.",
    url = "https://doi.org/10.1017/s1464793102006097",
    doi = "10.1017/s1464793102006097",
    openalex = "W2168524476",
    references = "doi10100797814899175155, doi1010079789401579261, doi1016680003156920000400718bgadbt20co2, doi1023071377078, doi1023072992444, openalexw1511255518, openalexw1593551567, openalexw1600651929, openalexw2163836228, openalexw635257420"
}

In this article we explore the paradox of why morphological data are currently utilized less for than are DNA sequence data, whereas most of what we know about stems from classifications founded on morphological data. The crucial difference between the two data sources relates to the number of potentially unambiguous characters available, their ease and speed of discovery, and their suitability for analysis using transformational models. We consider that the increased use of DNA sequence data, relative to morphology, for is inevitable and well founded, but that a crucial issue remains concerning the role of morphology in reconstruction. We present the view that rigorous and critical anatomical studies of fewer morphological characters, in the context of molecular phylogenies, is a more fruitful approach to integrating the strengths of morphological data with those of sequence data. This approach is preferable to compiling larger data matrices of increasingly ambiguous and problematic morphological characters. We argue below that a main constraint of morphologybased phylogenetic inference concerns the limited number of unambiguous characters available for analysis in a transformational framework. This problem of a limited number of unambiguous characters is further compounded by obstacles to accurate homology assessment and character coding, which further reduce the number of characters available for analysis. We discuss and disagree with the view that more morphological data should be used in reconstruction. Furthermore, we consider the claim that the greatest strength of morphological data-increased taxon sampling-to be mistaken. In the discussion that follows we use phylogeny reconstruction to refer to the computer-based algorithmic analyses routinely conducted in systematics today.

@article{doi10108010635150390223613,
    author = "Scotland, Robert W. and Olmstead, Richard G. and Bennett, Jonathan R.",
    title = "Phylogeny Reconstruction: The Role of Morphology",
    year = "2003",
    journal = "Systematic Biology",
    abstract = "In this article we explore the paradox of why morphological data are currently utilized less for than are DNA sequence data, whereas most of what we know about stems from classifications founded on morphological data. The crucial difference between the two data sources relates to the number of potentially unambiguous characters available, their ease and speed of discovery, and their suitability for analysis using transformational models. We consider that the increased use of DNA sequence data, relative to morphology, for is inevitable and well founded, but that a crucial issue remains concerning the role of morphology in reconstruction. We present the view that rigorous and critical anatomical studies of fewer morphological characters, in the context of molecular phylogenies, is a more fruitful approach to integrating the strengths of morphological data with those of sequence data. This approach is preferable to compiling larger data matrices of increasingly ambiguous and problematic morphological characters. We argue below that a main constraint of morphologybased phylogenetic inference concerns the limited number of unambiguous characters available for analysis in a transformational framework. This problem of a limited number of unambiguous characters is further compounded by obstacles to accurate homology assessment and character coding, which further reduce the number of characters available for analysis. We discuss and disagree with the view that more morphological data should be used in reconstruction. Furthermore, we consider the claim that the greatest strength of morphological data-increased taxon sampling-to be mistaken. In the discussion that follows we use phylogeny reconstruction to refer to the computer-based algorithmic analyses routinely conducted in systematics today.",
    url = "https://doi.org/10.1080/10635150390223613",
    doi = "10.1080/10635150390223613",
    openalex = "W2111931534",
    references = "crossref1995systematics, doi101111j109600311991tb00045x, doi101111j109600311995tb00092x, doi1023072992444, doi105860choice323881"
}

Accurately dating when the first bilaterally symmetrical animals arose is crucial to our understanding of early animal evolution. The earliest unequivocally bilaterian fossils are approximately 555 million years old. In contrast, molecular-clock analyses calibrated by using the fossil record of vertebrates estimate that vertebrates split from dipterans (Drosophila) approximately 900 million years ago (Ma). Nonetheless, comparative genomic analyses suggest that a significant rate difference exists between vertebrates and dipterans, because the percentage difference between the genomes of mosquito and fly is greater than between fish and mouse, even though the vertebrate divergence is almost twice that of the dipteran. Here we show that the dipteran rate of molecular evolution is similar to other invertebrate taxa (echinoderms and bivalve molluscs) but not to vertebrates, which significantly decreased their rate of molecular evolution with respect to invertebrates. Using a data set consisting of the concatenation of seven different amino acid sequences from 23 ingroup taxa (giving a total of 11 different invertebrate calibration points scattered throughout the bilaterian tree and across the Phanerozoic), we estimate that the last common ancestor of bilaterians arose somewhere between 573 and 656 Ma, depending on the value assigned to the parameter scaling molecular substitution rate heterogeneity. These results are in accord with the known fossil record and support the view that the Cambrian explosion reflects, in part, the diversification of bilaterian phyla.

@article{doi101073pnas0401670101,
    author = "Peterson, Kevin J. and Lyons, Jessica B. and Nowak, Kristin S. and Takacs, Carter M. and Wargo, Matthew J. and McPeek, Mark A.",
    title = "Estimating metazoan divergence times with a molecular clock",
    year = "2004",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Accurately dating when the first bilaterally symmetrical animals arose is crucial to our understanding of early animal evolution. The earliest unequivocally bilaterian fossils are approximately 555 million years old. In contrast, molecular-clock analyses calibrated by using the fossil record of vertebrates estimate that vertebrates split from dipterans (Drosophila) approximately 900 million years ago (Ma). Nonetheless, comparative genomic analyses suggest that a significant rate difference exists between vertebrates and dipterans, because the percentage difference between the genomes of mosquito and fly is greater than between fish and mouse, even though the vertebrate divergence is almost twice that of the dipteran. Here we show that the dipteran rate of molecular evolution is similar to other invertebrate taxa (echinoderms and bivalve molluscs) but not to vertebrates, which significantly decreased their rate of molecular evolution with respect to invertebrates. Using a data set consisting of the concatenation of seven different amino acid sequences from 23 ingroup taxa (giving a total of 11 different invertebrate calibration points scattered throughout the bilaterian tree and across the Phanerozoic), we estimate that the last common ancestor of bilaterians arose somewhere between 573 and 656 Ma, depending on the value assigned to the parameter scaling molecular substitution rate heterogeneity. These results are in accord with the known fossil record and support the view that the Cambrian explosion reflects, in part, the diversification of bilaterian phyla.",
    url = "https://doi.org/10.1073/pnas.0401670101",
    doi = "10.1073/pnas.0401670101",
    openalex = "W2143124634",
    references = "doi101017s009483730001681x, openalexw635257420"
}

A phylogenetic analysis of 36 species provides a test for the taxonomy and the history of Early Cretaceous spatangoids. Most taxonomic units from genera to suborders are consistent with the proposed phylogenetic framework. We retain Hemiasterina, Micrasterina, Hemiasteridae, Schizasteridae, Hemiaster, Heteraster, Mecaster, and Periaster as original monophyletic groups. However, all of these clades originate without the classical apomorphies normally ascribed to them. We suggest a revision of their diagnoses and of the generic attributions of basal species. Some ill‐defined, ‘primitive’, and paraphyletic taxa are recognised: Toxaster, Epiaster, Palhemiaster, and Toxasteridae. Even if they do not have phylogenetic meaning, they are retained here, pending a more complete revision.

@article{doi101111j00310239200400364x,
    author = "Villier, Loïc and Néraudeau, Didier and Clavel, Bernard and Neumann, Christian and David, Bruno",
    title = "Phylogeny of Early Cretaceous spatangoids (Echinodermata: Echinoidea) and taxonomic implications",
    year = "2004",
    journal = "Palaeontology",
    abstract = "A phylogenetic analysis of 36 species provides a test for the taxonomy and the history of Early Cretaceous spatangoids. Most taxonomic units from genera to suborders are consistent with the proposed phylogenetic framework. We retain Hemiasterina, Micrasterina, Hemiasteridae, Schizasteridae, Hemiaster, Heteraster, Mecaster, and Periaster as original monophyletic groups. However, all of these clades originate without the classical apomorphies normally ascribed to them. We suggest a revision of their diagnoses and of the generic attributions of basal species. Some ill‐defined, ‘primitive’, and paraphyletic taxa are recognised: Toxaster, Epiaster, Palhemiaster, and Toxasteridae. Even if they do not have phylogenetic meaning, they are retained here, pending a more complete revision.",
    url = "https://doi.org/10.1111/j.0031-0239.2004.00364.x",
    doi = "10.1111/j.0031-0239.2004.00364.x",
    openalex = "W2170259396",
    references = "doi101007978140206754912413, doi101016002555648290027x, doi101017s0022336000061321, doi101093oso97801985771880010001, doi1012019781003077831, doi10120197810030789205, doi1016660094837320000260056cefisg20co2, doi1023071483846, doi105281zenodo16046014, openalexw635257420"
}

The phylogenetic relationships among deuterostome animals have been debated for many years, and a diversity of hypotheses have been proposed based on both morphological and molecular data. Here we have assembled sequences of 217 nuclear-encoded proteins to address specific questions concerning their relationships and times of origin. We recovered significant support for urochordates as the closest relative of vertebrates with an analysis of 59 proteins (17,400 amino acids) and suggest that the basal position of urochordates found in previous molecular studies may have been the result of long-branch attraction biases. Our results also support Ambulacraria, the pairing of hemichordates with echinoderms (nine proteins; 2,382 amino acids), and Cyclostomata, the pairing of lampreys with hagfish (25 proteins; 6,895 amino acids). In addition, 325 shared proteins (102,110 amino acids) were obtained from the complete genomes of six vertebrates and a urochordate for phylogenetic analysis and divergence time estimation. An evolutionary timescale was estimated using a local (Bayesian) molecular clock method. We found that most major lineages of deuterostomes arose prior to the Cambrian Explosion of fossils (approximately 520 MYA) and that several lineages had originated before periods of global glaciation in the Precambrian.

@article{doi101093molbevmsi225,
    author = "Blair, Jaime E. and Hedges, S. Blair",
    title = "Molecular Phylogeny and Divergence Times of Deuterostome Animals",
    year = "2005",
    journal = "Molecular Biology and Evolution",
    abstract = "The phylogenetic relationships among deuterostome animals have been debated for many years, and a diversity of hypotheses have been proposed based on both morphological and molecular data. Here we have assembled sequences of 217 nuclear-encoded proteins to address specific questions concerning their relationships and times of origin. We recovered significant support for urochordates as the closest relative of vertebrates with an analysis of 59 proteins (17,400 amino acids) and suggest that the basal position of urochordates found in previous molecular studies may have been the result of long-branch attraction biases. Our results also support Ambulacraria, the pairing of hemichordates with echinoderms (nine proteins; 2,382 amino acids), and Cyclostomata, the pairing of lampreys with hagfish (25 proteins; 6,895 amino acids). In addition, 325 shared proteins (102,110 amino acids) were obtained from the complete genomes of six vertebrates and a urochordate for phylogenetic analysis and divergence time estimation. An evolutionary timescale was estimated using a local (Bayesian) molecular clock method. We found that most major lineages of deuterostomes arose prior to the Cambrian Explosion of fossils (approximately 520 MYA) and that several lineages had originated before periods of global glaciation in the Precambrian.",
    url = "https://doi.org/10.1093/molbev/msi225",
    doi = "10.1093/molbev/msi225",
    openalex = "W1975553093",
    references = "doi101007bf02101113, doi101017s0006323199005472, doi10103835057062, doi10103846965, doi101038nature01262, doi101038nature01851, doi101073pnas9794469, doi101086425183, doi101093bib52150, doi101093nar25173389, doi101093nar25244876, doi101093oxfordjournalsmolbeva004134, doi101093oxfordjournalsmolbeva025664, doi101093oxfordjournalsmolbeva025897, doi101093oxfordjournalsmolbeva026201, doi101111j109600311998tb00338x, doi101126science1058040, doi101126science28153811342, doi101126science28754612185, doi101130g205191, doi1023072413259, nieuwenhuys1998the, openalexw635257420"
}

@article{doi101038nature05110,
    author = "James, Timothy Y. and Kauff, Frank and Schoch, Conrad L. and Matheny, P. Brandon and Hofstetter, Valérie and Cox, Cymon J. and Celio, Gail J. and Gueidan, Cécile and Fraker, Emily and Miądlikowska, Jolanta and Lumbsch, H. Thorsten and Rauhut, Alexandra and Reeb, Valérie and Arnold, A. Elizabeth and Wynns, Anja Amtoft and Stajich, Jason and Hosaka, Kentaro and Sung, Gi‐Ho and Johnson, Desiree and O’Rourke, Ben and Crockett, Michael and Binder, Manfred and Curtis, Judd M. and Slot, Jason C. and Wang, Zheng and Wilson, Andrew W. and Schüßler, Arthur and Longcore, Joyce E. and O’Donnell, Kerry and Mozley-Standridge, Sharon E. and Porter, David and Letcher, Peter M. and Powell, Martha J. and Taylor, John W. and White, Merlin M. and Griffith, Gareth and Davies, D. R. and Humber, Richard A. and Morton, Joseph B. and Sugiyama, Junta and Rossman, Amy Y. and Rogers, Jack D. and Pfister, D.H. and Hewitt, David and Hansen, Karen and Hambleton, Sarah and Shoemaker, R. A. and Kohlmeyer, Jan and Volkmann‐Kohlmeyer, Brigitte and Spotts, Robert A. and Serdani, Maryna and Crous, P.W. and Hughes, Karen W. and Matsuura, Kenji and Langer, Ewald and Langer, Gitta Jutta and Untereiner, Wendy A. and Lücking, Robert and Büdel, Burkhard and Geiser, David M. and Aptroot, André and Diederich, Paul and Schmitt, Imke and Schultz, Matthias and Yahr, Rebecca and Hibbett, David S. and Lutzoni, François and McLaughlin, David J. and Spatafora, Joseph W. and Vilgalys, Rytas",
    title = "Reconstructing the early evolution of Fungi using a six-gene phylogeny",
    year = "2006",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature05110",
    doi = "10.1038/nature05110",
    openalex = "W2054908644",
    references = "doi10108010635150290069913, doi101093bioinformatics183502, openalexw2611511275"
}

Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique ("diagnostic") characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.

@article{doi10108010635150600852011,
    author = "Pons, Joan and Barraclough, Timothy G. and Gómez‐Zurita, Jesús and Cardoso, Anabela and Duran, Daniel P. and Hazell, Steaphan P. and Kamoun, Sophien and Sumlin, W D and Vogler, Alfried P.",
    title = "Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects",
    year = "2006",
    journal = "Systematic Biology",
    abstract = {Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique ("diagnostic") characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.},
    url = "https://doi.org/10.1080/10635150600852011",
    doi = "10.1080/10635150600852011",
    openalex = "W2102883209",
    references = "doi101007978140206754912413, doi10100797814615678136, doi101016s0169534701021619, doi101046j1365294x200001020x, doi101073pnas0406166101, doi101073pnas89178322, doi101073pnas91146491, doi101080106351502753475880, doi101093genetics1322619, doi101093oxfordjournalsmolbeva003974, doi101098rspb20022218, doi101111j109600311999tb00277x, doi101146annurevecolsys34011802132421, doi101146annureven10010165000525, doi101371journalpbio0020312, doi101371journalpbio0030422, doi1023072413039"
}

Parsimony analysis (cladistics) has long been one of the most widely used methods of phylogenetic inference in the fields of systematic and evolutionary biology. Moreover, it has mathematical attributes that lend themselves for use with complex, genomic-sacle data sets. In this book, specialists review philosophical, statistical, methodological, and mathematical aspects of parsimony analysis, and demonstrate the potential that this powerful hierarchical data summarization method has for both structural and functional genomics research.

@book{doi101093acprofoso97801992973060010001,
    author = "Albert, Victor A.",
    title = "Parsimony, Phylogeny, and Genomics",
    year = "2006",
    booktitle = "Oxford University Press eBooks",
    abstract = "Parsimony analysis (cladistics) has long been one of the most widely used methods of phylogenetic inference in the fields of systematic and evolutionary biology. Moreover, it has mathematical attributes that lend themselves for use with complex, genomic-sacle data sets. In this book, specialists review philosophical, statistical, methodological, and mathematical aspects of parsimony analysis, and demonstrate the potential that this powerful hierarchical data summarization method has for both structural and functional genomics research.",
    url = "https://doi.org/10.1093/acprof:oso/9780199297306.001.0001",
    doi = "10.1093/acprof:oso/9780199297306.001.0001",
    openalex = "W1527858535",
    references = "doi101016002555648290027x, doi101111j109600311995tb00092x, doi1023071220820, doi1023072412452, doi1023072992272"
}

Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.

@article{doi10118614712105788,
    author = "Bollback, Jonathan P.",
    title = "SIMMAP: Stochastic character mapping of discrete traits on phylogenies",
    year = "2006",
    journal = "BMC Bioinformatics",
    abstract = "Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.",
    url = "https://doi.org/10.1186/1471-2105-7-88",
    doi = "10.1186/1471-2105-7-88",
    openalex = "W2118207809",
    references = "doi101007bf01734359, doi101016b9781483232119500097, doi10103844766, doi101080106351501753462876, doi101086284325, doi101093bioinformatics178754, doi101093oso97801985464120010001, doi105860choice295104, doi105860choice392183, openalexw2611511275, openalexw638862129"
}

In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.

@article{doi101111j10963642200600293x,
    author = "Livezey, Bradley C. and Zusi, Richard L.",
    title = "Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion",
    year = "2007",
    journal = "Zoological Journal of the Linnean Society",
    abstract = "In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.",
    url = "https://doi.org/10.1111/j.1096-3642.2006.00293.x",
    doi = "10.1111/j.1096-3642.2006.00293.x",
    openalex = "W2153165351",
    references = "crossref1995systematics, doi101002jmor10382, doi101002jmor10406, doi101002jmor1052090107, doi101007bf02101113, doi101016b978012249408650011x, doi101017s0006323197005100, doi101017s1464793102006103, doi101017s1464793105006779, doi101038nature03150, doi101073pnas0507106102, doi10108002724634199410011524, doi10108010635150500234583, doi10108010635150590950326, doi101093oso97801951223430010001, doi101093oso97801985052350010001, doi101093oxfordjournalsmolbeva026092, doi101093sysbio33183, doi101093sysbio422182, doi101098rspb20001368, doi101111j109600311989tb00573x, doi101111j109600311993tb00217x, doi101111j109600312003tb00387x, doi101111j109636422001tb01313x, doi101111j109636422001tb01314x, doi101111j1469185x1997tb00024x, doi101111j146979981991tb04794x, doi101111j155856461959tb03005x, doi101111j155856461985tb00420x, doi101126science2665186779, doi1012060003008220023870001tmappo20co2, doi1012060003009020042860001mptaso20co2, doi1016660094837320050310192meam20co2, doi1023072408678, doi1023072413134, doi1023072992540, doi10230740168337, doi102992014590582006371pon20co2, doi105860choice323881, doi105860choice343307, doi105860choice392183, doi105860choice405235, doi105962bhltitle106607, gregor1988the, openalexw2506868775, openalexw3217097258"
}

Echinoderms have long been characterized by the presence of ambulacra that exhibit pentaradiate symmetry and define five primary body axes. In reality, truly pentaradial ambulacral symmetry is a condition derived only once in the evolutionary history of echinoderms and is restricted to eleutherozoans, the clade that contains most living echinoderm species. In contrast, early echinoderms have a bilaterally symmetrical 2-1-2 arrangement, with three ambulacra radiating from the mouth. Branching of the two side ambulacra during ontogeny produces the five adult rays. During the Cambrian Explosion and Ordovician Radiation, some 30 clades of echinoderms evolved, many of which have aberrant ambulacral systems with one to four rays. Unfortunately, no underlying model has emerged that explains ambulacral homologies among disparate forms. Here we show that most Paleozoic echinoderms are characterized by uniquely identifiable ambulacra that develop in three distinct postlarval stages. Nearly all “aberrant” echinoderm morphologies can be explained by the paedomorphic ambulacra reduction (PAR) model through the loss of some combination of these growth stages during ontogeny. Superficially similar patterns of ambulacral reduction in distantly related clades have resulted from the parallel loss of homologous ambulacra during ontogeny. Pseudo-fivefold symmetry seen in Blastoidea and the true fivefold symmetry seen in Eleutherozoa result from great reduction and total loss, respectively, of the 2–1–2 symmetry early in ontogeny. These ambulacral variations suggest that both developmental and ecological constraints affect the evolution of novel echinoderm body plans.

@article{doi101666060531,
    author = "Sumrall, Colin D. and Wray, Gregory A.",
    title = "Ontogeny in the fossil record: diversification of body plans and the evolution of “aberrant” symmetry in Paleozoic echinoderms",
    year = "2007",
    journal = "Paleobiology",
    abstract = "Echinoderms have long been characterized by the presence of ambulacra that exhibit pentaradiate symmetry and define five primary body axes. In reality, truly pentaradial ambulacral symmetry is a condition derived only once in the evolutionary history of echinoderms and is restricted to eleutherozoans, the clade that contains most living echinoderm species. In contrast, early echinoderms have a bilaterally symmetrical 2-1-2 arrangement, with three ambulacra radiating from the mouth. Branching of the two side ambulacra during ontogeny produces the five adult rays. During the Cambrian Explosion and Ordovician Radiation, some 30 clades of echinoderms evolved, many of which have aberrant ambulacral systems with one to four rays. Unfortunately, no underlying model has emerged that explains ambulacral homologies among disparate forms. Here we show that most Paleozoic echinoderms are characterized by uniquely identifiable ambulacra that develop in three distinct postlarval stages. Nearly all “aberrant” echinoderm morphologies can be explained by the paedomorphic ambulacra reduction (PAR) model through the loss of some combination of these growth stages during ontogeny. Superficially similar patterns of ambulacral reduction in distantly related clades have resulted from the parallel loss of homologous ambulacra during ontogeny. Pseudo-fivefold symmetry seen in Blastoidea and the true fivefold symmetry seen in Eleutherozoa result from great reduction and total loss, respectively, of the 2–1–2 symmetry early in ontogeny. These ambulacral variations suggest that both developmental and ecological constraints affect the evolution of novel echinoderm body plans.",
    url = "https://doi.org/10.1666/06053.1",
    doi = "10.1666/06053.1",
    openalex = "W2020391426"
}

BACKGROUND: Adaptive radiation, the evolution of ecological and phenotypic diversity from a common ancestor, is a central concept in evolutionary biology and characterizes the evolutionary histories of many groups of organisms. One such group is the Mustelidae, the most species-rich family within the mammalian order Carnivora, encompassing 59 species classified into 22 genera. Extant mustelids display extensive ecomorphological diversity, with different lineages having evolved into an array of adaptive zones, from fossorial badgers to semi-aquatic otters. Mustelids are also widely distributed, with multiple genera found on different continents. As with other groups that have undergone adaptive radiation, resolving the phylogenetic history of mustelids presents a number of challenges because ecomorphological convergence may potentially confound morphologically based phylogenetic inferences, and because adaptive radiations often include one or more periods of rapid cladogenesis that require a large amount of data to resolve. RESULTS: We constructed a nearly complete generic-level phylogeny of the Mustelidae using a data matrix comprising 22 gene segments (approximately 12,000 base pairs) analyzed with maximum parsimony, maximum likelihood and Bayesian inference methods. We show that mustelids are consistently resolved with high nodal support into four major clades and three monotypic lineages. Using Bayesian dating techniques, we provide evidence that mustelids underwent two bursts of diversification that coincide with major paleoenvironmental and biotic changes that occurred during the Neogene and correspond with similar bursts of cladogenesis in other vertebrate groups. Biogeographical analyses indicate that most of the extant diversity of mustelids originated in Eurasia and mustelids have colonized Africa, North America and South America on multiple occasions. CONCLUSION: Combined with information from the fossil record, our phylogenetic and dating analyses suggest that mustelid diversification may have been spurred by a combination of faunal turnover events and diversification at lower trophic levels, ultimately caused by climatically driven environmental changes. Our biogeographic analyses show Eurasia as the center of origin of mustelid diversity and that mustelids in Africa, North America and South America have been assembled over time largely via dispersal, which has important implications for understanding the ecology of mustelid communities.

@article{doi10118617417007610,
    author = "Koepfli, Klaus‐Peter and Deere, Kerry A and Slater, Graham J. and Begg, Colleen and Begg, Keith S. and Grassman, Lon I. and Lucherini, Mauro and Veron, Géraldine and Wayne, Robert K.",
    title = "Multigene phylogeny of the Mustelidae: Resolving relationships, tempo and biogeographic history of a mammalian adaptive radiation",
    year = "2008",
    journal = "BMC Biology",
    abstract = "BACKGROUND: Adaptive radiation, the evolution of ecological and phenotypic diversity from a common ancestor, is a central concept in evolutionary biology and characterizes the evolutionary histories of many groups of organisms. One such group is the Mustelidae, the most species-rich family within the mammalian order Carnivora, encompassing 59 species classified into 22 genera. Extant mustelids display extensive ecomorphological diversity, with different lineages having evolved into an array of adaptive zones, from fossorial badgers to semi-aquatic otters. Mustelids are also widely distributed, with multiple genera found on different continents. As with other groups that have undergone adaptive radiation, resolving the phylogenetic history of mustelids presents a number of challenges because ecomorphological convergence may potentially confound morphologically based phylogenetic inferences, and because adaptive radiations often include one or more periods of rapid cladogenesis that require a large amount of data to resolve. RESULTS: We constructed a nearly complete generic-level phylogeny of the Mustelidae using a data matrix comprising 22 gene segments (approximately 12,000 base pairs) analyzed with maximum parsimony, maximum likelihood and Bayesian inference methods. We show that mustelids are consistently resolved with high nodal support into four major clades and three monotypic lineages. Using Bayesian dating techniques, we provide evidence that mustelids underwent two bursts of diversification that coincide with major paleoenvironmental and biotic changes that occurred during the Neogene and correspond with similar bursts of cladogenesis in other vertebrate groups. Biogeographical analyses indicate that most of the extant diversity of mustelids originated in Eurasia and mustelids have colonized Africa, North America and South America on multiple occasions. CONCLUSION: Combined with information from the fossil record, our phylogenetic and dating analyses suggest that mustelid diversification may have been spurred by a combination of faunal turnover events and diversification at lower trophic levels, ultimately caused by climatically driven environmental changes. Our biogeographic analyses show Eurasia as the center of origin of mustelid diversity and that mustelids in Africa, North America and South America have been assembled over time largely via dispersal, which has important implications for understanding the ecology of mustelid communities.",
    url = "https://doi.org/10.1186/1741-7007-6-10",
    doi = "10.1186/1741-7007-6-10",
    openalex = "W1969810115",
    references = "doi101093oso97801985771880010001, doi101126science1122277"
}

@article{doi101016jtree201005002,
    author = "Quental, Tiago B. and Marshall, Charles R.",
    title = "Diversity dynamics: molecular phylogenies need the fossil record",
    year = "2010",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/j.tree.2010.05.002",
    doi = "10.1016/j.tree.2010.05.002",
    openalex = "W2157452947",
    references = "doi101017s0094837300016134, doi101073pnas111144698, doi101111j14754983200600612x"
}

It has been argued that increases in predation over geological time should result in increases in defensive adaptations in prey taxa. Recent in situ and laboratory observations indicate that cidaroid sea urchins feed on live stalked crinoids, leaving distinct bite marks on their skeletal elements. Similar bite marks on fossil crinoids from Poland strongly suggest that these animals have been subject to echinoid predation since the Triassic. Following their near-demise during the end-Permian extinction, crinoids underwent a major evolutionary radiation during the Middle-Late Triassic that produced distinct morphological and behavioral novelties, particularly motile taxa that contrasted strongly with the predominantly sessile Paleozoic crinoid faunas. We suggest that the appearance and subsequent evolutionary success of motile crinoids were related to benthic predation by post-Paleozoic echinoids with their stronger and more active feeding apparatus and that, in the case of crinoids, the predation-driven Mesozoic marine revolution started earlier than in other groups, perhaps soon after the end-Permian extinction.

@article{doi101073pnas0914199107,
    author = "Baumiller, Tomasz K. and Salamon, Mariusz A. and Gorzelak, Przemysław and Mooi, Rich and Messing, Charles G. and Gahn, Forest J.",
    title = "Post-Paleozoic crinoid radiation in response to benthic predation preceded the Mesozoic marine revolution",
    year = "2010",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "It has been argued that increases in predation over geological time should result in increases in defensive adaptations in prey taxa. Recent in situ and laboratory observations indicate that cidaroid sea urchins feed on live stalked crinoids, leaving distinct bite marks on their skeletal elements. Similar bite marks on fossil crinoids from Poland strongly suggest that these animals have been subject to echinoid predation since the Triassic. Following their near-demise during the end-Permian extinction, crinoids underwent a major evolutionary radiation during the Middle-Late Triassic that produced distinct morphological and behavioral novelties, particularly motile taxa that contrasted strongly with the predominantly sessile Paleozoic crinoid faunas. We suggest that the appearance and subsequent evolutionary success of motile crinoids were related to benthic predation by post-Paleozoic echinoids with their stronger and more active feeding apparatus and that, in the case of crinoids, the predation-driven Mesozoic marine revolution started earlier than in other groups, perhaps soon after the end-Permian extinction.",
    url = "https://doi.org/10.1073/pnas.0914199107",
    doi = "10.1073/pnas.0914199107",
    openalex = "W2064012062",
    references = "doi101017s0022336000061321, doi105281zenodo16046014, kier1974evolutionary"
}

The relationships of post-Palaeozoic echinoids at family level are established through phylogenetic analysis of 169 taxa and 306 skeletal characters (excluding pedicellariae). Previous phylogenetic analyses of echinoids have either examined specific subgroups in detail or have looked at a relatively small number of taxa selected from across the class, with sparse sampling potentially affecting the reliability of results adversely. Our new analyses represent a compromise between encompassing the diversity of form that exists, while keeping the number of taxa to a level that does not make rigorous analysis impossibly time-consuming. In constructing the taxon-character data matrix we have encountered a surprising lack of primary data on plating pattern, lantern, and girdle structure for many supposedly "well-known" taxa. A well-resolved phylogenetic hypothesis was obtained and is used as the basis for a formal classification. Characters generally have a high retention index (>0.7) but low consistency index (<0.25) suggesting that, although characters are largely retained after they first evolve, most also undergo occasional reversal or convergence. Although parts of the resulting trees are only weakly supported (e.g. the precise sister group of the Irregularia), other parts are unambiguously resolved. Not unexpectedly, deep nodes are often not supported by unique apomorphies and higher taxa acquire their characteristic set of features over time. Diagnoses based on crown group taxa thus often fail to encompass fossil stem-group members adequately. Establishing the relationships of taxa at the root of large groups is hampered by limited character resolution. The influence of fossil taxa on the topology was explored by comparing the tree topologies obtained with and without their inclusion. We show that removal of fossils from stem groups makes no difference where their crown group is morphologically conservative, but has a major influence where extant sister groups are separated by large morphological gaps. Completeness of the echinoid record and its match to the stratigraphical record of first occurrences is tested using various metrics and found to be highly congruent, with irregular echinoids showing a higher congruence than regular ones.

@article{doi10108014772011003603556,
    author = "Kroh, Andreas and Smith, Andrew B.",
    title = "The phylogeny and classification of post-Palaeozoic echinoids",
    year = "2010",
    journal = "Journal of Systematic Palaeontology",
    abstract = {The relationships of post-Palaeozoic echinoids at family level are established through phylogenetic analysis of 169 taxa and 306 skeletal characters (excluding pedicellariae). Previous phylogenetic analyses of echinoids have either examined specific subgroups in detail or have looked at a relatively small number of taxa selected from across the class, with sparse sampling potentially affecting the reliability of results adversely. Our new analyses represent a compromise between encompassing the diversity of form that exists, while keeping the number of taxa to a level that does not make rigorous analysis impossibly time-consuming. In constructing the taxon-character data matrix we have encountered a surprising lack of primary data on plating pattern, lantern, and girdle structure for many supposedly "well-known" taxa. A well-resolved phylogenetic hypothesis was obtained and is used as the basis for a formal classification. Characters generally have a high retention index (>0.7) but low consistency index (<0.25) suggesting that, although characters are largely retained after they first evolve, most also undergo occasional reversal or convergence. Although parts of the resulting trees are only weakly supported (e.g. the precise sister group of the Irregularia), other parts are unambiguously resolved. Not unexpectedly, deep nodes are often not supported by unique apomorphies and higher taxa acquire their characteristic set of features over time. Diagnoses based on crown group taxa thus often fail to encompass fossil stem-group members adequately. Establishing the relationships of taxa at the root of large groups is hampered by limited character resolution. The influence of fossil taxa on the topology was explored by comparing the tree topologies obtained with and without their inclusion. We show that removal of fossils from stem groups makes no difference where their crown group is morphologically conservative, but has a major influence where extant sister groups are separated by large morphological gaps. Completeness of the echinoid record and its match to the stratigraphical record of first occurrences is tested using various metrics and found to be highly congruent, with irregular echinoids showing a higher congruence than regular ones.},
    url = "https://doi.org/10.1080/14772011003603556",
    doi = "10.1080/14772011003603556",
    openalex = "W2072979411",
    references = "doi1010160031018268900989, doi101017s0022336000061321, doi101017s0094837300005248, doi101038019118a0, doi101038114085a0, doi10108010635150290102339, doi101093nqs5vi146318i, doi101111j00310239200400364x, doi101111j109600311999tb00277x, doi101111j10960031200800209x, doi101111j14636409200500201x, doi101111j146979981833tb06418x, doi101126science972526482b, doi103133pp321, doi105281zenodo16046014, doi105962bhltitle126954, doi105962bhltitle156765, doi105962bhltitle542, kier1974evolutionary, openalexw2894525608, openalexw635257420"
}

@article{doi101016jympev201209018,
    author = "Rouse, Greg W. and Jermiin, Lars S. and Wilson, Nerida G. and Eeckhaut, Igor and Lanterbecq, Déborah and Oji, Tatsuo and Young, Craig M. and Browning, Teena L. and Cisternas, Paula and Helgen, Lauren E. and Stuckey, Michelle and Messing, Charles G.",
    title = "Fixed, free, and fixed: The fickle phylogeny of extant Crinoidea (Echinodermata) and their Permian–Triassic origin",
    year = "2012",
    journal = "Molecular Phylogenetics and Evolution",
    url = "https://doi.org/10.1016/j.ympev.2012.09.018",
    doi = "10.1016/j.ympev.2012.09.018",
    openalex = "W2116958898",
    references = "doi1010160031018268900989, doi101111j1469185x1984tb00411x"
}

Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4--20 complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.].

@article{doi101093sysbiosys058,
    author = "Ronquist, Fredrik and Klopfstein, Seraina and Vilhelmsen, Lars and Schulmeister, Susanne and Murray, Debra L. and Rasnitsyn, Alexandr P.",
    title = "A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera",
    year = "2012",
    journal = "Systematic Biology",
    abstract = "Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4--20 complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95\% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.].",
    url = "https://doi.org/10.1093/sysbio/sys058",
    doi = "10.1093/sysbio/sys058",
    openalex = "W2159597448",
    references = "doi101016jympev201104003, doi10108010635150290102456, doi101093molbevmsm193, doi101093sysbiosyq085, doi101093sysbiosyr047, doi101093sysbiosyr107, openalexw1900040508, openalexw2733548038"
}

@incollection{doi101016b9780123964915000010,
    author = "Smith, Andrew B. and Kroh, Andreas",
    title = "Phylogeny of Sea Urchins",
    year = "2013",
    booktitle = "Developments in aquaculture and fisheries science",
    url = "https://doi.org/10.1016/b978-0-12-396491-5.00001-0",
    doi = "10.1016/b978-0-12-396491-5.00001-0",
    openalex = "W28941992",
    references = "doi101111j00310239200400364x"
}

A key measure of humanity's global impact is by how much it has increased species extinction rates. Familiar statements are that these are 100-1000 times pre-human or background extinction levels. Estimating recent rates is straightforward, but establishing a background rate for comparison is not. Previous researchers chose an approximate benchmark of 1 extinction per million species per year (E/MSY). We explored disparate lines of evidence that suggest a substantially lower estimate. Fossil data yield direct estimates of extinction rates, but they are temporally coarse, mostly limited to marine hard-bodied taxa, and generally involve genera not species. Based on these data, typical background loss is 0.01 genera per million genera per year. Molecular phylogenies are available for more taxa and ecosystems, but it is debated whether they can be used to estimate separately speciation and extinction rates. We selected data to address known concerns and used them to determine median extinction estimates from statistical distributions of probable values for terrestrial plants and animals. We then created simulations to explore effects of violating model assumptions. Finally, we compiled estimates of diversification-the difference between speciation and extinction rates for different taxa. Median estimates of extinction rates ranged from 0.023 to 0.135 E/MSY. Simulation results suggested over- and under-estimation of extinction from individual phylogenies partially canceled each other out when large sets of phylogenies were analyzed. There was no evidence for recent and widespread pre-human overall declines in diversity. This implies that average extinction rates are less than average diversification rates. Median diversification rates were 0.05-0.2 new species per million species per year. On the basis of these results, we concluded that typical rates of background extinction may be closer to 0.1 E/MSY. Thus, current extinction rates are 1,000 times higher than natural background rates of extinction and future rates are likely to be 10,000 times higher.

@article{doi101111cobi12380,
    author = "de Vos, Jurriaan M. and Joppa, Lucas and Gittleman, John L. and Stephens, Patrick R. and Pimm, Stuart L.",
    title = "Estimating the normal background rate of species extinction",
    year = "2014",
    journal = "Conservation Biology",
    abstract = "A key measure of humanity's global impact is by how much it has increased species extinction rates. Familiar statements are that these are 100-1000 times pre-human or background extinction levels. Estimating recent rates is straightforward, but establishing a background rate for comparison is not. Previous researchers chose an approximate benchmark of 1 extinction per million species per year (E/MSY). We explored disparate lines of evidence that suggest a substantially lower estimate. Fossil data yield direct estimates of extinction rates, but they are temporally coarse, mostly limited to marine hard-bodied taxa, and generally involve genera not species. Based on these data, typical background loss is 0.01 genera per million genera per year. Molecular phylogenies are available for more taxa and ecosystems, but it is debated whether they can be used to estimate separately speciation and extinction rates. We selected data to address known concerns and used them to determine median extinction estimates from statistical distributions of probable values for terrestrial plants and animals. We then created simulations to explore effects of violating model assumptions. Finally, we compiled estimates of diversification-the difference between speciation and extinction rates for different taxa. Median estimates of extinction rates ranged from 0.023 to 0.135 E/MSY. Simulation results suggested over- and under-estimation of extinction from individual phylogenies partially canceled each other out when large sets of phylogenies were analyzed. There was no evidence for recent and widespread pre-human overall declines in diversity. This implies that average extinction rates are less than average diversification rates. Median diversification rates were 0.05-0.2 new species per million species per year. On the basis of these results, we concluded that typical rates of background extinction may be closer to 0.1 E/MSY. Thus, current extinction rates are 1,000 times higher than natural background rates of extinction and future rates are likely to be 10,000 times higher.",
    url = "https://doi.org/10.1111/cobi.12380",
    doi = "10.1111/cobi.12380",
    openalex = "W2114051274",
    references = "doi101017s0094837300016134, doi101038ncomms2958, doi101098rspb20080630, doi101146annurevecolsys37091305110035, doi1016660094837320050310006poaeit20co2, doi10560219780801882210"
}

Abstract strap (S tratigraphic T ree A nalysis for P alaeontology) is a new package for the freely available statistical programming language R designed to perform three main tasks: (1) to time‐scale phylogenies of fossil taxa; (2) to plot those time‐scaled trees against stratigraphy; and (3) to assess congruence between phylogenies and stratigraphy. Time‐scaling is performed with the DatePhylo function, with three approaches offered. Plotting trees against a choice of five different geological time scaless is possible using the geoscalePhylo function. Finally, the function StratPhyloCongruence calculates stratigraphic congruence measures for one or more input phylogenies, with no taxon limit. All three major congruence measures are offered: S tratigraphic C onsistency I ndex (SCI), M anhattan S tratigraphic M easure (MSM *) and the gap excess ratio (GER; including GER t and GER *), as well as the pseudocongruence measure, the R elative C ompleteness I ndex (RCI). Each measure has an accompanying significance test that works by comparing the input trees against a user‐defined number of randomly generated topologies with the same taxon set and age ranges. Additional options for generating these random topologies allow the user to fix the outgroup or retain the input tree shape to make fairer comparisons. A tutorial that assumes no prior knowledge of R showcases all three functions using two different example data sets.

@article{doi101111pala12142,
    author = "Bell, Mark A. and Lloyd, Graeme T.",
    title = "strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence",
    year = "2014",
    journal = "Palaeontology",
    abstract = "Abstract strap (S tratigraphic T ree A nalysis for P alaeontology) is a new package for the freely available statistical programming language R designed to perform three main tasks: (1) to time‐scale phylogenies of fossil taxa; (2) to plot those time‐scaled trees against stratigraphy; and (3) to assess congruence between phylogenies and stratigraphy. Time‐scaling is performed with the DatePhylo function, with three approaches offered. Plotting trees against a choice of five different geological time scaless is possible using the geoscalePhylo function. Finally, the function StratPhyloCongruence calculates stratigraphic congruence measures for one or more input phylogenies, with no taxon limit. All three major congruence measures are offered: S tratigraphic C onsistency I ndex (SCI), M anhattan S tratigraphic M easure (MSM *) and the gap excess ratio (GER; including GER t and GER *), as well as the pseudocongruence measure, the R elative C ompleteness I ndex (RCI). Each measure has an accompanying significance test that works by comparing the input trees against a user‐defined number of randomly generated topologies with the same taxon set and age ranges. Additional options for generating these random topologies allow the user to fix the outgroup or retain the input tree shape to make fairer comparisons. A tutorial that assumes no prior knowledge of R showcases all three functions using two different example data sets.",
    url = "https://doi.org/10.1111/pala.12142",
    doi = "10.1111/pala.12142",
    openalex = "W2058630418",
    references = "crossref1995systematics, doi101093bioinformaticsbtg412, doi101093sysbio1811, doi101093sysbiosys058, doi101098rspb20080715, doi101111j10960031200800217x, doi101111j2041210x201200223x, doi101126science1161833, doi101126science1252243, doi1018814epiiugs2013v36i3002, doi1023072412407, doi1023072412810, doi105860choice323881, openalexw2611511275, openalexw2989049194, openalexw592572837"
}

How ecological and morphological diversity accrues over geological time has been much debated by paleobiologists. Evidence from the fossil record suggests that many clades reach maximal diversity early in their evolutionary history, followed by a decline in evolutionary rates as ecological space fills or due to internal constraints. Here, we apply recently developed methods for estimating rates of morphological evolution during the post-Paleozoic history of a major invertebrate clade, the Echinoidea. Contrary to expectation, rates of evolution were lowest during the initial phase of diversification following the Permo-Triassic mass extinction and increased over time. Furthermore, although several subclades show high initial rates and net decreases in rates of evolution, consistent with "early bursts" of morphological diversification, at more inclusive taxonomic levels, these bursts appear as episodic peaks. Peak rates coincided with major shifts in ecological morphology, primarily associated with innovations in feeding strategies. Despite having similar numbers of species in today's oceans, regular echinoids have accrued far less morphological diversity than irregular echinoids due to lower intrinsic rates of morphological evolution and less morphological innovation, the latter indicative of constrained or bounded evolution. These results indicate that rates of evolution are extremely heterogenous through time and their interpretation depends on the temporal and taxonomic scale of analysis.

@article{doi101073pnas1418153112,
    author = "Hopkins, Melanie J. and Smith, Andrew B.",
    title = "Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution",
    year = "2015",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = {How ecological and morphological diversity accrues over geological time has been much debated by paleobiologists. Evidence from the fossil record suggests that many clades reach maximal diversity early in their evolutionary history, followed by a decline in evolutionary rates as ecological space fills or due to internal constraints. Here, we apply recently developed methods for estimating rates of morphological evolution during the post-Paleozoic history of a major invertebrate clade, the Echinoidea. Contrary to expectation, rates of evolution were lowest during the initial phase of diversification following the Permo-Triassic mass extinction and increased over time. Furthermore, although several subclades show high initial rates and net decreases in rates of evolution, consistent with "early bursts" of morphological diversification, at more inclusive taxonomic levels, these bursts appear as episodic peaks. Peak rates coincided with major shifts in ecological morphology, primarily associated with innovations in feeding strategies. Despite having similar numbers of species in today's oceans, regular echinoids have accrued far less morphological diversity than irregular echinoids due to lower intrinsic rates of morphological evolution and less morphological innovation, the latter indicative of constrained or bounded evolution. These results indicate that rates of evolution are extremely heterogenous through time and their interpretation depends on the temporal and taxonomic scale of analysis.},
    url = "https://doi.org/10.1073/pnas.1418153112",
    doi = "10.1073/pnas.1418153112",
    openalex = "W2068132819",
    references = "doi10108014772011003603556, doi1016660094837320000260056cefisg20co2"
}

Abstract Phylogenetic relationships among early crinoids are evaluated by maximizing parsimonious‐informative characters that are unordered and unweighted. Primarily T remadocian– D arriwilian (E arly– M iddle O rdovician) taxa are analysed. Stratigraphic congruence metrics support the best phylogenetic hypothesis derived using parsimony methods. This study confirms the traditionally recognized lineages of P alaeozoic crinoids and provides new information on the branching order of evolving lineages. Camerates are basal crinoids with progressively more tipward groups (from an O rdovician perspective) being protocrinoids, cladids (paraphyletic), hybocrinids and disparids. The P rotocrinoida should be maintained, but the A ethocrinida should be placed within the C ladida. The results of this study identify phylogenetic structure amongst the major early crinoid lineages and delineate the relative positions of crinoid higher taxa along a tree. Each valid higher taxon discussed herein requires a comprehensive treatment to delimit within‐lineage phylogenetic relationships.

@article{doi101111pala12204,
    author = "Ausich, William I. and Kammer, Thomas and Rhenberg, Elizabeth C. and Wright, David F.",
    title = "Early phylogeny of crinoids within the pelmatozoan clade",
    year = "2015",
    journal = "Palaeontology",
    abstract = "Abstract Phylogenetic relationships among early crinoids are evaluated by maximizing parsimonious‐informative characters that are unordered and unweighted. Primarily T remadocian– D arriwilian (E arly– M iddle O rdovician) taxa are analysed. Stratigraphic congruence metrics support the best phylogenetic hypothesis derived using parsimony methods. This study confirms the traditionally recognized lineages of P alaeozoic crinoids and provides new information on the branching order of evolving lineages. Camerates are basal crinoids with progressively more tipward groups (from an O rdovician perspective) being protocrinoids, cladids (paraphyletic), hybocrinids and disparids. The P rotocrinoida should be maintained, but the A ethocrinida should be placed within the C ladida. The results of this study identify phylogenetic structure amongst the major early crinoid lineages and delineate the relative positions of crinoid higher taxa along a tree. Each valid higher taxon discussed herein requires a comprehensive treatment to delimit within‐lineage phylogenetic relationships.",
    url = "https://doi.org/10.1111/pala.12204",
    doi = "10.1111/pala.12204",
    openalex = "W1934510031"
}

Abstract Xiphosurids are an archaic group of aquatic chelicerate arthropods, generally known by the colloquial misnomer of ‘horseshoe crabs’. Known from marine environments as far back as the early O rdovician, horseshoe crabs are generally considered ‘living fossils’ – descendants of a bradytelic lineage exhibiting little morphological or ecological variation throughout geological time. However, xiphosurids are known from freshwater sediments in the P alaeozoic and M esozoic; furthermore, the contention that xiphosurids show little morphological variation has never been tested empirically. Attempts to test this are hampered by the lack of a modern phylogenetic framework with which to explore different evolutionary scenarios. Here, I present a phylogenetic analysis of X iphosurida and explore patterns of morphospace and environmental occupation of the group throughout the P hanerozoic. X iphosurids are shown to have invaded non‐marine environments independently at least five times throughout their evolutionary history, twice resulting in the radiation of major clades – bellinurines and austrolimulids – that occupied novel regions of morphospace. These clades show a convergent ecological pattern of differentiation, speciation and subsequent extinction. Horseshoe crabs are shown to have a more dynamic and complex evolutionary history than previously supposed, with the extant species representing only a fraction of the group's past ecological and morphological diversity.

@article{doi101111pala12220,
    author = "Lamsdell, James C.",
    title = "Horseshoe crab phylogeny and independent colonizations of fresh water: ecological invasion as a driver for morphological innovation",
    year = "2015",
    journal = "Palaeontology",
    abstract = "Abstract Xiphosurids are an archaic group of aquatic chelicerate arthropods, generally known by the colloquial misnomer of ‘horseshoe crabs’. Known from marine environments as far back as the early O rdovician, horseshoe crabs are generally considered ‘living fossils’ – descendants of a bradytelic lineage exhibiting little morphological or ecological variation throughout geological time. However, xiphosurids are known from freshwater sediments in the P alaeozoic and M esozoic; furthermore, the contention that xiphosurids show little morphological variation has never been tested empirically. Attempts to test this are hampered by the lack of a modern phylogenetic framework with which to explore different evolutionary scenarios. Here, I present a phylogenetic analysis of X iphosurida and explore patterns of morphospace and environmental occupation of the group throughout the P hanerozoic. X iphosurids are shown to have invaded non‐marine environments independently at least five times throughout their evolutionary history, twice resulting in the radiation of major clades – bellinurines and austrolimulids – that occupied novel regions of morphospace. These clades show a convergent ecological pattern of differentiation, speciation and subsequent extinction. Horseshoe crabs are shown to have a more dynamic and complex evolutionary history than previously supposed, with the extant species representing only a fraction of the group's past ecological and morphological diversity.",
    url = "https://doi.org/10.1111/pala.12220",
    doi = "10.1111/pala.12220",
    openalex = "W2173155428",
    references = "doi101111j14754983201101103x, doi101111pala12142"
}

Despite their profound adaptations to the aquatic realm and their apparent success throughout the Triassic and the Jurassic, ichthyosaurs became extinct roughly 30 million years before the end-Cretaceous mass extinction. Current hypotheses for this early demise involve relatively minor biotic events, but are at odds with recent understanding of the ichthyosaur fossil record. Here, we show that ichthyosaurs maintained high but diminishing richness and disparity throughout the Early Cretaceous. The last ichthyosaurs are characterized by reduced rates of origination and phenotypic evolution and their elevated extinction rates correlate with increased environmental volatility. In addition, we find that ichthyosaurs suffered from a profound Early Cenomanian extinction that reduced their ecological diversity, likely contributing to their final extinction at the end of the Cenomanian. Our results support a growing body of evidence revealing that global environmental change resulted in a major, temporally staggered turnover event that profoundly reorganized marine ecosystems during the Cenomanian.

@article{doi101038ncomms10825,
    author = "Fischer, Valentin and Bardet, Nathalie and Benson, Roger and Arkhangelsky, M. S. and Friedman, Matt",
    title = "Extinction of fish-shaped marine reptiles associated with reduced evolutionary rates and global environmental volatility",
    year = "2016",
    journal = "Nature Communications",
    abstract = "Despite their profound adaptations to the aquatic realm and their apparent success throughout the Triassic and the Jurassic, ichthyosaurs became extinct roughly 30 million years before the end-Cretaceous mass extinction. Current hypotheses for this early demise involve relatively minor biotic events, but are at odds with recent understanding of the ichthyosaur fossil record. Here, we show that ichthyosaurs maintained high but diminishing richness and disparity throughout the Early Cretaceous. The last ichthyosaurs are characterized by reduced rates of origination and phenotypic evolution and their elevated extinction rates correlate with increased environmental volatility. In addition, we find that ichthyosaurs suffered from a profound Early Cenomanian extinction that reduced their ecological diversity, likely contributing to their final extinction at the end of the Cenomanian. Our results support a growing body of evidence revealing that global environmental change resulted in a major, temporally staggered turnover event that profoundly reorganized marine ecosystems during the Cenomanian.",
    url = "https://doi.org/10.1038/ncomms10825",
    doi = "10.1038/ncomms10825",
    openalex = "W2295669701",
    references = "doi101016jcub201410064, doi101016jgloplacha201312007, doi101017cbo9780511802461005, doi101017s0016756812000994, doi1010292001pa000623, doi10108002724634199910011160, doi101080027246342011595464, doi101093bioinformaticsbtg180, doi101093bioinformaticsbtg412, doi101098rspb20091845, doi101111brv12038, doi101111brv12203, doi101111j2041210x201200223x, doi101111pala12142, doi101126scienceaaa3716, doi101371journalpone0029234, doi101371journalpone0031838, doi101371journalpone0103152, doi1023071268794, doi1023073802723, druckenmiller2010a, openalexw2896296657"
}

Ophiuroid systematics is currently in a state of upheaval, with recent molecular estimates fundamentally clashing with traditional, morphology-based classifications. Here, we attempt a long overdue recast of a morphological phylogeny estimate of the Ophiuroidea taking into account latest insights on microstructural features of the arm skeleton. Our final estimate is based on a total of 45 ingroup taxa, including 41 recent species covering the full range of extant ophiuroid higher taxon diversity and 4 fossil species known from exceptionally preserved material, and the Lower Carboniferous Aganaster gregarius as the outgroup. A total of 130 characters were scored directly on specimens. The tree resulting from the Bayesian inference analysis of the full data matrix is reasonably well resolved and well supported, and refutes all previous classifications, with most traditional families discredited as poly- or paraphyletic. In contrast, our tree agrees remarkably well with the latest molecular estimate, thus paving the way towards an integrated new classification of the Ophiuroidea. Among the characters which were qualitatively found to accord best with our tree topology, we selected a list of potential synapomorphies for future formal clade definitions. Furthermore, an analysis with 13 of the ingroup taxa reduced to the lateral arm plate characters produced a tree which was essentially similar to the full dataset tree. This suggests that dissociated lateral arm plates can be analysed in combination with fully known taxa and thus effectively unlocks the extensive record of fossil lateral arm plates for phylogenetic estimates. Finally, the age and position within our tree implies that the ophiuroid crown-group had started to diversify by the Early Triassic.

@article{doi101371journalpone0156140,
    author = "Thuy, Ben and Stöhr, Sabine",
    title = "A New Morphological Phylogeny of the Ophiuroidea (Echinodermata) Accords with Molecular Evidence and Renders Microfossils Accessible for Cladistics",
    year = "2016",
    journal = "PLoS ONE",
    abstract = "Ophiuroid systematics is currently in a state of upheaval, with recent molecular estimates fundamentally clashing with traditional, morphology-based classifications. Here, we attempt a long overdue recast of a morphological phylogeny estimate of the Ophiuroidea taking into account latest insights on microstructural features of the arm skeleton. Our final estimate is based on a total of 45 ingroup taxa, including 41 recent species covering the full range of extant ophiuroid higher taxon diversity and 4 fossil species known from exceptionally preserved material, and the Lower Carboniferous Aganaster gregarius as the outgroup. A total of 130 characters were scored directly on specimens. The tree resulting from the Bayesian inference analysis of the full data matrix is reasonably well resolved and well supported, and refutes all previous classifications, with most traditional families discredited as poly- or paraphyletic. In contrast, our tree agrees remarkably well with the latest molecular estimate, thus paving the way towards an integrated new classification of the Ophiuroidea. Among the characters which were qualitatively found to accord best with our tree topology, we selected a list of potential synapomorphies for future formal clade definitions. Furthermore, an analysis with 13 of the ingroup taxa reduced to the lateral arm plate characters produced a tree which was essentially similar to the full dataset tree. This suggests that dissociated lateral arm plates can be analysed in combination with fully known taxa and thus effectively unlocks the extensive record of fossil lateral arm plates for phylogenetic estimates. Finally, the age and position within our tree implies that the ophiuroid crown-group had started to diversify by the Early Triassic.",
    url = "https://doi.org/10.1371/journal.pone.0156140",
    doi = "10.1371/journal.pone.0156140",
    openalex = "W2408106615",
    references = "doi10108014772011003603556"
}

@article{doi101016jympev201702014,
    author = "Miller, Allison K. and Kerr, Alexander M. and Paulay, Gustav and Reich, Mike and Wilson, Nerida G. and Carvajal, Jose I. and Rouse, Greg W.",
    title = "Molecular phylogeny of extant Holothuroidea (Echinodermata)",
    year = "2017",
    journal = "Molecular Phylogenetics and Evolution",
    url = "https://doi.org/10.1016/j.ympev.2017.02.014",
    doi = "10.1016/j.ympev.2017.02.014",
    openalex = "W2593325434",
    references = "doi101111j1469185x1984tb00411x"
}

Abstract The subclass Camerata (Crinoidea, Echinodermata) is a major group of Paleozoic crinoids that represents an early divergence in the evolutionary history and morphologic diversification of class Crinoidea, yet phylogenetic relationships among early camerates remain unresolved. This study conducted a series of quantitative phylogenetic analyses using parsimony methods to infer relationships of all well-preserved Ordovician camerate genera (52 taxa), establish the branching sequence of early camerates, and test the monophyly of traditionally recognized higher taxa, including orders Monobathrida and Diplobathrida. The first phylogenetic analysis identified a suitable outroup for rooting the Ordovician camerate tree and assessed affinities of the atypical dicyclic family Reteocrinidae. The second analysis inferred the phylogeny of all well-preserved Ordovician camerate genera. Inferred phylogenies confirm: (1) the Tremadocian genera Cnemecrinus and Eknomocrinus are sister to the Camerata; (2) as historically defined, orders Monobathrida and Diplobathrida do not represent monophyletic groups; (3) with minimal revision, Monobathrida and Diplobathrida can be re-diagnosed to represent monophyletic clades; (4) family Reteocrinidae is more closely related to camerates than to other crinoid groups currently recognized at the subclass level; and (5) several genera in subclass Camerata represent stem taxa that cannot be classified as either true monobathrids or true diplobathrids. The clade containing Monobathrida and Diplobathrida, as recognized herein, is termed Eucamerata to distinguish its constituent taxa from more basally positioned taxa, termed stem eucamerates. The results of this study provide a phylogenetic framework for revising camerate classification, elucidating patterns of morphologic evolution, and informing outgroup selection for future phylogenetic analyses of post-Ordovician camerates.

@article{doi101017jpa2016137,
    author = "Cole, Selina R.",
    title = "Phylogeny and morphologic evolution of the Ordovician Camerata (Class Crinoidea, Phylum Echinodermata)",
    year = "2017",
    journal = "Journal of Paleontology",
    abstract = "Abstract The subclass Camerata (Crinoidea, Echinodermata) is a major group of Paleozoic crinoids that represents an early divergence in the evolutionary history and morphologic diversification of class Crinoidea, yet phylogenetic relationships among early camerates remain unresolved. This study conducted a series of quantitative phylogenetic analyses using parsimony methods to infer relationships of all well-preserved Ordovician camerate genera (52 taxa), establish the branching sequence of early camerates, and test the monophyly of traditionally recognized higher taxa, including orders Monobathrida and Diplobathrida. The first phylogenetic analysis identified a suitable outroup for rooting the Ordovician camerate tree and assessed affinities of the atypical dicyclic family Reteocrinidae. The second analysis inferred the phylogeny of all well-preserved Ordovician camerate genera. Inferred phylogenies confirm: (1) the Tremadocian genera Cnemecrinus and Eknomocrinus are sister to the Camerata; (2) as historically defined, orders Monobathrida and Diplobathrida do not represent monophyletic groups; (3) with minimal revision, Monobathrida and Diplobathrida can be re-diagnosed to represent monophyletic clades; (4) family Reteocrinidae is more closely related to camerates than to other crinoid groups currently recognized at the subclass level; and (5) several genera in subclass Camerata represent stem taxa that cannot be classified as either true monobathrids or true diplobathrids. The clade containing Monobathrida and Diplobathrida, as recognized herein, is termed Eucamerata to distinguish its constituent taxa from more basally positioned taxa, termed stem eucamerates. The results of this study provide a phylogenetic framework for revising camerate classification, elucidating patterns of morphologic evolution, and informing outgroup selection for future phylogenetic analyses of post-Ordovician camerates.",
    url = "https://doi.org/10.1017/jpa.2016.137",
    doi = "10.1017/jpa.2016.137",
    openalex = "W2586606587",
    references = "doi1010029781444313918, doi1010160031018268900989, doi101017jpa2016142, doi101017jpa201720, doi101017s009483730001280x, doi101017s0094837300016134, doi101111j109600311989tb00573x, doi101111pala12142, doi101130spe46p1, doi101666009483731999251mditer20co2, doi105860choice323881, openalexw2611511275"
}

Abstract Knowledge of phylogenetic relationships among species is fundamental to understanding basic patterns in evolution and underpins nearly all research programs in biology and paleontology. However, most methods of phylogenetic inference typically used by paleontologists do not accommodate the idiosyncrasies of fossil data and therefore do not take full advantage of the information provided by the fossil record. The advent of Bayesian ‘tip-dating’ approaches to phylogeny estimation is especially promising for paleosystematists because time-stamped comparative data can be combined with probabilistic models tailored to accommodate the study of fossil taxa. Under a Bayesian framework, the recently developed fossilized birth–death (FBD) process provides a more realistic tree prior model for paleontological data that accounts for macroevolutionary dynamics, preservation, and sampling when inferring phylogenetic trees containing fossils. In addition, the FBD tree prior allows for the possibility of sampling ancestral morphotaxa. Although paleontologists are increasingly embracing probabilistic phylogenetic methods, these recent developments have not previously been applied to the deep-time invertebrate fossil record. Here, I examine phylogenetic relationships among Ordovician through Devonian crinoids using a Bayesian tip-dating approach. Results support several clades recognized in previous analyses sampling only Ordovician taxa, but also reveal instances where phylogenetic affinities are more complex and extensive revisions are necessary, particularly among the Cladida. The name Porocrinoidea is proposed for a well-supported clade of Ordovician ‘cyathocrine’ cladids and hybocrinids. The Eucladida is proposed as a clade name for the sister group of the Flexibilia herein comprised of cladids variously considered ‘cyathocrines,’ ‘dendrocrines,’ and/or ‘poteriocrines’ by other authors.

@article{doi101017jpa2016141,
    author = "Wright, David F.",
    title = "Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata)",
    year = "2017",
    journal = "Journal of Paleontology",
    abstract = "Abstract Knowledge of phylogenetic relationships among species is fundamental to understanding basic patterns in evolution and underpins nearly all research programs in biology and paleontology. However, most methods of phylogenetic inference typically used by paleontologists do not accommodate the idiosyncrasies of fossil data and therefore do not take full advantage of the information provided by the fossil record. The advent of Bayesian ‘tip-dating’ approaches to phylogeny estimation is especially promising for paleosystematists because time-stamped comparative data can be combined with probabilistic models tailored to accommodate the study of fossil taxa. Under a Bayesian framework, the recently developed fossilized birth–death (FBD) process provides a more realistic tree prior model for paleontological data that accounts for macroevolutionary dynamics, preservation, and sampling when inferring phylogenetic trees containing fossils. In addition, the FBD tree prior allows for the possibility of sampling ancestral morphotaxa. Although paleontologists are increasingly embracing probabilistic phylogenetic methods, these recent developments have not previously been applied to the deep-time invertebrate fossil record. Here, I examine phylogenetic relationships among Ordovician through Devonian crinoids using a Bayesian tip-dating approach. Results support several clades recognized in previous analyses sampling only Ordovician taxa, but also reveal instances where phylogenetic affinities are more complex and extensive revisions are necessary, particularly among the Cladida. The name Porocrinoidea is proposed for a well-supported clade of Ordovician ‘cyathocrine’ cladids and hybocrinids. The Eucladida is proposed as a clade name for the sister group of the Flexibilia herein comprised of cladids variously considered ‘cyathocrines,’ ‘dendrocrines,’ and/or ‘poteriocrines’ by other authors.",
    url = "https://doi.org/10.1017/jpa.2016.141",
    doi = "10.1017/jpa.2016.141",
    openalex = "W2586407476",
    references = "doi10100703064746897, doi1010160016003258906884, doi1010160025556481900432, doi1010160031018268900989, doi101017jpa2016137, doi101017jpa2016142, doi101017jpa201720, doi10108001621459199510476572, doi101080106351501753462876, doi101086284325, doi101093bioinformaticsbtg412, doi101111pala12142, doi101130spe46p1, doi101186147121487214, doi101214ss1177011136, doi101306st6398c26, openalexw3135630760"
}

Abstract Evolutionary transitions to marine habitats occurred frequently among Mesozoic reptiles. Only one such clade survives to the present: sea turtles (Chelonioidea). Other marine turtles originated during the Mesozoic, but uncertain affinities of key fossils have obscured the number of transitions to marine life, and the timing of the origin of marine adaptation in chelonioids. Phylogenetic studies support either a highly‐inclusive chelonioid total‐group including fossil marine clades from the Jurassic and Cretaceous (e.g. protostegids, thalassochelydians, sandownids) or a less inclusive chelonioid total‐group excluding those clades. Under this paradigm, these clades belong outside Cryptodira, and represent at least one additional evolutionary transition to marine life in turtles. We present a new phylogenetic hypothesis informed by high resolution computed tomographic data of living and fossil taxa. Besides a well‐supported Chelonioidea, which includes protostegids, we recover a previously unknown clade of stem‐group turtles, Angolachelonia, which includes the Late Jurassic thalassochelydians, and the Cretaceous–Palaeogene sandownids. Accounting for the Triassic Odontochelys, our results indicate three independent evolutionary transitions to marine life in non‐pleurodiran turtles (plus an additional two‐three in pleurodires). Among all independent origins of marine habits, a pelagic ecology only evolved once, among chelonioids. All turtle groups that independently invaded marine habitats in the Jurassic–Cretaceous (chelonioids, angolachelonians, bothremydid pleurodires) survived the Cretaceous–Palaeogene mass extinction event. This highlights extensive survival of marine turtles compared to other marine reptiles. Furthermore, deeply‐nested clades such as chelonioids are found by the middle Early Cretaceous, suggesting a rapid diversification of crown‐group turtles during the Early Cretaceous.

@article{doi101111pala12384,
    author = "Evers, Serjoscha and Benson, Roger",
    title = "A new phylogenetic hypothesis of turtles with implications for the timing and number of evolutionary transitions to marine lifestyles in the group",
    year = "2018",
    journal = "Palaeontology",
    abstract = "Abstract Evolutionary transitions to marine habitats occurred frequently among Mesozoic reptiles. Only one such clade survives to the present: sea turtles (Chelonioidea). Other marine turtles originated during the Mesozoic, but uncertain affinities of key fossils have obscured the number of transitions to marine life, and the timing of the origin of marine adaptation in chelonioids. Phylogenetic studies support either a highly‐inclusive chelonioid total‐group including fossil marine clades from the Jurassic and Cretaceous (e.g. protostegids, thalassochelydians, sandownids) or a less inclusive chelonioid total‐group excluding those clades. Under this paradigm, these clades belong outside Cryptodira, and represent at least one additional evolutionary transition to marine life in turtles. We present a new phylogenetic hypothesis informed by high resolution computed tomographic data of living and fossil taxa. Besides a well‐supported Chelonioidea, which includes protostegids, we recover a previously unknown clade of stem‐group turtles, Angolachelonia, which includes the Late Jurassic thalassochelydians, and the Cretaceous–Palaeogene sandownids. Accounting for the Triassic Odontochelys, our results indicate three independent evolutionary transitions to marine life in non‐pleurodiran turtles (plus an additional two‐three in pleurodires). Among all independent origins of marine habits, a pelagic ecology only evolved once, among chelonioids. All turtle groups that independently invaded marine habitats in the Jurassic–Cretaceous (chelonioids, angolachelonians, bothremydid pleurodires) survived the Cretaceous–Palaeogene mass extinction event. This highlights extensive survival of marine turtles compared to other marine reptiles. Furthermore, deeply‐nested clades such as chelonioids are found by the middle Early Cretaceous, suggesting a rapid diversification of crown‐group turtles during the Early Cretaceous.",
    url = "https://doi.org/10.1111/pala.12384",
    doi = "10.1111/pala.12384",
    openalex = "W2883587102",
    references = "doi101007s1205200901192, doi101016jympev201705008, doi10103827421, doi101086425183, doi101098rsbl20080022, doi101111brv12038, doi101111pala12142, doi10166612149, doi1033740140580105"
}

Abstract Order Diplobathrida is a major clade of camerate crinoids spanning the Ordovician–Mississippian, yet phylogenetic relationships have only been inferred for Ordovician taxa. This has hampered efforts to construct a comprehensive tree of life for crinoids and develop a classification scheme that adequately reflects diplobathrid evolutionary history. Here, I apply maximum parsimony and Bayesian phylogenetic approaches to the fossil record of diplobathrids to infer the largest tree of fossil crinoids to date, with over 100 genera included. Recovered trees provide a framework for evaluating the current classification of diplobathrids. Notably, previous suborder divisions are not supported, and superfamily divisions will require significant modification. Although numerous revisions are required for families, most can be retained through reassignment of genera. In addition, recovered trees were used to produce phylogeny‐based estimates of diplobathrid lineage diversity. By accounting for ghost lineages, phylogeny‐based richness estimates offer greater insight into diversification and extinction dynamics than traditional taxonomy‐based approaches alone and provide a detailed summary of the ~150 million‐year evolutionary history of Diplobathrida. This study constitutes a major step toward producing a phylogeny of the Crinoidea and documenting crinoid diversity dynamics. In addition, it will serve as a framework for subsequent phylogeny‐based investigations of macroevolutionary questions.

@article{doi101111pala12401,
    author = "Cole, Selina R.",
    title = "Phylogeny and evolutionary history of diplobathrid crinoids (Echinodermata)",
    year = "2018",
    journal = "Palaeontology",
    abstract = "Abstract Order Diplobathrida is a major clade of camerate crinoids spanning the Ordovician–Mississippian, yet phylogenetic relationships have only been inferred for Ordovician taxa. This has hampered efforts to construct a comprehensive tree of life for crinoids and develop a classification scheme that adequately reflects diplobathrid evolutionary history. Here, I apply maximum parsimony and Bayesian phylogenetic approaches to the fossil record of diplobathrids to infer the largest tree of fossil crinoids to date, with over 100 genera included. Recovered trees provide a framework for evaluating the current classification of diplobathrids. Notably, previous suborder divisions are not supported, and superfamily divisions will require significant modification. Although numerous revisions are required for families, most can be retained through reassignment of genera. In addition, recovered trees were used to produce phylogeny‐based estimates of diplobathrid lineage diversity. By accounting for ghost lineages, phylogeny‐based richness estimates offer greater insight into diversification and extinction dynamics than traditional taxonomy‐based approaches alone and provide a detailed summary of the \textasciitilde 150 million‐year evolutionary history of Diplobathrida. This study constitutes a major step toward producing a phylogeny of the Crinoidea and documenting crinoid diversity dynamics. In addition, it will serve as a framework for subsequent phylogeny‐based investigations of macroevolutionary questions.",
    url = "https://doi.org/10.1111/pala.12401",
    doi = "10.1111/pala.12401",
    openalex = "W2897788581",
    references = "doi101017jpa2016137, doi101017jpa2016142, doi101017jpa2017151, doi101017jpa201720, doi101017s0094837300003778, doi101093acprofosobl97801995871000010001, doi101093sysbiosys029, doi101111j2041210x201200223x, doi101126science1160006, doi101126science21545391501, doi101146annurevearth33092203122654, doi1012019781003077831, doi107312webb12678, openalexw2611511275"
}

Timescales are of fundamental importance to evolutionary biology as they facilitate hypothesis tests of historical evolutionary processes. Through the incorporation of fossil occurrence data, the fossilized birth-death (FBD) process provides a framework for estimating divergence times using more paleontological data than traditional node calibration approaches have allowed. The inclusion of more data can refine evolutionary timescale estimates, but for many taxonomic groups it is computationally infeasible to include all available fossil occurrence data. Here, we utilize both empirical data and a simulation framework to identify approaches to subsampling fossil occurrence data that result in the most accurate estimates of divergence times. To achieve this we assess the performance of the FBD-Skyline model when implementing multiple approaches to incorporating subsampled fossil occurrence data. Our results demonstrate that it is necessary to account for all available fossil occurrence data to achieve the most accurate estimates of clade age. We show that this can be achieved if an empirical Bayes approach, accounting for fossil sampling through time, is applied to the FBD process. Random subsampling of occurrence data can lead to estimates of clade age that are incompatible with fossil evidence if no control over the affinities of fossil occurrences is enforced. Our results call into question the accuracy of previous divergence time studies incorporating the FBD process that have used only a subsample of all available fossil occurrence data.

@article{doi101093sysbiosyz037,
    author = "O’Reilly, Joseph and Donoghue, Philip C. J.",
    title = "The Effect of Fossil Sampling on the Estimation of Divergence Times with the Fossilized Birth–Death Process",
    year = "2019",
    journal = "Systematic Biology",
    abstract = "Timescales are of fundamental importance to evolutionary biology as they facilitate hypothesis tests of historical evolutionary processes. Through the incorporation of fossil occurrence data, the fossilized birth-death (FBD) process provides a framework for estimating divergence times using more paleontological data than traditional node calibration approaches have allowed. The inclusion of more data can refine evolutionary timescale estimates, but for many taxonomic groups it is computationally infeasible to include all available fossil occurrence data. Here, we utilize both empirical data and a simulation framework to identify approaches to subsampling fossil occurrence data that result in the most accurate estimates of divergence times. To achieve this we assess the performance of the FBD-Skyline model when implementing multiple approaches to incorporating subsampled fossil occurrence data. Our results demonstrate that it is necessary to account for all available fossil occurrence data to achieve the most accurate estimates of clade age. We show that this can be achieved if an empirical Bayes approach, accounting for fossil sampling through time, is applied to the FBD process. Random subsampling of occurrence data can lead to estimates of clade age that are incompatible with fossil evidence if no control over the affinities of fossil occurrences is enforced. Our results call into question the accuracy of previous divergence time studies incorporating the FBD process that have used only a subsample of all available fossil occurrence data.",
    url = "https://doi.org/10.1093/sysbio/syz037",
    doi = "10.1093/sysbio/syz037",
    openalex = "W2946805451",
    references = "doi101017jpa2016141"
}

Abstract Members of the echinoid order Spatangoida, a highly diverse and abundant marine invertebrate clade, were important denizens of the Cretaceous Western Interior Seaway (WIS), an epicontinental seaway that divided North America in two during an interval of greenhouse conditions between roughly 100 and 65 million years ago. A phylogenetic analysis of spatangoids was conducted using a character matrix of 32 characters from 21 species. Species that occur in the WIS were considered comprehensively, and species from other regions such as South America, Europe, and North Africa were also incorporated into the analysis. Phylogenetic patterns retrieved are largely congruent with preexisting family-level classifications; however, species within several genera, especially Hemiaster and Heteraster, need to be reassigned so that classification better reflects phylogeny. The genera Washitaster and Heteraster are closely related, as are Mecaster, Palhemiaster, and Proraster; Pliotoxaster, Macraster, and Hemiaster; and Micraster and Diplodetus. Biogeographic patterns were also considered using the phylogeny, and several episodes of vicariance and range expansion were identified. These were possibly related to some of the various major episodes of sea-level rise and fall during the Cretaceous. In particular, Valangian–mid-Aptian regressions may have caused vicariance within Heteraster and Washitaster while other early spatangoid vicariance may be related to regressions during the late Aptian–early Cenomanian. Further, vicariance caused by regressions during the mid-Cenomanian–Maastrichtian may have driven diversification within Micraster and Diplodetus. Last, transgressions during the late Aptian–early Cenomanian seem to have spurred prominent range expansions in Mecaster and Hemiaster.

@article{doi101017jpa2020102,
    author = "Byrum, Steven and Lieberman, Bruce S.",
    title = "Phylogeny and biogeography of some Cretaceous spatangoid echinoids with special emphasis on taxa from the Western Interior Seaway",
    year = "2020",
    journal = "Journal of Paleontology",
    abstract = "Abstract Members of the echinoid order Spatangoida, a highly diverse and abundant marine invertebrate clade, were important denizens of the Cretaceous Western Interior Seaway (WIS), an epicontinental seaway that divided North America in two during an interval of greenhouse conditions between roughly 100 and 65 million years ago. A phylogenetic analysis of spatangoids was conducted using a character matrix of 32 characters from 21 species. Species that occur in the WIS were considered comprehensively, and species from other regions such as South America, Europe, and North Africa were also incorporated into the analysis. Phylogenetic patterns retrieved are largely congruent with preexisting family-level classifications; however, species within several genera, especially Hemiaster and Heteraster, need to be reassigned so that classification better reflects phylogeny. The genera Washitaster and Heteraster are closely related, as are Mecaster, Palhemiaster, and Proraster; Pliotoxaster, Macraster, and Hemiaster; and Micraster and Diplodetus. Biogeographic patterns were also considered using the phylogeny, and several episodes of vicariance and range expansion were identified. These were possibly related to some of the various major episodes of sea-level rise and fall during the Cretaceous. In particular, Valangian–mid-Aptian regressions may have caused vicariance within Heteraster and Washitaster while other early spatangoid vicariance may be related to regressions during the late Aptian–early Cenomanian. Further, vicariance caused by regressions during the mid-Cenomanian–Maastrichtian may have driven diversification within Micraster and Diplodetus. Last, transgressions during the late Aptian–early Cenomanian seem to have spurred prominent range expansions in Mecaster and Hemiaster.",
    url = "https://doi.org/10.1017/jpa.2020.102",
    doi = "10.1017/jpa.2020.102",
    openalex = "W3112581246",
    references = "arachchige2019taxonomy, doi101016002555648290027x, doi101016jgloplacha201312007, doi101017jpa201879, doi10108014772011003603556, doi101111j109600311994tb00179x, doi101144gslsp19880370119, doi101306m56578, doi1023073515270, doi105962bhltitle40014, openalexw3217097258, openalexw592572837"
}

Phylogenomic and paleontological data constitute complementary resources for unraveling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthesizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic data set for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic data sets that selects loci with high phylogenetic signal, low systematic biases, and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two. [Echinoidea; fossils; paleontology; phylogenomics; time calibration; total evidence.].

@article{doi101093sysbiosyaa069,
    author = "Koch, Nicolás Mongiardino and Thompson, Jeffrey R.",
    title = "A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data",
    year = "2020",
    journal = "Systematic Biology",
    abstract = "Phylogenomic and paleontological data constitute complementary resources for unraveling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthesizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic data set for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic data sets that selects loci with high phylogenetic signal, low systematic biases, and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two. [Echinoidea; fossils; paleontology; phylogenomics; time calibration; total evidence.].",
    url = "https://doi.org/10.1093/sysbio/syaa069",
    doi = "10.1093/sysbio/syaa069",
    openalex = "W3083369987",
    references = "doi101017s0022336000061321, doi10108014772011003603556, doi101093sysbiosyw107, doi105281zenodo16046014, kier1974evolutionary"
}

Abstract Cambrian bivalved arthropods are a polyphyletic group of carapace‐bearing arthropods that includes stem euarthropods, stem mandibulates and crustaceans. Here, we describe Pakucaris apatis gen. et sp. nov., a new stem mandibulate bivalved arthropod from the middle Cambrian (Wuliuan Stage) Burgess Shale (Marble Canyon, Kootenay National Park, British Columbia, Canada). Two morphotypes of this small arthropod (11.6–26.6 mm long) are recognized, which differ mainly in their size and number of segments, possibly reflecting sexual dimorphism or different anamorphic stages. The carapace presents a dorsal crest extending anteriorly into a small recurved rostrum and two anterolateral processes. Around 20% of the posteriormost body segments and limbs are covered by a large spine‐bearing shield. The head bears a pair of eyes, a possible pair of unsegmented appendicular projections and two pairs of segmented appendages. The thorax is multisegmented, homonomous, with weakly sclerotized segments bearing biramous limbs, composed of a stenopodous endopod with c. 20 podomeres and a paddle‐shaped exopod. Pakucaris is interpreted as a nektobenthic suspension feeder. Bayesian phylogenetic analysis implies a position within Hymenocarina as stem mandibulates. The posterior shield is regarded as a pygidium, and represents a case of morphofunctional convergent evolution between mandibulates, artiopodans and mollisoniids. Furthermore, Pakucaris adds to a growing number of pygidium‐bearing arthropods, potentially hinting at a common developmental pattern across early arthropod evolution. This study not only increases our understanding of the early evolution of mandibulates, but also illustrates a unique case of early evolutionary convergence during the Cambrian Explosion.

@article{doi101002spp21366,
    author = "Izquierdo‐López, Alejandro and Caron, Jean‐Bernard",
    title = "A Burgess Shale mandibulate arthropod with a pygidium: a case of convergent evolution",
    year = "2021",
    journal = "Papers in Palaeontology",
    abstract = "Abstract Cambrian bivalved arthropods are a polyphyletic group of carapace‐bearing arthropods that includes stem euarthropods, stem mandibulates and crustaceans. Here, we describe Pakucaris apatis gen. et sp. nov., a new stem mandibulate bivalved arthropod from the middle Cambrian (Wuliuan Stage) Burgess Shale (Marble Canyon, Kootenay National Park, British Columbia, Canada). Two morphotypes of this small arthropod (11.6–26.6 mm long) are recognized, which differ mainly in their size and number of segments, possibly reflecting sexual dimorphism or different anamorphic stages. The carapace presents a dorsal crest extending anteriorly into a small recurved rostrum and two anterolateral processes. Around 20\% of the posteriormost body segments and limbs are covered by a large spine‐bearing shield. The head bears a pair of eyes, a possible pair of unsegmented appendicular projections and two pairs of segmented appendages. The thorax is multisegmented, homonomous, with weakly sclerotized segments bearing biramous limbs, composed of a stenopodous endopod with c. 20 podomeres and a paddle‐shaped exopod. Pakucaris is interpreted as a nektobenthic suspension feeder. Bayesian phylogenetic analysis implies a position within Hymenocarina as stem mandibulates. The posterior shield is regarded as a pygidium, and represents a case of morphofunctional convergent evolution between mandibulates, artiopodans and mollisoniids. Furthermore, Pakucaris adds to a growing number of pygidium‐bearing arthropods, potentially hinting at a common developmental pattern across early arthropod evolution. This study not only increases our understanding of the early evolution of mandibulates, but also illustrates a unique case of early evolutionary convergence during the Cambrian Explosion.",
    url = "https://doi.org/10.1002/spp2.1366",
    doi = "10.1002/spp2.1366",
    openalex = "W3171801394",
    references = "doi101016jcub202002054, doi101098rsos191350"
}