@article{bateson1886the,
    author = "Bateson, William",
    title = "The Ancestry of the Chordata",
    year = "1886",
    journal = "Journal of Cell Science",
    url = "https://doi.org/10.1242/jcs.s2-26.104.535",
    doi = "10.1242/jcs.s2-26.104.535",
    number = "104",
    openalex = "W2572595438",
    pages = "535-572",
    volume = "S2-26"
}

@article{bateson1886the3,
    author = "Bateson, W",
    title = "The ancestry of the Chordata",
    year = "1886",
    journal = "Quarterly Journal of Microscopical Science, v. 26, p. 535-571",
    note = "talkorigins\_source = {true}; raw\_reference = {Bateson, W., 1886, The ancestry of the Chordata: Quarterly Journal of Microscopical Science, v. 26, p. 535-571.}"
}

@misc{garstang1894preliminary6,
    author = "Garstang, W",
    title = "Preliminary note on a New Theory of the Phylogeny of the Chordata",
    year = "1894",
    howpublished = "Zoologischer Anzeiger, v. 17, p. 122-125",
    note = "talkorigins\_source = {true}; raw\_reference = {Garstang, W., 1894, Preliminary note on a New Theory of the Phylogeny of the Chordata: Zoologischer Anzeiger, v. 17, p. 122-125.}"
}

@misc{gaskell1908the8,
    author = "Gaskell, W. H",
    title = "The Origin of Vertebrates",
    year = "1908",
    howpublished = "London, Longman",
    note = "talkorigins\_source = {true}; raw\_reference = {Gaskell, W. H., 1908, The Origin of Vertebrates: London, Longman.}"
}

@article{garstang1928the7,
    author = "Garstang, W",
    title = "The morphology of the Tunicata and its bearings on the phylogeny of the Chordata",
    year = "1928",
    journal = "Quarterly Journal of Microscopical Science, v. 72, p. 51-187",
    note = "talkorigins\_source = {true}; raw\_reference = {Garstang, W., 1928, The morphology of the Tunicata and its bearings on the phylogeny of the Chordata: Quarterly Journal of Microscopical Science, v. 72, p. 51-187.}"
}

@article{barrington1938the1,
    author = "Barrington, E. J. W",
    title = "The digestive system of Amphioxus ( Branchiostoma) lanceolatus",
    year = "1938",
    journal = "Philosophical Transactions of the Royal Society, London B, v. 228, p. 269-311",
    note = "talkorigins\_source = {true}; raw\_reference = {Barrington, E. J. W., 1938, The digestive system of Amphioxus ( Branchiostoma) lanceolatus: Philosophical Transactions of the Royal Society, London B, v. 228, p. 269-311.}"
}

@article{barrington1940observations2,
    author = "Barrington, E. J. W",
    title = "Observations on feeding and digestion in Glossobalanus minutus",
    year = "1940",
    journal = "Quarterly Journal of Microscopical Science, v. 82, p. 227-260",
    note = "talkorigins\_source = {true}; raw\_reference = {Barrington, E. J. W., 1940, Observations on feeding and digestion in Glossobalanus minutus: Quarterly Journal of Microscopical Science, v. 82, p. 227-260.}"
}

@article{crossref1951the,
    title = "The Chordates",
    year = "1951",
    journal = "Gastroenterology",
    url = "https://doi.org/10.1016/s0016-5085(51)80057-x",
    doi = "10.1016/s0016-5085(51)80057-x",
    number = "1",
    openalex = "W4252394996",
    pages = "150",
    volume = "18"
}

@article{doi101111j155856461965tb01722x,
    author = "Camin, Joseph H. and Sokal, Robert R.",
    title = "A METHOD FOR DEDUCING BRANCHING SEQUENCES IN PHYLOGENY",
    year = "1965",
    journal = "Evolution",
    abstract = {With the advent of relatively objective classifications, such as the phenetic classifications produced by the operational techniques of numerical taxonomy (Sokal and Sneath, 1963), it was inevitable that biologists would wonder what phylogenetic conclusions could be drawn from them and with what reliability.If these phenetic taxonomies did not reflect all of the elements of phyletics (Sokal and Camin, 1965), could techniques be devised for deducing the latter?For example, could operational methods be devised for deducing the cladistic relationships among taxa, so that, given the same initial information, different investigators would obtain the same results?By cladistic relationships we mean the evolutionary branching sequences among taxonomic units without regard to phenetic similarities among them or to an absolute time scale.There is no question that phylogenies could probably be reconstructed without error for any taxonomic group if complete fossil sequences for that group were available.However, can cladistic reconstructions be carried out with any degree of 1 This paper was presented on December 29, 1964, at a symposium entitled "Interactions between numerical and orthodox taxonomies" at Knoxville, Tennessee, before the Society of Systematic Zoology.2 Contribution No.},
    url = "https://doi.org/10.1111/j.1558-5646.1965.tb01722.x",
    doi = "10.1111/j.1558-5646.1965.tb01722.x",
    openalex = "W2120653759",
    references = "doi101038202147a0, doi1015159783112551080005, doi1023071377831, doi1023072411550, doi1023072411730, doi104324978020376680411, doi105962bhltitle84425, openalexw1541749163, openalexw3201999275"
}

@article{doi101111j155856461965tb01734x,
    author = "Dillon, L.",
    title = "THE HYDROCOEL AND THE ANCESTRY OF THE CHORDATES",
    year = "1965",
    journal = "Evolution",
    url = "https://doi.org/10.1111/j.1558-5646.1965.tb01734.x",
    doi = "10.1111/j.1558-5646.1965.tb01734.x",
    is_oa = "true",
    number = "3",
    pages = "436-446",
    semanticscholar_citation_count = "6",
    semanticscholar_id = "d372bec96512a803a7bf29e0d2a6dc93a163a468",
    volume = "19"
}

@article{crossref1973palaeozoology,
    title = "Palaeozoology: Ancestry of Chordates",
    year = "1973",
    journal = "Nature",
    url = "https://doi.org/10.1038/245123c0",
    doi = "10.1038/245123c0",
    number = "5421",
    pages = "123-124",
    volume = "245"
}

@article{doi101098rstb19730032,
    author = "Jefferies, R.",
    title = "The Ordovician Fossil Lagynocystis pyramidalis (Barrande) and the Ancestry of Amphioxus",
    year = "1973",
    journal = "Philosophical Transactions of the Royal Society B",
    abstract = "Lagynocystis pyramidalis (Barrande) from the marine Lower Ordovician of Bohemia (Šárka Formation (Llanvirn)), has features which suggest that it is ancestral, or nearly so, to living cephalochordates such as amphioxus (Branchiostoma). L. pyramidalis belongs to a strange group of fossils classified by some workers as ‘carpoid’ echinoderms (phylum Echinodermata, subphylum Homalozoa, class Stylophora). They are better seen, however, as primitive chordates with echinoderm affinities (phylum Chordata, subphylum Calcichordata Jefferies, 1967, class Stylophora). The most striking echinoderm-like feature of the calcichordates is their calcite skeleton with each plate a single crystal of calcite. Their chordate characters include: (1) branchial slits; (2) a postanal tail (stem) with muscle blocks, notochord, dorsal nerve cord and segmental ganglia; (3) a brain and cranial nervous system like those of a fish; and (4) various asymmetries like those of recent primitive chordates. The calcichordates are divided into a more primitive order, Cornuta, and a more advanced order Mitrata, which evolved from Cornuta. L. pyramidalis is a specialized member of the order Mitrata. Forms up till now associated with it in the suborder Lagynocystida of the Mitrata are better separated from it to form a new suborder Peltocystida (Kirkocystidae plus Peltocystidae). The features which ally L. pyramidalis to amphioxus are as follows: (1) a median ventral atrium opening by a median ventral atriopore; (2) a probably excretory posterior coelom which could give rise to the nephridia of amphioxus by upward growth of the gill slits; (3) evidence that the anus opened externally on the left; (4) evidence that the mouth and buccal cavity was innervated more strongly from the left than from the right; (5) evidence suggesting that, if it swam, L. pyramidalis would rotate about its long axis, clockwise as seen from behind, like late larval amphioxus and larval tunicates. The amphioxus-like features of L. pyramidalis are imposed on the pattern of a very primitive mitrate. There existed thus: (1) a well-developed brain and the cranial nerves were more of the vertebrate pattern than those of amphioxus; (2) left and right branchial openings in addition to the median atriopore; and (3) the tail or stem had paired segmental ganglia. The latest common ancestor of vertebrates and amphioxus would be a primitive mitrate. It follows, since Lagynocystis had a calcite skeleton, that such a skeleton has been lost at least twice in the evolution of the chordates.",
    url = "https://www.semanticscholar.org/paper/ca5b8f2f3a69f4cfcceb8adb101609f40eb57b2e",
    doi = "10.1098/RSTB.1973.0032",
    is_oa = "true",
    number = "871",
    pages = "409-469",
    semanticscholar_citation_count = "50",
    semanticscholar_id = "ca5b8f2f3a69f4cfcceb8adb101609f40eb57b2e",
    volume = "265"
}

@article{jefferies1973the,
    author = "Jefferies, R. P. S.",
    title = "The Ordovician fossil Lagynocystis pyramidalis (Barrande) and the ancestry of amphioxus",
    year = "1973",
    journal = "Philosophical Transactions of the Royal Society of London. B, Biological Sciences",
    abstract = "Lagynocystis pyramidalis (Barrande) from the marine Lower Ordovician of Bohemia (Šárka Formation (Llanvirn)), has features which suggest that it is ancestral, or nearly so, to living cephalochordates such as amphioxus (Branchiostoma). L. pyramidalis belongs to a strange group of fossils classified by some workers as ‘carpoid’ echinoderms (phylum Echinodermata, subphylum Homalozoa, class Stylophora). They are better seen, however, as primitive chordates with echinoderm affinities (phylum Chordata, subphylum Calcichordata Jefferies, 1967, class Stylophora). The most striking echinoderm-like feature of the calcichordates is their calcite skeleton with each plate a single crystal of calcite. Their chordate characters include: (1) branchial slits; (2) a postanal tail (stem) with muscle blocks, notochord, dorsal nerve cord and segmental ganglia; (3) a brain and cranial nervous system like those of a fish; and (4) various asymmetries like those of recent primitive chordates. The calcichordates are divided into a more primitive order, Cornuta, and a more advanced order Mitrata, which evolved from Cornuta. L. pyramidalis is a specialized member of the order Mitrata. Forms up till now associated with it in the suborder Lagynocystida of the Mitrata are better separated from it to form a new suborder Peltocystida (Kirkocystidae plus Peltocystidae). The features which ally L. pyramidalis to amphioxus are as follows: (1) a median ventral atrium opening by a median ventral atriopore; (2) a probably excretory posterior coelom which could give rise to the nephridia of amphioxus by upward growth of the gill slits; (3) evidence that the anus opened externally on the left; (4) evidence that the mouth and buccal cavity was innervated more strongly from the left than from the right; (5) evidence suggesting that, if it swam, L. pyramidalis would rotate about its long axis, clockwise as seen from behind, like late larval amphioxus and larval tunicates. The amphioxus-like features of L. pyramidalis are imposed on the pattern of a very primitive mitrate. There existed thus: (1) a well-developed brain and the cranial nerves were more of the vertebrate pattern than those of amphioxus; (2) left and right branchial openings in addition to the median atriopore; and (3) the tail or stem had paired segmental ganglia. The latest common ancestor of vertebrates and amphioxus would be a primitive mitrate. It follows, since Lagynocystis had a calcite skeleton, that such a skeleton has been lost at least twice in the evolution of the chordates.",
    url = "https://doi.org/10.1098/rstb.1973.0032",
    doi = "10.1098/rstb.1973.0032",
    number = "871",
    pages = "409-469",
    volume = "265"
}

@article{jefferies1973the10,
    author = "Jefferies, R. P. S",
    title = "The Ordovician fossil Lagynocystis pyramidalis (Barrande) and the ancestry of amphioxus",
    year = "1973",
    journal = "Philosophical Transactions of the Royal Society, London B, v. 265, p. 409-469",
    note = "talkorigins\_source = {true}; raw\_reference = {Jefferies, R. P. S., 1973, The Ordovician fossil Lagynocystis pyramidalis (Barrande) and the ancestry of amphioxus: Philosophical Transactions of the Royal Society, London B, v. 265, p. 409-469.}"
}

@book{godeaux1974primitive9,
    author = "Godeaux, J. E. A",
    title = "Primitive Deuterostomians, in Florkin, M., and Scheer, B. T., eds., Chemical Zoology",
    year = "1974",
    publisher = "London, Academic Press, v. VIII, p. 4-60",
    note = "talkorigins\_source = {true}; raw\_reference = {Godeaux, J. E. A., 1974, Primitive Deuterostomians, in Florkin, M., and Scheer, B. T., eds., Chemical Zoology: London, Academic Press, v. VIII, p. 4-60.}"
}

@incollection{berrill1975chordata4,
    author = "Berrill, N. J",
    editor = "Giese, A. C. and Pearse, J. S.",
    title = "Chordata: Tunicata",
    year = "1975",
    booktitle = "Reproduction of Marine Invertebrates II. Ectoprocts and Lesser Coelomates",
    publisher = "New York, Academic Press, p. 241-282",
    note = "talkorigins\_source = {true}; raw\_reference = {Berrill, N. J., 1975, Chordata: Tunicata, in Giese, A. C., and Pearse, J. S., eds., Reproduction of Marine Invertebrates II. Ectoprocts and Lesser Coelomates: New York, Academic Press, p. 241-282.}"
}

@inproceedings{jefferies1975fossil11,
    author = "Jefferies, R. P. S",
    title = "Fossil evidence concerning the origin of the chordates",
    year = "1975",
    booktitle = "Symposium of the Zoological Society, London, v. 36, p. 253-318",
    note = "talkorigins\_source = {true}; raw\_reference = {Jefferies, R. P. S., 1975, Fossil evidence concerning the origin of the chordates: Symposium of the Zoological Society, London, v. 36, p. 253-318.}"
}

@inproceedings{watts1975evolution12,
    author = "Watts, D. C",
    title = "Evolution of phosphagen kinases in the chordate line",
    year = "1975",
    booktitle = "Symposium of the Zoological Society, London, v. 36, p. 105-127",
    note = "talkorigins\_source = {true}; raw\_reference = {Watts, D. C., 1975, Evolution of phosphagen kinases in the chordate line: Symposium of the Zoological Society, London, v. 36, p. 105-127.}"
}

@incollection{wickstead1975chordata13,
    author = "Wickstead, J. H",
    editor = "Giese, A. C. and Pearse, J. S.",
    title = "Chordata: Acrania (Cephalochordata)",
    year = "1975",
    booktitle = "Reproduction of Marine Invertebrates II, Entoprocts and Lesser Coelomates",
    publisher = "New York, Academic Press, p. 283-319",
    note = "talkorigins\_source = {true}; raw\_reference = {Wickstead, J. H., 1975, Chordata: Acrania (Cephalochordata), in Giese, A. C., and Pearse, J. S., eds., Reproduction of Marine Invertebrates II, Entoprocts and Lesser Coelomates: New York, Academic Press, p. 283-319.}"
}

@incollection{crossref1976chordates,
    title = "Chordates",
    year = "1976",
    booktitle = "Animal Biochromes and Structural Colours",
    url = "https://doi.org/10.1525/9780520339422-020",
    doi = "10.1525/9780520339422-020",
    openalex = "W4246051787",
    pages = "138-181"
}

@book{openalexw2506868775,
    author = "Gould, Stephen Jay",
    title = "Ontogeny and Phylogeny",
    year = "1977",
    abstract = "* *1. Prospectus * Part I: Recapitulation *2. The Analogistic Tradition from Anaximander to Bonnet * The Seeds of Recapitulation in Greek Science? * Ontogeny and Phylogeny in the Conflict of and Epigenesis: The Idyll of Charles Bonnet * Appendix: The Revolution in *3. Transcendental Origins, 1793--1860 * Naturphilosophie: An Expression of Developmentalism * Two Leading Recapitulationists among the Naturphilosophen: Oken and Meckel * Oken's Classification of Animals Linear Additions of Organs * J. F. Meckel's Sober Statement of the Same Principles * Serres and the French Transcendentalists * Recapitulation and the Theory of Developmental Arrests * Von Baer's Critique of Recapitulation * The Direction of Development and Classification of Animals * Von Baer and Naturphilosophie: What Is the Universal Direction of Development? * Louis Agassiz and the Threefold Parallelism *4. Evolutionary Triumph, 1859--1900 * Evolutionary Theory and Zoological Practice * Darwin and the Evolution of Von Baer' Laws * Evolution and the Mechanics of Recapitulation * Ernst Haeckel: Phylogeny as the Mechanical Cause of Ontogeny * The Mechanism of Recapitulation * The American Neo-Lamarckians: The Law of Acceleration as Evolution's Motor * Progressive Evolution by Acceleration * The Extent of Parallelism * Why Does Recapitulation Dominate the History of Life? * Alpheus Hyatt and Universal Acceleration * Lamarckism and the Memory Analogy * Recapitulation and Darwinism * Appendix: The Evolutionary Translation of von Baer's Laws *5. Pervasive Influence * Criminal Anthropology * Racism * Child Development * Primary Education * Freudian Psychoanalysis * Epilogue *6. Decline, Fall, and Generalization * A Clever Argument * An Empirical Critique * Organs or Ancestors: The Transformation of Haeckel's Heterochrony * Interpolations into Juvenile Stages * Introduction of Juvenile Features into the Adults of Descendants * What Had Become of von Baer's Critique? * Benign Neglect: Recapitulation and the Rise of Experimental Embryology * The Prior Assumptions of Recapitulation * Wilhelm His and His Physiological Embryology: A Preliminary Skirmish * Roux's Entwicklungsmechanik and the Biogenetic Low * Recapitulation and Substantive Issues in Experimental Embryology: The New Preformationism * Mendel's Resurrection, Haeckel's Fall, and the Generalization of Recapitulation * Part II: Heterocrony and Paedomorphosis *7. Heterochrony and the Parallel of Ontogeny and Phylogeny * Acceleration and Retardation * Confusion in and after Haeckel's Wake * Guidelines for a Resolution * The Reduction of de Beer's Categories of Heterochrony to Acceleration and Retardation * A Historical Paradox: The Supposed Dominance of Recapitulation * Dissociability and Heterochrony * Correlation and Disociability * Dissociation of the Three Processes * A Metric for Dissociation * Temporal Shift as a Mechanism of Dissociation * A Clock Model of Heterochrony * Appendix: A Note on the Multivariate Representation of Dissociation *8. The Ecological and Evolutionary Significance of Heterochrony * The Argument from Frequency * The Importance of Recapitulation * The Importance of Heterochronic Change: Selected Cases * Frequency of Paedomorphosis in the Origin of Higher Taxa * A Critique of the Classical Significance of Heterochrony * The Classical Arguments * Retrospective and Immediate Significance * Heterochrony, Ecology, and Life-History Strategies * The Potential Ease and Rapidity of Heterochronic Change * The Control of Metamorphosis in Insects * Amphibian Paedomorphosis and the Thyroid Gland *9. Progenesis and Neoteny Insect Progenesis * Prothetely and Metathetely * Paedogenesis (Parthenogenetic Progenesis) in Gall Midges and Beetles * Progenesis in Wingless, Parthenogenetic Aphids * Additional Cases of Progenesis with a Similar Ecological Basis * Neotenic Solitary Locusts: Are They an Exception to the Rule? * Amphibian Neoteny * The Ecological Determinants of Progenesis * Unstable Environments * Colonization * Parasites * Male Dispersal * Progenesis as an Adaptive Response to Pressures for Small Size * The Role of Heterochrony in Macroevolution: Contrasting Flexibilities for Progenesis and Neoteny * Progenesis * Neoteny * The Social Correlates of Neoteny in Higher Vertebrates *10. Retardation and Neoteny in Human Evolution * The Seeds of Neoteny * The Fetalization Theory of Louis Bolk * Bolk's Data * Bolk's Interpretation * Bolk's Evolutionary Theory * A Tradition of Argument * Retardation in Human Evolution * Morphology in the Matrix of Retardation * Of Enumeration * Of Prototypes * Of Correlation * The Adaptive Significance of Retarded Development *11. Epilogue * Notes * Bibliography * Glossary * Index",
    openalex = "W2506868775",
    references = "doi101086409052, doi101146annureves08110177001045"
}

@article{doi101098rstb19780013,
    author = "Jefferies, R. and Lewis, D. N.",
    title = "The English Silurian fossil Placocystites forbesianus and the ancestry of the vertebrates",
    year = "1978",
    journal = "Philosophical Transactions of the Royal Society B",
    abstract = "Placocystites forbesianus de Koninck, from the Silurian Dudley Limestone, near Dudley, West Midlands, is here interpreted as a primitive chordate with a calcite skeleton of echinoderm type. This agrees with earlier papers by the senior author and disagrees with the work of Ubaghs (1968 etc.). Applying Hennig’s terminology, Placocystites probably belongs to the stem group of the vertebrates and therefore throws light on primitive vertebrate anatomy. It also belongs to the group Calcichordata, set up by one of us as a subphylum (Jefferies 1967). The Calcichordata, however, are not comparable in phylogenetic position with the living chordate subphyla, so the word calcichordate will henceforth be used only informally, for any chordate with a skeleton of echinoderm type. Ubaghs, who has developed a totally different interpretation, assigns Placocystites to the subphylum Homalozoa of the phylum Echinodermata. In assigning it to that phylum, Ubaghs’s work is more traditional than ours. Within the calcichordates, Placocystites forbesianus belongs to the more advanced group known as mitrates. These are distinguished from more primitive calcichordates (cornutes) by having right gill slits in addition to left ones. Within the mitrates it is possible to suggest the stem groups, in the Hennigian sense, of acraniates, tunicates and vertebrates. The term standard vertebrate is proposed to denote vertebrates in the usual sense, as contrasted with those stem vertebrates included in the mitrates. The two obvious parts of a calcichordate, formerly called theca and stem, or body and tail, are best called head and tail by homology with standard vertebrates. Mitrates correspond to the tunicate-tadpole-like protovertebrate of ‘antisegmentationist’ morphologists such as Froriep, Starck and Romer. The uniformly segmented protovertebrate of 'segmentationist’ morphologists such as Goodrich would represent a real but later stage in the ancestry of standard vertebrates, descended from a mitrate. The somites of standard vertebrates and acraniates can be plausibly identified inside calcichordates. The premandibular and mandibular somites would be located in the head, along with the buccal cavity, pharynx, gill slits and viscera. The left and right mandibular somites were probably represented in mitrates by the left and right anterior coeloms. The paired premandibular somites would be represented by a crescentic body situated in the posterior part of the head just in front of the brain. The hyoidean somites would be the most anterior pair of somites of the tail, totally separated from gill slits and gill bars. More posterior somites would also be in the tail, behind the hyoidean somites. The homologues of the paired eyes of standard vertebrates can also be recognized as having existed in mitrates (cispharyngeal eyes). The presumed premandibular, mandibular and hyoidean somites were grouped round them in an arrangement which could give rise to the extrinsic eye muscles of standard vertebrates. The ears of mitrates were lateral to the hyoidean somites as they are in living vertebrate embryos. The nervous system of Placocystites and its relatives is comparable with that of a fish. The brain was divided into two parts broadly corresponding to the prosencephalon and rhombencephalon of an early standard vertebrate (though the rhombencephalon of vertebrates also includes derivatives of the mitrate tail). The cranial nerves are deduced to have included olfactory, perhaps terminalis, optic, trigeminal and acusticolateralis complexes. The trigeminal complex included opthalmicus superficialis and ophthalmicus profundus branches and a single pair of ganglia. Contrary to classical theory, it was not divided into profundus and ‘true’ trigeminal subcomplexes. The pharynx of Placocystites and related mitrates was like that of a tunicate, particularly in certain asymmetries. Details of the skeleton strongly indicate that the pharynx in life would have contained an endostylar mucous trap of tunicate or ammocoete type, as classical theory would predict. The neural gland (‘hypophysis’) seems to have had the same relations as in a fully formed tunicate tadpole, but was probably endodermal in origin, homologous with Seessel’s pouch of a vertebrate. The anatomy of the head of the primitive calcichordate Cothurnocystis, which was a cornute, and like other cornutes and larval amphioxus had left gill slits only, is reconstructed by working backwards from mitrates and by direct evidence from its skeleton. The hypothetical latest common ancestor of lampreys and gnathostomes is deduced. The parts derived from the mitrate head can be distinguished from those derived from the mitrate tail. The animal probably possessed a notochordal head region and a trunk. These would have formed when gill slits and viscera migrated backwards ventral to the anterior part of the mitrate tail. The pericardium would have arisen by ventral growth of mitrate tail somites down the gill bars and their fusion ventrally to form a cavity. The visceral coelom arose by the ventral growth of mitrate tail somites round the viscera, accompanied by the development and fusion of cavities in the ventral parts of these somites. The branchial nerves of standard vertebrates are a mixture of placodal elements, probably derived from the mitrate head, and neural crest elements, probably derived from the mitrate tail. This hypothetical animal probably evolved from the mitrates when one of them took to habitual forwards swimming. Placocystites probably crept backwards through the sediment just below the sea bottom, pulled by the tail. A pair of spines near the mouth would serve to cut into the sediment, probably assisted by water squirted along them from the buccal cavity.",
    url = "https://www.semanticscholar.org/paper/16b6f461c900ef5cd7480fbcd4ca74bc161ac131",
    doi = "10.1098/RSTB.1978.0013",
    is_oa = "true",
    number = "990",
    pages = "205-323",
    semanticscholar_citation_count = "86",
    semanticscholar_id = "16b6f461c900ef5cd7480fbcd4ca74bc161ac131",
    volume = "282"
}

@misc{bone1979the5,
    author = "Bone, Q",
    title = "The Origin of the Chordates [2nd ed.]",
    year = "1979",
    howpublished = "Burlington, N.C., Carolina Biological Supply",
    note = "talkorigins\_source = {true}; raw\_reference = {Bone, Q., 1979, The Origin of the Chordates [2nd ed.]: Burlington, N.C., Carolina Biological Supply.}"
}

@article{doi101017s0094837300006588,
    author = "Alberch, Pere and Gould, Stephen Jay and Oster, George and Wake, David B.",
    title = "Size and shape in ontogeny and phylogeny",
    year = "1979",
    journal = "Paleobiology",
    abstract = "We present a quantitative method for describing how heterochronic changes in ontogeny relate to phyletic trends. This is a step towards creating a unified view of developmental biology and evolutionary ecology in the study of morphological evolution. Using this representation, we obtain a greatly simplified and logical scheme of classification. We believe that this scheme will be particularly useful in studying the data of paleontology and comparative morphology and in the analysis of processes leading to adaptive radiation. We illustrate this scheme by examples drawn from the literature and our own work.",
    url = "https://doi.org/10.1017/s0094837300006588",
    doi = "10.1017/s0094837300006588",
    openalex = "W1860355084",
    references = "doi101086404940, doi101086409052, doi101111j1469185x1966tb01624x, doi101111j155856461949tb00010x, doi101111j155856461976tb00911x, doi101146annurevbi46070177003041, doi101146annureves08110177001045, doi1023072412825, doi1043249781315765471, doi105962bhltitle146947, openalexw1525434908, openalexw2506868775"
}

@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"
}

@article{doi101111j155856461985tb00420x,
    author = "Felsenstein, Joseph",
    title = "CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP",
    year = "1985",
    journal = "Evolution",
    abstract = {The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95\% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.},
    url = "https://doi.org/10.1111/j.1558-5646.1985.tb00420.x",
    doi = "10.1111/j.1558-5646.1985.tb00420.x",
    openalex = "W2030966943",
    references = "doi1010160025556478900895, doi101038scientificamerican0583116, doi10108000031305198310483087, doi101111j155856461965tb01722x, doi101111j155856461983tb05533x, doi10113719781611970319, doi101214aos1176344552, doi1023072413323, doi1023072685844, doi102307sysbio342152"
}

@article{doi1023072408678,
    author = "Felsenstein, Joseph",
    title = "Confidence Limits on Phylogenies: An Approach Using the Bootstrap",
    year = "1985",
    journal = "Evolution",
    url = "https://doi.org/10.2307/2408678",
    doi = "10.2307/2408678",
    openalex = "W4254275792"
}

@article{doi101126science3277277,
    author = "Field, Katharine G. and Olsen, Gary J. and Lane, David and Giovannoni, Stephen J. and Ghiselin, Michael T. and Raff, Elizabeth C. and Pace, Norman R. and Raff, Rudolf A.",
    title = "Molecular Phylogeny of the Animal Kingdom",
    year = "1988",
    journal = "Science",
    abstract = "A rapid sequencing method for ribosomal RNA was applied to the resolution of evolutionary relationships among Metazoa. Representatives of 22 classes in 10 animal phyla were used to infer phylogenetic relationships, based on evolutionary distances determined from pairwise comparisons of the 18S ribosomal RNA sequences. The classical Eumetazoa are divided into two groups. Cnidarians arose from a protist ancestry different from the second group, the Bilateria. Within the Bilateria, an early split gave rise to Platyhelminthes (flatworms) and the coelomate lineage. Coelomates are thus monophyletic, and they radiated rapidly into four groups: chordates, echinoderms, arthropods, and eucoelomate protostomes.",
    url = "https://doi.org/10.1126/science.3277277",
    doi = "10.1126/science.3277277",
    openalex = "W2002638704",
    references = "cloud1976beginnings, crossref1977patterns, doi101007bf01653945, doi101016c20130056265, doi101017s009483730000498x, doi101073pnas74125463, doi101073pnas82206955, doi101073pnas8351383, doi101093oxfordjournalsmolbeva040362, doi101126science1553760279, doi101126science202030, doi101126science3082006, doi101128mr5122212711987"
}

@article{doi1010160092867489909471,
    author = "Patel, Nipam H. and Martı́n-Blanco, Enrique and Coleman, Kevin and Poole, Stephen J. and Ellis, Michael C. and Kornberg, Thomas B. and Goodman, Corey S.",
    title = "Expression of engrailed proteins in arthropods, annelids, and chordates",
    year = "1989",
    journal = "Cell",
    url = "https://doi.org/10.1016/0092-8674(89)90947-1",
    doi = "10.1016/0092-8674(89)90947-1",
    openalex = "W2012092107",
    references = "doi101002jmor1050880104, doi1010160003269783904189, doi1010160022283686903852, doi1010160769262581900374, doi101016s0168952500891295, doi101038256495a0, doi101038287795a0, doi101038335025a0, doi101073pnas74125463, doi101126science3277277, doi1023071439568, doi1023072412988"
}

@incollection{crossref1990primitive,
    title = "Primitive chordates",
    year = "1990",
    booktitle = "Animals",
    url = "https://doi.org/10.1017/cbo9780511565267.013",
    doi = "10.1017/cbo9780511565267.013",
    openalex = "W209725464",
    pages = "295-322"
}

@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"
}

@article{doi101038376479a0,
    author = "Carroll, Sean B.",
    title = "Homeotic genes and the evolution of arthropods and chordates",
    year = "1995",
    journal = "Nature",
    url = "https://doi.org/10.1038/376479a0",
    doi = "10.1038/376479a0",
    openalex = "W2008004759",
    references = "doi1010079783642866593, doi101016009286749290471n, doi1010160092867494902909, doi101038095550b0, doi101038276565a0, doi101038308428a0, doi101038361219a0, doi101038370563a0, doi101126science860134, doi101242dev1212333, doi101242dev1994supplement125, doi1023071437764, doi1023073514548, openalexw2506868775"
}

@article{doi101111j146363951996tb01256x,
    author = "Jefferies, R. and Brown, N. A. and Daley, Paul E. J.",
    title = "The Early Phylogeny of Chordates and Echinoderms and the Origin of Chordate Left–Right Asymmetry and Bilateral Symmetry",
    year = "1996",
    journal = "Acta Zoologica",
    abstract = "Left–right asymmetry in Dexiothetica (= echinoderms + chordates) results mainly from dexiothetism—an episode in their ancestry when an animal resembling the Recent pterobranch Cephalodiscus lay right‐side‐downwards on the sea floor. Castericystis sprinklei belongs to the dexiothete stem group. The history of the echinoderm stem group is reconstructed. Chordate bilateral symmetry evolved by six successive steps. Tail–head overlap occurred independently in craniates and acraniates. The neural crest would have existed in the latest common ancestor of extant chordates, or even earlier. Gross asymmetries occur in extant chordates in organs derived from the calcichordate head, but not in those derived from the calcichordate tail. The anterior boundary of hox gene expression in vertebrates corresponds to the anterior end of the calcichordate tail. Left–right organ pairing (an important step in the origin of chordate bilateral symmetry) may have involved the interaction of a symmetrizing morphogen, produced from the anterior end of the tail, with a lateral morphogen (Wilhelmi's morphogen), produced in ontogeny at first from the left and later from the right. This mechanism may still act in the metamorphosis of amphioxus and in mirror‐imaging in vertebrate twins. Wilhelmi's morphogen may be related to one or more members of the dorsal cascade of Drosophila.",
    url = "https://www.semanticscholar.org/paper/ed43e37abb0502fb22eb83089d464f5feeaab118",
    doi = "10.1111/J.1463-6395.1996.TB01256.X",
    is_oa = "true",
    number = "2",
    pages = "101-122",
    semanticscholar_citation_count = "92",
    semanticscholar_id = "ed43e37abb0502fb22eb83089d464f5feeaab118",
    volume = "77",
    references = "doi101126science1403568820, doi101242jcss231123445, doi101242jcss232126183"
}

@article{doi10103841710,
    author = "Shubin, Neil and Tabin, Cliff and Carroll, Sean B.",
    title = "Fossils, genes and the evolution of animal limbs",
    year = "1997",
    journal = "Nature",
    url = "https://doi.org/10.1038/41710",
    doi = "10.1038/41710",
    openalex = "W1601043516",
    references = "doi101002jez1401080304, doi1010160092867493906262, doi1010160092867493906273, doi1010160092867493906284, doi101016s0092867400811149, doi101017s0263593300006787, doi101038368208a0, doi101038376479a0, doi10108011035899509546213, doi101093aesa283408, doi101111j109636421995tb00110x, doi101111j109636421995tb00119x, doi101111j150239311996tb01839x, doi101126science2504981658, doi10182618200376605199601, doi1023072992562, doi1023073223017, doi105281zenodo16171435, doi107208chicago97802262565730010001"
}

@article{doi101111j109636421997tb00137x,
    author = "Ponder, Winston F. and Lindberg, David R.",
    title = "Towards a phylogeny of gastropod molluscs: an analysis using morphological characters",
    year = "1997",
    journal = "Zoological Journal of the Linnean Society",
    abstract = "Morphological (including ultrastructural) and developmental characters utilized in recent literature are critically reviewed as the basis to reassess the phylogenetic relationships of gastropods. The purpose of this paper is to provide a framework of characters for future studies and a testable phylogenetic hypothesis. This is one of the first attempts to use such characters to assess the relationships of all major clades using parsimony methods. The analysis uses 117 characters and includes 40 taxa, predominantly 'prosobranchs'. Five outgroup taxa are included, representing four conchiferan groups and Poly-placophora. Of the 117 characters reviewed and included in the analyses, nine are shell characters (four of these are shell structure), two opercular, two muscular, four ctenidial, 12 renopericardial and 24 reproductive (including 17 based on sperm and spermatogenesis), 27 of the digestive system, 32 of the nervous system and sense organs; the remainder are developmental (3) and of the foot and hypobranchial gland. In the initial analysis the data set included a mixture of binary and multistate characters with all characters unordered. These data were also analysed after scaling so that each character had equal weight. A third data set was constructed in which all characters were coded as binary characters. These analyses resulted in some implausible character transformations, mainly-involving the regaining of lost pallial structures. Additional analyses were run on all three sets of data after removing five characters showing the most unlikely transformations. These analyses resulted in generally similar topologies. The robustness of the clades was tested using clade decay. The adaptive radiation of gastropods and their life history traits are briefly described and discussed and the terminology for simultaneous hermaphroditism refined. A scenario for the evolution of torsion equated with the fossil record is proposed and the effects of torsion and coiling on gastropods are discussed along with asymmetry imposed by limpet-shaped body forms. It is suggested that the first gastropods were ultradextral. The idea that heterochrony has played a major part in gastropod evolution is developed and discussed, particularly the paedomorphic stamp imposed on the apogastropods. The veliger larvae of caenogastropods and heterobranchs are contrasted and found to differ in many respects. The evolution of planktotrophy within gastropods is discussed. Recent phylogenetic hypotheses for gastropods based on molecular data are generally in broad agreement with the present results. On the basis of our analyses we discuss the major monophyletic groups within gastropods. Gastropods appear to be a monophyletic clade, and divide into two primary groups, the Eogastropoda (incorporating the patellogastropods and their (probably sinistrally coiled) ancestors and the Orthogastropoda - the remainder of the gastropods. Orthogastropoda comprises several well defined clades. The vetigastropod clade encompasses most of the groups previously included in the paraphyletic Archaeogastropoda (fissurellids, trochoideans, scissurelloideans, halioroideans pleurotomarioideans) as well as lepeto-driloidean and lepetelloidean limpets and seguenzids. The location of the hot vent taxa Peltospiridae and Neomphalidae varies with each analysis, probably because there is a lack of ultrastructural data for these taxa and parallelism in many characters. They either form a paraphyletic or monophyletic group at or near the base of the vetigastropods or a clade with the neritopsines and cocculinoideans. The neritopsines (Neritoidea etc.) consistently form a clade with the cocculinoidean limpets, but their position on the tree also differs depending on the data set used and (in the case of the scaled data) whether or not the full suite of characters is used. They are either the sister to the rest of the orthogastropods or to the apogastropods. Caenogastropods [Mesogastropoda (+ architaenioglossan groups) + Neogastropoda] are consistently monophyletic as are the heterobranchs ('Heterostropha'+ Opisthobranchia + Pulmo-nata). The caenogastropods and heterobranchs also form a clade in all the analyses and the name Apogastropoda is redefined to encompass this group. New taxa are proposed, Sorbeoconcha for the caenogastropods exclusive of the architaenioglossan taxa, and Hypsogastropoda for the 'higher caenogastropods' – the Sorbeoconcha exclusive of the Cerithioidea and Campaniloidea.",
    url = "https://doi.org/10.1111/j.1096-3642.1997.tb00137.x",
    doi = "10.1111/j.1096-3642.1997.tb00137.x",
    openalex = "W1971435248",
    references = "doi1010079781489957405, doi101007bf02537225, doi1010160012825272900724, doi1010160016003258902862, doi1010160305197885900559, doi101016b9780122825057500129, doi101017s0022336000021454, doi101017s0094837300006588, doi101017s0094837300012793, doi10110809504120610655222, doi101111j146363951995tb00988x, doi101111j1469185x1950tb00585x, doi101126science3277277, doi1023071292581, doi1023072412182, doi1023072992272, doi1023073225209, openalexw2264583994, openalexw2506868775, openalexw638862129, openalexw659399033"
}

@article{doi101002mmng19980010106,
    author = "Bergström, J. and Naumann, W. and Viehweg, J. and Martí-Mus, M.",
    title = "Conodonts, Calcichordates and the Origin of Vertebrates",
    year = "1998",
    journal = "Fossil Record",
    abstract = "Abstract. Interpretation of early deuterostome evolution and relationships has been hampered by the lack of soft-part preservation in most groups. In addition, a recently revealed upside-down life orientation of vertebrates (the only real notoneuralians) compared to other bilateral animals has been misinterpreted as evidence for a unique body design in all deuterostomes, misleading any search for relatives. Regarding echinoderms, the variety of body plans is confusing. The interpretation of some fossils with echinoderm-type calcite skeletons as “calcichordate” ancestors of chordates, however, involves a hypothetical reconstruction of an unusual body plan and a long series of hypothetical transitions. The number of necessary steps is much lower if cephalochordates (amphioxus or lancelet) are derived directly from hemichordate enteropneusts. “Sensation interpretations” of fossils (Yunnanozoon, Cathaymyrus) from Burgess Shale type deposits have added further confusion. Soft-part preservation of conodont animals, with V-shaped myomeres and a notochord, shows that they were segmented chordates, while probable eyes and teeth suggest that they were already on the vertebrate side. Die Interpretation fruher Deuterostomia hinsichtlich ihrer Evolution und verwandtschaftlichen Beziehungen ist in den meisten Gruppen durch den Mangel an Weichkorpererhaltung sehr erschwert. Die kurzlich entdeckte Tatsache, das Vertebraten, d. h. die einzigen echten Notoneuralia, im Gegensatz zu anderen bilateral symmetrischen Organismen eine mit ihrer ursprunglichen Oberseite nach unten gerichtete Lebensstellung einnehmen, hat zu der irrtumlichen Ansicht gefuhrt, das alle Deuostomia uber einen im Tierreich einzigartigen Bauplan verfugen. Diese Interpretation brachte naturgemas jede Suche nach Verwandtschaftsverhaltnissen auf Abwege. Hinsichtlich der Echinodermata ist die bauplanmasige Variation in der Tat verwirrend. Die Interpretation einiger Fossilien mit Echinodermen-ahnlichen Kalzitskeletten als “calcichordate” Vorfahren der Chordata setzt jedoch die hypothetische Rekonstruktion eines ungewohnlichen Bauplans sowie eine lange Serie hypothetischer Ubergange voraus. Die Anzahl der notwendigen Schritte ist sehr viel geringer. wenn Cephalochordaten (Amphioxus oder das Lanzettfischchen) von hemichordaten Enteropneusta abgeleitet werden. Zusatzliche Verwirrung hat es durch sensationelle Interpretationen von Fossilien, Wie Yunnanozoon und Cathaymyrus aus Burgess-Schiefer-artigen Ablagerungen gegeben. Weichkorpererhaltung von Conodontentieren, die V-formige Myomere sowie einen Notochord besitzen, zeigen, das es sich um segmentierte Chordata handelte, wahrend sie die Prasenz moglicher Augenstrukturen und Zahne bereits auf die Seite der Vertebraten stellt. doi: 10.1002/mmng.19980010106",
    url = "https://fr.copernicus.org/articles/1/81/1998/fr-1-81-1998.pdf",
    doi = "10.1002/MMNG.19980010106",
    is_oa = "true",
    number = "1",
    pages = "81-91",
    semanticscholar_citation_count = "20",
    semanticscholar_id = "f366bb142ee9180100c34ce2b6934f0ff4dc6d40",
    volume = "1"
}

@article{doi101017s000632310000548x,
    author = "Budd, Graham E. and Jensen, Sören",
    title = "A critical reappraisal of the fossil record of the bilaterian phyla",
    year = "2000",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "It has long been assumed that the extant bilaterian phyla generally have their origin in the Cambrian explosion, when they appear in an essentially modern form. Both these assumptions are questionable. A strict application of stem- and crown-group concepts to phyla shows that although the branching points of many clades may have occurred in the Early Cambrian or before, the appearance of the modern body plans was in most cases later: very few bilaterian phyla sensu stricto have demonstrable representatives in the earliest Cambrian. Given that the early branching points of major clades is an inevitable result of the geometry of clade diversi®cation, the alleged phenomenon of phyla appearing early and remaining morphologically static is seen not to require particular explanation. Confusion in the de®nition of a phylum has thus led to attempts to explain (especially from a developmental perspective) a feature that is partly inevitable, partly illusory. We critically discuss models for Proterozoic diversi®cation based on small body size, limited developmental capacity and poor preservation and cryptic habits, and show that the prospect of lineage diversi®cation occurring early in the Proterozoic can be seen to be unlikely on grounds of both parsimonyand functional morphology. Indeed, the combination of the body and trace fossil record demonstrates a progressive diversi®cation through the end of the Proterozoic well into the Cambrian and beyond, a picture consistent with body plans being assembled during this time. Body-plan characters are likely to have been acquired monophyletically in the history of the bilaterians, and a model explaining the diversity in just oneof them, the coelom, is presented. This analysis points to the requirement for a careful application of systematic methodology before explanations are sought for alleged patterns of constraint and ¯fexibility.",
    url = "https://doi.org/10.1017/s000632310000548x",
    doi = "10.1017/s000632310000548x",
    openalex = "W2148377177",
    references = "doi101002aja1002030302, doi101002jmor1050540103, doi101017s0022336000024963, doi101017s0094837300012793, doi101017s009483730001681x, doi10103835318, doi101038361490a0, doi101038377720a0, doi101038382127a0, doi101038387489a0, doi10103846965, doi101098rstb19780005, doi101098rstb19790006, doi101098rstb19950029, doi101111j109583121996tb01693x, doi101111j109600311991tb00045x, doi101111j146363951991tb00312x, doi101111j146363951995tb00988x, doi101111j146364091991tb00303x, doi101111j1469185x1988tb00631x, doi101111j150239311975tb01311x, doi101111j150239311990tb01373x, doi101111j150239311998tb00509x, doi101126science28354091919, doi101126science28454232129, doi101126science7886451, doi101139e87124, doi101508300037918, doi101826182003741571989, doi101826182003769311997, doi1023073515360, doi1023073515362, doi1023073515363, doi105281zenodo16238847, dzik1988the, openalexw2055967869, openalexw2598873191, openalexw2754161204"
}

@article{doi101073pnas9794453,
    author = "Adoutte, André and Balavoine, Guillaume and Lartillot, Nicolas and Lespinet, Olivier and Prud’homme, Benjamin and de Rosa, Renaud",
    title = "The new animal phylogeny: Reliability and implications",
    year = "2000",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = {DNA sequence analysis dictates new interpretation of phylogenic trees. Taxa that were once thought to represent successive grades of complexity at the base of the metazoan tree are being displaced to much higher positions inside the tree. This leaves no evolutionary "intermediates" and forces us to rethink the genesis of bilaterian complexity.},
    url = "https://doi.org/10.1073/pnas.97.9.4453",
    doi = "10.1073/pnas.97.9.4453",
    openalex = "W2162160001",
    references = "doi101111j109600311998tb00338x, doi101126science28354091919, doi101126science7886451, doi105860choice334500"
}

@misc{bone2001chordata,
    author = "Bone, Quentin",
    title = "Chordata (Chordates)",
    year = "2001",
    booktitle = "Encyclopedia of Life Sciences",
    abstract = "The Chordata are a group of animals characterized by a dorsal tubular nerve cord, a notochord and gill slits. The group includes the Vertebrata (Craniata), Tunicata, Acrania and Conodonta.",
    url = "https://doi.org/10.1038/npg.els.0001528",
    doi = "10.1038/npg.els.0001528"
}

@article{doi101046j1525142x2001003003170x,
    author = "Peterson, Kevin J. and Eernisse, Douglas J.",
    title = "Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences",
    year = "2001",
    journal = "Evolution \& Development",
    abstract = "Insight into the origin and early evolution of the animal phyla requires an understanding of how animal groups are related to one another. Thus, we set out to explore animal phylogeny by analyzing with maximum parsimony 138 morphological characters from 40 metazoan groups, and 304 18S rDNA sequences, both separately and together. Both types of data agree that arthropods are not closely related to annelids: the former group with nematodes and other molting animals (Ecdysozoa), and the latter group with molluscs and other taxa with spiral cleavage. Furthermore, neither brachiopods nor chaetognaths group with deuterostomes; brachiopods are allied with the molluscs and annelids (Lophotrochozoa), whereas chaetognaths are allied with the ecdysozoans. The major discordance between the two types of data concerns the rooting of the bilaterians, and the bilaterian sister-taxon. Morphology suggests that the root is between deuterostomes and protostomes, with ctenophores the bilaterian sister-group, whereas 18S rDNA suggests that the root is within the Lophotrochozoa with acoel flatworms and gnathostomulids as basal bilaterians, and with cnidarians the bilaterian sister-group. We suggest that this basal position of acoels and gnathostomulids is artifactal because for 1,000 replicate phylogenetic analyses with one random sequence as outgroup, the majority root with an acoel flatworm or gnathostomulid as the basal ingroup lineage. When these problematic taxa are eliminated from the matrix, the combined analysis suggests that the root lies between the deuterostomes and protostomes, and Ctenophora is the bilaterian sister-group. We suggest that because chaetognaths and lophophorates, taxa traditionally allied with deuterostomes, occupy basal positions within their respective protostomian clades, deuterostomy most likely represents a suite of characters plesiomorphic for bilaterians.",
    url = "https://doi.org/10.1046/j.1525-142x.2001.003003170.x",
    doi = "10.1046/j.1525-142x.2001.003003170.x",
    openalex = "W2128919173",
    references = "burdonjones1952development, doi1010079789401149044, doi101016b9780122825057x50015, doi101017s0022336000059977, doi10103821631, doi101038387489a0, doi101073pnas972111359, doi101073pnas9794469, doi101093oxfordjournalsmolbeva026241, doi101093oxfordjournalsmolbeva040071, doi101098rspb20001111, doi101098rstb19940059, doi101098rstb19950029, doi101111j109600311995tb00092x, doi101111j109600311998tb00338x, doi101111j109600311999tb00277x, doi101111j109600311999tb00278x, doi101111j146363951991tb00312x, doi101111j146364091997tb00412x, doi101111j1469185x1988tb00631x, doi101111j150239311995tb01591x, doi101111j155856461985tb00420x, doi101111j155856461988tb02497x, doi101126science28354091919, doi101126science2905493972, doi101126science7886451, doi105860choice334500, doi105860choice501469, openalexw654005152, openalexw659399033"
}

@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"
}

@article{doi101126science1065889,
    author = "Huelsenbeck, John P. and Ronquist, Fredrik and Nielsen, Rasmus and Bollback, Jonathan P.",
    title = "Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology",
    year = "2001",
    journal = "Science",
    abstract = "As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.",
    url = "https://doi.org/10.1126/science.1065889",
    doi = "10.1126/science.1065889",
    openalex = "W2141913814",
    references = "doi101093bioinformatics178754, doi101093oxfordjournalsmolbeva025892, doi1023072412923"
}

@article{doi101016s1055790302003329,
    author = "Miya, Masaki and Takeshima, Hirohiko and Endo, Hiromitsu and Ishiguro, Naoya B. and Inoue, Jun and Mukai, Takahiko and Satoh, Takashi and Yamaguchi, Motoomi and Kawaguchi, Akira and Mabuchi, Kohji and Shirai, Shigeru and Nishida, Mutsumi",
    title = "Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences",
    year = "2002",
    journal = "Molecular Phylogenetics and Evolution",
    url = "https://doi.org/10.1016/s1055-7903(02)00332-9",
    doi = "10.1016/s1055-7903(02)00332-9",
    openalex = "W2170114989",
    references = "applegate1967phyletic, bonde1974interrelationships, doi101007bf00160154, doi101016s0016699588800664, doi101093bioinformatics149817, doi101093oxfordjournalsmolbeva003741, doi101111j109600311996tb00196x, doi101111j109600311999tb00277x, doi101111j155856461982tb05453x, doi101111j155856461983tb05533x, doi101111j155856461988tb02497x, doi101146annureven10010165000525, doi1023071375442, doi1023071437499, doi1023071444873, doi1023073514548, openalexw571605905"
}

@article{doi10108010635150390235520,
    author = "Guindon, Stéphane and Gascuel, Olivier",
    title = "A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood",
    year = "2003",
    journal = "Systematic Biology",
    abstract = "The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximum- likelihood principle, which clearly satisfies these requirements. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximum-likelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distance-based and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/.",
    url = "https://doi.org/10.1080/10635150390235520",
    doi = "10.1080/10635150390235520",
    openalex = "W2103546861",
    references = "doi101007bf00160154, doi101007bf01731581, doi101007bf01734359, doi101007bf02101694, doi101016b9781483232119500097, doi101093bioinformatics178754, doi101093oxfordjournalsmolbeva025664, doi101093oxfordjournalsmolbeva040023, doi101093oxfordjournalsmolbeva040454, doi101111j155856461985tb00420x, openalexw2002446259, openalexw2170120409, openalexw2994240441, openalexw3199943451, openalexw3217097258"
}

@article{doi101146annurevecolsys35112202130124,
    author = "Halanych, Kenneth M.",
    title = "The New View of Animal Phylogeny",
    year = "2004",
    journal = "Annual Review of Ecology Evolution and Systematics",
    abstract = "▪ Abstract Molecular tools have profoundly rearranged our understanding of metazoan phylogeny. Initially based on the nuclear small ribosomal subunit (SSU or 18S) gene, recent hypotheses have been corroborated by several sources of data (including the nuclear large ribosomal subunit, Hox genes, mitochondrial gene order, concatenated mitochondrial genes, and the myosin II heavy chain gene). Herein, the evidence supporting our current understanding is discussed on a clade by clade basis. Bilaterian animals consist of three clades: Deuterostomia, Lophotrochozoa, and Ecdysozoa. Each clade is supported by molecular and morphological data. Deuterostomia is smaller than traditionally recognized, consisting of hemichordates, echinoderms, chordates, and Xenoturbella (an enigmatic worm-like animal). Lophotrochozoa groups animals with a lophophore feeding apparatus (Brachiopoda, Bryozoa, and Phoronida) and trochophore larvae (e.g., annelids and mollusk), as well as several other recognized phyla (e.g., platyhelmin thes, sipunculans, nemerteans). Ecdysozoa comprises molting animals (e.g., arthropods, nematodes, tardigrades, priapulids), grouping together two major model organisms (Drosophila and Caenorhabditis) in the same lineage. Platyhelminthes do not appear to be monophyletic, with Acoelomorpha holding a basal position in Bilateria. Before the emergence of bilateral animals, sponges, ctenophorans, cnidarians, and placozoans split from the main animal lineage, but order of divergence is less than certain. Many questions persist concerning relationships within Ecdysozoa and Lophotrochozoa, poriferan monophyly, and the placement of many less-studied taxa (e.g., kinorhynchs, gastrotrichs, gnathostomulids, and entoprocts).",
    url = "https://doi.org/10.1146/annurev.ecolsys.35.112202.130124",
    doi = "10.1146/annurev.ecolsys.35.112202.130124",
    openalex = "W2114395497",
    references = "doi1010079789401149044, doi101016003101829390065q, doi101016jtig200312003, doi101016s0092867403004690, doi101017s0006323198005167, doi10103835318, doi101038387489a0, doi10103846965, doi101038nature01851, doi101046j1525142x2001003003170x, doi101073pnas972111359, doi101073pnas9794469, doi101093oxfordjournalsmolbeva004134, doi101093oxfordjournalsmolbeva026241, doi101098rspb20032631, doi101098rstb19950029, doi101111j109600311998tb00338x, doi101111j146363951987tb00892x, doi101111j146364091997tb00412x, doi101126science2705236598, doi101126science28354091919, doi101126science28454232129, doi101126science3277277, doi101146annurevge22120188002513, doi105860choice501469, openalexw2076004673"
}

@article{doi101242dev01201,
    author = "Takahashi, Tokiharu and Holland, P.",
    title = "Amphioxus and ascidian Dmbx homeobox genes give clues to the vertebrate origins of midbrain development",
    year = "2004",
    journal = "Development",
    abstract = "The ancestral chordate neural tube had a tripartite structure, comprising anterior, midbrain-hindbrain boundary (MHB) and posterior regions. The most anterior region encompasses both forebrain and midbrain in vertebrates. It is not clear when or how the distinction between these two functionally and developmentally distinct regions arose in evolution. Recently, we reported a mouse PRD-class homeobox gene, Dmbx1, expressed in the presumptive midbrain at early developmental stages, and the hindbrain at later stages,with exclusion from the MHB. This gene provides a route to investigate the evolution of midbrain development. We report the cloning, genomic structure,phylogeny and embryonic expression of Dmbx genes from amphioxus and from Ciona, representing the two most closely related lineages to the vertebrates. Our analyses show that Dmbx genes form a distinct, ancient,homeobox gene family, with highly conserved sequence and genomic organisation,albeit more divergent in Ciona. In amphioxus, no Dmbx expression is observed in the neural tube, supporting previous arguments that the MHB equivalent region has been secondarily modified in evolution. In Ciona, the CiDmbx gene is detected in neural cells caudal to Pax2/5/8-positive cells (MHB homologue), in the Hox-positive region, but,interestingly, not in any cells rostral to them. These results suggest that a midbrain homologue is missing in Ciona, and argue that midbrain development is a novelty that evolved specifically on the vertebrate lineage. We discuss the evolution of midbrain development in relation to the ancestry of the tripartite neural ground plan and the origin of the MHB organiser.",
    url = "http://dev.biologists.org/content/131/14/3285.full.pdf",
    doi = "10.1242/dev.01201",
    is_oa = "true",
    number = "14",
    pages = "3285-3294",
    semanticscholar_citation_count = "78",
    semanticscholar_id = "34d71e3f355023009bea8722d4b8b13d41ae1156",
    volume = "131"
}

@article{doi101017s0031182006001934,
    author = "Nakao, Miki and McManus, Donald P. and Schantz, Peter M. and Craig, Philip S. and Ito, Akira",
    title = "A molecular phylogeny of the genus Echinococcus inferred from complete mitochondrial genomes",
    year = "2006",
    journal = "Parasitology",
    abstract = "Taxonomic revision by molecular phylogeny is needed to categorize members of the genus Echinococcus (Cestoda: Taeniidae). We have reconstructed the phylogenetic relationships of E. oligarthrus, E. vogeli, E. multilocularis, E. shiquicus, E. equinus, E. ortleppi, E. granulosus sensu stricto and 3 genotypes of E. granulosus sensu lato (G6, G7 and G8) from their complete mitochondrial genomes. Maximum likelihood and partitioned Bayesian analyses using concatenated data sets of nucleotide and amino acid sequences depicted phylogenetic trees with the same topology. The 3 E. granulosus genotypes corresponding to the camel, pig, and cervid strains were monophyletic, and their high level of genetic similarity supported taxonomic species unification of these genotypes into E. canadensis. Sister species relationships were confirmed between E. ortleppi and E. canadensis, and between E. multilocularis and E. shiquicus, regardless of the analytical approach employed. The basal positions of the phylogenetic tree were occupied by the neotropical endemic species, E. oligarthrus and E. vogeli, whose definitive hosts are derived from carnivores that immigrated from North America after the formation of the Panamanian land bridge. Host-parasite co-evolution comparisons suggest that the ancestral homeland of Echinococcus was North America or Asia, depending on whether the ancestral definitive hosts were canids or felids.",
    url = "https://doi.org/10.1017/s0031182006001934",
    doi = "10.1017/s0031182006001934",
    openalex = "W2160073440",
    references = "doi101073pnas972111359, doi101126science1122277"
}

@article{doi101038nature05241,
    author = "Bourlat, Sarah J. and Juliusdottir, Thorhildur and Lowe, Christopher J. and Freeman, Robert M. and Aronowicz, Jochanan and Kirschner, Mark and Lander, Eric S. and Thorndyke, Michael C. and Nakano, Hiroaki and Kohn, Andrea B. and Heyland, Andreas and Moroz, Leonid L. and Copley, Richard R. and Telford, Maximilian J.",
    title = "Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida",
    year = "2006",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature05241",
    doi = "10.1038/nature05241",
    openalex = "W2062955619",
    references = "doi101016s0092867403004690, doi101038nature01851, doi101038nature02975, doi101038nature04336, doi101073pnas972111359, doi10108010635150500234583, doi101093molbevmsi111, doi101093molbevmsj055, doi101093sysbio274401, doi101126science28354091919, doi101126science7886451, doi101139z04158, doi1023072412923"
}

@article{doi101371journalpbio0040291,
    author = "Lowe, Christopher J. and Terasaki, Mark and Wu, Michael and Freeman, Robert M. and Runft, Linda L. and Kwan, Kristen M. and Haigo, Saori L. and Aronowicz, Jochanan and Lander, Eric S. and Gruber, Chris and Smith, Mark A. and Kirschner, Marc W. and Gerhart, John C.",
    title = "Dorsoventral Patterning in Hemichordates: Insights into Early Chordate Evolution",
    year = "2006",
    journal = "PLoS Biology",
    abstract = {We have compared the dorsoventral development of hemichordates and chordates to deduce the organization of their common ancestor, and hence to identify the evolutionary modifications of the chordate body axis after the lineages split. In the hemichordate embryo, genes encoding bone morphogenetic proteins (Bmp) 2/4 and 5/8, as well as several genes for modulators of Bmp activity, are expressed in a thin stripe of ectoderm on one midline, historically called "dorsal." On the opposite midline, the genes encoding Chordin and Anti-dorsalizing morphogenetic protein (Admp) are expressed. Thus, we find a Bmp-Chordin developmental axis preceding and underlying the anatomical dorsoventral axis of hemichordates, adding to the evidence from Drosophila and chordates that this axis may be at least as ancient as the first bilateral animals. Numerous genes encoding transcription factors and signaling ligands are expressed in the three germ layers of hemichordate embryos in distinct dorsoventral domains, such as pox neuro, pituitary homeobox, distalless, and tbx2/3 on the Bmp side and netrin, mnx, mox, and single-minded on the Chordin-Admp side. When we expose the embryo to excess Bmp protein, or when we deplete endogenous Bmp by small interfering RNA injections, these expression domains expand or contract, reflecting their activation or repression by Bmp, and the embryos develop as dorsalized or ventralized limit forms. Dorsoventral patterning is independent of anterior/posterior patterning, as in Drosophila but not chordates. Unlike both chordates and Drosophila, neural gene expression in hemichordates is not repressed by high Bmp levels, consistent with their development of a diffuse rather than centralized nervous system. We suggest that the common ancestor of hemichordates and chordates did not use its Bmp-Chordin axis to segregate epidermal and neural ectoderm but to pattern many other dorsoventral aspects of the germ layers, including neural cell fates within a diffuse nervous system. Accordingly, centralization was added in the chordate line by neural-epidermal segregation, mediated by the pre-existing Bmp-Chordin axis. Finally, since hemichordates develop the mouth on the non-Bmp side, like arthropods but opposite to chordates, the mouth and Bmp-Chordin axis may have rearranged in the chordate line, one relative to the other.},
    url = "https://doi.org/10.1371/journal.pbio.0040291",
    doi = "10.1371/journal.pbio.0040291",
    openalex = "W2129829180",
    references = "doi101007s004270050225, doi1010160092867493906273, doi1010160092867494904219, doi1010160092867494905142, doi1010160092867495902767, doi101016jgde200506004, doi101016s009286740081795x, doi101016s0092867403004690, doi10103835049541, doi101038nature01851, doi101038nature02415, doi101038nrn1175, openalexw1809736813, openalexw659399033"
}

@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"
}

@article{doi101186147121487s1s4,
    author = "Lartillot, Nicolas and Brinkmann, Henner and Philippe, Hervé",
    title = "Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model",
    year = "2007",
    journal = "BMC Evolutionary Biology",
    abstract = "The CAT model appears to be more robust than WAG against LBA artefacts, essentially because it correctly anticipates the high probability of convergences and reversions implied by the small effective size of the amino-acid alphabet at each site of the alignment. More generally, our results provide strong evidence that site-specificities in the substitution process need be accounted for in order to obtain more reliable phylogenetic trees.",
    url = "https://doi.org/10.1186/1471-2148-7-s1-s4",
    doi = "10.1186/1471-2148-7-s1-s4",
    openalex = "W2131527832",
    references = "doi101093molbevmsi111"
}

@article{doi101038nature06967,
    author = "Putnam, Nicholas H. and Butts, Thomas and Ferrier, David and Furlong, Rebecca F. and Hellsten, Uffe and Kawashima, Takeshi and Robinson‐Rechavi, Marc and Shoguchi, Eiichi and Terry, Astrid and Yu, Jr‐Kai and Benito-Gutiérrez, E`lia and Dubchak, Inna and García‐Fernàndez, Jordi and Gibson-Brown, Jeremy J. and Grigoriev, Igor V. and Horton, Amy C. and de Jong, Pieter J. and Jurka, Jerzy and Kapitonov, Vladimir V. and Kohara, Yuji and Kuroki, Yoko and Lindquist, Erika and Lucas, Susan and Osoegawa, Kazutoyo and Pennacchio, L and Salamov, Asaf A. and Satou, Yutaka and Sauka‐Spengler, Tatjana and Schmutz, Jeremy and Shin‐I, Tadasu and Toyoda, Atsushi and Bronner‐Fraser, Marianne and Fujiyama, Asao and Holland, Linda Z. and Holland, Peter W. H. and Satoh, Nori and Rokhsar, Daniel S.",
    title = "The amphioxus genome and the evolution of the chordate karyotype",
    year = "2008",
    journal = "Nature",
    abstract = "Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.",
    url = "https://doi.org/10.1038/nature06967",
    doi = "10.1038/nature06967",
    openalex = "W2131871062",
    references = "doi1010079783642866593, doi101016jtree200504008, doi101016s0092867403004690, doi10103835057062, doi101038370563a0, doi101038377720a0, doi101038nature04336, doi101038nature05241, doi101038scientificamerican0779122, doi101073pnas9794469, doi10108010635150390235520, doi101093bioinformatics178754, doi101093bioinformaticsbtg180, doi101093molbevmsi225, doi101093nar22224673, doi101093nar25173389, doi101093oxfordjournalsmolbeva026334, doi101101gr073676107, doi101126science1058040, doi101126science1080049, doi101126science1128691, doi101242dev1994supplement125, doi101371journalpbio0030007, doi101371journalpbio0030314, openalexw3217097258"
}

@article{doi101098rstb20072246,
    author = "Swalla, Billie J. and Smith, Andrew B.",
    title = "Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives",
    year = "2008",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "Deuterostomes are a monophyletic group of animals that include the vertebrates, invertebrate chordates, ambulacrarians and xenoturbellids. Fossil representatives from most major deuterostome groups, including some phylum-level crown groups, are found in the Lower Cambrian, suggesting that evolutionary divergence occurred in the Late Precambrian, in agreement with some molecular clock estimates. Molecular phylogenies, larval morphology and the adult heart/kidney complex all support echinoderms and hemichordates as a sister grouping (Ambulacraria). Xenoturbellids are a relatively newly discovered phylum of worm-like deuterostomes that lacks a fossil record, but molecular evidence suggests that these animals are a sister group to the Ambulacraria. Within the chordates, cephalochordates share large stretches of chromosomal synteny with the vertebrates, have a complete Hox complex and are sister group to the vertebrates based on ribosomal and mitochondrial gene evidence. In contrast, tunicates have a highly derived adult body plan and are sister group to the vertebrates based on the analyses of concatenated genomic sequences. Cephalochordates and hemichordates share gill slits and an acellular cartilage, suggesting that the ancestral deuterostome also shared these features. Gene network data suggest that the deuterostome ancestor had an anterior-posterior body axis specified by Hox and Wnt genes, a dorsoventral axis specified by a BMP/chordin gradient, and was bilaterally symmetrical with left-right asymmetry determined by expression of nodal.",
    url = "https://doi.org/10.1098/rstb.2007.2246",
    doi = "10.1098/rstb.2007.2246",
    openalex = "W2102660198",
    references = "doi101038377720a0, doi101038nature01264, doi101093oxfordjournalsmolbeva025897, doi101139z04158, doi101139z04160, doi101139z04190, doi101146annureves10110179001551, doi101371journalpbio0040291, morris1979the"
}

@incollection{crossref2009chordates,
    title = "Chordates",
    year = "2009",
    booktitle = "Encyclopedia of Neuroscience",
    url = "https://doi.org/10.1007/978-3-540-29678-2\_1012",
    doi = "10.1007/978-3-540-29678-2\_1012",
    openalex = "W4249900450",
    pages = "709-709"
}

@incollection{crossref2009phylogeny,
    title = "Phylogeny and Evolution of Chordates",
    year = "2009",
    booktitle = "Encyclopedia of Neuroscience",
    url = "https://doi.org/10.1007/978-3-540-29678-2\_4581",
    doi = "10.1007/978-3-540-29678-2\_4581",
    pages = "3160-3160"
}

@incollection{mallatt2009evolution,
    author = "Mallatt, Jon",
    title = "Evolution and Phylogeny of Chordates",
    year = "2009",
    booktitle = "Encyclopedia of Neuroscience",
    url = "https://doi.org/10.1007/978-3-540-29678-2\_3116",
    doi = "10.1007/978-3-540-29678-2\_3116",
    pages = "1201-1208"
}

@article{doi101016jympev201110008,
    author = "Park, Eunji and Hwang, Dae‐Sik and Lee, Jae‐Seong and Song, Jun‐Im and Seo, Tae‐Kun and Won, Yong‐Jin",
    title = "Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record",
    year = "2011",
    journal = "Molecular Phylogenetics and Evolution",
    url = "https://doi.org/10.1016/j.ympev.2011.10.008",
    doi = "10.1016/j.ympev.2011.10.008",
    openalex = "W2057007227",
    references = "doi101038hdy200862, doi101111j14754983200700692x, doi101371journalpone0001121"
}

@article{doi101016jcub201410016,
    author = "Cannon, Johanna T. and Kocot, Kevin M. and Waits, Damien S. and Weese, David and Swalla, Billie J. and Santos, Scott R. and Halanych, Kenneth M.",
    title = "Phylogenomic Resolution of the Hemichordate and Echinoderm Clade",
    year = "2014",
    journal = "Current Biology",
    url = "https://doi.org/10.1016/j.cub.2014.10.016",
    doi = "10.1016/j.cub.2014.10.016",
    openalex = "W1986400158",
    references = "doi101016jcub200905063, doi101111j15023931201200319x, doi101139z04190"
}

@article{doi101093bioinformaticsbtu033,
    author = "Stamatakis, Alexandros",
    title = "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies",
    year = "2014",
    journal = "Bioinformatics",
    abstract = "Abstract Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.",
    url = "https://doi.org/10.1093/bioinformatics/btu033",
    doi = "10.1093/bioinformatics/btu033",
    openalex = "W2141052558",
    references = "doi101038nature12130, doi101080106351501753462876, doi10108010635150802429642, doi101089cmb20090179, doi101093bioinformaticsbtl446, doi101093molbevmss112, doi101093molbevmst024, doi101093sysbiosyq010, doi101093sysbiosyr010, doi101109ipdps201370"
}

@article{osugi2014evolutionary,
    author = "Osugi, Tomohiro and Okamura, Tomoki and Son, You Lee and Ohkubo, Makoto and Ubuka, Takayoshi and Henmi, Yasuhisa and Tsutsui, Kazuyoshi",
    title = "Evolutionary Origin of GnIH and NPFF in Chordates: Insights from Novel Amphioxus RFamide Peptides",
    year = "2014",
    journal = "PLoS ONE",
    url = "https://doi.org/10.1371/journal.pone.0100962",
    doi = "10.1371/journal.pone.0100962",
    number = "7",
    openalex = "W2071326593",
    pages = "e100962",
    volume = "9",
    references = "doi101006bbrc20003350, doi101006jmbi19970951, doi101016jyfrne201003001, doi101016s0006899399019095, doi101038nature04336, doi101093molbevmsr121, doi101093nar14114683, doi101126science1132040, doi101210en20111110, doi101371journalpbio0050101"
}

@article{doi101016jympev201510009,
    author = "Zheng, Yuchi and Wiens, John J.",
    title = "Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species",
    year = "2015",
    journal = "Molecular Phylogenetics and Evolution",
    url = "https://doi.org/10.1016/j.ympev.2015.10.009",
    doi = "10.1016/j.ympev.2015.10.009",
    openalex = "W2175367716",
    references = "doi101038nature09864, doi10108010635150500234583, doi101093molbevmsu080"
}

@incollection{crossref2016chordates,
    title = "Chordates",
    year = "2016",
    booktitle = "The Marine World",
    url = "https://doi.org/10.1515/9780691232447-022",
    doi = "10.1515/9780691232447-022",
    openalex = "W4252901577",
    pages = "306-313"
}

@misc{s27fd27686b95842cdc75b89c9ea4da5d36ad5f61b,
    author = "Subbotin, V.",
    title = "Arguments on the origin of the vertebrAte liver And the Amphioxus hepAtic diverticulum : A hypothesis on evolutionAry novelties *",
    year = "2017",
    url = "https://www.semanticscholar.org/paper/7fd27686b95842cdc75b89c9ea4da5d36ad5f61b",
    is_oa = "true",
    semanticscholar_citation_count = "5",
    semanticscholar_id = "7fd27686b95842cdc75b89c9ea4da5d36ad5f61b"
}

@incollection{berman2019phylogeny,
    author = "Berman, Jules J.",
    title = "Phylogeny: Eukaryotes to Chordates",
    year = "2019",
    booktitle = "Evolution's Clinical Guidebook",
    url = "https://doi.org/10.1016/b978-0-12-817126-4.00005-9",
    doi = "10.1016/b978-0-12-817126-4.00005-9",
    pages = "173-205"
}

@article{doi101371journalpbio3000494,
    author = "Upham, Nathan S. and Esselstyn, Jacob A. and Jetz, Walter",
    title = "Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation",
    year = "2019",
    journal = "PLoS Biology",
    abstract = {Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.},
    url = "https://doi.org/10.1371/journal.pbio.3000494",
    doi = "10.1371/journal.pbio.3000494",
    openalex = "W2991998196",
    references = "doi10100703064746897, doi101007s1091401693638, doi101023a1011317930838, doi101038416816a, doi101038nature05634, doi101038nature06277, doi101038nature10291, doi101038nature11631, doi101038nature22897, doi101038nature25794, doi101073pnas1319091111, doi101073pnas1519387112, doi101093acprofoso97801985670280010001, doi101093bioinformaticsbts199, doi101093jmammalgyx147, doi101093jmammalgyy179, doi101093molbevmsm193, doi101093molbevmsv037, doi101093sysbiosyr047, doi101093sysbiosyr107, doi101093sysbiosyv080, doi101098rspb20120683, doi101111evo12681, doi101126science1157704, doi101126science1211028, doi101126science1229237, doi101371journalpone0089543, doi101371journalpone0183070, doi1026879424"
}

@article{doi101111brv12908,
    author = "Nanglu, Karma and Cole, Selina R. and Wright, David F. and Souto, Camilla",
    title = "Worms and gills, plates and spines: the evolutionary origins and incredible disparity of deuterostomes revealed by fossils, genes, and development",
    year = "2022",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Deuterostomes are the major division of animal life which includes sea stars, acorn worms, and humans, among a wide variety of ecologically and morphologically disparate taxa. However, their early evolution is poorly understood, due in part to their disparity, which makes identifying commonalities difficult, as well as their relatively poor early fossil record. Here, we review the available morphological, palaeontological, developmental, and molecular data to establish a framework for exploring the origins of this important and enigmatic group. Recent fossil discoveries strongly support a vermiform ancestor to the group Hemichordata, and a fusiform active swimmer as ancestor to Chordata. The diverse and anatomically bewildering variety of forms among the early echinoderms show evidence of both bilateral and radial symmetry. We consider four characteristics most critical for understanding the form and function of the last common ancestor to Deuterostomia: Hox gene expression patterns, larval morphology, the capacity for biomineralization, and the morphology of the pharyngeal region. We posit a deuterostome last common ancestor with a similar antero-posterior gene regulatory system to that found in modern acorn worms and cephalochordates, a simple planktonic larval form, which was later elaborated in the ambulacrarian lineage, the ability to secrete calcium minerals in a limited fashion, and a pharyngeal respiratory region composed of simple pores. This animal was likely to be motile in adult form, as opposed to the sessile origins that have been historically suggested. Recent debates regarding deuterostome monophyly as well as the wide array of deuterostome-affiliated problematica further suggest the possibility that those features were not only present in the last common ancestor of Deuterostomia, but potentially in the ur-bilaterian. The morphology and development of the early deuterostomes, therefore, underpin some of the most significant questions in the study of metazoan evolution.",
    url = "https://doi.org/10.1111/brv.12908",
    doi = "10.1111/brv.12908",
    openalex = "W4306738504",
    references = "doi101016jcub202002054, doi101017jpa201720, doi101017pab201942, doi101111brv12614, doi101111j1469185x201200220x, doi101111j15023931201200319x, doi101111pala12475, doi101139z04190, doi101144jgs2015017, doi101186s1291501602714, doi101242dev066712, doi101371journalpone0009586, jefferies1973the"
}

@article{doi101016jcub202405026,
    author = "Mussini, Giovanni and Smith, M. P. and Vinther, Jakob and Rahman, Imran A. and Murdock, Duncan J. E. and Harper, D. and Dunn, F. S.",
    title = "A new interpretation of Pikaia reveals the origins of the chordate body plan.",
    year = "2024",
    journal = "Current biology : CB",
    abstract = {Our understanding of the evolutionary origin of Chordata, one of the most disparate and ecologically significant animal phyla, is hindered by a lack of unambiguous stem-group relatives. Problematic Cambrian fossils that have been considered as candidate chordates include vetulicolians,1Yunnanozoon,2 and the iconic Pikaia.3 However, their phylogenetic placement has remained poorly constrained, impeding reconstructions of character evolution along the chordate stem lineage. Here we reinterpret the morphology of Pikaia, providing evidence for a gut canal and, crucially, a dorsal nerve cord-a robust chordate synapomorphy. The identification of these structures underpins a new anatomical model of Pikaia that shows that this fossil was previously interpreted upside down. We reveal a myomere configuration intermediate between amphioxus and vertebrates and establish morphological links between Yunnanozoon, Pikaia, and uncontroversial chordates. In this light, we perform a new phylogenetic analysis, using a revised, comprehensive deuterostome dataset, and establish a chordate stem lineage. We resolve vetulicolians as a paraphyletic group comprising the earliest diverging stem chordates, subtending a grade of more derived stem-group chordates comprising Yunnanozoon and Pikaia. Our phylogenetic results reveal the stepwise acquisition of characters diagnostic of the chordate crown group. In addition, they chart a phase in early chordate evolution defined by the gradual integration of the pharyngeal region with a segmented axial musculature, supporting classical evolutionary-developmental hypotheses of chordate origins4 and revealing a "lost chapter" in the history of the phylum.},
    url = "http://www.cell.com/article/S0960982224006699/pdf",
    doi = "10.1016/j.cub.2024.05.026",
    is_oa = "true",
    number = "13",
    pages = "2980-2989.e2",
    semanticscholar_citation_count = "10",
    semanticscholar_id = "b304b4ce4cef6e205468689c766d7bb9d61fbda4",
    volume = "34"
}

@article{doi101093icbicae134,
    author = "Swalla, B.",
    title = "Deuterostome Ancestors and Chordate Origins.",
    year = "2024",
    journal = "Integrative and comparative biology",
    abstract = "Synopsis The Deuterostomia are a monophyletic group, consisting of the Ambulacraria, with two phyla, Hemichordata and Echinodermata, and the phylum Chordata, containing the subphyla Cephalochordata (lancelets or Amphioxus), Tunicata (Urochordata), and Vertebrata. Hemichordates and echinoderms are sister groups and are critical for understanding the deuterostome ancestor and the origin and evolution of the chordates within the deuterostomes. Enteropneusta, worm-like hemichordates, share many chordate features as adults, including a post-anal tail, gill slits, and a central nervous system (CNS) that deploys similar developmental genetic regulatory networks (GRNs). Genomic comparisons show that cephalochordates share synteny and a vermiform body plan similar to vertebrates, but phylogenomic analyses place tunicates as the sister group of vertebrates. Tunicates have a U-shaped gut and a very different adult body plan than the rest of the chordates, and all tunicates have small genomes and many gene losses, although the GRNs underlying specific tissues, such as notochord and muscle, are conserved. Echinoderms and vertebrates have extensive fossil records, with fewer specimens found for tunicates and enteropneusts, or worm-like hemichordates. The data is mounting that the deuterostome ancestor was a complex benthic worm, with gill slits, a cartilaginous skeleton, and a CNS. Two extant groups, echinoderms and tunicates, have evolved highly derived body plans, remarkably different than the deuterostome ancestor. We review the current genomic and GRN data on the different groups of deuterostomes’ characters to re-evaluate different hypotheses of chordate origins. Notochord loss in echinoderms and hemichordates is as parsimonious as notochord gain in the chordates but has implications for the deuterostome ancestor. The chordate ancestor lost an ancestral nerve net, retained the CNS, and evolved neural crest cells.",
    url = "https://www.semanticscholar.org/paper/93487d300190de7211de1d528192f4364b31d1ec",
    doi = "10.1093/icb/icae134",
    is_oa = "true",
    number = "5",
    pages = "1175-1181",
    semanticscholar_citation_count = "4",
    semanticscholar_id = "93487d300190de7211de1d528192f4364b31d1ec",
    volume = "64",
    references = "doi101186s12915022012827"
}

@misc{crossrefNoneevolution,
    title = "Evolution of aplacophoran mollusks",
    year = "None",
    booktitle = "AccessScience",
    url = "https://doi.org/10.1036/1097-8542.yb150943",
    doi = "10.1036/1097-8542.yb150943"
}