Invertebrates

@misc{moore1952invertebrate41,
    author = "Moore, R. C. and Lalicker, C. G. and Fischer, A. G",
    title = "Invertebrate Fossils",
    year = "1952",
    note = "talkorigins\_source = {true}; raw\_reference = {Moore, R. C., Lalicker, C. G., and Fischer, A. G., 1952, Invertebrate Fossils:}"
}

@misc{schrock1953principles50,
    author = "Schrock, R. R. and Twenhofel, W. H",
    title = "Principles of Invertebrate",
    year = "1953",
    note = "talkorigins\_source = {true}; raw\_reference = {Schrock, R. R., and Twenhofel, W. H., 1953, Principles of Invertebrate}"
}

@misc{wells1956scleractinia58,
    author = "Wells, J. W",
    title = "Scleractinia",
    year = "1956",
    howpublished = "p.F328-F444, in Moore, R. C., ed., Treatise",
    note = "talkorigins\_source = {true}; raw\_reference = {Wells, J. W., 1956, Scleractinia: p.F328-F444, in Moore, R. C., ed., Treatise}"
}

@misc{arkell1957mesozoic3,
    author = "Arkell, W. J. and Kummel, B. and Wright, C. W",
    title = "Mesozoic Ammonoidea, in",
    year = "1957",
    note = "talkorigins\_source = {true}; raw\_reference = {Arkell, W. J., Kummel, B., and Wright, C. W., 1957, Mesozoic Ammonoidea, in}"
}

@misc{scott1959intraspecific52,
    author = "Scott, A. J. and Collinson, C",
    title = "Intraspecific variability in conodonts -",
    year = "1959",
    note = "talkorigins\_source = {true}; raw\_reference = {Scott, A. J., and Collinson, C., 1959, Intraspecific variability in conodonts -}"
}

Starting from the premise that oscillations are dangerous for any system and that violent oscillations may be lethal, this paper contrasts the highly stable production systems of tropical waters with the seasonal and longer-term oscillations of temperate and polar waters. The differences are climatically determined, and since the present glacial type of climate is young in the climatic history of the earth, the ecological systems of the higher latitudes are considered as immature and at a low level of adaptation. That they may be in process of evolution toward greater stability is suggested by a number of phenomena, such as the development of large, slow-respiring, slow-growing individuals, and the production of the young in many arctic invertebrates in mid-winter or late fall. These and other observed peculiarities of high latitude fauna tend to make the most efficient use of the available plant food and to spread the cropping pressure over as much of the year as possible. Oceanic birds are cited as examples in which stable populations have been achieved by evolution of lower breeding rates, and the phosphate and nitrate cycles in the upper layers of tropical seas are discussed. It is emphasized that selection here is operating at the level of the ecosystem; competition is between systems rather than between individuals or specific populations.

@article{doi101086282114,
    author = "Dunbar, M. J.",
    title = "The Evolution of Stability in Marine Environments Natural Selection at the Level of the Ecosystem",
    year = "1960",
    journal = "The American Naturalist",
    abstract = "Starting from the premise that oscillations are dangerous for any system and that violent oscillations may be lethal, this paper contrasts the highly stable production systems of tropical waters with the seasonal and longer-term oscillations of temperate and polar waters. The differences are climatically determined, and since the present glacial type of climate is young in the climatic history of the earth, the ecological systems of the higher latitudes are considered as immature and at a low level of adaptation. That they may be in process of evolution toward greater stability is suggested by a number of phenomena, such as the development of large, slow-respiring, slow-growing individuals, and the production of the young in many arctic invertebrates in mid-winter or late fall. These and other observed peculiarities of high latitude fauna tend to make the most efficient use of the available plant food and to spread the cropping pressure over as much of the year as possible. Oceanic birds are cited as examples in which stable populations have been achieved by evolution of lower breeding rates, and the phosphate and nitrate cycles in the upper layers of tropical seas are discussed. It is emphasized that selection here is operating at the level of the ecosystem; competition is between systems rather than between individuals or specific populations.",
    url = "https://doi.org/10.1086/282114",
    doi = "10.1086/282114",
    openalex = "W1983080188"
}

@misc{easton1960invertebrate24,
    author = "Easton, W. H",
    title = "Invertebrate Paleontology",
    year = "1960",
    howpublished = "New York, Harper, 701 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Easton, W. H., 1960, Invertebrate Paleontology: New York, Harper, 701 p.}"
}

@misc{knight1960monoplacophora39,
    author = "Knight, J. B. and Yochelson, E. L",
    title = "Monoplacophora",
    year = "1960",
    howpublished = "P. I77-I84, in",
    note = "talkorigins\_source = {true}; raw\_reference = {Knight, J. B., and Yochelson, E. L., 1960, Monoplacophora: P. I77-I84, in}"
}

@book{borradale1961the10,
    author = "Borradale, L. A. et al",
    title = "The Invertebrata",
    year = "1961",
    publisher = "Cambridge, Cambridge University",
    note = "talkorigins\_source = {true}; raw\_reference = {Borradale, L. A. et al., 1961, The Invertebrata: Cambridge, Cambridge University}"
}

@misc{connell1961the15,
    author = "Connell, J. H",
    title = "The effects of competition, predation by Thais lapillus",
    year = "1961",
    note = "talkorigins\_source = {true}; raw\_reference = {Connell, J. H., 1961, The effects of competition, predation by Thais lapillus}"
}

@misc{connell1961the18,
    author = "Connell, J. H",
    title = "The influence of interspecific competition and other factors on the",
    year = "1961",
    note = "talkorigins\_source = {true}; raw\_reference = {Connell, J. H., 1961, The influence of interspecific competition and other factors on the}"
}

@misc{ross1962pennsylvanian48,
    author = "Ross, C. A. and Ross, J. P",
    title = "Pennsylvanian, Permian rugose corals, Glass",
    year = "1962",
    note = "talkorigins\_source = {true}; raw\_reference = {Ross, C. A., and Ross, J. P., 1962, Pennsylvanian, Permian rugose corals, Glass}"
}

@article{doi101111j1469185x1966tb01624x,
    author = "Gould, Stephen Jay",
    title = "ALLOMETRY AND SIZE IN ONTOGENY AND PHYLOGENY",
    year = "1966",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    url = "https://doi.org/10.1111/j.1469-185x.1966.tb01624.x",
    doi = "10.1111/j.1469-185x.1966.tb01624.x",
    openalex = "W2082598566",
    references = "colbert1948evolution, doi101001jama196203050110085031, doi101007bf02982279, doi101038114895a0, doi101038137780b0, doi101038164820b0, doi101086280573, doi101093biomet371230, doi101111j155856461949tb00010x, doi101152physrev1947274511, doi1015159780691183978018, doi1023071538742, doi1023072405671, doi1023072527939, doi1023072532815, doi107312rens91062, doi107312simp93764, kermack1954a"
}

Stratigraphic and paleontologic studies in eastern Nevada and western Utah show that at least eight major marine and paralic fossil communities occur in rocks of Early Permian age. The eight communities, named for characteristic faunal elements, are: palaeotextulariid, fusulinid, coral, dictyoclostid- Composita, chonetoid, Heteralosia, nuculanid, and euphemitid. The palaeotextulariid, fusulinid, coral, dictyoclostid- Composita, and chonetoid communities probably required a salinity close to 35 per mil. The palaeotextulariid community probably lived at a depth of 50–70 m; fusulinid at 20–50 m; and coral at 10–30 m. The dictyoclostid- Composita and chonetoid communities may have lived at a depth of 4-10 m, the latter in a lower energy environment than the former. The Heteralosia, nuculanid, and euphemitid communities apparently were euryhaline and occupied very shallow bottoms.

@article{doi101130001676061966771121pioepf20co2,
    author = "Stevens, Calvin H.",
    title = "Paleoecologic Implications of Early Permian Fossil Communities in Eastern Nevada and Western Utah",
    year = "1966",
    journal = "Geological Society of America Bulletin",
    abstract = "Stratigraphic and paleontologic studies in eastern Nevada and western Utah show that at least eight major marine and paralic fossil communities occur in rocks of Early Permian age. The eight communities, named for characteristic faunal elements, are: palaeotextulariid, fusulinid, coral, dictyoclostid- Composita, chonetoid, Heteralosia, nuculanid, and euphemitid. The palaeotextulariid, fusulinid, coral, dictyoclostid- Composita, and chonetoid communities probably required a salinity close to 35 per mil. The palaeotextulariid community probably lived at a depth of 50–70 m; fusulinid at 20–50 m; and coral at 10–30 m. The dictyoclostid- Composita and chonetoid communities may have lived at a depth of 4-10 m, the latter in a lower energy environment than the former. The Heteralosia, nuculanid, and euphemitid communities apparently were euryhaline and occupied very shallow bottoms.",
    url = "https://doi.org/10.1130/0016-7606(1966)77[1121:pioepf]2.0.co;2",
    doi = "10.1130/0016-7606(1966)77[1121:pioepf]2.0.co;2",
    openalex = "W2132239955"
}

@misc{beaver1967morphology6,
    author = "Beaver, H. H",
    title = "Morphology, in Moore, R",
    year = "1967",
    howpublished = "C., ed., Treatise on",
    note = "talkorigins\_source = {true}; raw\_reference = {Beaver, H. H., 1967, Morphology, in Moore, R. C., ed., Treatise on}"
}

@article{doi1010160025322767900515,
    author = "Seilacher, Adolf",
    title = "Bathymetry of trace fossils",
    year = "1967",
    journal = "Marine Geology",
    url = "https://doi.org/10.1016/0025-3227(67)90051-5",
    doi = "10.1016/0025-3227(67)90051-5",
    openalex = "W1975115126",
    references = "doi1010079783662010204, doi101007bf01820746, doi101007bf02986976, doi101086626811, doi101126science150369260, doi10130674d70c452b2111d78648000102c1865d, doi1023071483846, openalexw2049573044, openalexw2343619380, openalexw574363047"
}

@misc{fay1967phylogeny27,
    author = "Fay, R. O",
    title = "Phylogeny and Evolution, p",
    year = "1967",
    howpublished = "S392-S396, in Moore, R. C",
    note = "talkorigins\_source = {true}; raw\_reference = {Fay, R. O., 1967, Phylogeny and Evolution, p. S392-S396, in Moore, R. C.,}"
}

Communities of Paleozoic shelf invertebrates underwent varied rates of change in faunal composition. Notable changes took place during Late Devonian-Early Mississippian time and were most noticeable in offshore brachiopod-dominated communities. Near-shore molluscan communities remained relatively stable throughout the Paleozoic.

@article{bretsky1968evolution,
    author = "Bretsky, Peter W.",
    title = "Evolution of Paleozoic Marine Invertebrate Communities",
    year = "1968",
    journal = "Science",
    abstract = "Communities of Paleozoic shelf invertebrates underwent varied rates of change in faunal composition. Notable changes took place during Late Devonian-Early Mississippian time and were most noticeable in offshore brachiopod-dominated communities. Near-shore molluscan communities remained relatively stable throughout the Paleozoic.",
    url = "https://doi.org/10.1126/science.159.3820.1231",
    doi = "10.1126/science.159.3820.1231",
    number = "3820",
    openalex = "W2087658969",
    pages = "1231-1233",
    volume = "159",
    references = "doi101038207270a0, doi101086282070, doi101086282114, doi101130001676061966771121pioepf20co2, doi101130gsab48403, doi101130mem67v1p461, doi105962bhltitle7199, openalexw2602415691, openalexw574363047"
}

@misc{beklemishev1969principles8,
    author = "Beklemishev, W. N",
    title = "Principles of Comparative Anatomy of Invertebrates",
    year = "1969",
    note = "talkorigins\_source = {true}; raw\_reference = {Beklemishev, W. N., 1969, Principles of Comparative Anatomy of Invertebrates:}"
}

@misc{glaessner1969decapoda33,
    author = "Glaessner, M. F",
    title = "Decapoda, p",
    year = "1969",
    howpublished = "R399-R533, in Moore, R. C., ed",
    note = "talkorigins\_source = {true}; raw\_reference = {Glaessner, M. F., 1969, Decapoda, p. R399-R533, in Moore, R. C., ed.,}"
}

@misc{kaufmann1969form37,
    author = "Kaufmann, E. G",
    title = "Form, function, and evolution",
    year = "1969",
    howpublished = "P. N129-N205, in Moore",
    note = "talkorigins\_source = {true}; raw\_reference = {Kaufmann, E. G., 1969, Form, function, and evolution: P. N129-N205, in Moore,}"
}

@misc{connell1970a21,
    author = "Connell, J. H",
    title = "A predator-prey system in the marine intertidal region",
    year = "1970",
    howpublished = "I. Balanus",
    note = "talkorigins\_source = {true}; raw\_reference = {Connell, J. H., 1970, A predator-prey system in the marine intertidal region. I. Balanus}"
}

Benthic invertebrates living in low oxygen regions of the Black Sea, Gulf of California, and basins off Southern California form three major biofacies associated with the following concentrations of dissolved oxygen: (1) an azoic region (≤ 0.1 ml/1), (2) a low diversity, small, soft-bodied infauna (0.3–1.0 ml/1), and (3) a diverse calcareous fauna (2 1.0 ml/l). These biofacies recapitulate the chronologic appearance of Pre-Cambrian trace fossils followed by a diverse calcified fauna in the Cambrian. The basin model has been used to reconstruct a Lower Cambrian oxygen level of 0.1 P.A.L. (present atmospheric level). This value is ten-fold that proposed in the Berkner-Marshall hypothesis.

@article{doi101111j150239311971tb01864x,
    author = "Rhoads, Donald C. and Morse, John W.",
    title = "EVOLUTIONARY AND ECOLOGIC SIGNIFICANCE OF OXYGEN‐DEFICIENT MARINE BASINS",
    year = "1971",
    journal = "Lethaia",
    abstract = "Benthic invertebrates living in low oxygen regions of the Black Sea, Gulf of California, and basins off Southern California form three major biofacies associated with the following concentrations of dissolved oxygen: (1) an azoic region (≤ 0.1 ml/1), (2) a low diversity, small, soft-bodied infauna (0.3–1.0 ml/1), and (3) a diverse calcareous fauna (2 1.0 ml/l). These biofacies recapitulate the chronologic appearance of Pre-Cambrian trace fossils followed by a diverse calcified fauna in the Cambrian. The basin model has been used to reconstruct a Lower Cambrian oxygen level of 0.1 P.A.L. (present atmospheric level). This value is ten-fold that proposed in the Berkner-Marshall hypothesis.",
    url = "https://doi.org/10.1111/j.1502-3931.1971.tb01864.x",
    doi = "10.1111/j.1502-3931.1971.tb01864.x",
    openalex = "W2032752559",
    references = "doi101007bf00355712, doi101007bf00367496, doi1010160012825266900407, doi101017s0022336000061655, doi101073pnas5361205, doi101073pnas5361205a, doi101073pnas654781, doi101093icb93881, doi101111j150239311970tb01265x, doi101111j150239311970tb01854x, doi101126science1543750766, doi101144gslsp19670020104, doi1011751520046919650220225otoaro20co2"
}

@misc{eldredge1971the25,
    author = "Eldredge, N",
    title = "The allopatric model and phylogeny of Paleozoic",
    year = "1971",
    note = "talkorigins\_source = {true}; raw\_reference = {Eldredge, N., 1971, The allopatric model and phylogeny of Paleozoic}"
}

@misc{stenzel1971oysters55,
    author = "Stenzel, H. B",
    title = "Oysters",
    year = "1971",
    howpublished = "p. N953-N1214, in Moore, R. C., ed., Treatise",
    note = "talkorigins\_source = {true}; raw\_reference = {Stenzel, H. B., 1971, Oysters: p. N953-N1214, in Moore, R. C., ed., Treatise}"
}

Infaunal bivalves able to live in depths of 1 meter or less have significantly wider geographic distributions than infaunal bivalves restricted to deeper waters (not including deep-sea species). Shallower species tolerate a wider range of environmental conditions and probably have longer-lived larvae than species limited to depths greater than 1 meter. As a result of differences in geographic distribution, species able to live as shallow as 1 meter should be less likely to speciate or go extinct than species restricted to deeper waters. Low-diversity species associations (⩽ 1 meter) should therefore also be evolutionarily more stable than high-diversity (>1 meter) associations. These predictions are supported by evidence from the fossil record.

@article{doi101086282933,
    author = "Jackson, Jeremy B. C.",
    title = "Biogeographic Consequences of Eurytopy and Stenotopy Among Marine Bivalves and Their Evolutionary Significance",
    year = "1974",
    journal = "The American Naturalist",
    abstract = "Infaunal bivalves able to live in depths of 1 meter or less have significantly wider geographic distributions than infaunal bivalves restricted to deeper waters (not including deep-sea species). Shallower species tolerate a wider range of environmental conditions and probably have longer-lived larvae than species limited to depths greater than 1 meter. As a result of differences in geographic distribution, species able to live as shallow as 1 meter should be less likely to speciate or go extinct than species restricted to deeper waters. Low-diversity species associations (⩽ 1 meter) should therefore also be evolutionarily more stable than high-diversity (>1 meter) associations. These predictions are supported by evidence from the fossil record.",
    url = "https://doi.org/10.1086/282933",
    doi = "10.1086/282933",
    openalex = "W2037439741",
    references = "bretsky1968evolution"
}

The distribution of numbers of species and the median number of species from 386 selected fossil communities are tabulated for high stress, variable nearshore, and open marine environments during the Lower, Middle, and Upper Paleozoic, the Mesozoic and the Cenozoic. The number of species always increases from high stress to variable nearshore to open marine environments. Within-habitat variation in number of species is small for long intervals of the Phanerozoic. The median number of species in communities from high stress environments remains fixed at about 8 from the Cambrian to the Pleistocene. In open marine environments, the median is near 30 for the Middle and Upper Paleozoic and almost the same for the Mesozoic. Increases of 50% in median number of species between the Lower and Middle Paleozoic and 2 times between the Mesozoic and Cenozoic occur in open marine environments with parallel, but less pronounced, increases in variable nearshore environments. Conditions controlling overall within-habitat species richness changed at those times. These changes do not correlate directly with evolution of new major taxa, change in physical conditions, predation, space availability or oxygen supply. They may be related to changes in resource availability influenced by factors such as the developing terrestrial flora, to lag-time inherent in the evolutionary process of diversification, or to as yet undetermined factors. Although provinciality determines total species richness for the biosphere, the within-habitat data suggest that the number of marine invertebrate species in the world has increased since the Middle Paleozoic, contrary to Raup's (1976b) contention, but possibly only by about 4 times, not the order of magnitude or more suggested by Valentine (1970).

@article{doi101017s0094837300005236,
    author = "Bambach, Richard K.",
    title = "Species richness in marine benthic habitats through the Phanerozoic",
    year = "1977",
    journal = "Paleobiology",
    abstract = "The distribution of numbers of species and the median number of species from 386 selected fossil communities are tabulated for high stress, variable nearshore, and open marine environments during the Lower, Middle, and Upper Paleozoic, the Mesozoic and the Cenozoic. The number of species always increases from high stress to variable nearshore to open marine environments. Within-habitat variation in number of species is small for long intervals of the Phanerozoic. The median number of species in communities from high stress environments remains fixed at about 8 from the Cambrian to the Pleistocene. In open marine environments, the median is near 30 for the Middle and Upper Paleozoic and almost the same for the Mesozoic. Increases of 50\% in median number of species between the Lower and Middle Paleozoic and 2 times between the Mesozoic and Cenozoic occur in open marine environments with parallel, but less pronounced, increases in variable nearshore environments. Conditions controlling overall within-habitat species richness changed at those times. These changes do not correlate directly with evolution of new major taxa, change in physical conditions, predation, space availability or oxygen supply. They may be related to changes in resource availability influenced by factors such as the developing terrestrial flora, to lag-time inherent in the evolutionary process of diversification, or to as yet undetermined factors. Although provinciality determines total species richness for the biosphere, the within-habitat data suggest that the number of marine invertebrate species in the world has increased since the Middle Paleozoic, contrary to Raup's (1976b) contention, but possibly only by about 4 times, not the order of magnitude or more suggested by Valentine (1970).",
    url = "https://doi.org/10.1017/s0094837300005236",
    doi = "10.1017/s0094837300005236",
    openalex = "W2148395366",
    references = "dayton1971competition, doi1010079783642659232, doi1010160031018268900473, doi101017s0094837300004930, doi101086282070, doi101086282400, doi101086282541, doi101086627723, doi101111j155856461963tb03295x, doi101130001676061968791315tailif20co2, doi101146annureves05110174001441, doi1015159781400881376, doi1023071948498, doi1023072258550, doi1023072485224, doi103133pp323, doi105281zenodo16238847, openalexw574363047"
}

@article{cloney1978ascidian12,
    author = "Cloney, R. A",
    title = "Ascidian metamorphosis",
    year = "1978",
    journal = "review and analysis, in Chia, F",
    note = "talkorigins\_source = {true}; raw\_reference = {Cloney, R. A., 1978, Ascidian metamorphosis: review and analysis, in Chia, F.}"
}

@misc{plough1978sea43,
    author = "Plough, H. H",
    title = "Sea Squirts of the Atlantic Continental Shelf from Maine to",
    year = "1978",
    note = "talkorigins\_source = {true}; raw\_reference = {Plough, H. H., 1978, Sea Squirts of the Atlantic Continental Shelf from Maine to}"
}

@misc{ford1979precambrian30,
    author = "Ford, T. D",
    title = "Precambrian Fossils and the Origin of the Phyla, in House",
    year = "1979",
    note = "talkorigins\_source = {true}; raw\_reference = {Ford, T. D., 1979, Precambrian Fossils and the Origin of the Phyla, in House,}"
}

@misc{rolf1980early45,
    author = "Rolf, W. D. I",
    title = "Early Invertebrate Terrestrial Faunas, in Panchen, A",
    year = "1980",
    note = "talkorigins\_source = {true}; raw\_reference = {Rolf, W. D. I., 1980, Early Invertebrate Terrestrial Faunas, in Panchen, A.}"
}

@article{bengtson1981fossils,
    author = "Bengtson, Stefan",
    title = "Fossils, phylogeny, evolution and science",
    year = "1981",
    journal = "Lethaia",
    url = "https://doi.org/10.1111/j.1502-3931.1981.tb01921.x",
    doi = "10.1111/j.1502-3931.1981.tb01921.x",
    number = "2",
    openalex = "W2076884206",
    pages = "166-166",
    volume = "14"
}

Data on numbers of marine families within 91 metazoan classes known from the Phanerozoic fossil record are analyzed. The distribution of the 2800 fossil families among the classes is very uneven, with most belonging to a small minority of classes. Similarly, the stratigraphic distribution of the classes is very uneven, with most first appearing early in the Paleozoic and with many of the smaller classes becoming extinct before the end of that era. However, despite this unevenness, a Q -mode factor analysis indicates that the structure of these data is rather simple. Only three factors are needed to account for more than 90% of the data. These factors are interpreted as reflecting the three great “evolutionary faunas” of the Phanerozoic marine record: a trilobite-dominated Cambrian fauna, a brachiopod-dominated later Paleozoic fauna, and a mollusc-dominated Mesozoic-Cenozoic, or “modern,” fauna. Lesser factors relate to slow taxonomic turnover within the major faunas through time and to unique aspects of particular taxa and times. Each of the three major faunas seems to have its own characteristic diversity so that its expansion or contraction appears as being intimately associated with a particular phase in the history of total marine diversity. The Cambrian fauna expands rapidly during the Early Cambrian radiations and maintains dominance during the Middle to Late Cambrian “equilibrium.” The Paleozoic fauna then ascends to dominance during the Ordovician radiations, which increase diversity dramatically; this new fauna then maintains dominance throughout the long interval of apparent equilibrium that lasts until the end of the Paleozoic Era. The modern fauna, which slowly increases in importance during the Paleozoic Era, quickly rises to dominance with the Late Permian extinctions and maintains that status during the general rise in diversity to the apparent maximum in the Neogene. The increase in diversity associated with the expansion of each new fauna appears to coincide with an approximately exponential decline of the previously dominant fauna, suggesting possible displacement of each evolutionary fauna by its successor.

@article{doi101017s0094837300003778,
    author = "Sepkoski, J. John",
    title = "A factor analytic description of the Phanerozoic marine fossil record",
    year = "1981",
    journal = "Paleobiology",
    abstract = "Data on numbers of marine families within 91 metazoan classes known from the Phanerozoic fossil record are analyzed. The distribution of the 2800 fossil families among the classes is very uneven, with most belonging to a small minority of classes. Similarly, the stratigraphic distribution of the classes is very uneven, with most first appearing early in the Paleozoic and with many of the smaller classes becoming extinct before the end of that era. However, despite this unevenness, a Q -mode factor analysis indicates that the structure of these data is rather simple. Only three factors are needed to account for more than 90\% of the data. These factors are interpreted as reflecting the three great “evolutionary faunas” of the Phanerozoic marine record: a trilobite-dominated Cambrian fauna, a brachiopod-dominated later Paleozoic fauna, and a mollusc-dominated Mesozoic-Cenozoic, or “modern,” fauna. Lesser factors relate to slow taxonomic turnover within the major faunas through time and to unique aspects of particular taxa and times. Each of the three major faunas seems to have its own characteristic diversity so that its expansion or contraction appears as being intimately associated with a particular phase in the history of total marine diversity. The Cambrian fauna expands rapidly during the Early Cambrian radiations and maintains dominance during the Middle to Late Cambrian “equilibrium.” The Paleozoic fauna then ascends to dominance during the Ordovician radiations, which increase diversity dramatically; this new fauna then maintains dominance throughout the long interval of apparent equilibrium that lasts until the end of the Paleozoic Era. The modern fauna, which slowly increases in importance during the Paleozoic Era, quickly rises to dominance with the Late Permian extinctions and maintains that status during the general rise in diversity to the apparent maximum in the Neogene. The increase in diversity associated with the expansion of each new fauna appears to coincide with an approximately exponential decline of the previously dominant fauna, suggesting possible displacement of each evolutionary fauna by its successor.",
    url = "https://doi.org/10.1017/s0094837300003778",
    doi = "10.1017/s0094837300003778",
    openalex = "W2505144080",
    references = "doi10100797814613088367, doi1010160012825272900724, doi101017s0094837300004917, doi101017s009483730000508x, doi101017s0094837300005236, doi101017s0094837300005352, doi101017s0094837300005649, doi101017s0094837300005972, doi101017s0094837300012549, doi101126science17740541065, doi101126science2064415217, doi101130spe89p63, doi1023071483846, doi1023071796560, doi1023072405671, doi1023072412725, doi1023072412728, doi1023072806339, doi107312simp93764, openalexw1504049102, openalexw645218623"
}

Because of fundamental differences between trace fossils and body fossils, ichnologic nomenclature is beset with difficulties. Foremost is inconsistent treatment by the International Commission on Zoological Nomenclature (lack of sanction for post-1930 names, confusion over the rule of priority) and inadequate curation of type specimens. However, ichnologists have contributed their own problems via inadequate diagnoses and descriptions, misconceptions of ichnologic and taxonomic principles, proliferation of names and failure to engage in true monographic revisions. All these difficulties are illustrated in a thorough reevaluation of the ichnogenera Planolites Nicholson and Palaeophycus Hall. Contrary to a popular but ill-founded scheme in which these ichnogenera are differentiated simply on the presence or absence of branches, Planolites is an unlined burrow infilled with sediments having textural and fabricational characters unlike those of the host rock, whereas Palaeophycus is a lined burrow filled with sediments typically identical to those of the surrounding matrix. Planolites represents active backfilling of sediment in an ephemeral burrow constructed by a mobile deposit feeder and Palaeophycus represents passive sedimentation within an open dwelling burrow constructed by a predaceous or suspension-feeding animal. In addition to ichnological nomenclature and ethology, the ramifications are important in paleoecology, sedimentology and diagenetic studies. Currently recognized ichnospecies of Planolites include P. montanus Richter, P. beverleyensis (Billings) and P. annularis Walcott. Those of Palaeophycus include P. heberti (Saporta), P. tubularis Hall, P. striatus Hall, P. sulcatus (Miller and Dyer) and P. alternatus n. ichnosp.

@article{openalexw2344228935,
    author = "Pemberton, S. George and Frey, Robert W.",
    title = "Trace fossil nomenclature and the Planolites-Palaeophycus dilemma",
    year = "1982",
    journal = "Journal of Paleontology",
    abstract = "Because of fundamental differences between trace fossils and body fossils, ichnologic nomenclature is beset with difficulties. Foremost is inconsistent treatment by the International Commission on Zoological Nomenclature (lack of sanction for post-1930 names, confusion over the rule of priority) and inadequate curation of type specimens. However, ichnologists have contributed their own problems via inadequate diagnoses and descriptions, misconceptions of ichnologic and taxonomic principles, proliferation of names and failure to engage in true monographic revisions. All these difficulties are illustrated in a thorough reevaluation of the ichnogenera Planolites Nicholson and Palaeophycus Hall. Contrary to a popular but ill-founded scheme in which these ichnogenera are differentiated simply on the presence or absence of branches, Planolites is an unlined burrow infilled with sediments having textural and fabricational characters unlike those of the host rock, whereas Palaeophycus is a lined burrow filled with sediments typically identical to those of the surrounding matrix. Planolites represents active backfilling of sediment in an ephemeral burrow constructed by a mobile deposit feeder and Palaeophycus represents passive sedimentation within an open dwelling burrow constructed by a predaceous or suspension-feeding animal. In addition to ichnological nomenclature and ethology, the ramifications are important in paleoecology, sedimentology and diagenetic studies. Currently recognized ichnospecies of Planolites include P. montanus Richter, P. beverleyensis (Billings) and P. annularis Walcott. Those of Palaeophycus include P. heberti (Saporta), P. tubularis Hall, P. striatus Hall, P. sulcatus (Miller and Dyer) and P. alternatus n. ichnosp.",
    openalex = "W2344228935",
    references = "doi1010079783642659232, doi101111j150239311980tb00632x, doi101130gsab10199, doi1023071485443, openalexw3127114020, openalexw574363047"
}

@incollection{doi101007978147570740311,
    author = "Thayer, Charles W.",
    title = "Sediment-Mediated Biological Disturbance and the Evolution of Marine Benthos",
    year = "1983",
    booktitle = "Topics in geobiology",
    url = "https://doi.org/10.1007/978-1-4757-0740-3\_11",
    doi = "10.1007/978-1-4757-0740-3\_11",
    openalex = "W119980067",
    references = "doi1010160022098181901118, doi101016s0920544608703261, doi101038207270a0"
}

Summary 1. Modes of larval development play important roles in the ecology, biogeography, and evolution of marine benthic organisms. Studies of the larval ecology of fossil organisms can contribute greatly to our understanding of such roles by allowing us to race effects on evolutionary time scales. 2. Modes of development can be inferred for well preserved molluscan fossils because the size of the initial larval shell (Protoconch I in gastropods, Prodissoconch I in bivalves) reflects egg size. Other morphological criteria are also available, and a comparative approach based on related taxa with known development may be the most reliable method. By combining larval and adult traits, it is possible to recognize modes of larval development in at least some fossil bryozoans, brachiopods, and echinoderms as well. (a) Planktotrophic larvae arise from small eggs, are released in enormous numbers with little parental investment per offspring, and suffer tremendous mortality during and shortly after a planktic existence. These larvae feed on the plankton during development, and are commonly capable of a prolonged free‐swimming existence, and thus wide dispersal. (b) Nonplanktotrophic larvae (which include both planktic lecithotrophic forms and ‘direct developers’) generally arise from large eggs, with relatively few young produced per parent. Relative to planktotrophic larvae, nonplanktotrophic larvae generally receive greater parental investment per larva, and larval mortality is generally lower. These larvae rely on yolk for nutrition during development, and planktic durations are generally much briefer than for species with planktotrophic larvae, so that dispersal capability is considerably less. Energetic investment per egg is generally higher than in planktotrophs, but as there are lower fecundities as well it is difficult to generalize about the total energetic cost of one mode of reproduction against the other. 3. Owing to the high dispersal capability of planktotrophic larvae, it has been suggested that species with such larvae will be geographically widespread, geologically long‐ranging, and exhibit low speciation and extinction rates. Species with nonplanktotrophic larvae will tend to be geographically more restricted, geologically short‐ranging, and exhibit high speciation and extinction rates (again, as a consequence of their characteristically low larval dispersal capabilities). 4. Recognition of differential dispersal capabilities can play a role in paleobiogeo‐graphic analyses. Concurrent study of the distribution of groups with contrasting modes of development will permit testing of hypotheses concerning timing, magnitudes and frequencies of migration and vicariance events. 5. Larval types are not randomly distributed in the oceans, but relationships with other aspects of the organisms' biology and habitats are very complex. Mode of development varies with: (a) Ecology. A simple r–––K model of adaptive strategies is clearly insufficient to explain the observed relationships: while many ‘equilibrium’ species have nonplanktotrophic larvae, and organisms living in less prdictable environments often have planktotrophic larvae, some of the most opportunistic marine species have nonplanktotrophic larvae. Nonetheless, planktotrophic development seems most suited for exploitation of patchy but widespread habitats. (b) Latitude. At shelf depths, planktotrophy is predominant in the tropics, and decreases sharply at high latitudes. (c) Depth. Incidence of planktotrophy decreases with depth across the continental shelf, at least in some taxa. Beyond the shelf, many deep‐sea organisms are nonplanktotrophic (e.g. most bivalves, peracarid crustaceans), but planktotrophic development appears to be present in other groups (prosobranch gastropods, ophiuroids, and bivalves inhabiting transient habitats such as sunken wood and hydrothermal vents). These trends in developmental types will be accompanied by trends in evolutionary rates and patterns as outlined above. The study of larval ecology by paleobiologists will yield insights into the processes that gave rise to ancient evolutionary and biogeographic patterns, and will permit the development and testing of hypotheses on the origins of the patterns observed in modern seas.

@article{doi101111j1469185x1983tb00380x,
    author = "Jablonski, David and Lutz, Richard A.",
    title = "LARVAL ECOLOGY OF MARINE BENTHIC INVERTEBRATES: PALEOBIOLOGICAL IMPLICATIONS",
    year = "1983",
    journal = "Biological reviews/Biological reviews of the Cambridge Philosophical Society",
    abstract = "Summary 1. Modes of larval development play important roles in the ecology, biogeography, and evolution of marine benthic organisms. Studies of the larval ecology of fossil organisms can contribute greatly to our understanding of such roles by allowing us to race effects on evolutionary time scales. 2. Modes of development can be inferred for well preserved molluscan fossils because the size of the initial larval shell (Protoconch I in gastropods, Prodissoconch I in bivalves) reflects egg size. Other morphological criteria are also available, and a comparative approach based on related taxa with known development may be the most reliable method. By combining larval and adult traits, it is possible to recognize modes of larval development in at least some fossil bryozoans, brachiopods, and echinoderms as well. (a) Planktotrophic larvae arise from small eggs, are released in enormous numbers with little parental investment per offspring, and suffer tremendous mortality during and shortly after a planktic existence. These larvae feed on the plankton during development, and are commonly capable of a prolonged free‐swimming existence, and thus wide dispersal. (b) Nonplanktotrophic larvae (which include both planktic lecithotrophic forms and ‘direct developers’) generally arise from large eggs, with relatively few young produced per parent. Relative to planktotrophic larvae, nonplanktotrophic larvae generally receive greater parental investment per larva, and larval mortality is generally lower. These larvae rely on yolk for nutrition during development, and planktic durations are generally much briefer than for species with planktotrophic larvae, so that dispersal capability is considerably less. Energetic investment per egg is generally higher than in planktotrophs, but as there are lower fecundities as well it is difficult to generalize about the total energetic cost of one mode of reproduction against the other. 3. Owing to the high dispersal capability of planktotrophic larvae, it has been suggested that species with such larvae will be geographically widespread, geologically long‐ranging, and exhibit low speciation and extinction rates. Species with nonplanktotrophic larvae will tend to be geographically more restricted, geologically short‐ranging, and exhibit high speciation and extinction rates (again, as a consequence of their characteristically low larval dispersal capabilities). 4. Recognition of differential dispersal capabilities can play a role in paleobiogeo‐graphic analyses. Concurrent study of the distribution of groups with contrasting modes of development will permit testing of hypotheses concerning timing, magnitudes and frequencies of migration and vicariance events. 5. Larval types are not randomly distributed in the oceans, but relationships with other aspects of the organisms' biology and habitats are very complex. Mode of development varies with: (a) Ecology. A simple r–––K model of adaptive strategies is clearly insufficient to explain the observed relationships: while many ‘equilibrium’ species have nonplanktotrophic larvae, and organisms living in less prdictable environments often have planktotrophic larvae, some of the most opportunistic marine species have nonplanktotrophic larvae. Nonetheless, planktotrophic development seems most suited for exploitation of patchy but widespread habitats. (b) Latitude. At shelf depths, planktotrophy is predominant in the tropics, and decreases sharply at high latitudes. (c) Depth. Incidence of planktotrophy decreases with depth across the continental shelf, at least in some taxa. Beyond the shelf, many deep‐sea organisms are nonplanktotrophic (e.g. most bivalves, peracarid crustaceans), but planktotrophic development appears to be present in other groups (prosobranch gastropods, ophiuroids, and bivalves inhabiting transient habitats such as sunken wood and hydrothermal vents). These trends in developmental types will be accompanied by trends in evolutionary rates and patterns as outlined above. The study of larval ecology by paleobiologists will yield insights into the processes that gave rise to ancient evolutionary and biogeographic patterns, and will permit the development and testing of hypotheses on the origins of the patterns observed in modern seas.",
    url = "https://doi.org/10.1111/j.1469-185x.1983.tb00380.x",
    doi = "10.1111/j.1469-185x.1983.tb00380.x",
    openalex = "W2060347297",
    references = "doi1010160016003258902862, doi1010160302352475900389, doi101016b9780122825057500129, doi101016b9780122825057x50015, doi101017s0094837300003778, doi101017s0094837300005224, doi101017s0094837300005236, doi101017s0094837300005649, doi101017s0094837300005662, doi101017s0094837300016894, doi101086282697, doi101086409052, doi101093icb153717, doi101111j150239311977tb00628x, doi101111j155856461978tb04642x, doi101126science150369228, doi101126science18040931377, doi1015159781400881376, doi101525aa195052402a00270, doi1023071292581, doi1023071483846, doi1023072407204, doi1025773v5jaxgtq24, doi104159harvard9780674865327, hartnoll1975chemoreception, howells1950genetics, openalexw1549886310, openalexw2506868775, openalexw2531009674, openalexw3135630760, openalexw3208881761, openalexw565715315, stanley1978chronospecies"
}

@book{ali1984photoreception1,
    author = "Ali, M. A",
    title = "Photoreception and Vision in Invertebrates",
    year = "1984",
    publisher = "New York, Plenum Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Ali, M. A., 1984, Photoreception and Vision in Invertebrates: New York, Plenum Press.}"
}

Four basic types of skeletal concentrations are modeled in terms of changes in sedimentation rate alone. The model categorizes fossil concentrations on the relatively objective basis of their bed contacts, and uses this criterion to infer directional shifts in net sedimentation. This radical simplification of accumulation histories, in which hardpart input is held constant, yields a surprisingly powerful model capable of predicting a broad spectrum of taphonomic and paleobiologic phenomena. Type I concentrations grade from less fossiliferous sediments and terminate in omission surfaces; if hardpart supply is held constant, they record a slowdown from positive to zero net sedimentation. Type II concentrations are the same as Type I but terminate in erosion surfaces (slowdown to negative net sedimentation), and Type III and IV concentrations are characterized by basal erosion or omission surfaces, respectively, grade upward into less fossiliferous sediments, and record increases in net sedimentation from negative or zero rates to positive rates. According to the model, samples collected from successive horizons within any of these shell beds will differ in the degree and type of post-mortem bias owing to differing histories of hardpart exposure at the depositional interface. Moreover, because rates of sediment accumulation govern the abundance of hardparts at the depositional interface and thus many of the physical characteristics of the benthic habitat, the dynamics of fossil accumulation have direct consequences for the structure of benthic communities (taphonomic feedback) and for ecologically controlled species morphometry. The model is highly robust to fluctuations in hardpart input, as judged by its ability to correctly infer modes of formation of concentrations in synthetic stratigraphic sections. In addition, field examples of Type I–IV concentrations show independent evidence of formation during intervals of reduced net sedimentation, and many exhibit trends in taphonomic and paleobiologic features expected from the postulated changes in net sedimentation. The model thus provides a testable working hypothesis for the accumulation of fossil material in a wide range of environments, and should be applicable to concentrations of any taxonomic composition, state of preservation, or geologic age. The power and robustness of this heuristic model in fact argue that fossil-rich and fossil-poor strata provide fundamentally different records of past conditions, and that sedimentation rather than hardpart input is the primary control on the nature of the fossil record.

@article{doi101017s0094837300002943,
    author = "Kidwell, Susan M.",
    title = "Models for fossil concentrations: paleobiologic implications",
    year = "1986",
    journal = "Paleobiology",
    abstract = "Four basic types of skeletal concentrations are modeled in terms of changes in sedimentation rate alone. The model categorizes fossil concentrations on the relatively objective basis of their bed contacts, and uses this criterion to infer directional shifts in net sedimentation. This radical simplification of accumulation histories, in which hardpart input is held constant, yields a surprisingly powerful model capable of predicting a broad spectrum of taphonomic and paleobiologic phenomena. Type I concentrations grade from less fossiliferous sediments and terminate in omission surfaces; if hardpart supply is held constant, they record a slowdown from positive to zero net sedimentation. Type II concentrations are the same as Type I but terminate in erosion surfaces (slowdown to negative net sedimentation), and Type III and IV concentrations are characterized by basal erosion or omission surfaces, respectively, grade upward into less fossiliferous sediments, and record increases in net sedimentation from negative or zero rates to positive rates. According to the model, samples collected from successive horizons within any of these shell beds will differ in the degree and type of post-mortem bias owing to differing histories of hardpart exposure at the depositional interface. Moreover, because rates of sediment accumulation govern the abundance of hardparts at the depositional interface and thus many of the physical characteristics of the benthic habitat, the dynamics of fossil accumulation have direct consequences for the structure of benthic communities (taphonomic feedback) and for ecologically controlled species morphometry. The model is highly robust to fluctuations in hardpart input, as judged by its ability to correctly infer modes of formation of concentrations in synthetic stratigraphic sections. In addition, field examples of Type I–IV concentrations show independent evidence of formation during intervals of reduced net sedimentation, and many exhibit trends in taphonomic and paleobiologic features expected from the postulated changes in net sedimentation. The model thus provides a testable working hypothesis for the accumulation of fossil material in a wide range of environments, and should be applicable to concentrations of any taxonomic composition, state of preservation, or geologic age. The power and robustness of this heuristic model in fact argue that fossil-rich and fossil-poor strata provide fundamentally different records of past conditions, and that sedimentation rather than hardpart input is the primary control on the nature of the fossil record.",
    url = "https://doi.org/10.1017/s0094837300002943",
    doi = "10.1017/s0094837300002943",
    openalex = "W1810485278",
    references = "doi101007978364265923211, openalexw574363047"
}

@misc{jablonski1986larval35,
    author = "Jablonski, D",
    title = "Larval ecology and macroevolution in marine invertebrates",
    year = "1986",
    note = "talkorigins\_source = {true}; raw\_reference = {Jablonski, D., 1986, Larval ecology and macroevolution in marine invertebrates:}"
}

Actualistic experiments have quantified rate of anaerobic decay and associated mineralization around proteinaceous macro-organisms. Carcasses of the polychaete worm Nereis and the eumalacostracans Nephrops and Palaemon were buried in airtight glass jars filled with sediment and water from marine, brackish, and lacustrine environments. Over a period of 25 weeks the contents were examined to determine the state of decay and were chemically analyzed to monitor early diagenetic mineralization (two methods for such analysis are reviewed). Decay processes were active in the experimental conditions despite anoxia and had virtually destroyed the carcasses within 25 weeks. However, decay-rate in the sulfate-reducing marine system was greater than in the methanogenic freshwater environments. Petrological and geochemical analyses of the organic remains identified discrete layers of authigenic iron monosulfide (a pyrite precursor) on the surface of the decaying Nephrops cuticle within weeks of initiating the experiment. Chemical analysis of decomposing flesh showed a marked increase in pore-water calcium content with time. The results clearly show that anoxia is ineffective as a long-term conservation medium in the preservation of soft-bodied fossils. However, decay-induced mineralization can be very rapid so that even a slight reduction in decay rate can lead to improved levels of fossil preservation. Traditionally, stagnation and rapid burial are considered to be the main prerequisites for the preservation of soft-bodied fossils and the formation of Konservat-Lagerstätten. Clearly these factors are only important in that they promote early diagenetic mineralization. This is the only way to halt information loss through decay.

@article{allison1988the,
    author = "Allison, Peter A.",
    title = "The role of anoxia in the decay and mineralization of proteinaceous macro-fossils",
    year = "1988",
    journal = "Paleobiology",
    abstract = "Actualistic experiments have quantified rate of anaerobic decay and associated mineralization around proteinaceous macro-organisms. Carcasses of the polychaete worm Nereis and the eumalacostracans Nephrops and Palaemon were buried in airtight glass jars filled with sediment and water from marine, brackish, and lacustrine environments. Over a period of 25 weeks the contents were examined to determine the state of decay and were chemically analyzed to monitor early diagenetic mineralization (two methods for such analysis are reviewed). Decay processes were active in the experimental conditions despite anoxia and had virtually destroyed the carcasses within 25 weeks. However, decay-rate in the sulfate-reducing marine system was greater than in the methanogenic freshwater environments. Petrological and geochemical analyses of the organic remains identified discrete layers of authigenic iron monosulfide (a pyrite precursor) on the surface of the decaying Nephrops cuticle within weeks of initiating the experiment. Chemical analysis of decomposing flesh showed a marked increase in pore-water calcium content with time. The results clearly show that anoxia is ineffective as a long-term conservation medium in the preservation of soft-bodied fossils. However, decay-induced mineralization can be very rapid so that even a slight reduction in decay rate can lead to improved levels of fossil preservation. Traditionally, stagnation and rapid burial are considered to be the main prerequisites for the preservation of soft-bodied fossils and the formation of Konservat-Lagerstätten. Clearly these factors are only important in that they promote early diagenetic mineralization. This is the only way to halt information loss through decay.",
    url = "https://doi.org/10.1017/s009483730001188x",
    doi = "10.1017/s009483730001188x",
    number = "2",
    openalex = "W2487864689",
    pages = "139-154",
    volume = "14",
    references = "doi1010160016703784900899, doi101017s0094837300005996, doi101017s009483730000676x, doi101098rstb19850134, doi101130001676061968791315tailif20co2, doi1015159780691209401, doi102475ajs26811, doi104319lo19842920236, doi105962bhlpart22969, doi105962bhltitle7199, openalexw2754161204, openalexw599354073, schopf1978fossilization"
}

@article{doi1010160031018288900545,
    author = "Gray, Jane",
    title = "Evolution of the freshwater ecosystem: The fossil record",
    year = "1988",
    journal = "Palaeogeography Palaeoclimatology Palaeoecology",
    url = "https://doi.org/10.1016/0031-0182(88)90054-5",
    doi = "10.1016/0031-0182(88)90054-5",
    openalex = "W1984241346",
    references = "applegate1967phyletic, doi1010079783642814983, doi1010079789400958517, doi1010160031018275900279, doi1010160031018279901123, doi1010160304377087900416, doi101038164766a0, doi10108002724634198410012014, doi10108003115518108567003, doi101093icb12177, doi101130001676061972831299peboto20co2, doi10113000917613198614567ltpots20co2, doi1023071292217, doi1023071441916, doi1023071442263, doi1023071797104, doi1023071933240, doi1023072258117, doi102475ajs242274, doi102475ajs2628975, doi102475ajs28211, doi103133pp690, doi105281zenodo16298542, doi105281zenodo3382461, doi105962bhltitle54054, doi105962p150189, openalexw1504637003, openalexw2163397885, openalexw2246336267, openalexw2982931797, openalexw337536883, openalexw568207017, openalexw637324698, sohl1960archeogastropoda, thomson1969the"
}

@incollection{doi101016b9780126709506500047,
    author = "de Carvalho, Marcelo R.",
    title = "Higher-Level Elasmobranch Phylogeny, Basal Squaleans, and Paraphyly",
    year = "1996",
    booktitle = "Elsevier eBooks",
    url = "https://doi.org/10.1016/b978-012670950-6/50004-7",
    doi = "10.1016/b978-012670950-6/50004-7",
    openalex = "W2496781023",
    references = "doi101093icb172303, doi101111j109636421996tb02189x, doi101111j146363951940tb00339x, openalexw595691412"
}

@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"
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many benthic marine invertebrates develop by means of free-livlng, dispersive larval stages. The presumed advantages of such larvae include the avoidance of competition for resources with adults, temporary reduct~on of benthic mortality while in the plankton, decreased likelihood of inbreeding in the next generation, and increased ability to withstand local extinction However, the direct~on of evolutionary change appears generally b ~a s e d toward the loss of larvae in many clades, implying that larvae are somehow disadvantageous. Poss~ble disadvantages include dispersal away from favorable habitat, mismatches between larval and luvenile physiological tolerances, greater sus-ceptib~lity to env~ronmental stresses, greater susceptibihty to predation. and vanous costs that may be associated with n~etanlorphosing in response to specific chemical cues and postponing n~etamorphosis in the absence of those cues. Understanding the forces responsible for the present distribution of larval and non-larval (aplanktonlc) development among benthic marine invertebrates, and the potential influence of human activities on the direct~on of future evolutionary change in 1-eproductlve patterns, will require a better understanding of the following issues. the role of macro-evolutionary forces in selecting for or against dispersive larvae, the relative tolerances of encapsulated embryos and free-living larvae to salinity, pollutant, and other environmental stresses; the degree to which egg masses, e g g capsules, and brood chambers protect developing embryos from environmental stresses; the relative magmtude of predation by planktonic and benthic predators on both larvae and early juveniles; the way In which larval and juvenile size affect vulnerability to predators; the extent to w h ~c h encapsulation and brooding protect against predators; the amount of genetic change associated with loss of larvae from invertebrate life cycles and the time required to accomplish that change; and the degree to which continued input of larvae from other populations deters selection against dispersive larvae The prominence of larval development in modern life cycles may reflect difficulties In loslng larvae from llfe cycles more than selection for their retention.

@article{doi103354meps177269,
    author = "Pechenik, JA",
    title = "On the advantages and disadvantages of larval stages in benthic marine invertebrate life cycles",
    year = "1999",
    journal = "Marine Ecology Progress Series",
    abstract = "many benthic marine invertebrates develop by means of free-livlng, dispersive larval stages. The presumed advantages of such larvae include the avoidance of competition for resources with adults, temporary reduct\textasciitilde on of benthic mortality while in the plankton, decreased likelihood of inbreeding in the next generation, and increased ability to withstand local extinction However, the direct\textasciitilde on of evolutionary change appears generally b \textasciitilde a s e d toward the loss of larvae in many clades, implying that larvae are somehow disadvantageous. Poss\textasciitilde ble disadvantages include dispersal away from favorable habitat, mismatches between larval and luvenile physiological tolerances, greater sus-ceptib\textasciitilde lity to env\textasciitilde ronmental stresses, greater susceptibihty to predation. and vanous costs that may be associated with n\textasciitilde etanlorphosing in response to specific chemical cues and postponing n\textasciitilde etamorphosis in the absence of those cues. Understanding the forces responsible for the present distribution of larval and non-larval (aplanktonlc) development among benthic marine invertebrates, and the potential influence of human activities on the direct\textasciitilde on of future evolutionary change in 1-eproductlve patterns, will require a better understanding of the following issues. the role of macro-evolutionary forces in selecting for or against dispersive larvae, the relative tolerances of encapsulated embryos and free-living larvae to salinity, pollutant, and other environmental stresses; the degree to which egg masses, e g g capsules, and brood chambers protect developing embryos from environmental stresses; the relative magmtude of predation by planktonic and benthic predators on both larvae and early juveniles; the way In which larval and juvenile size affect vulnerability to predators; the extent to w h \textasciitilde c h encapsulation and brooding protect against predators; the amount of genetic change associated with loss of larvae from invertebrate life cycles and the time required to accomplish that change; and the degree to which continued input of larvae from other populations deters selection against dispersive larvae The prominence of larval development in modern life cycles may reflect difficulties In loslng larvae from llfe cycles more than selection for their retention.",
    url = "https://doi.org/10.3354/meps177269",
    doi = "10.3354/meps177269",
    openalex = "W2065268282",
    references = "doi1010160169534796100288, doi101016b9780122825057x50015, doi101016s006528810860187x, doi10103841710, doi101126science11538249, doi101146annurevecolsys271237, doi101146annurevecolsys271477, doi101146annureves16110185002011, doi101146annureves16110185002141, doi105860choice341536, thorson1950reproductive"
}

@misc{doi10100797836425967425,
    author = "Zapata, A. and Amemiya, Chris T.",
    title = "Phylogeny of Lower Vertebrates and Their Immunological Structures",
    year = "2000",
    booktitle = "Current topics in microbiology and immunology",
    url = "https://doi.org/10.1007/978-3-642-59674-2\_5",
    doi = "10.1007/978-3-642-59674-2\_5",
    openalex = "W1611932380",
    references = "crossref1997interrelationships, doi101001jama281242351, doi101002j146020751992tb05120x, doi101002jmor1051730108, doi1010079783642866593, doi1010160145305x81900458, doi1010160145305x87900103, doi101016b9780126709506500035, doi101016b9780126709506500187, doi10103831927, doi101073pnas89188794, doi10108002724634198110011886, doi101093icb112183, doi101093icb172303, doi101126science28253941711, doi101146annureven10010165000525, doi101242dev1994supplement125, doi1023071442263, doi1023073514548, openalexw2081952897, openalexw3041320757, openalexw3211386673"
}

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.

@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"
}

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

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

@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{doi101016s0012825202001319,
    author = "Taylor, Paul D. and Wilson, Mark A.",
    title = "Palaeoecology and evolution of marine hard substrate communities",
    year = "2003",
    journal = "Earth-Science Reviews",
    url = "https://doi.org/10.1016/s0012-8252(02)00131-9",
    doi = "10.1016/s0012-8252(02)00131-9",
    openalex = "W1998311295",
    references = "crossref1977patterns, doi1010079781475707403, doi1010079783642659232, doi101007s003380000129, doi1010160037073894900264, doi101016c20090029031, doi101016s0301926896000617, doi101016s0967065397808939, doi101017s0022336000025567, doi101017s0022336000038932, doi101017s0094837300005352, doi101046j13653091200000003x, doi10108008927019809378348, doi101086283381, doi101086629241, doi101111j136530911990tb00147x, doi101111j136530911993tb01364x, doi101111j1469185x1983tb00380x, doi101126science11538249, doi1011300091761319980261091afrfoh23co2, doi101144pygs5211, doi101146annurevecolsys271477, doi1012019781003077831, doi1023071936969, doi1023072403105, doi1023073514631, doi1023073514786, doi1023073515314, doi1023073515363, doi103354meps058175, jablonski1983larval, openalexw1528487914, openalexw1608366422, openalexw2152529191, simpson1978patterns"
}

The evolution of subtropical (30–35°N) upper ocean temperatures through the Cretaceous is inferred from the oxygen isotope compositions of 64 fish teeth (enamel) coming from the western Tethyan platform. Mean δ 18 O values of 22‰ at the Berriasian‐Valanginian boundary decrease, with oscillations to 18.5‰ around the Cenomanian‐Turonian boundary, and progressively increase to 21.5‰ by the end of the Cretaceous. The similarity of this oxygen isotope curve for bioapatites from platform environments with those for foraminifera and bulk carbonates that were deposited in deeper waters and at other paleolatitudes indicates that they record global climatic signals. Major cooling events at the million‐year scale can be distinguished: (1) at the Berriasian‐Valanginian boundary and (2) during the earliest Late Valanginian. A third cooling event is detected during the earliest Aptian. These events, already proposed as icehouse interludes during the lower Cretaceous, are also recorded at subtropical latitudes. A progressive warming is identified from the Aptian to the Cenomanian‐Turonian interval that corresponds to a thermal optimum, and then upper ocean temperatures decreased to the Maastrichtian. Minimum isotopic temperatures range from 15°C to 28°C, assuming a δ 18 O seawater of −1‰, for an ice‐free world. Taking more realistic δ 18 O seawater values of ∼0‰ for tropical waters, during glacial periods (within the Berriasian‐Valanginian interval, and earliest Aptian) or with above average salinities (possibly the Maastrichtian), temperatures are increased by 4–5°C. Temperature differences between climatic extremes of the Valanginian and Cenomanian‐Turonian are estimated to have been 10°C. Latitudinal thermal gradients for the Albian‐Cenomanian, Turonian, and Maastrichtian were 0.2–0.3°C/° latitude and thus weaker than modern oceanic values at about 0.4°C/° latitude.

@article{doi1010292002pa000823,
    author = "Pucéat, Emmanuelle and Lécuyer, Christophe and Sheppard, Simon M.F. and Dromart, Gilles and Reboulet, Stéphane and Grandjean, Patricia",
    title = "Thermal evolution of Cretaceous Tethyan marine waters inferred from oxygen isotope composition of fish tooth enamels",
    year = "2003",
    journal = "Paleoceanography",
    abstract = "The evolution of subtropical (30–35°N) upper ocean temperatures through the Cretaceous is inferred from the oxygen isotope compositions of 64 fish teeth (enamel) coming from the western Tethyan platform. Mean δ 18 O values of 22‰ at the Berriasian‐Valanginian boundary decrease, with oscillations to 18.5‰ around the Cenomanian‐Turonian boundary, and progressively increase to 21.5‰ by the end of the Cretaceous. The similarity of this oxygen isotope curve for bioapatites from platform environments with those for foraminifera and bulk carbonates that were deposited in deeper waters and at other paleolatitudes indicates that they record global climatic signals. Major cooling events at the million‐year scale can be distinguished: (1) at the Berriasian‐Valanginian boundary and (2) during the earliest Late Valanginian. A third cooling event is detected during the earliest Aptian. These events, already proposed as icehouse interludes during the lower Cretaceous, are also recorded at subtropical latitudes. A progressive warming is identified from the Aptian to the Cenomanian‐Turonian interval that corresponds to a thermal optimum, and then upper ocean temperatures decreased to the Maastrichtian. Minimum isotopic temperatures range from 15°C to 28°C, assuming a δ 18 O seawater of −1‰, for an ice‐free world. Taking more realistic δ 18 O seawater values of ∼0‰ for tropical waters, during glacial periods (within the Berriasian‐Valanginian interval, and earliest Aptian) or with above average salinities (possibly the Maastrichtian), temperatures are increased by 4–5°C. Temperature differences between climatic extremes of the Valanginian and Cenomanian‐Turonian are estimated to have been 10°C. Latitudinal thermal gradients for the Albian‐Cenomanian, Turonian, and Maastrichtian were 0.2–0.3°C/° latitude and thus weaker than modern oceanic values at about 0.4°C/° latitude.",
    url = "https://doi.org/10.1029/2002pa000823",
    doi = "10.1029/2002pa000823",
    openalex = "W1639686691",
    references = "doi1010160012821x89900186, doi101016s0012825299000483, doi101126science28253972241, doi10113000917613198614703pefcnp20co2, doi1011300091761319880160022lctvan23co2, doi1011300091761319980260995adswat23co2"
}

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/.

@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{doi101086383584,
    author = "Wooding, Stephen",
    title = "Inferring Phylogenies.",
    year = "2004",
    journal = "The American Journal of Human Genetics",
    url = "https://doi.org/10.1086/383584",
    doi = "10.1086/383584",
    openalex = "W4233815609"
}

A phylogenetic approach to the origin and maintenance of species diversity ideally requires the sampling of all species within a clade, confirmation that they are evolutionarily distinct entities, and knowledge of their geographical distributions. In the marine tropics such studies have mostly been of fish and reef-associated organisms, usually with high dispersal. In contrast, snails of the genus Echinolittorina (Littorinidae) are restricted to rocky shores, have a four-week pelagic development (and recorded dispersal up to 1400 km), and show different evolutionary patterns. We present a complete molecular phylogeny of Echinolittorina, derived from Bayesian analysis of sequences from nuclear 28S rRNA and mitochondrial 12S rRNA and COI genes (nodal support indicated by posterior probabilities, maximum likelihood, and neighbor-joining bootstrap). This consists of 59 evolutionarily significant units (ESUs), including all 50 known taxonomic species. The 26 ESUs found in the Indo-West Pacific region form a single clade, whereas the eastern Pacific and Atlantic species are basal. The earliest fossil occurred in the Tethys during the middle Eocene and we suggest that the Indo-West Pacific clade has been isolated since closure of the Tethyan seaway in the early Miocene. The geographical distributions of all species (based on more than 3700 locality records) appear to be circumscribed by barriers of low temperature, unsuitable sedimentary habitat, stretches of open water exceeding about 1400 km, and differences in oceanographic conditions on the continuum between oceanic and continental. The geographical ranges of sister species show little or no overlap, indicating that the speciation mode is predominantly allopatric. Furthermore, range expansion following speciation appears to have been limited, because a high degree of allopatry is maintained through three to five branching points of the phylogeny. This may be explained by infrequent long-distance colonization, habitat specialization on the oceanic/continental gradient, and perhaps by interspecific competition. In the eastern Pacific plus Atlantic we identify five cases of divergence on either side of the Isthmus of Panama, but our estimates of their ages pre-date the emergence of the Isthmus. There are three examples of sister relationships between species in the western Atlantic and eastern Atlantic, all resulting from dispersal to the east. Within the Indo-West Pacific, we find no geographical pattern of speciation events; narrowly endemic species of recent origin are present in both peripheral and central parts of the region. Evidence from estimated divergence times of sister species, and from a plot of the number of lineages over time, suggest that there has been no acceleration of diversification during the glacio-eustatic cycles of the Plio-Pleistocene. In comparison with reefal organisms, species of Echinolittorina on rocky shores may be less susceptible to extinction or isolation during sea-level fluctuations. The species richness of Echinolittorina in the classical biogeographic provinces conforms to the common pattern of highest diversity (11 species) in the central "East Indies Triangle" of the Indo-West Pacific, with a subsidiary focus in the eastern Pacific and western Atlantic, and lowest diversity in the eastern Atlantic. The diversity focus in the East Indies Triangle is produced by a mosaic of restricted allopatric species and overlap of a few widespread ones, and is the result of habitat specialization rather than historical vicariance. This study emphasizes the plurality of biogeographic histories and speciation patterns in the marine tropics.

@article{doi101111j001438202004tb01600x,
    author = "Williams, S T and Reid, D G",
    title = "Speciation and diversity on tropical rocky shores: a global phylogeny of snails of the genus Echinolittorina.",
    year = "2004",
    journal = "Evolution; international journal of organic evolution",
    abstract = {A phylogenetic approach to the origin and maintenance of species diversity ideally requires the sampling of all species within a clade, confirmation that they are evolutionarily distinct entities, and knowledge of their geographical distributions. In the marine tropics such studies have mostly been of fish and reef-associated organisms, usually with high dispersal. In contrast, snails of the genus Echinolittorina (Littorinidae) are restricted to rocky shores, have a four-week pelagic development (and recorded dispersal up to 1400 km), and show different evolutionary patterns. We present a complete molecular phylogeny of Echinolittorina, derived from Bayesian analysis of sequences from nuclear 28S rRNA and mitochondrial 12S rRNA and COI genes (nodal support indicated by posterior probabilities, maximum likelihood, and neighbor-joining bootstrap). This consists of 59 evolutionarily significant units (ESUs), including all 50 known taxonomic species. The 26 ESUs found in the Indo-West Pacific region form a single clade, whereas the eastern Pacific and Atlantic species are basal. The earliest fossil occurred in the Tethys during the middle Eocene and we suggest that the Indo-West Pacific clade has been isolated since closure of the Tethyan seaway in the early Miocene. The geographical distributions of all species (based on more than 3700 locality records) appear to be circumscribed by barriers of low temperature, unsuitable sedimentary habitat, stretches of open water exceeding about 1400 km, and differences in oceanographic conditions on the continuum between oceanic and continental. The geographical ranges of sister species show little or no overlap, indicating that the speciation mode is predominantly allopatric. Furthermore, range expansion following speciation appears to have been limited, because a high degree of allopatry is maintained through three to five branching points of the phylogeny. This may be explained by infrequent long-distance colonization, habitat specialization on the oceanic/continental gradient, and perhaps by interspecific competition. In the eastern Pacific plus Atlantic we identify five cases of divergence on either side of the Isthmus of Panama, but our estimates of their ages pre-date the emergence of the Isthmus. There are three examples of sister relationships between species in the western Atlantic and eastern Atlantic, all resulting from dispersal to the east. Within the Indo-West Pacific, we find no geographical pattern of speciation events; narrowly endemic species of recent origin are present in both peripheral and central parts of the region. Evidence from estimated divergence times of sister species, and from a plot of the number of lineages over time, suggest that there has been no acceleration of diversification during the glacio-eustatic cycles of the Plio-Pleistocene. In comparison with reefal organisms, species of Echinolittorina on rocky shores may be less susceptible to extinction or isolation during sea-level fluctuations. The species richness of Echinolittorina in the classical biogeographic provinces conforms to the common pattern of highest diversity (11 species) in the central "East Indies Triangle" of the Indo-West Pacific, with a subsidiary focus in the eastern Pacific and western Atlantic, and lowest diversity in the eastern Atlantic. The diversity focus in the East Indies Triangle is produced by a mosaic of restricted allopatric species and overlap of a few widespread ones, and is the result of habitat specialization rather than historical vicariance. This study emphasizes the plurality of biogeographic histories and speciation patterns in the marine tropics.},
    url = "https://pubmed.ncbi.nlm.nih.gov/15562687/",
    doi = "10.1111/j.0014-3820.2004.tb01600.x",
    openalex = "W2180951634",
    pmid = "15562687",
    references = "doi101016s016953470102198x, doi101038324137a0, doi101073pnas86166196, doi101093bioinformatics178754, doi101093nar22224673, doi101093nar25244876, doi1023071447682, openalexw1505736461, openalexw1840956397, openalexw3217097258"
}

The origins of evolutionary innovations have been intensively studied, but relatively little is known about their large-scale ecological patterns. For post-Paleozoic benthic marine invertebrates, which have the richest and most densely sampled fossil record, order-level taxa tend to appear first in onshore, disturbed habitats, even in groups that are now exclusively deep-water (so that present-day distributions are not reliable indicators of original environments). New results presented here show that the onshore-origination pattern is robust to shifts in taxonomic methods and to new paleontological discoveries, and the few available studies suggest that this pattern can also be seen in terms of excursions in morphospace or the acquisition of derived character states, without reference to taxonomic categories. The environmental pattern at high levels contrasts significantly with the origin of low-level novelties (such as defined genera and families) in crinoids, echinoids, and bryozoans, where first appearances tend to conform to their clade-specific bathymetric diversity gradients. This discordance seems to eliminate potential driving mechanisms that simply scale up within-population genetic or ecological processes. Little is known about the factors that promote the onshore-offshore expansion of orders across the continental shelf, or that drive some clades to abandon ancestral habitats for an exclusively deep-water distribution. The origin of evolutionary innovation must ultimately reside in developmental changes, but the onshore-origination bias could emerge from two different dynamics: the pattern could be primarily genetic and developmental, i.e., innovations truly arise onshore; or primarily ecological, i.e., innovations arise randomly but preferentially survive onshore. Whatever the ultimate driving mechanisms, these macroevolutionary patterns show that theories of large-scale evolutionary novelty must include an ecological dimension.

@article{doi101002jezb21075,
    author = "Jablonski, David",
    title = "Evolutionary innovations in the fossil record: the intersection of ecology, development, and macroevolution",
    year = "2005",
    journal = "Journal of Experimental Zoology Part B Molecular and Developmental Evolution",
    abstract = "The origins of evolutionary innovations have been intensively studied, but relatively little is known about their large-scale ecological patterns. For post-Paleozoic benthic marine invertebrates, which have the richest and most densely sampled fossil record, order-level taxa tend to appear first in onshore, disturbed habitats, even in groups that are now exclusively deep-water (so that present-day distributions are not reliable indicators of original environments). New results presented here show that the onshore-origination pattern is robust to shifts in taxonomic methods and to new paleontological discoveries, and the few available studies suggest that this pattern can also be seen in terms of excursions in morphospace or the acquisition of derived character states, without reference to taxonomic categories. The environmental pattern at high levels contrasts significantly with the origin of low-level novelties (such as defined genera and families) in crinoids, echinoids, and bryozoans, where first appearances tend to conform to their clade-specific bathymetric diversity gradients. This discordance seems to eliminate potential driving mechanisms that simply scale up within-population genetic or ecological processes. Little is known about the factors that promote the onshore-offshore expansion of orders across the continental shelf, or that drive some clades to abandon ancestral habitats for an exclusively deep-water distribution. The origin of evolutionary innovation must ultimately reside in developmental changes, but the onshore-origination bias could emerge from two different dynamics: the pattern could be primarily genetic and developmental, i.e., innovations truly arise onshore; or primarily ecological, i.e., innovations arise randomly but preferentially survive onshore. Whatever the ultimate driving mechanisms, these macroevolutionary patterns show that theories of large-scale evolutionary novelty must include an ecological dimension.",
    url = "https://doi.org/10.1002/jez.b.21075",
    doi = "10.1002/jez.b.21075",
    openalex = "W2071059397",
    references = "bretsky1968evolution, doi1016660094837320000260056cefisg20co2"
}

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

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

Americanae nace como un proyecto conjunto que surge dentro de la Red Europea de Información y Documentación sobre América Latina (REDIAL), y que ha afrontado la Biblioteca de la Agencia Española de Cooperación Internacional para el Desarrollo (AECID). Esta nueva biblioteca virtual hace más accesibles los libros digitales de tema americanista a los investigadores y usuarios interesados de cualquier parte del mundo.

@incollection{doi1012019781420006391ch7,
    author = "Thiel, Martín and Haye, Pilar A.",
    title = "The Ecology Of Rafting In The Marine Environment. Iii. Biogeographical And Evolutionary Consequences",
    year = "2006",
    booktitle = "Oceanography and Marine Biology/Oceanography and marine biology - an annual review",
    abstract = "Americanae nace como un proyecto conjunto que surge dentro de la Red Europea de Información y Documentación sobre América Latina (REDIAL), y que ha afrontado la Biblioteca de la Agencia Española de Cooperación Internacional para el Desarrollo (AECID). Esta nueva biblioteca virtual hace más accesibles los libros digitales de tema americanista a los investigadores y usuarios interesados de cualquier parte del mundo.",
    url = "https://doi.org/10.1201/9781420006391.ch7",
    doi = "10.1201/9781420006391.ch7",
    openalex = "W24039824",
    references = "doi101111j001438202004tb01600x"
}

Temperature controls the rate of fundamental biochemical processes and thereby regulates organismal attributes including development rate and survival. The increase in metabolic rate with temperature explains substantial among-species variation in life-history traits, population dynamics, and ecosystem processes. Temperature can also cause variability in metabolic rate within species. Here, we compare the effect of temperature on a key component of marine life cycles among a geographically and taxonomically diverse group of marine fish and invertebrates. Although innumerable lab studies document the negative effect of temperature on larval development time, little is known about the generality versus taxon-dependence of this relationship. We present a unified, parameterized model for the temperature dependence of larval development in marine animals. Because the duration of the larval period is known to influence larval dispersal distance and survival, changes in ocean temperature could have a direct and predictable influence on population connectivity, community structure, and regional-to-global scale patterns of biodiversity.

@article{doi101073pnas0603422104,
    author = "O’Connor, Mary I. and Bruno, John F. and Gaines, Steven D. and Halpern, Benjamin S. and Lester, Sarah E. and Kinlan, Brian P. and Weiss, Jack M.",
    title = "Temperature control of larval dispersal and the implications for marine ecology, evolution, and conservation",
    year = "2007",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Temperature controls the rate of fundamental biochemical processes and thereby regulates organismal attributes including development rate and survival. The increase in metabolic rate with temperature explains substantial among-species variation in life-history traits, population dynamics, and ecosystem processes. Temperature can also cause variability in metabolic rate within species. Here, we compare the effect of temperature on a key component of marine life cycles among a geographically and taxonomically diverse group of marine fish and invertebrates. Although innumerable lab studies document the negative effect of temperature on larval development time, little is known about the generality versus taxon-dependence of this relationship. We present a unified, parameterized model for the temperature dependence of larval development in marine animals. Because the duration of the larval period is known to influence larval dispersal distance and survival, changes in ocean temperature could have a direct and predictable influence on population connectivity, community structure, and regional-to-global scale patterns of biodiversity.",
    url = "https://doi.org/10.1073/pnas.0603422104",
    doi = "10.1073/pnas.0603422104",
    openalex = "W2157367008",
    references = "doi101016b9780122825057x50015, doi101086381872, doi101111j1469185x1950tb00585x, doi101146annureves16110185002011, thorson1950reproductive"
}

The importance of ecological interactions in driving the evolution of animals has been the focus of intense debate among paleontologists, evolutionary biologists, and macroecologists. To test whether the intensity of such interactions covaries with the secular evolutionary trend in global biodiversity, we compiled a species-level database of predation intensity, as measured by the frequency of common predation traces (drillings and repair scars ranging in age from Ediacaran to Holocene). The results indicate that the frequency of predation traces increased notably by the Ordovician, and not in the mid-Paleozoic as suggested by multiple previous studies. Importantly, these estimates of predation intensity and global diversity of marine metazoans correlate throughout the Phanerozoic fossil record regardless of corrections and methods applied. This concordance may represent (i) an ecological signal: long-term coupling of diversity and predation; (ii) a diversity-driven diffusion of predatory behaviors: an increased probability of more complex predatory strategies to appear at higher diversity levels; or (iii) a spurious concordance in signal capture: an artifact where rare species and less-frequent (e.g., trace-producing) predatory behaviors are both more detectable at times when sampling improves. The coupling of predation and diversity records suggests that macroevolutionary and macroecological patterns share common causative mechanisms that may reflect either historical processes or sampling artifacts.

@article{doi101073pnas0704960104,
    author = "Huntley, John Warren and Kowalewski, Michał",
    title = "Strong coupling of predation intensity and diversity in the Phanerozoic fossil record",
    year = "2007",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "The importance of ecological interactions in driving the evolution of animals has been the focus of intense debate among paleontologists, evolutionary biologists, and macroecologists. To test whether the intensity of such interactions covaries with the secular evolutionary trend in global biodiversity, we compiled a species-level database of predation intensity, as measured by the frequency of common predation traces (drillings and repair scars ranging in age from Ediacaran to Holocene). The results indicate that the frequency of predation traces increased notably by the Ordovician, and not in the mid-Paleozoic as suggested by multiple previous studies. Importantly, these estimates of predation intensity and global diversity of marine metazoans correlate throughout the Phanerozoic fossil record regardless of corrections and methods applied. This concordance may represent (i) an ecological signal: long-term coupling of diversity and predation; (ii) a diversity-driven diffusion of predatory behaviors: an increased probability of more complex predatory strategies to appear at higher diversity levels; or (iii) a spurious concordance in signal capture: an artifact where rare species and less-frequent (e.g., trace-producing) predatory behaviors are both more detectable at times when sampling improves. The coupling of predation and diversity records suggests that macroevolutionary and macroecological patterns share common causative mechanisms that may reflect either historical processes or sampling artifacts.",
    url = "https://doi.org/10.1073/pnas.0704960104",
    doi = "10.1073/pnas.0704960104",
    openalex = "W2043156007",
    references = "doi101038337695c0, doi1011300091761319980261091afrfoh23co2"
}

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.

@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"
}

Associations of fossil genera and species commonly display repeated and predictable patterns of change in stratigraphic sections. These changes exhibit some analogies with the phenomenon of ecological succession but are longer-term allogenic temporal changes, occurring over time scales of tens to hundreds of thousands of years, that should be referred to as biotic (faunal-floral) replacement. Habitat tracking is one of a suite of possible mechanisms of biotic replacement, but one that may be important in certain marine settings. Evidence of tracking includes (1) recurrence of similar replacement series of differing age; (2) mirroring of vertical replacement of faunas by lateral gradients of species associations along single time planes; (3) the occurrence of similar gradient transects at different time planes; (4) the correlatability of highs and lows of quantitative faunal curves (e.g., variations of detrended correspondence analysis scores) at different localities despite offsets of absolute scores; and (5) the high fidelity recurrence of stenotopic species in particular associations representing narrowly defined environments. The degree of ecological fidelity (e.g., similarity of species richness, guild structure) that is maintained during tracking is variable. Recurrent assemblages in different cycles, separated by as much as several million years, can be very similar in terms of species composition and trophic structure. Common species, however, may show significant differences in rank and relative abundances. This evidence indicates individualistic tracking of preferred habitat by various species. In shallow-shelf and ramp settings, sea-level fluctuations may produce approximately symmetrical patterns of biotic replacement where biofacies are arrayed typically in elongate belts parallel to depositional strike. Asymmetries, however, are common and may result from variations in sediment supply during sea-level fluctuation. Hence, the low siliciclastic input typical of transgressions predictably favors those organisms that require lower sedimentation or turbidity and perhaps firmgrounds to hardgrounds, whereas the regressive half cycle at analogous depths favors more eurytopic organisms that tolerate or prefer higher sedimentation or turbidity. The phenomenon of tracking may be of considerable importance in evolutionary paleoecology. Tracking implies that species commonly respond to long-term physical changes, not by adaptation, but primarily by migration of species to preferred habitats, if the rate or magnitude of environmental change is not too great. Provided that the same basic environment existed through time, despite lateral shifting by up to hundreds of kilometers, most species of benthic invertebrates were capable of surviving with little or no evolutionary change. Tracking may be the primary basis of patterns of morphological stasis, as well as relative stability in biofacies richness, composition, and trophic structure.

@article{doi102110palo2005p05028r,
    author = "BRETT, C. E. and Hendy, Austin and Bartholomew, Alexander and Bonelli, James R. and McLaughlin, Patrick I.",
    title = "RESPONSE OF SHALLOW MARINE BIOTAS TO SEA-LEVEL FLUCTUATIONS: A REVIEW OF FAUNAL REPLACEMENT AND THE PROCESS OF HABITAT TRACKING",
    year = "2007",
    journal = "Palaios",
    abstract = "Associations of fossil genera and species commonly display repeated and predictable patterns of change in stratigraphic sections. These changes exhibit some analogies with the phenomenon of ecological succession but are longer-term allogenic temporal changes, occurring over time scales of tens to hundreds of thousands of years, that should be referred to as biotic (faunal-floral) replacement. Habitat tracking is one of a suite of possible mechanisms of biotic replacement, but one that may be important in certain marine settings. Evidence of tracking includes (1) recurrence of similar replacement series of differing age; (2) mirroring of vertical replacement of faunas by lateral gradients of species associations along single time planes; (3) the occurrence of similar gradient transects at different time planes; (4) the correlatability of highs and lows of quantitative faunal curves (e.g., variations of detrended correspondence analysis scores) at different localities despite offsets of absolute scores; and (5) the high fidelity recurrence of stenotopic species in particular associations representing narrowly defined environments. The degree of ecological fidelity (e.g., similarity of species richness, guild structure) that is maintained during tracking is variable. Recurrent assemblages in different cycles, separated by as much as several million years, can be very similar in terms of species composition and trophic structure. Common species, however, may show significant differences in rank and relative abundances. This evidence indicates individualistic tracking of preferred habitat by various species. In shallow-shelf and ramp settings, sea-level fluctuations may produce approximately symmetrical patterns of biotic replacement where biofacies are arrayed typically in elongate belts parallel to depositional strike. Asymmetries, however, are common and may result from variations in sediment supply during sea-level fluctuation. Hence, the low siliciclastic input typical of transgressions predictably favors those organisms that require lower sedimentation or turbidity and perhaps firmgrounds to hardgrounds, whereas the regressive half cycle at analogous depths favors more eurytopic organisms that tolerate or prefer higher sedimentation or turbidity. The phenomenon of tracking may be of considerable importance in evolutionary paleoecology. Tracking implies that species commonly respond to long-term physical changes, not by adaptation, but primarily by migration of species to preferred habitats, if the rate or magnitude of environmental change is not too great. Provided that the same basic environment existed through time, despite lateral shifting by up to hundreds of kilometers, most species of benthic invertebrates were capable of surviving with little or no evolutionary change. Tracking may be the primary basis of patterns of morphological stasis, as well as relative stability in biofacies richness, composition, and trophic structure.",
    url = "https://doi.org/10.2110/palo.2005.p05-028r",
    doi = "10.2110/palo.2005.p05-028r",
    openalex = "W2029752719",
    references = "doi101038207270a0, doi101111j150239311978tb01893x, doi101111j150239311985tb00697x, doi1023073515180"
}

@article{openalexw2898156694,
    author = "Klug, Stefanie and Kriwet, Jürgen and Lirio, Mary Rose and Núñez, Héctor",
    title = "Mesozoic Fishes 4 - Homology and Phylogeny",
    year = "2008",
    openalex = "W2898156694",
    references = "brinkman2002teleost, doi1010029780470715253ch10, doi101029pa002i001p00001, doi101093icesjms233366, doi101126science1059412, doi1016710272463420010210172dteotr20co2, doi1023071269588, doi1023071292845, doi1023071445079, doi1023071446835, openalexw2040817479, openalexw2588677549"
}

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

@article{doi101093sysbiosyq010,
    author = "Guindon, Stéphane and Dufayard, Jean-François and Lefort, Vincent and Anisimova, Maria and Hordijk, Wim and Gascuel, Olivier",
    title = "New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0",
    year = "2010",
    journal = "Systematic Biology",
    abstract = "PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.",
    url = "https://doi.org/10.1093/sysbio/syq010",
    doi = "10.1093/sysbio/syq010",
    openalex = "W2111211467",
    references = "doi101007bf02100115, doi101007bf02101990, doi101016b9781483232119500097, doi10108010635150390235520, doi10108010635150802429642, doi101086383584, doi101093bioinformaticsbtg180, doi101093bioinformaticsbtl446, doi101093molbevmsn067, doi101093oxfordjournalsmolbeva026201, doi101111j155856461985tb00420x, doi101146annurevge22120188002513, doi101371journalpone0009490"
}

The fossil record demonstrates that each major taxonomic group has a consistent net rate of diversification and a limit to its species richness. It has been thought that long-term changes in the dominance of major taxonomic groups can be predicted from these characteristics. However, new analyses show that diversity limits may rise or fall in response to adaptive radiations or extinctions. These changes are idiosyncratic and occur at different times in each taxa. For example, the end-Permian mass extinction permanently reduced the diversity of important, previously dominant groups such as brachiopods and crinoids. The current global crisis may therefore permanently alter the biosphere's taxonomic composition by changing the rules of evolution.

@article{doi101126science1189910,
    author = "Alroy, John",
    title = "The Shifting Balance of Diversity Among Major Marine Animal Groups",
    year = "2010",
    journal = "Science",
    abstract = "The fossil record demonstrates that each major taxonomic group has a consistent net rate of diversification and a limit to its species richness. It has been thought that long-term changes in the dominance of major taxonomic groups can be predicted from these characteristics. However, new analyses show that diversity limits may rise or fall in response to adaptive radiations or extinctions. These changes are idiosyncratic and occur at different times in each taxa. For example, the end-Permian mass extinction permanently reduced the diversity of important, previously dominant groups such as brachiopods and crinoids. The current global crisis may therefore permanently alter the biosphere's taxonomic composition by changing the rules of evolution.",
    url = "https://doi.org/10.1126/science.1189910",
    doi = "10.1126/science.1189910",
    openalex = "W1980420809",
    references = "doi101017s0022336000040026, doi101017s0094837300003778, doi101017s0094837300005352, doi101017s0094837300005972, doi101017s0094837300006539, doi101017s0094837300008186, doi101073pnas0802597105, doi101126science1156963, doi101126science21545391501, doi101126science7701342"
}

Cephalopods are extraordinary molluscs equipped with vertebrate-like intelligence and a unique buoyancy system for locomotion. A growing body of evidence from the fossil record, embryology and Bayesian molecular divergence estimations provides a comprehensive picture of their origins and evolution. Cephalopods evolved during the Cambrian (∼530 Ma) from a monoplacophoran-like mollusc in which the conical, external shell was modified into a chambered buoyancy apparatus. During the mid-Palaeozoic (∼416 Ma) cephalopods diverged into nautiloids and the presently dominant coleoids. Coleoids (i.e. squids, cuttlefish and octopods) internalised their shells and, in the late Palaeozoic (∼276 Ma), diverged into Vampyropoda and the Decabrachia. This shell internalisation appears to be a unique evolutionary event. In contrast, the loss of a mineralised shell has occurred several times in distinct coleoid lineages. The general tendency of shell reduction reflects a trend towards active modes of life and much more complex behaviour.

@article{doi101002bies201100001,
    author = "Kröger, Björn and Vinther, Jakob and Fuchs, Dirk",
    title = "Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules",
    year = "2011",
    journal = "BioEssays",
    abstract = "Cephalopods are extraordinary molluscs equipped with vertebrate-like intelligence and a unique buoyancy system for locomotion. A growing body of evidence from the fossil record, embryology and Bayesian molecular divergence estimations provides a comprehensive picture of their origins and evolution. Cephalopods evolved during the Cambrian (∼530 Ma) from a monoplacophoran-like mollusc in which the conical, external shell was modified into a chambered buoyancy apparatus. During the mid-Palaeozoic (∼416 Ma) cephalopods diverged into nautiloids and the presently dominant coleoids. Coleoids (i.e. squids, cuttlefish and octopods) internalised their shells and, in the late Palaeozoic (∼276 Ma), diverged into Vampyropoda and the Decabrachia. This shell internalisation appears to be a unique evolutionary event. In contrast, the loss of a mineralised shell has occurred several times in distinct coleoid lineages. The general tendency of shell reduction reflects a trend towards active modes of life and much more complex behaviour.",
    url = "https://doi.org/10.1002/bies.201100001",
    doi = "10.1002/bies.201100001",
    openalex = "W1924968197",
    references = "doi1010079781402068065, doi1023072406301"
}

Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule, with replacement rates established (calibrated) using paleontological age estimates from textbooks (e.g., Dodson 1960). Since that time, the amount of molecular sequence data has increased dramatically, affording ever-greater opportunities to apply molecular divergence approaches to fundamental problems in evolutionary biology.

@article{doi101093sysbiosyr107,
    author = "Parham, James F. and Donoghue, Philip C. J. and Bell, Christopher J. and Calway, Tyler and Head, Jason J. and Holroyd, Patricia A. and Inoue, Jun and Irmis, Randall B. and Joyce, Walter G. and Ksepka, Daniel T. and Patané, José Salvatore Leister and Smith, Nathan D. and Tarver, James E. and van Tuinen, Marcel and Yang, Ziheng and Angielczyk, Kenneth D. and Greenwood, Jenny M. and Hipsley, Christy A. and Jacobs, Louis L. and Makovicky, Peter J. and Müller, Johannes and Smith, Krister T. and Theodor, Jessica M. and Warnock, Rachel C. M. and Benton, Michael J.",
    title = "Best Practices for Justifying Fossil Calibrations",
    year = "2011",
    journal = "Systematic Biology",
    abstract = "Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule, with replacement rates established (calibrated) using paleontological age estimates from textbooks (e.g., Dodson 1960). Since that time, the amount of molecular sequence data has increased dramatically, affording ever-greater opportunities to apply molecular divergence approaches to fundamental problems in evolutionary biology.",
    url = "https://doi.org/10.1093/sysbio/syr107",
    doi = "10.1093/sysbio/syr107",
    openalex = "W2113525598",
    references = "doi101016jepsl200909013, doi101016jgca201006017, doi101016jtig200403007, doi101017cbo9780511536045, doi101038nature08745, doi101093molbevmsj024, doi101093molbevmsl150, doi101093oxfordjournalsmolbeva025892, doi101093sysbio3817, doi101111j00310239200300301x, doi101111j14698137201103794x, doi101126science1101012, doi101126science13334591105, doi1012060003009020073021taoeoa20co2, doi101371journalpbio0040088, doi101371journalpone0009329, doi1023072992432, doi104095215638, openalexw1535663436, openalexw2989049194, openalexw592572837"
}

Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes."

@article{doi101073pnas1206625109,
    author = "Near, Thomas J. and Eytan, Ron I. and Dornburg, Alex and Kuhn, Kristen L. and Moore, Jon A. and Davis, Matthew P. and Wainwright, Peter C. and Friedman, Matt and Smith, W. Leo",
    title = "Resolution of ray-finned fish phylogeny and timing of diversification",
    year = "2012",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = {Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes."},
    url = "https://doi.org/10.1073/pnas.1206625109",
    doi = "10.1073/pnas.1206625109",
    openalex = "W2081778808",
    references = "doi101016b9780126709506500138, doi101016s1055790302003329, doi101073pnas0811087106, doi101093bioinformaticsbtl446, doi101093bioinformaticsbtq228, doi101093oso97801985404720010001, doi101111j14754983201201165x, doi101126science1157704, doi101126science1211028, doi101186147121487214, doi101371journalpbio0040088, doi1023072412685, openalexw653978695"
}

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

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

The Subclass Elasmobranchii is widely considered nowadays to be the sister group of the Subclass Holocephali, although chimaeroid fishes were originally classified as elasmobranchs along with modern sharks and rays. While this modern systematic treatment provides an accurate reflection of the phylogenetic relationships among extant taxa, the classification of many extinct non-holocephalan shark-like chondrichthyans as elasmobranchs is challenged. A revised, apomorphy-based definition of elasmobranchs is presented in which they are considered the equivalent of neoselachians, i.e. a monophyletic group of modern sharks and rays which not only excludes all stem and crown holocephalans, but also many Palaeozoic shark-like chondrichthyans and even close extinct relatives of neoselachians such as hybodonts. The fossil record of elasmobranchs (i.e. neoselachians) is reviewed, focusing not only on their earliest records but also on their subsequent distribution patterns through time. The value and limitations of the fossil record in answering questions about elasmobranch phylogeny are discussed. Extinction is seen as a major factor in shaping early elasmobranch history, especially during the Triassic. Extinctions may also have helped shape modern lamniform diversity, despite uncertainties surrounding the phylogenetic affinities of supposedly extinct clades such as cretoxyrhinids, anacoracids and odontids. Apart from these examples, and the supposed Cretaceous extinction of 'sclerorhynchids', elasmobranch evolution since the Jurassic has mostly involved increased diversification (especially during the Cretaceous). The biogeographical distribution of early elasmobranchs may be obscured by sampling bias, but the earliest records of numerous groups are located within the Tethyan realm. The break-up of Gondwana, and particularly the opening of the South Atlantic Ocean (together with the development of epicontinental seaways across Brazil and Africa during the Cretaceous), provided repeated opportunities for dispersal from both eastern (European) and western (Caribbean) Tethys into newly formed ocean basins.

@article{doi101111j10958649201203245x,
    author = "Maisey, John G.",
    title = "What is an ‘elasmobranch’? The impact of palaeontology in understanding elasmobranch phylogeny and evolution",
    year = "2012",
    journal = "Journal of Fish Biology",
    abstract = "The Subclass Elasmobranchii is widely considered nowadays to be the sister group of the Subclass Holocephali, although chimaeroid fishes were originally classified as elasmobranchs along with modern sharks and rays. While this modern systematic treatment provides an accurate reflection of the phylogenetic relationships among extant taxa, the classification of many extinct non-holocephalan shark-like chondrichthyans as elasmobranchs is challenged. A revised, apomorphy-based definition of elasmobranchs is presented in which they are considered the equivalent of neoselachians, i.e. a monophyletic group of modern sharks and rays which not only excludes all stem and crown holocephalans, but also many Palaeozoic shark-like chondrichthyans and even close extinct relatives of neoselachians such as hybodonts. The fossil record of elasmobranchs (i.e. neoselachians) is reviewed, focusing not only on their earliest records but also on their subsequent distribution patterns through time. The value and limitations of the fossil record in answering questions about elasmobranch phylogeny are discussed. Extinction is seen as a major factor in shaping early elasmobranch history, especially during the Triassic. Extinctions may also have helped shape modern lamniform diversity, despite uncertainties surrounding the phylogenetic affinities of supposedly extinct clades such as cretoxyrhinids, anacoracids and odontids. Apart from these examples, and the supposed Cretaceous extinction of 'sclerorhynchids', elasmobranch evolution since the Jurassic has mostly involved increased diversification (especially during the Cretaceous). The biogeographical distribution of early elasmobranchs may be obscured by sampling bias, but the earliest records of numerous groups are located within the Tethyan realm. The break-up of Gondwana, and particularly the opening of the South Atlantic Ocean (together with the development of epicontinental seaways across Brazil and Africa during the Cretaceous), provided repeated opportunities for dispersal from both eastern (European) and western (Caribbean) Tethys into newly formed ocean basins.",
    url = "https://doi.org/10.1111/j.1095-8649.2012.03245.x",
    doi = "10.1111/j.1095-8649.2012.03245.x",
    openalex = "W2036104980",
    references = "doi101016b9780126709506500035, doi101038003342a0, doi101038142004a0, doi101093icb172303, doi101093oso97801985404720010001, doi1012060003009020042840001fsotgr20co2, doi101371journalpone, doi1016710272463420050250478r20co2, doi1023071441916, doi105860choice421559, doi105962bhltitle20094, doi105962bhltitle82144, openalexw3041320757"
}

@incollection{doi101201b118674,
    author = "Naylor, Gavin J. P. and Caira, Janine N. and Jensen, Kirsten and Rosana, K. A. M. and Straube, Nicolas and Lakner, Clemens",
    title = "Elasmobranch Phylogeny",
    year = "2012",
    booktitle = "Marine biology/CRC marine biology series",
    url = "https://doi.org/10.1201/b11867-4",
    doi = "10.1201/b11867-4",
    openalex = "W4243664349"
}

Interest in elasmobranch biodiversity and taxonomy has grown in recent years, catalyzed primarily by four inuences: (1) the large number of new species that have been described over the past 30 years (e.g., Last and Stevens, 2009); (2) the recognition that many species of elasmobranchs, several of which have not yet been formally described, may be threatened with extinction from shing pressures and habitat destruction (Stevens et al., 2000); (3) the growing interest in DNA “barcoding” as a tool to augment taxonomic description (e.g., Ward et al., 2007); and (4) an emerging recognition of the important role that elasmobranchs play as top predators in marine ecosystems (Heithaus et al., 2008).

@incollection{doi101201b118679,
    author = "Naylor, Janine N. Caira Gavin",
    title = "Elasmobranch Phylogeny: A Mitochondrial Estimate Based on 595 Species",
    year = "2012",
    abstract = "Interest in elasmobranch biodiversity and taxonomy has grown in recent years, catalyzed primarily by four inuences: (1) the large number of new species that have been described over the past 30 years (e.g., Last and Stevens, 2009); (2) the recognition that many species of elasmobranchs, several of which have not yet been formally described, may be threatened with extinction from shing pressures and habitat destruction (Stevens et al., 2000); (3) the growing interest in DNA “barcoding” as a tool to augment taxonomic description (e.g., Ward et al., 2007); and (4) an emerging recognition of the important role that elasmobranchs play as top predators in marine ecosystems (Heithaus et al., 2008).",
    url = "https://doi.org/10.1201/b11867-9",
    doi = "10.1201/b11867-9",
    openalex = "W2500401673",
    references = "doi101093icb172303, doi101111j109636421996tb02189x, doi1012060003009020042840001fsotgr20co2, doi1023071447424, openalexw3211386673"
}

@article{doi101038ncomms2633,
    author = "Neenan, James M. and Klein, Nicole and Scheyer, Torsten M.",
    title = "European origin of placodont marine reptiles and the evolution of crushing dentition in Placodontia",
    year = "2013",
    journal = "Nature Communications",
    url = "https://doi.org/10.1038/ncomms2633",
    doi = "10.1038/ncomms2633",
    openalex = "W1977901493"
}

Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the “bush at the top” of the teleost tree, and indicates acanthomorphs originated in the Early Cretaceous. Paleontological evidence suggests acanthomorphs exhibit a pulse of morphological diversification following the end Cretaceous mass extinction; however, the role of this event on the accumulation of living acanthomorph diversity remains unclear. Lineage diversification rates through time exhibit no shifts associated with the end Cretaceous mass extinction, but there is a global decrease in lineage diversification rates 50 Ma that occurs during a period when morphological disparity among fossil acanthomorphs increases sharply. Analysis of clade-specific shifts in diversification rates reveal that the hyperdiversity of living acanthomorphs is highlighted by several rapidly radiating lineages including tunas, gobies, blennies, snailfishes, and Afro-American cichlids. These lineages with high diversification rates are not associated with a single habitat type, such as coral reefs, indicating there is no single explanation for the success of acanthomorphs, as exceptional bouts of diversification have occurred across a wide array of marine and freshwater habitats.

@article{doi101073pnas1304661110,
    author = "Near, Thomas J. and Dornburg, Alex and Eytan, Ron I. and Keck, Benjamin P. and Smith, W. Leo and Kuhn, Kristen L. and Moore, Jon A. and Price, Samantha A. and Burbrink, Frank T. and Friedman, Matt and Wainwright, Peter C.",
    title = "Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes",
    year = "2013",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the “bush at the top” of the teleost tree, and indicates acanthomorphs originated in the Early Cretaceous. Paleontological evidence suggests acanthomorphs exhibit a pulse of morphological diversification following the end Cretaceous mass extinction; however, the role of this event on the accumulation of living acanthomorph diversity remains unclear. Lineage diversification rates through time exhibit no shifts associated with the end Cretaceous mass extinction, but there is a global decrease in lineage diversification rates 50 Ma that occurs during a period when morphological disparity among fossil acanthomorphs increases sharply. Analysis of clade-specific shifts in diversification rates reveal that the hyperdiversity of living acanthomorphs is highlighted by several rapidly radiating lineages including tunas, gobies, blennies, snailfishes, and Afro-American cichlids. These lineages with high diversification rates are not associated with a single habitat type, such as coral reefs, indicating there is no single explanation for the success of acanthomorphs, as exceptional bouts of diversification have occurred across a wide array of marine and freshwater habitats.",
    url = "https://doi.org/10.1073/pnas.1304661110",
    doi = "10.1073/pnas.1304661110",
    openalex = "W2073550716",
    references = "doi101073pnas1110395108, doi101073pnas1206625109, doi101073pnas1211526110, doi101371currentstol53ba26640df0ccaee75bb165c8c26288"
}

We integrated the evidence for evolutionary and plastic trait changes in situ in response to climate change in freshwater invertebrates (aquatic insects and zooplankton). The synthesis on the trait changes in response to the expected reductions in hydroperiod and increases in salinity indicated little evidence for adaptive, plastic, and genetic trait changes and for local adaptation. With respect to responses to temperature, there are many studies on temporal trait changes in phenology and body size in the wild that are believed to be driven by temperature increases, but there is a general lack of rigorous demonstration whether these trait changes are genetically based, adaptive, and causally driven by climate change. Current proof for genetic trait changes under climate change in freshwater invertebrates stems from a limited set of common garden experiments replicated in time. Experimental thermal evolution experiments and common garden warming experiments associated with space-for-time substitutions along latitudinal gradients indicate that besides genetic changes, also phenotypic plasticity and evolution of plasticity are likely to contribute to the observed phenotypic changes under climate change in aquatic invertebrates. Apart from plastic and genetic thermal adjustments, also genetic photoperiod adjustments are widespread and may even dominate the observed phenological shifts.

@article{doi101111eva12108,
    author = "Stoks, Robby and Geerts, Aurora and Meester, Luc De",
    title = "Evolutionary and plastic responses of freshwater invertebrates to climate change: realized patterns and future potential",
    year = "2013",
    journal = "Evolutionary Applications",
    abstract = "We integrated the evidence for evolutionary and plastic trait changes in situ in response to climate change in freshwater invertebrates (aquatic insects and zooplankton). The synthesis on the trait changes in response to the expected reductions in hydroperiod and increases in salinity indicated little evidence for adaptive, plastic, and genetic trait changes and for local adaptation. With respect to responses to temperature, there are many studies on temporal trait changes in phenology and body size in the wild that are believed to be driven by temperature increases, but there is a general lack of rigorous demonstration whether these trait changes are genetically based, adaptive, and causally driven by climate change. Current proof for genetic trait changes under climate change in freshwater invertebrates stems from a limited set of common garden experiments replicated in time. Experimental thermal evolution experiments and common garden warming experiments associated with space-for-time substitutions along latitudinal gradients indicate that besides genetic changes, also phenotypic plasticity and evolution of plasticity are likely to contribute to the observed phenotypic changes under climate change in aquatic invertebrates. Apart from plastic and genetic thermal adjustments, also genetic photoperiod adjustments are widespread and may even dominate the observed phenological shifts.",
    url = "https://doi.org/10.1111/eva.12108",
    doi = "10.1111/eva.12108",
    openalex = "W2141011783",
    references = "doi101146annurevento120710100557"
}

The Purbeck and Wealden formations of southern England represent marginal marine and continental deposition during the latest Jurassic and Early Cretaceous periods. More famous for their fossil dinosaurs and mammals, these units also yield the remains of fishes. In this work, first published in three parts between 1916 and 1919, Arthur Smith Woodward (1864–1944) provides the most extensive overview of the Purbeck and Wealden ichthyofauna, describing and illustrating some thirty genera of cartilaginous, lobe-finned, and ray-finned fishes. Woodward finds the preservation of fishes from both deposits to be suboptimal, but nevertheless comes to some important conclusions: he shows that the fish fauna of the English Wealden is nearly identical to that of the famous coeval deposits of Bernissart in Belgium, and finds that the species from both the Wealden and Purbeck show closer affinities with Jurassic forms than with later Cretaceous lineages like those described in his monograph on fishes from the Chalk.

@book{doi101017cbo9781139680851,
    author = "Woodward, Arthur Smith",
    title = "The Fossil Fishes of the English Wealden and Purbeck Formations",
    year = "2014",
    booktitle = "Cambridge University Press eBooks",
    abstract = "The Purbeck and Wealden formations of southern England represent marginal marine and continental deposition during the latest Jurassic and Early Cretaceous periods. More famous for their fossil dinosaurs and mammals, these units also yield the remains of fishes. In this work, first published in three parts between 1916 and 1919, Arthur Smith Woodward (1864–1944) provides the most extensive overview of the Purbeck and Wealden ichthyofauna, describing and illustrating some thirty genera of cartilaginous, lobe-finned, and ray-finned fishes. Woodward finds the preservation of fishes from both deposits to be suboptimal, but nevertheless comes to some important conclusions: he shows that the fish fauna of the English Wealden is nearly identical to that of the famous coeval deposits of Bernissart in Belgium, and finds that the species from both the Wealden and Purbeck show closer affinities with Jurassic forms than with later Cretaceous lineages like those described in his monograph on fishes from the Chalk.",
    url = "https://doi.org/10.1017/cbo9781139680851",
    doi = "10.1017/cbo9781139680851",
    openalex = "W612406501"
}

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.

@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"
}

Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%. IQ-TREE is freely available at http://www.cibiv.at/software/iqtree.

@article{doi101093molbevmsu300,
    author = "Nguyen, Lam-Tung and Schmidt, Heiko A. and von Haeseler, Arndt and Minh, Bùi Quang",
    title = "IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies",
    year = "2014",
    journal = "Molecular Biology and Evolution",
    abstract = "Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2\% and 87.1\% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7\% and 47.1\% of the DNA alignments and 42.2\% and 100\% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1\%. IQ-TREE is freely available at http://www.cibiv.at/software/iqtree.",
    url = "https://doi.org/10.1093/molbev/msu300",
    doi = "10.1093/molbev/msu300",
    openalex = "W2111647009",
    references = "doi101002fedr4910860506, doi101007bf00160154, doi101007bf01734359, doi101007bf02101990, doi10108010635150390235520, doi101086383584, doi101093bioinformaticsbtl446, doi101093molbevmst024, doi101093sysbio204406, doi101093sysbiosyq010, doi1023072412116, openalexw1514875444, openalexw3217097258"
}

Coleoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and represent nearly the entire diversity of modern cephalopods. Sophisticated adaptations such as the use of colour for camouflage and communication, jet propulsion and the ink sac highlight the unique nature of the group. Despite these striking adaptations, there are clear parallels in ecology between coleoids and bony fishes. The coleoid fossil record is limited, however, hindering confident analysis of the tempo and pattern of their evolution. Here we use a molecular dataset (180 genes, approx. 36 000 amino acids) of 26 cephalopod species to explore the phylogeny and timing of cephalopod evolution. We show that crown cephalopods diverged in the Silurian-Devonian, while crown coleoids had origins in the latest Palaeozoic. While the deep-sea vampire squid and dumbo octopuses have ancient origins extending to the Early Mesozoic Era, 242 ± 38 Ma, incirrate octopuses and the decabrachian coleoids (10-armed squid) diversified in the Jurassic Period. These divergence estimates highlight the modern diversity of coleoid cephalopods emerging in the Mesozoic Marine Revolution, a period that also witnessed the radiation of most ray-finned fish groups in addition to several other marine vertebrates. This suggests that that the origin of modern cephalopod biodiversity was contingent on ecological competition with marine vertebrates.

@article{doi101098rspb20162818,
    author = "Tanner, Alastair R and Fuchs, Dirk and Winkelmann, Inger E and Gilbert, M Thomas P and Pankey, M Sabrina and Ribeiro, Ângela M and Kocot, Kevin M and Halanych, Kenneth M and Oakley, Todd H and da Fonseca, Rute R and Pisani, Davide and Vinther, Jakob",
    title = "Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution.",
    year = "2017",
    journal = "Proceedings. Biological sciences",
    abstract = "Coleoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and represent nearly the entire diversity of modern cephalopods. Sophisticated adaptations such as the use of colour for camouflage and communication, jet propulsion and the ink sac highlight the unique nature of the group. Despite these striking adaptations, there are clear parallels in ecology between coleoids and bony fishes. The coleoid fossil record is limited, however, hindering confident analysis of the tempo and pattern of their evolution. Here we use a molecular dataset (180 genes, approx. 36 000 amino acids) of 26 cephalopod species to explore the phylogeny and timing of cephalopod evolution. We show that crown cephalopods diverged in the Silurian-Devonian, while crown coleoids had origins in the latest Palaeozoic. While the deep-sea vampire squid and dumbo octopuses have ancient origins extending to the Early Mesozoic Era, 242 ± 38 Ma, incirrate octopuses and the decabrachian coleoids (10-armed squid) diversified in the Jurassic Period. These divergence estimates highlight the modern diversity of coleoid cephalopods emerging in the Mesozoic Marine Revolution, a period that also witnessed the radiation of most ray-finned fish groups in addition to several other marine vertebrates. This suggests that that the origin of modern cephalopod biodiversity was contingent on ecological competition with marine vertebrates.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC5360930/",
    doi = "10.1098/rspb.2016.2818",
    openalex = "W2593801679",
    pmcid = "PMC5360930",
    pmid = "28250188",
    references = "doi101017s0094837300005352, doi101073pnas1206625109, doi101093bioinformaticsbtu033, doi101093molbevmsm193, doi101093molbevmsn067, doi101093sysbiosyt022, doi101098rspb20162818, doi101111j1469185x1972tb00975x, doi101126science1116412, doi101146annurevearth040809152556, doi1015159780691224244, openalexw1528487914"
}

@article{doi101038nbt4229,
    author = "Parks, Donovan H. and Chuvochina, Maria and Waite, David W. and Rinke, Christian and Skarshewski, Adam and Chaumeil, Pierre-Alain and Hugenholtz, Philip",
    title = "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life",
    year = "2018",
    journal = "Nature Biotechnology",
    url = "https://doi.org/10.1038/nbt.4229",
    doi = "10.1038/nbt.4229",
    openalex = "W2889019390",
    references = "doi101038nature12352, doi101038nature14486, doi101038nmicrobiol201648, doi101038nrmicro1341, doi101038nrmicro3330, doi101093bioinformaticsbtu033, doi101093molbevmsn067, doi101093molbevmsx116, doi101371journalpcbi1002195"
}

Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.

@article{doi101073pnas1719358115,
    author = "Hughes, Lily C. and Ortı́, Guillermo and Huang, Yu and Sun, Ying and Baldwin, Carole C. and Thompson, Andrew W. and Arcila, Dahiana and Betancur‐R, Ricardo and Li, Chenhong and Becker, L.A. and Bellora, Nicolás and Zhao, Xiaomeng and Li, Xiaofeng and Wang, Min and Fang, Chao and Xie, Bing and Zhou, Zhuocheng and Huang, Hai and Chen, Songlin and Venkatesh, Byrappa and Shi, Qiong",
    title = "Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data",
    year = "2018",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.",
    url = "https://doi.org/10.1073/pnas.1719358115",
    doi = "10.1073/pnas.1719358115",
    openalex = "W2803572653",
    references = "doi101073pnas1206625109, doi10108010635150290069913, doi101093bioinformatics17121246, doi101093bioinformaticsbtt403, doi101093bioinformaticsbtu033, doi101093bioinformaticsbtu462, doi101093molbevmsm088, doi101093sysbiosys004, doi101111j109636421981tb01575x, doi101186s1286201709583, doi101371currentstol53ba26640df0ccaee75bb165c8c26288, doi101371journalpbio0030314, doi1023072412448"
}

@article{doi101016jcub201904057,
    author = "Giribet, Gonzalo and Edgecombe, Gregory D.",
    title = "The Phylogeny and Evolutionary History of Arthropods",
    year = "2019",
    journal = "Current Biology",
    url = "https://doi.org/10.1016/j.cub.2019.04.057",
    doi = "10.1016/j.cub.2019.04.057",
    openalex = "W2950592321",
    references = "doi101007s0042700600854, doi101016jasd200910002, doi101016jasd201610011, doi101016jcub201205018, doi101038nature10689, doi101038nature12520, doi101038nature14256, doi101038ncomms3485, doi101038s41467019102447, doi101073pnas1719962115, doi101093molbevmss216, doi101098rsos172206, doi101111brv12168, doi101111j10960031201200413x, doi101111j14754983201101124x, doi1011861471214812162, doi101186s1286201710887, doi1023072412988"
}

@article{doi101016jearscirev201902020,
    author = "Klompmaker, Adiël A. and Kelley, Patricia H. and Chattopadhyay, Devapriya and Clements, Jeff C. and Huntley, John Warren and Kowalewski, Michał",
    title = "Predation in the marine fossil record: Studies, data, recognition, environmental factors, and behavior",
    year = "2019",
    journal = "Earth-Science Reviews",
    url = "https://doi.org/10.1016/j.earscirev.2019.02.020",
    doi = "10.1016/j.earscirev.2019.02.020",
    openalex = "W2917611271",
    references = "doi101016001669959180043y, doi1010160195667182900416, doi101016jpalaeo200909010, doi101016jpalwor201104001, doi101016s001282520300014x, doi101080027246342011601714, doi101111j150239312002tb00062x, doi101111pala12042, doi101111pala12254, doi101146annureves10110179001551, doi101371journalpone0052200, morris1979the"
}

Understanding heterogeneity in species richness between closely related clades is a key research question in ecology and evolutionary biology. Multiple hypotheses have been proposed to interpret such diversity contrasts across the tree of life, with most studies focusing on speciation rates to explain clades' evolutionary radiations, while often neglecting extinction rates. Here we study a notorious biological model as exemplified by the sister relationships between mackerel sharks (Lamniformes, 15 extant species) and ground sharks (Carcharhiniformes, ∼290 extant species). Using a comprehensive fossil dataset, we found that the diversity dynamics of lamniforms waxed and waned following repeated cycles of radiation phases and declining phases. Radiation phases peaked up to 3 times the current diversity in the early Late Cretaceous. In the last 20 million years, the group declined to its present-day diversity. Along with a higher extinction risk for young species, we further show that this declining pattern is likely attributed to a combination of abiotic and biotic factors, with a cooling-driven extinction (negative correlation between temperature and extinction) and clade competition with some ground sharks. Competition from multiple clades successively drove the demise and replacement of mackerel sharks due to a failure to originate facing the rise of ground sharks, particularly since the Eocene. These effects came from ecologically similar carcharhiniform species inhibiting diversification of medium- and large-sized lamniforms. These results imply that the interplay between abiotic and biotic drivers had a substantial role in extinction and speciation, respectively, which determines the sequential rise and decline of marine apex predators.

@article{doi101073pnas1902693116,
    author = "Condamine, Fabien L. and Romieu, Jules and Guinot, Guillaume",
    title = "Climate cooling and clade competition likely drove the decline of lamniform sharks",
    year = "2019",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Understanding heterogeneity in species richness between closely related clades is a key research question in ecology and evolutionary biology. Multiple hypotheses have been proposed to interpret such diversity contrasts across the tree of life, with most studies focusing on speciation rates to explain clades' evolutionary radiations, while often neglecting extinction rates. Here we study a notorious biological model as exemplified by the sister relationships between mackerel sharks (Lamniformes, 15 extant species) and ground sharks (Carcharhiniformes, ∼290 extant species). Using a comprehensive fossil dataset, we found that the diversity dynamics of lamniforms waxed and waned following repeated cycles of radiation phases and declining phases. Radiation phases peaked up to 3 times the current diversity in the early Late Cretaceous. In the last 20 million years, the group declined to its present-day diversity. Along with a higher extinction risk for young species, we further show that this declining pattern is likely attributed to a combination of abiotic and biotic factors, with a cooling-driven extinction (negative correlation between temperature and extinction) and clade competition with some ground sharks. Competition from multiple clades successively drove the demise and replacement of mackerel sharks due to a failure to originate facing the rise of ground sharks, particularly since the Eocene. These effects came from ecologically similar carcharhiniform species inhibiting diversification of medium- and large-sized lamniforms. These results imply that the interplay between abiotic and biotic drivers had a substantial role in extinction and speciation, respectively, which determines the sequential rise and decline of marine apex predators.",
    url = "https://doi.org/10.1073/pnas.1902693116",
    doi = "10.1073/pnas.1902693116",
    openalex = "W2976793806",
    references = "doi101016jearscirev200712003, doi101017s1464793104006517, doi101038nature06588, doi101038ncomms2958, doi101073pnas0603587103, doi101111brv12203, doi101126science1061967, doi101126science1116412, doi101126science1157719, doi101198016214502760047131, doi101371journalpone0185185, doi105860choice344488"
}

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.

@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"
}

Lamniformes (Chondrichthyes: Elasmobranchii) is a group of sharks that consists of 15 extant species with a wide range of morphological diversity. The most rarely captured lamniform is Odontaspis noronhai, and many aspects of its biology remain unknown to date. In this study, the skeletal anatomy of a previously described specimen of O. noronhai was examined using computed tomography. The new skeletal data were then added to a previously published morphology-based character matrix to conduct a new phylogenetic analysis of the Lamniformes. Our phylogenetic study strongly suggests non-monophyly of Odontaspididae, that traditionally consisted of Carcharias taurus, O. ferox, and O. noronhai. Thus, the family Carchariidae is formally resurrected for the genus Carcharias to separate it from the family Odontaspididae sensu stricto for Odontaspis. The overall topology of our phylogenetic trees is similar to that of previously published morphology-based trees and drastically different from the tree topology generally attained by molecular data that cluster Alopias, Megachasma, Odontaspis, and Pseudocarcharias together as a separate clade. The major topological discrepancy between molecular and morphological trees may be attributed to unconventionally asynchronous rates between morphological and molecular evolution, at least in certain species within the Lamniformes, along with likely manifestation of mosaic evolution. The recognition of the family Carchariidae is important to conservation biology, because the extinction of C. taurus would not only mean the elimination of the genus Carcharias, but also the entire family Carchariidae. Our study demonstrates the importance of the integration of both morphological and molecular information to understand organismal evolution.

@article{doi101643cg18160,
    author = "Stone, Nicholas R. and Shimada, Kenshu",
    title = "Skeletal Anatomy of the Bigeye Sand Tiger Shark, Odontaspis noronhai (Lamniformes: Odontaspididae), and Its Implications for Lamniform Phylogeny, Taxonomy, and Conservation Biology",
    year = "2019",
    journal = "Copeia",
    abstract = "Lamniformes (Chondrichthyes: Elasmobranchii) is a group of sharks that consists of 15 extant species with a wide range of morphological diversity. The most rarely captured lamniform is Odontaspis noronhai, and many aspects of its biology remain unknown to date. In this study, the skeletal anatomy of a previously described specimen of O. noronhai was examined using computed tomography. The new skeletal data were then added to a previously published morphology-based character matrix to conduct a new phylogenetic analysis of the Lamniformes. Our phylogenetic study strongly suggests non-monophyly of Odontaspididae, that traditionally consisted of Carcharias taurus, O. ferox, and O. noronhai. Thus, the family Carchariidae is formally resurrected for the genus Carcharias to separate it from the family Odontaspididae sensu stricto for Odontaspis. The overall topology of our phylogenetic trees is similar to that of previously published morphology-based trees and drastically different from the tree topology generally attained by molecular data that cluster Alopias, Megachasma, Odontaspis, and Pseudocarcharias together as a separate clade. The major topological discrepancy between molecular and morphological trees may be attributed to unconventionally asynchronous rates between morphological and molecular evolution, at least in certain species within the Lamniformes, along with likely manifestation of mosaic evolution. The recognition of the family Carchariidae is important to conservation biology, because the extinction of C. taurus would not only mean the elimination of the genus Carcharias, but also the entire family Carchariidae. Our study demonstrates the importance of the integration of both morphological and molecular information to understand organismal evolution.",
    url = "https://doi.org/10.1643/cg-18-160",
    doi = "10.1643/cg-18-160",
    openalex = "W2986461835",
    references = "doi101002jmor10342"
}

Preface Pattern and Diversity in Reproduction and Development, L.A. Levin and T.S. Bridges Variation in Size, Energy Content, and Biochemical Composition of Invertebrate Eggs: Correlates to the Mode of Larval Development, W.B. Jaeckle Evolutionary Ecology of Larval Types, J.N. Havenhand The Ecology of Fertilization in Free-Spawning Invertebrates, D.R. Levitan The Timing of Larval Release, S.G. Morgan Mechanisms and Rates of Suspension Feeding, M.W. Hart and R.R. Strathmann Larval Nutrition, I.F. Boidron-Metairon Behavior and Locomotion during the Dispersal Phase of Larval Life, C.M. Young Life and Death in the Plankton: Larval Mortality and Adaptation, S.G. Morgan Mechanisms of Cross-Shelf Dispersal of Larval Invertebrates and Fish, A.L. Shanks Using Genetics as an Indirect Estimator of Larval Dispersal, S.R. Palumbi Modeling the Dynamics of Marine Species: The Importance of Incorporating Larval Dispersal, S.D. Gaines and K.D. Lafferty Evolution of Larvae and Development Modes, G.A. Wray Index

@book{doi1012019780138758950,
    author = "McEdward, Larry R.",
    title = "Ecology of Marine Invertebrate Larvae",
    year = "2020",
    abstract = "Preface Pattern and Diversity in Reproduction and Development, L.A. Levin and T.S. Bridges Variation in Size, Energy Content, and Biochemical Composition of Invertebrate Eggs: Correlates to the Mode of Larval Development, W.B. Jaeckle Evolutionary Ecology of Larval Types, J.N. Havenhand The Ecology of Fertilization in Free-Spawning Invertebrates, D.R. Levitan The Timing of Larval Release, S.G. Morgan Mechanisms and Rates of Suspension Feeding, M.W. Hart and R.R. Strathmann Larval Nutrition, I.F. Boidron-Metairon Behavior and Locomotion during the Dispersal Phase of Larval Life, C.M. Young Life and Death in the Plankton: Larval Mortality and Adaptation, S.G. Morgan Mechanisms of Cross-Shelf Dispersal of Larval Invertebrates and Fish, A.L. Shanks Using Genetics as an Indirect Estimator of Larval Dispersal, S.R. Palumbi Modeling the Dynamics of Marine Species: The Importance of Incorporating Larval Dispersal, S.D. Gaines and K.D. Lafferty Evolution of Larvae and Development Modes, G.A. Wray Index",
    url = "https://doi.org/10.1201/9780138758950",
    doi = "10.1201/9780138758950",
    openalex = "W641111994"
}

Ecdysozoans (Phyla Arthropoda, Kinorhyncha, Loricifera, Nematoda, Nematomorpha, Onychophora, Priapulida, Tardigrada) are invertebrates bearing a tough, periodically moulted cuticle that predisposes them to exceptional preservation. Ecdysozoans dominate the oldest exceptionally preserved bilaterian animal biotas in the early to mid-Cambrian (c. 520–508 Ma), with possible trace fossils in the latest Ediacaran (<556 Ma). The fossil record of Ecdysozoa is among the best understood of major animal clades and is believed to document their origins and evolutionary history well. Strikingly, however, molecular clock analyses have implied a considerably deeper Precambrian origin for Ecdysozoa, much older than their earliest fossils. Here, using an improved set of fossil calibrations, we performed Bayesian analyses to estimate an evolutionary time-tree for Ecdysozoa, sampling all eight phyla for the first time. Our results recover Scalidophora as the sister group to Nematoida + Panarthropoda (= Cryptovermes nov.) and suggest that the Ediacaran divergence of Ecdysozoa occurred at least 23 myr before the first potential ecdysozoan trace fossils. This finding is impervious to the use of all plausible phylogenies, fossil prior distributions, evolutionary rate models and matrix partitioning strategies. Arthropods exhibit more precision and less incongruence between fossil- and clock-based estimates of clade ages than other ecdysozoan phyla. Supplementary material: Full methodologies used and an appendix of fossil calibration points are available at https://doi.org/10.6084/m9.figshare.c.5811381 Thematic collection: This article is part of the Advances in the Cambrian Explosion collection available at: https://www.lyellcollection.org/cc/advances-cambrian-explosion

@article{doi101144jgs2021107,
    author = "Howard, Richard J. and Giacomelli, Mattia and Lozano-Fernández, Jesús and Edgecombe, Gregory D. and Fleming, James F. and Kristensen, Reinhardt Møbjerg and Ma, Xiaoya and Olesen, Jørgen and Sørensen, Martin V. and Thomsen, Philip Francis and Wills, Matthew A. and Donoghue, Philip C. J. and Pisani, Davide",
    title = "The Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data",
    year = "2022",
    journal = "Journal of the Geological Society",
    abstract = "Ecdysozoans (Phyla Arthropoda, Kinorhyncha, Loricifera, Nematoda, Nematomorpha, Onychophora, Priapulida, Tardigrada) are invertebrates bearing a tough, periodically moulted cuticle that predisposes them to exceptional preservation. Ecdysozoans dominate the oldest exceptionally preserved bilaterian animal biotas in the early to mid-Cambrian (c. 520–508 Ma), with possible trace fossils in the latest Ediacaran (<556 Ma). The fossil record of Ecdysozoa is among the best understood of major animal clades and is believed to document their origins and evolutionary history well. Strikingly, however, molecular clock analyses have implied a considerably deeper Precambrian origin for Ecdysozoa, much older than their earliest fossils. Here, using an improved set of fossil calibrations, we performed Bayesian analyses to estimate an evolutionary time-tree for Ecdysozoa, sampling all eight phyla for the first time. Our results recover Scalidophora as the sister group to Nematoida + Panarthropoda (= Cryptovermes nov.) and suggest that the Ediacaran divergence of Ecdysozoa occurred at least 23 myr before the first potential ecdysozoan trace fossils. This finding is impervious to the use of all plausible phylogenies, fossil prior distributions, evolutionary rate models and matrix partitioning strategies. Arthropods exhibit more precision and less incongruence between fossil- and clock-based estimates of clade ages than other ecdysozoan phyla. Supplementary material: Full methodologies used and an appendix of fossil calibration points are available at https://doi.org/10.6084/m9.figshare.c.5811381 Thematic collection: This article is part of the Advances in the Cambrian Explosion collection available at: https://www.lyellcollection.org/cc/advances-cambrian-explosion",
    url = "https://doi.org/10.1144/jgs2021-107",
    doi = "10.1144/jgs2021-107",
    openalex = "W4210420449",
    references = "doi101038s415590160022, doi101093gbeevz097, doi101098rspb20182505, doi101111ter12368, doi102110palo2009p09004r"
}

Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced researchers, conquering the large number of software programs required for a multilocus-based phylogenetic reconstruction can be somewhat daunting and time-consuming. PhyloSuite, a software with a user-friendly GUI, was designed to make this process more accessible by integrating multiple software programs needed for multilocus and single-gene phylogenies and further streamlining the whole process. In this protocol, we aim to explain how to conduct each step of the phylogenetic pipeline and tree-based analyses in PhyloSuite. We also present a new version of PhyloSuite (v1.2.3), wherein we fixed some bugs, made some optimizations, and introduced some new functions, including a number of tree-based analyses, such as signal-to-noise calculation, saturation analysis, spurious species identification, and etc. The step-by-step protocol includes background information (i.e., what the step does), reasons (i.e., why do the step), and operations (i.e., how to do it). This protocol will help researchers quick-start their way through the multilocus phylogenetic analysis, especially those interested in conducting organelle-based analyses.

@article{doi101002imt287,
    author = "Xiang, Chuan‐Yu and Gao, Fangluan and Jakovlić, Ivan and Lei, Hong‐Peng and Hu, Ye and Zhang, Hong and Zou, Hong and Wang, Gui‐Tang and Zhang, Dong",
    title = "Using PhyloSuite for molecular phylogeny and tree‐based analyses",
    year = "2023",
    journal = "iMeta",
    abstract = "Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced researchers, conquering the large number of software programs required for a multilocus-based phylogenetic reconstruction can be somewhat daunting and time-consuming. PhyloSuite, a software with a user-friendly GUI, was designed to make this process more accessible by integrating multiple software programs needed for multilocus and single-gene phylogenies and further streamlining the whole process. In this protocol, we aim to explain how to conduct each step of the phylogenetic pipeline and tree-based analyses in PhyloSuite. We also present a new version of PhyloSuite (v1.2.3), wherein we fixed some bugs, made some optimizations, and introduced some new functions, including a number of tree-based analyses, such as signal-to-noise calculation, saturation analysis, spurious species identification, and etc. The step-by-step protocol includes background information (i.e., what the step does), reasons (i.e., why do the step), and operations (i.e., how to do it). This protocol will help researchers quick-start their way through the multilocus phylogenetic analysis, especially those interested in conducting organelle-based analyses.",
    url = "https://doi.org/10.1002/imt2.87",
    doi = "10.1002/imt2.87",
    openalex = "W4321242087",
    references = "doi101038s41467019102447, doi101093molbevmsu080, doi101371journalpone0051629"
}

The origin of vertebrate paired appendages is one of the most investigated and debated examples of evolutionary novelty 1-7. Paired appendages are widely considered as key innovations that enabled new opportunities for controlled swimming and gill ventilation and were prerequisites for the eventual transition from water to land. The past 150 years of debate 8-10 has been shaped by two contentious theories 4,5: the ventrolateral fin-fold hypothesis 9,10 and the archipterygium hypothesis 8. The latter proposes that fins and girdles evolved from an ancestral gill arch. Although studies in animal development have revived interest in this idea 11-13, it is apparently unsupported by fossil evidence. Here we present palaeontological support for a pharyngeal basis for the vertebrate shoulder girdle. We use computed tomography scanning to reveal details of the braincase of Kolymaspis sibirica 14, an Early Devonian placoderm fish from Siberia, that suggests a pharyngeal component of the shoulder. We combine these findings with refreshed comparative anatomy of placoderms and jawless outgroups to place the origin of the shoulder girdle on the sixth branchial arch. These findings provide a novel framework for understanding the origin of the pectoral girdle. Our evidence clarifies the location of the presumptive head-trunk interface in jawless fishes and explains the constraint on branchial arch number in gnathostomes 15. The results revive a key aspect of the archipterygium hypothesis and help reconcile it with the ventrolateral fin-fold model.

@article{doi101038s41586023067024,
    author = "Brazeau, Martin and Castiello, Marco and Fehri, Amin El Fassi El and Hamilton, Louis and Ivanov, Alexander O. and Johanson, Zerina and Friedman, Matt",
    title = "Fossil evidence for a pharyngeal origin of the vertebrate pectoral girdle",
    year = "2023",
    journal = "Nature",
    abstract = "The origin of vertebrate paired appendages is one of the most investigated and debated examples of evolutionary novelty 1-7. Paired appendages are widely considered as key innovations that enabled new opportunities for controlled swimming and gill ventilation and were prerequisites for the eventual transition from water to land. The past 150 years of debate 8-10 has been shaped by two contentious theories 4,5: the ventrolateral fin-fold hypothesis 9,10 and the archipterygium hypothesis 8. The latter proposes that fins and girdles evolved from an ancestral gill arch. Although studies in animal development have revived interest in this idea 11-13, it is apparently unsupported by fossil evidence. Here we present palaeontological support for a pharyngeal basis for the vertebrate shoulder girdle. We use computed tomography scanning to reveal details of the braincase of Kolymaspis sibirica 14, an Early Devonian placoderm fish from Siberia, that suggests a pharyngeal component of the shoulder. We combine these findings with refreshed comparative anatomy of placoderms and jawless outgroups to place the origin of the shoulder girdle on the sixth branchial arch. These findings provide a novel framework for understanding the origin of the pectoral girdle. Our evidence clarifies the location of the presumptive head-trunk interface in jawless fishes and explains the constraint on branchial arch number in gnathostomes 15. The results revive a key aspect of the archipterygium hypothesis and help reconcile it with the ventrolateral fin-fold model.",
    url = "https://doi.org/10.1038/s41586-023-06702-4",
    doi = "10.1038/s41586-023-06702-4",
    openalex = "W4388126757",
    references = "doi101002dvdy192, doi101038nature20806, doi101111cla12524"
}

The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80% of animal species and half of animal biomass. It has been the subject of several recent phylogenomic analyses, yet relationships within Pancrustacea show a notable lack of stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly of malacostracans. We show small changes in taxon sampling have large impacts on phylogenetic estimation. By analyzing identical orthologs between two slightly different taxon sets, we show that the differences in the resulting topologies are due primarily to the effects of taxon sampling on the phylogenetic reconstruction method. We compare trees resulting from our phylogenomic analyses with those from the literature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statistical topology tests reject the previously published trees in favor of the maximum likelihood trees produced here. Our results reject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. Notably, we find Copepoda nested within Allotriocarida with high support and recover a novel relationship between decapods, euphausiids, and syncarids that we refer to as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister to this latter clade, which we collectively name Stomatocarida, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocarida. A new Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results in the context of other pancrustacean phylogenetic hypotheses and highlight 15 key taxa to sample in future studies.

@article{doi101093molbevmsad175,
    author = "Bernot, James P. and Owen, Christopher L. and Wolfe, Joanna M. and Meland, Kenneth and Olesen, Jørgen and Crandall, Keith A.",
    title = "Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling",
    year = "2023",
    journal = "Molecular Biology and Evolution",
    abstract = "The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80\% of animal species and half of animal biomass. It has been the subject of several recent phylogenomic analyses, yet relationships within Pancrustacea show a notable lack of stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly of malacostracans. We show small changes in taxon sampling have large impacts on phylogenetic estimation. By analyzing identical orthologs between two slightly different taxon sets, we show that the differences in the resulting topologies are due primarily to the effects of taxon sampling on the phylogenetic reconstruction method. We compare trees resulting from our phylogenomic analyses with those from the literature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statistical topology tests reject the previously published trees in favor of the maximum likelihood trees produced here. Our results reject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. Notably, we find Copepoda nested within Allotriocarida with high support and recover a novel relationship between decapods, euphausiids, and syncarids that we refer to as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister to this latter clade, which we collectively name Stomatocarida, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocarida. A new Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results in the context of other pancrustacean phylogenetic hypotheses and highlight 15 key taxa to sample in future studies.",
    url = "https://doi.org/10.1093/molbev/msad175",
    doi = "10.1093/molbev/msad175",
    openalex = "W4385652026",
    references = "doi101038s41586023059366, doi101073pnas1719962115, doi101093gbeevz097, doi101353book31448"
}

@inproceedings{andzhou2024applications,
    author = "Zhou, Ethan and Ess, Madeline P. and Banker, Roxanne M.W. and Maciech, Samantha A. and Tyler, Carrie L.",
    title = "APPLICATIONS FOR 3D SCANNED FOSSILS OF ORDOVICIAN MARINE INVERTEBRATES",
    year = "2024",
    booktitle = "Geological Society of America Abstracts with Programs",
    url = "https://doi.org/10.1130/abs/2024am-401300",
    doi = "10.1130/abs/2024am-401300",
    openalex = "W4403859025"
}

The fossil fish Ptychodus Agassiz, 1834, characterized by a highly distinctive grinding dentition and an estimated gigantic body size (up to around 10 m), has remained one of the most enigmatic extinct elasmobranchs (i.e. sharks, skates and rays) for nearly two centuries. This widespread Cretaceous taxon is common in Albian to Campanian deposits from almost all continents. However, specimens mostly consist of isolated teeth or more or less complete dentitions, whereas cranial and post-cranial skeletal elements are very rare. Here we describe newly discovered material from the early Late Cretaceous of Mexico, including complete articulated specimens with preserved body outline, which reveals crucial information on the anatomy and systematic position of Ptychodus. Our phylogenetic and ecomorphological analyses indicate that ptychodontids were high-speed (tachypelagic) durophagous lamniforms (mackerel sharks), which occupied a specialized predatory niche previously unknown in fossil and extant elasmobranchs. Our results support the view that lamniforms were ecomorphologically highly diverse and represented the dominant group of sharks in Cretaceous marine ecosystems. Ptychodus may have fed predominantly on nektonic hard-shelled prey items such as ammonites and sea turtles rather than on benthic invertebrates, and its extinction during the Campanian, well before the end-Cretaceous crisis, might have been related to competition with emerging blunt-toothed globidensine and prognathodontine mosasaurs.

@article{doi101098rspb20240262,
    author = "Vullo, Romain and Villalobos-Segura, Eduardo and Amadori, Manuel and Kriwet, Jürgen and Frey, Eberhard and González González, Margarito A and Padilla Gutiérrez, José M and Ifrim, Christina and Stinnesbeck, Eva S and Stinnesbeck, Wolfgang",
    title = "Exceptionally preserved shark fossils from Mexico elucidate the long-standing enigma of the Cretaceous elasmobranch Ptychodus.",
    year = "2024",
    journal = "Proceedings. Biological sciences",
    abstract = "The fossil fish Ptychodus Agassiz, 1834, characterized by a highly distinctive grinding dentition and an estimated gigantic body size (up to around 10 m), has remained one of the most enigmatic extinct elasmobranchs (i.e. sharks, skates and rays) for nearly two centuries. This widespread Cretaceous taxon is common in Albian to Campanian deposits from almost all continents. However, specimens mostly consist of isolated teeth or more or less complete dentitions, whereas cranial and post-cranial skeletal elements are very rare. Here we describe newly discovered material from the early Late Cretaceous of Mexico, including complete articulated specimens with preserved body outline, which reveals crucial information on the anatomy and systematic position of Ptychodus. Our phylogenetic and ecomorphological analyses indicate that ptychodontids were high-speed (tachypelagic) durophagous lamniforms (mackerel sharks), which occupied a specialized predatory niche previously unknown in fossil and extant elasmobranchs. Our results support the view that lamniforms were ecomorphologically highly diverse and represented the dominant group of sharks in Cretaceous marine ecosystems. Ptychodus may have fed predominantly on nektonic hard-shelled prey items such as ammonites and sea turtles rather than on benthic invertebrates, and its extinction during the Campanian, well before the end-Cretaceous crisis, might have been related to competition with emerging blunt-toothed globidensine and prognathodontine mosasaurs.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC11040243/",
    doi = "10.1098/rspb.2024.0262",
    openalex = "W4395081355",
    pmcid = "PMC11040243",
    pmid = "38654646",
    references = "doi101002jmor10342, doi101016b9780126709506500035, doi101016jzool2020125799, doi101073pnas1902693116, doi101093icb172303, doi101098rspb20240262, doi101111cla12456, doi101111cla12524, doi105962p150189, openalexw3126673768"
}

The extensive chondrichthyan fossil record spans 400+ million years and has a global distribution. Paleontological studies provide a foundation of description and taxonomy to support deeper forays into ecology and evolution considering geographic, morphologic, and functional changes through time with nonanalog species and climate states. Although chondrichthyan teeth are most studied, analyses of dermal denticle metrics and soft tissue imprints are increasing. Recent methodological advances in morphology and geochemistry are elucidating fine-scale details, whereas large datasets and ecological modeling are broadening taxonomic, temporal, and geographic perspectives. The combination of ecological metrics and modeling with environmental reconstruction and climate simulations is opening new horizons to explore form and function, demographic dynamics, and food web structure in ancient marine ecosystems. Ultimately, the traits and taxa that endured or perished during the many catastrophic upheaval events in Earth's history contribute to conservation paleobiology, which is a much-needed perspective for extant chondrichthyans. ▪ The longevity and abundance of the chondrichthyan fossil record elucidates facets of ecological, evolutionary, and environmental histories. ▪ Though lacking postcranial, mineralized skeletons, dental enameloid and dermal denticles exquisitely preserve morphology and geochemistry. ▪ Technical advances in imaging, geochemistry, and modeling clarify the linkages between form and function with respect to physiology, diet, and environment. ▪ Conservation efforts can benefit from the temporal and spatial perspective of chondrichthyan persistence through past global change events.

@article{doi101146annurevearth040523010455,
    author = "Kim, Sora L. and Balk, Meghan A. and Sibert, Elizabeth C and Whitenack, Lisa B.",
    title = "Diving Deeper: Leveraging the Chondrichthyan Fossil Record to Investigate Environmental, Ecological, and Biological Change",
    year = "2024",
    journal = "Annual Review of Earth and Planetary Sciences",
    abstract = "The extensive chondrichthyan fossil record spans 400+ million years and has a global distribution. Paleontological studies provide a foundation of description and taxonomy to support deeper forays into ecology and evolution considering geographic, morphologic, and functional changes through time with nonanalog species and climate states. Although chondrichthyan teeth are most studied, analyses of dermal denticle metrics and soft tissue imprints are increasing. Recent methodological advances in morphology and geochemistry are elucidating fine-scale details, whereas large datasets and ecological modeling are broadening taxonomic, temporal, and geographic perspectives. The combination of ecological metrics and modeling with environmental reconstruction and climate simulations is opening new horizons to explore form and function, demographic dynamics, and food web structure in ancient marine ecosystems. Ultimately, the traits and taxa that endured or perished during the many catastrophic upheaval events in Earth's history contribute to conservation paleobiology, which is a much-needed perspective for extant chondrichthyans. ▪ The longevity and abundance of the chondrichthyan fossil record elucidates facets of ecological, evolutionary, and environmental histories. ▪ Though lacking postcranial, mineralized skeletons, dental enameloid and dermal denticles exquisitely preserve morphology and geochemistry. ▪ Technical advances in imaging, geochemistry, and modeling clarify the linkages between form and function with respect to physiology, diet, and environment. ▪ Conservation efforts can benefit from the temporal and spatial perspective of chondrichthyan persistence through past global change events.",
    url = "https://doi.org/10.1146/annurev-earth-040523-010455",
    doi = "10.1146/annurev-earth-040523-010455",
    openalex = "W4405708318",
    references = "doi101006jmsc20000724, doi101016jcub202108062, doi101093icb232347, doi101098rspb20240262, doi101126science1205106, doi101126science1239352, doi101126science1251817, doi101126science2795352860, doi101126scienceaad2622, doi101126scienceaad8745, doi107554elife00590"
}

Abstract The megatoothed shark genus Otodus has only been recorded previously from one locality in western Washington State, USA: Otodus auriculatus in the lower Eocene (Ypresian) part of the Crescent Formation in the Hamma Hamma River area, eastern Olympic Peninsula. Previously unpublished fossils from Washington expand the Otodus record from early Eocene to early or early middle Miocene. New specimens of O. auriculatus are from the middle Eocene (Lutetian) part of the Crescent Formation in the Canyon River area, southern Olympic Peninsula, and a fragmentary tooth from the middle Eocene (Bartonian) Aldwell Formation. Uppermost Eocene or lower Oligocene strata of the lower Lincoln Creek Formation south of the Olympic Mountains yielded a tooth fragment and a large vertebra of Otodus sp., and a large partial tooth referred to O. angustidens is from the uppermost Oligocene part of the Pysht Formation, northern Olympic Peninsula. Otodus cf. chubutensis is reported from the lower to middle Miocene Astoria Formation in southwestern Washington and coastal Oregon. Although rare, the fossils demonstrate that Otodus inhabited the northeastern Pacific Ocean from at least the early Eocene and even well past the period of cooling after the Eocene/Oligocene transition. Together, these fossils comprise the northernmost fossil record of the genus Otodus for the eastern Pacific Ocean.

@article{doi101007s12542025007585,
    author = "Goedert, James L. and Anderson, Katherine L. and Burns, Casey and Kiel, Steffen",
    title = "Fossils of the megatoothed shark Otodus (Chondrichthyes, Lamniformes) from Washington State, USA",
    year = "2025",
    journal = "Paläontologische Zeitschrift",
    abstract = "Abstract The megatoothed shark genus Otodus has only been recorded previously from one locality in western Washington State, USA: Otodus auriculatus in the lower Eocene (Ypresian) part of the Crescent Formation in the Hamma Hamma River area, eastern Olympic Peninsula. Previously unpublished fossils from Washington expand the Otodus record from early Eocene to early or early middle Miocene. New specimens of O. auriculatus are from the middle Eocene (Lutetian) part of the Crescent Formation in the Canyon River area, southern Olympic Peninsula, and a fragmentary tooth from the middle Eocene (Bartonian) Aldwell Formation. Uppermost Eocene or lower Oligocene strata of the lower Lincoln Creek Formation south of the Olympic Mountains yielded a tooth fragment and a large vertebra of Otodus sp., and a large partial tooth referred to O. angustidens is from the uppermost Oligocene part of the Pysht Formation, northern Olympic Peninsula. Otodus cf. chubutensis is reported from the lower to middle Miocene Astoria Formation in southwestern Washington and coastal Oregon. Although rare, the fossils demonstrate that Otodus inhabited the northeastern Pacific Ocean from at least the early Eocene and even well past the period of cooling after the Eocene/Oligocene transition. Together, these fossils comprise the northernmost fossil record of the genus Otodus for the eastern Pacific Ocean.",
    url = "https://doi.org/10.1007/s12542-025-00758-5",
    doi = "10.1007/s12542-025-00758-5",
    openalex = "W4417216703",
    references = "doi10268791502"
}

and extant parascylliids have a distinctive vertebral morphology previously described only in Carcharhiniformes, contributing a skeletal perspective to the picture emerging from macroevolutionary analyses of coastal, small-bodied origins for galeomorphs.

@article{doi101098rsos242011,
    author = "Dearden, Richard P. and Johanson, Zerina and O’Neill, Helen L. and Miles, K.J. and Bernard, Emma and Clark, Brett and Underwood, Charlie J. and Rücklin, Martin",
    title = "Three-dimensional fossils of a Cretaceous collared carpet shark (Parascylliidae, Orectolobiformes) shed light on skeletal evolution in galeomorphs",
    year = "2025",
    journal = "Royal Society Open Science",
    abstract = "and extant parascylliids have a distinctive vertebral morphology previously described only in Carcharhiniformes, contributing a skeletal perspective to the picture emerging from macroevolutionary analyses of coastal, small-bodied origins for galeomorphs.",
    url = "https://doi.org/10.1098/rsos.242011",
    doi = "10.1098/rsos.242011",
    openalex = "W4409912826",
    references = "doi101038s4155901704484, doi101093bioinformaticsbty633, doi101093sysbiosyr107, doi101093sysbiosys029, doi101093sysbiosyy032, doi101098rspb20240262, doi101126science1155674, doi101201b118674, doi101666040691, openalexw2898156694, openalexw349215600"
}

Using a new character matrix composed of revised matrices of previous analyses and new morphological findings, the phylogeny of Malacostraca (Pancrustacea) is analysed anew with 207 characters for 35 terminal taxa across all recognized orders. Particular emphasis was placed on methodological versatility, including different degrees of implied weighting and one of the first applications of methods recently developed in TNT (with the xlinks-command) for considering character dependencies. With >67% of ontological dependencies our character matrix offers a perfect opportunity for putting this new methodology to the test. In particular, we can demonstrate the significant impact of character dependencies and conclusively argue the usefulness of "xlinks" (or the consideration of character dependencies in general). Furthermore, the multimethod framework also enables a comparative evaluation of established and new approaches, and the resulting cladograms thereof. Although our various results leave many questions about the phylogeny of Malacostraca unanswered, clear support is emerging for some monophyla, whereas some surprising findings give reason for methodological reflection. Also, the necessity for an increased attention in terms of taxon sampling and additional character examinations in certain groups becomes obvious. We herein provide (i) an R-function for automatically translating the character dependency syntax proposed by Grams and Richter (Cladistics, 2023, 39, 437) into xlinks-commands for TNT; and (ii) a TNT-script for analysing a character matrix successively under various k-values for implied weighting.

@article{doi101111cla12611,
    author = "Grams, Markus and Torres, Ambrosio and Wirkner, Christian S. and Richter, Stefan",
    title = "A new morphological phylogeny of Malacostraca comparing the application of character dependencies and implied weighting",
    year = "2025",
    journal = "Cladistics",
    abstract = {Using a new character matrix composed of revised matrices of previous analyses and new morphological findings, the phylogeny of Malacostraca (Pancrustacea) is analysed anew with 207 characters for 35 terminal taxa across all recognized orders. Particular emphasis was placed on methodological versatility, including different degrees of implied weighting and one of the first applications of methods recently developed in TNT (with the xlinks-command) for considering character dependencies. With >67\% of ontological dependencies our character matrix offers a perfect opportunity for putting this new methodology to the test. In particular, we can demonstrate the significant impact of character dependencies and conclusively argue the usefulness of "xlinks" (or the consideration of character dependencies in general). Furthermore, the multimethod framework also enables a comparative evaluation of established and new approaches, and the resulting cladograms thereof. Although our various results leave many questions about the phylogeny of Malacostraca unanswered, clear support is emerging for some monophyla, whereas some surprising findings give reason for methodological reflection. Also, the necessity for an increased attention in terms of taxon sampling and additional character examinations in certain groups becomes obvious. We herein provide (i) an R-function for automatically translating the character dependency syntax proposed by Grams and Richter (Cladistics, 2023, 39, 437) into xlinks-commands for TNT; and (ii) a TNT-script for analysing a character matrix successively under various k-values for implied weighting.},
    url = "https://doi.org/10.1111/cla.12611",
    doi = "10.1111/cla.12611",
    openalex = "W4409183060",
    references = "doi101111cla12456, doi101111cla12581"
}

Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups-gastropods, bivalves, and cephalopods-each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans. Our analyses confirm a phylogeny proposed from morphology and show widespread genomic variation. The flexibility of the molluscan genome likely explains both historic challenges with their genomes and their evolutionary success.

@article{doi101126scienceads0215,
    author = "Chen, Zeyuan and Baeza, J. Antonio and Chen, Chong and González, María Teresa and González, Vanessa L. and Greve, Carola and Kocot, Kevin M. and Arbizu, Pedro Martínez and Moles, Juan and Schell, Tilman and Schwabe, Enrico and Sun, Jin and Wong, Nur Leena W. S. and Yap-Chiongco, Meghan K. and Sigwart, Julia D.",
    title = "A genome-based phylogeny for Mollusca is concordant with fossils and morphology",
    year = "2025",
    journal = "Science",
    abstract = "Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups-gastropods, bivalves, and cephalopods-each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans. Our analyses confirm a phylogeny proposed from morphology and show widespread genomic variation. The flexibility of the molluscan genome likely explains both historic challenges with their genomes and their evolutionary success.",
    url = "https://doi.org/10.1126/science.ads0215",
    doi = "10.1126/science.ads0215",
    openalex = "W4408016799",
    references = "doi101038s4146702229748w, doi101038s41559021014486, doi101093sysbiosyae010, doi101093sysbiosyu105, doi101111brv12614"
}