@misc{garstang1894preliminary11,
    author = "Garstang, W",
    title = "Preliminary note on a New Theory of the Phylogeny of the Chordata",
    year = "1894",
    howpublished = "Zoologischer Anzeiger, v. 17, p. 122-125",
    note = "talkorigins\_source = {true}; raw\_reference = {Garstang, W., 1894, Preliminary note on a New Theory of the Phylogeny of the Chordata: Zoologischer Anzeiger, v. 17, p. 122-125.}"
}

@article{garstang1928the12,
    author = "Garstang, W",
    title = "The morphology of the Tunicata and its bearings on the phylogeny of the Chordata",
    year = "1928",
    journal = "Quarterly Journal of Microscopical Science, v. 72, p. 51-187",
    note = "talkorigins\_source = {true}; raw\_reference = {Garstang, W., 1928, The morphology of the Tunicata and its bearings on the phylogeny of the Chordata: Quarterly Journal of Microscopical Science, v. 72, p. 51-187.}"
}

@misc{franz1932vivaparus10,
    author = "Franz, V",
    title = "Vivaparus; Morphometrie, Phylogenie und Geographie der europischen, fossilen und rezenten Paludinen",
    year = "1932",
    howpublished = "Med.-Naturw. Ges. Jena, Denkschr., v. 18",
    note = "talkorigins\_source = {true}; raw\_reference = {Franz, V., 1932, Vivaparus; Morphometrie, Phylogenie und Geographie der europischen, fossilen und rezenten Paludinen: Med.-Naturw. Ges. Jena, Denkschr., v. 18.}"
}

@book{baker1938the1,
    author = "Baker, J. R",
    title = "The Evolution of Breeding Systems, in Evolution, Essays presented to E.S. Goodrich",
    year = "1938",
    publisher = "Oxford, Oxford University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Baker, J. R., 1938, The Evolution of Breeding Systems, in Evolution, Essays presented to E.S. Goodrich: Oxford, Oxford University Press.}"
}

@book{camp1942phylogeny3,
    author = "Camp, C. L. and Smith, N",
    title = "Phylogeny and function of the digital ligaments of the horse",
    year = "1942",
    publisher = "Memoirs of the University of California, Berkeley, v. 13, p. 69-124",
    note = "talkorigins\_source = {true}; raw\_reference = {Camp, C. L., and Smith, N., 1942, Phylogeny and function of the digital ligaments of the horse: Memoirs of the University of California, Berkeley, v. 13, p. 69-124.}"
}

@techreport{greenwood1966phyletic17,
    author = "Greenwood, P. H. and Miles, R. S. and Patterson, C. and Rosen, D. E. and Weitzman, S. H. and Myers, G. S",
    title = "Phyletic studies of teleostean fishes, with a provisional classification of living forms",
    year = "1966",
    howpublished = "Bulletin of the American Museum of Natural History, v. 131, no. Art. 4, p. 339-456",
    note = "talkorigins\_source = {true}; raw\_reference = {Greenwood, P. H., Miles, R. S., Patterson, C., Rosen, D. E., Weitzman, S. H., and Myers, G. S., 1966, Phyletic studies of teleostean fishes, with a provisional classification of living forms: Bulletin of the American Museum of Natural History, v. 131, no. Art. 4, p. 339-456.}"
}

@book{hennig1966phylogenetic18,
    author = "Hennig, W",
    title = "Phylogenetic Systematics",
    year = "1966",
    publisher = "Urbana, Illinois, University of Illinois Press; [2nd edition, 1979]",
    note = "talkorigins\_source = {true}; raw\_reference = {Hennig, W., 1966, Phylogenetic Systematics: Urbana, Illinois, University of Illinois Press; [2nd edition, 1979].}"
}

@misc{fay1967phylogeny8,
    author = "Fay, R. O",
    title = "Phylogeny and Evolution, p",
    year = "1967",
    howpublished = "S392-S396, in Moore, R. C., ed., Treatise on Invertebrate Paleontology, pt. S (Echinodermata I), v.2 (Blastoids), p. S297-S650",
    note = "talkorigins\_source = {true}; raw\_reference = {Fay, R. O., 1967, Phylogeny and Evolution, p. S392-S396, in Moore, R. C., ed., Treatise on Invertebrate Paleontology, pt. S (Echinodermata I), v.2 (Blastoids), p. S297-S650.}"
}

@misc{fitch1967construction9,
    author = "Fitch, W. M. and Margoliash, E",
    title = "Construction of phylogenetic trees",
    year = "1967",
    howpublished = "Science, v. 155, p. 279-284",
    note = "talkorigins\_source = {true}; raw\_reference = {Fitch, W. M., and Margoliash, E., 1967, Construction of phylogenetic trees: Science, v. 155, p. 279-284.}"
}

@incollection{rvig1967phylogeny25,
    author = "rvig, T",
    editor = "Miles, A. E. W.",
    title = "Phylogeny of Tooth Tissue: Evolution of Some Calcified Tissues in Early Vertebrates",
    year = "1967",
    booktitle = "Structural and Chemical Organization of Teeth",
    publisher = "London, Academic Press",
    note = "talkorigins\_source = {true}; raw\_reference = {rvig, T., 1967, Phylogeny of Tooth Tissue: Evolution of Some Calcified Tissues in Early Vertebrates, in Miles, A. E. W., ed., Structural and Chemical Organization of Teeth: London, Academic Press.}"
}

@misc{eldredge1971the7,
    author = "Eldredge, N",
    title = "The allopatric model and phylogeny of Paleozoic invertebrates",
    year = "1971",
    howpublished = "Evolution, v. 25, p. 156-167",
    note = "talkorigins\_source = {true}; raw\_reference = {Eldredge, N., 1971, The allopatric model and phylogeny of Paleozoic invertebrates: Evolution, v. 25, p. 156-167.}"
}

@book{hubbs1971distribution19,
    author = "Hubbs, C. L. and Potter, I. C",
    title = "Distribution, Phylogeny and Taxonomy, in Hardisty, M. W., and Potter, I. C., eds., The Biology of Lampreys",
    year = "1971",
    publisher = "London, Academic Press, v. 1, p. 1-65",
    note = "talkorigins\_source = {true}; raw\_reference = {Hubbs, C. L., and Potter, I. C., 1971, Distribution, Phylogeny and Taxonomy, in Hardisty, M. W., and Potter, I. C., eds., The Biology of Lampreys: London, Academic Press, v. 1, p. 1-65.}"
}

@misc{kavanaugh1972hennigs20,
    author = "Kavanaugh, D. H",
    title = "Hennig's principles and methods of phylogenetic systematics",
    year = "1972",
    howpublished = "The Biologist, v. 54, p. 115-127",
    note = "talkorigins\_source = {true}; raw\_reference = {Kavanaugh, D. H., 1972, Hennig's principles and methods of phylogenetic systematics: The Biologist, v. 54, p. 115-127.}"
}

@article{greenwood1973interrelationships16,
    author = "Greenwood, P. H. and Miles, R. S. and Patterson, C",
    title = "Interrelationships of Fishes",
    year = "1973",
    journal = "London, Academic Press; [Supplement No.1 to the Zoological Journal of the Linnean Society, 53]",
    note = "talkorigins\_source = {true}; raw\_reference = {Greenwood, P. H., Miles, R. S., and Patterson, C., 1973, Interrelationships of Fishes: London, Academic Press; [Supplement No.1 to the Zoological Journal of the Linnean Society, 53].}"
}

@article{raup1973stochastic22,
    author = "Raup, D. M. and Gould, S. J. and Schopf, T. J. M. and Simberloff, D. S",
    title = "Stochastic models of phylogeny and the evolution of diversity",
    year = "1973",
    journal = "Journal of Geology, v. 81, no. 5, p. 525-542",
    note = "talkorigins\_source = {true}; raw\_reference = {Raup, D. M., Gould, S. J., Schopf, T. J. M., and Simberloff, D. S., 1973, Stochastic models of phylogeny and the evolution of diversity: Journal of Geology, v. 81, no. 5, p. 525-542.}"
}

@inproceedings{dilly1975the6,
    author = "Dilly, P. N",
    title = "The pterobranch Rhabdopleura compacta",
    year = "1975",
    booktitle = "its nervous system and phylogenetic position: Symposium of the Zoological Society, London, v. 36, p. 1-16",
    note = "talkorigins\_source = {true}; raw\_reference = {Dilly, P. N., 1975, The pterobranch Rhabdopleura compacta: its nervous system and phylogenetic position: Symposium of the Zoological Society, London, v. 36, p. 1-16.}"
}

@inproceedings{southward1975fine24,
    author = "Southward, E. C",
    title = "Fine structure and phylogeny of the Pogonomorpha",
    year = "1975",
    booktitle = "Symposium of the Zoological Society, London, v. 36, p. 235-251",
    note = "talkorigins\_source = {true}; raw\_reference = {Southward, E. C., 1975, Fine structure and phylogeny of the Pogonomorpha: Symposium of the Zoological Society, London, v. 36, p. 235-251.}"
}

@inproceedings{willner1975the26,
    author = "Willner, E. N",
    title = "The possible contribution of nemertines to the problem of the phylogeny of the protochordates",
    year = "1975",
    booktitle = "Symposium of the Zoological Society, London, v. 36, p. 319-345",
    note = "talkorigins\_source = {true}; raw\_reference = {Willner, E. N., 1975, The possible contribution of nemertines to the problem of the phylogeny of the protochordates: Symposium of the Zoological Society, London, v. 36, p. 319-345.}"
}

@article{gingerich1976paleontology14,
    author = "Gingerich, P. D",
    title = "Paleontology and phylogeny",
    year = "1976",
    journal = "patterns of evolution of the species level in early Tertiary mammals: American Journal of Science, v. 276, p. 1-28",
    note = "talkorigins\_source = {true}; raw\_reference = {Gingerich, P. D., 1976, Paleontology and phylogeny: patterns of evolution of the species level in early Tertiary mammals: American Journal of Science, v. 276, p. 1-28.}"
}

@misc{compagno1977phyletic5,
    author = "Compagno, L. J. V",
    title = "Phyletic relationships of living sharks and rays",
    year = "1977",
    howpublished = "American Zoologist, v. 17, p. 303-322",
    note = "talkorigins\_source = {true}; raw\_reference = {Compagno, L. J. V., 1977, Phyletic relationships of living sharks and rays: American Zoologist, v. 17, p. 303-322.}"
}

@book{gould1977ontogeny15,
    author = "Gould, S. J",
    title = "Ontogeny and Phylogeny",
    year = "1977",
    publisher = "Cambridge, Mass., Harvard University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Gould, S. J., 1977, Ontogeny and Phylogeny: Cambridge, Mass., Harvard University Press.}"
}

@article{brace1981tales2,
    author = "Brace, C. L",
    title = "Tales of the phylogenetic woods",
    year = "1981",
    journal = "the evolution and significance of evolutionary trees: American Journal of Physical Anthropology, v. 56, no. 4, p. 411-429",
    note = "talkorigins\_source = {true}; raw\_reference = {Brace, C. L., 1981, Tales of the phylogenetic woods: the evolution and significance of evolutionary trees: American Journal of Physical Anthropology, v. 56, no. 4, p. 411-429.}"
}

@misc{chatterjee1982phylogeny4,
    author = "Chatterjee, S",
    title = "Phylogeny and classification of thecodontian reptiles",
    year = "1982",
    howpublished = "Nature, v. 295, p. 317-320",
    note = "talkorigins\_source = {true}; raw\_reference = {Chatterjee, S., 1982, Phylogeny and classification of thecodontian reptiles: Nature, v. 295, p. 317-320.}"
}

@misc{gauthier1984phylogenetic13,
    author = "Gauthier, J. and Padian, K",
    title = "Phylogenetic, Functional and Aerodynamic Analysis of the Origin of Birds, in Hecht, M. K., Ostrom, J. H., Viohl, G., and Wellnhofer, P., eds., The Beginnings of Birds",
    year = "1984",
    howpublished = "Eichstatt, Fruende des Jura-Museums, p. 185-198",
    note = "talkorigins\_source = {true}; raw\_reference = {Gauthier, J., and Padian, K., 1984, Phylogenetic, Functional and Aerodynamic Analysis of the Origin of Birds, in Hecht, M. K., Ostrom, J. H., Viohl, G., and Wellnhofer, P., eds., The Beginnings of Birds: Eichstatt, Fruende des Jura-Museums, p. 185-198.}"
}

@incollection{paul1984the21,
    author = "Paul, G. S",
    editor = "Reif, W. E. and Westphal, F.",
    title = "The Archosaurs: A Phylogenetic Study",
    year = "1984",
    booktitle = "Third Symposium on Mesozoic Terrestrial Ecosystems",
    publisher = "Tbingen, ATTEMPTO-Verlag, p. 175-180",
    note = "talkorigins\_source = {true}; raw\_reference = {Paul, G. S., 1984, The Archosaurs: A Phylogenetic Study, in Reif, W. E., and Westphal, F., eds., Third Symposium on Mesozoic Terrestrial Ecosystems: Tbingen, ATTEMPTO-Verlag, p. 175-180.}"
}

@inproceedings{sereno1984the23,
    author = "Sereno, P. C",
    title = "The Phylogeny of the Ornithischia, a reappraisal, in Reif, W. E., and Westphal, F., eds., Third Symposium on Mesozoic Terrestrial Environments",
    year = "1984",
    booktitle = "Tbingen, ATTEMPTO-Verlag, p. 219-226",
    note = "talkorigins\_source = {true}; raw\_reference = {Sereno, P. C., 1984, The Phylogeny of the Ornithischia, a reappraisal, in Reif, W. E., and Westphal, F., eds., Third Symposium on Mesozoic Terrestrial Environments: Tbingen, ATTEMPTO-Verlag, p. 219-226.}"
}

@article{ferraris2000phylogeny,
    author = "Ferraris, Carl J.",
    title = "Phylogeny and Classification of Neotropical Fishes",
    year = "2000",
    journal = "Copeia",
    url = "https://doi.org/10.1643/0045-8511(2000)2000[0314:br]2.0.co;2",
    doi = "10.1643/0045-8511(2000)2000[0314:br]2.0.co;2",
    number = "1",
    pages = "314-315",
    volume = "2000"
}

@incollection{kapoor2004evolution,
    author = "Kapoor, B. G. and Khanna, Bhavna",
    title = "Evolution; Phylogeny; Classification",
    year = "2004",
    booktitle = "Ichthyology Handbook",
    url = "https://doi.org/10.1007/978-3-662-07844-0\_1",
    doi = "10.1007/978-3-662-07844-0\_1",
    pages = "1-30"
}

@article{betancurr2017phylogenetic,
    author = "Betancur-R, Ricardo and Wiley, Edward O. and Arratia, Gloria and Acero, Arturo and Bailly, Nicolas and Miya, Masaki and Lecointre, Guillaume and Ortí, Guillermo",
    title = "Phylogenetic classification of bony fishes",
    year = "2017",
    journal = "BMC Evolutionary Biology",
    url = "https://doi.org/10.1186/s12862-017-0958-3",
    doi = "10.1186/s12862-017-0958-3",
    number = "1",
    volume = "17"
}

@incollection{ji2021phylogeny,
    author = "Ji, Yunheng",
    title = "Phylogeny, Classification, Biogeography, and Evolution",
    year = "2021",
    booktitle = "A Monograph of Paris (Melanthiaceae)",
    url = "https://doi.org/10.1007/978-981-15-7903-5\_5",
    doi = "10.1007/978-981-15-7903-5\_5",
    pages = "69-81"
}

@article{near2024phylogenetic,
    author = "Near, Thomas J. and Thacker, Christine E.",
    title = "Phylogenetic Classification of Living and Fossil Ray-Finned Fishes (Actinopterygii)",
    year = "2024",
    journal = "Bulletin of the Peabody Museum of Natural History",
    url = "https://doi.org/10.3374/014.065.0101",
    doi = "10.3374/014.065.0101",
    number = "1",
    volume = "65"
}

@article{doi101016jcub202508008,
    author = "Troyer, Emily M and Rivero-Vega, Rafael A and Cui, Xindong and Zhu, Min and Qiao, Tuo and Saad, Hadeel H and Figueroa, Rodrigo T and Andrews, James V and Clement, Alice M and Lebedev, Oleg A and Higgins, Robert and Igielman, Benjamin and Pierce, Stephanie E and Giles, Sam and Friedman, Matt",
    title = "Macroevolutionary role reversals in the earliest radiation of bony fishes.",
    year = "2025",
    journal = "Current biology: CB",
    abstract = {The evolution of jaws is hypothesized to have fueled radiations among vertebrates, contributing to their overwhelming success in the present day. Past work shows rapid early expansion of diversity in jaw structure in many lineages; however, the evolutionary dynamics underlying this pattern are unclear and hindered by the lack of a robust comparative framework. Here, using a macroevolutionary approach, we explore the diversification of lower jaws in early bony fishes, a major contributor to this initial radiation. Using newly generated three-dimensional mandibular shape data from 86 species, we find evidence of adaptive radiation in jaws during the earliest interval of bony fish evolutionary history (423-359 Ma). These patterns are principally driven by early lungfishes and coelacanths, which display high rates of jaw diversification, rapid shifts into novel functional regions of trait space, and substantial innovation in jaw morphology and feeding ecology, standing in contrast to their "living fossil" descendants of today. Conversely, ray-finned fishes and tetrapodomorphs, morphologically diverse groups in the present day, show little indication of their future success, possessing slow rates of jaw evolution and low functional diversity. This profound inversion of patterns in modern taxa highlights the significance of paleontological data in understanding drivers of evolutionary diversification and the limitations of approaches using only living species. Overall, our findings provide insight into the evolutionary dynamics associated with the evolution of jaws and provide context for the role of jaws in vertebrate success.},
    url = "https://pubmed.ncbi.nlm.nih.gov/40897172/",
    doi = "10.1016/j.cub.2025.08.008",
    pmid = "40897172"
}

@article{doi101101gr280800125,
    author = "Wang, Cheng and Brownstein, Chase D and Chen, Wenjun and Ding, Zufa and Yu, Dan and Deng, Yu and Feng, Chenguang and Near, Thomas J and He, Shunping and Yang, Liandong",
    title = "Stable genome structures in living fossil fishes.",
    year = "2026",
    journal = "Genome research",
    abstract = "Genomic evolution can propel and restrict species diversification. Rapid molecular evolution and genomic rearrangement is often associated with increased species diversification, but whether genome structural evolution shows a slow tempo in long-lived, species-poor lineages remains unclear. Here, we present two chromosome-level genomes of gars, a lineage of seven living species of freshwater fishes that are nearly identical in anatomy to extinct species from tens of millions of years ago. Using the new genomes, we show that gars have the slowest rates of genomic structural and sequence evolution of all vertebrates. In species of the two living gar genera Atractosteus and Lepisosteus, 83.35\% of the genomes remain identical even though they diverged over 100 million years ago. Genome size variation among gars is almost entirely attributable to single base pair insertions and deletions. Yet, we also detect inflated GC repeat numbers on Chromosomes 14 and 23 of Atractosteus spatula that are absent in Lepisosteus and show that gar microchromosomes and macrochromosomes display different rates of structural evolution. Our analyses suggest that the genomic stability of gars, which may explain the ability of deeply divergent gar species to hybridize and has contributed to their higher structural similarity to tetrapod genomes than those of the far more closely related teleost fishes, may result from very low rates of transposable element origination and high inactivity compared to other vertebrates. Beyond providing a reference point for comparative vertebrate genomic studies, the new gar genomes illuminate a structural component of slow genomic evolution in living fossils and molecular mechanisms that may underlie exceptional genome stability.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC12863190/",
    doi = "10.1101/gr.280800.125",
    pmcid = "PMC12863190",
    pmid = "41530049"
}

@article{doi101186s12915026025444,
    author = "Frédérich, Bruno and Mittelheiser, Laurent and Gillet, Amandine and Hodge, Jennifer R and Laudet, Vincent and Dornburg, Alex",
    title = "Rapid and repeated evolution of pigmentation patterns in reef fishes.",
    year = "2026",
    journal = "BMC biology",
    abstract = "BACKGROUND: Pigmentation patterns are central to animal biology-shaping camouflage, signaling, and mate selection-and uncovering the mechanisms driving their diversification is key to understanding the evolutionary principles that generate this fundamental dimension of biodiversity. Reef fishes exhibit an incredible variety of patterns, from simple spots to intricate designs. To date, the underlying evolutionary processes that govern their diversification remain unclear. RESULTS: Here, we investigate the relationship between pigmentation pattern diversity, species richness, and geography across six iconic reef fish families. We provide evidence for a positive correlation between pattern diversity and species richness, with a high divergence of pigmentation patterns in every biogeographic region. Then, by using a suit of phylogenetically informed comparative analyses, we demonstrate that the evolution of pigmentation patterns is characterized by a combination of rapid and constrained phenotypic diversification. CONCLUSIONS: Overall, our findings illuminate factors that explain pigmentation pattern diversity in living reef fishes, revealing that speciation events have driven constant high levels of pigmentation pattern disparity within subclades and across globally variable reef fish assemblages.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC12927226/",
    doi = "10.1186/s12915-026-02544-4",
    pmcid = "PMC12927226",
    pmid = "41724958"
}