Monophyly

@article{crossref1926heilmann,
    title = "Heilmann on 'The Origin of Birds' The Origin of Birds Gerhard Heilmann",
    year = "1926",
    journal = "The Auk",
    url = "https://doi.org/10.2307/4075461",
    doi = "10.2307/4075461",
    number = "3",
    pages = "390-391",
    volume = "43"
}

@incollection{swinton1960the,
    author = "SWINTON, W.E.",
    title = "The Origin of Birds",
    year = "1960",
    booktitle = "Biology and Comparative Physiology of Birds",
    url = "https://doi.org/10.1016/b978-1-4832-3142-6.50006-9",
    doi = "10.1016/b978-1-4832-3142-6.50006-9",
    pages = "1-14"
}

@article{valen1968monophyly,
    author = "Valen, Leigh Van",
    title = "MONOPHYLY OR DIPHYLY IN THE ORIGIN OF WHALES",
    year = "1968",
    journal = "Evolution",
    url = "https://doi.org/10.1111/j.1558-5646.1968.tb03446.x",
    doi = "10.1111/j.1558-5646.1968.tb03446.x",
    number = "1",
    pages = "37-41",
    volume = "22"
}

@article{doi101111j155856461970tb01775x,
    author = "Galton, P.",
    title = "ORNITHISCHIAN DINOSAURS AND THE ORIGIN OF BIRDS",
    year = "1970",
    journal = "Evolution",
    url = "https://doi.org/10.1111/j.1558-5646.1970.tb01775.x",
    doi = "10.1111/j.1558-5646.1970.tb01775.x",
    is_oa = "true",
    number = "2",
    pages = "448-462",
    semanticscholar_citation_count = "37",
    semanticscholar_id = "d49bad7f9650d2e659f488b75b2cbde8c1f98494",
    volume = "24"
}

@article{ostrom1975the,
    author = "Ostrom, John H.",
    title = "The Origin of Birds",
    year = "1975",
    journal = "Annual Review of Earth and Planetary Sciences",
    url = "https://doi.org/10.1146/annurev.ea.03.050175.000415",
    doi = "10.1146/annurev.ea.03.050175.000415",
    number = "1",
    pages = "55-77",
    volume = "3"
}

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

@article{gauthier1986saurischian,
    author = "Gauthier, Jacques",
    title = "Saurischian monophyly and the origin of birds",
    year = "1986",
    publisher = "The Academy",
    abstract = "(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.",
    url = "https://zenodo.org/doi/10.5281/zenodo.16171435",
    doi = "10.5281/zenodo.16171435"
}

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

@article{s25fa512b11dd3cb39575b0e1b6ca7c486b5f6c73d,
    author = "Gauthier, J.",
    title = "Saurischian monophyly and the origin of birds",
    year = "1986",
    publisher = "The Academy",
    abstract = "(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.",
    url = "https://www.semanticscholar.org/paper/5fa512b11dd3cb39575b0e1b6ca7c486b5f6c73d",
    doi = "10.5281/zenodo.16171435",
    is_oa = "true",
    semanticscholar_citation_count = "1363",
    semanticscholar_id = "5fa512b11dd3cb39575b0e1b6ca7c486b5f6c73d"
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Inter and intrafamilial relationships within the New World Piciformes were examined through an electrophoretic analysis of 20 protein-coding loci (19 of which varied between taxa). One individual from each of 26 species representing 25 genera and 5 families was analyzed; Monotus momota (Coraciiformes, Momotidae) was used as an outgroup. Although levels of genetic differentiation were high (the mean Nei's unbiased distance was 1.07), the data proved useful for phylogenetic inference. The jackknife technique was used to estimate the robustness of phylogenetic hypotheses. At the interfamilial level, the results suggest the following groupings: [[[(Bucconidae) (Galbulidae)]{(Picidae)[(Capitonidae) (Ramphastidae)]}]]. These results were consistent with hypotheses of familial relationships proposed by two recent cladistic analyses of morphological character complexes (Simpson and Cracraft 1981, Swierczewski and Raikow 1981). Our data challenge the currently accepted monophyly of the Piciformes, however, in much the same way as do DNA-DNA hybridization data. Agreement among independently derived hypotheses of interfamilial relationships suggests confidence in our knowledge of evolutionary patterns among piciform taxa. Hypotheses of intrafamilial relationships, some of which agreed with morphological patterns obtained in other studies, were presented. This study shows that starch-gel electrophoresis may be useful at higher taxonomic levels.

@article{doi101093auk1044724,
    author = "Lanyon, S. and Zink, R.",
    title = "Genetic variation in piciform birds: monophyly and generic and familial relationships",
    year = "1987",
    journal = "The Auk",
    abstract = "Inter and intrafamilial relationships within the New World Piciformes were examined through an electrophoretic analysis of 20 protein-coding loci (19 of which varied between taxa). One individual from each of 26 species representing 25 genera and 5 families was analyzed; Monotus momota (Coraciiformes, Momotidae) was used as an outgroup. Although levels of genetic differentiation were high (the mean Nei's unbiased distance was 1.07), the data proved useful for phylogenetic inference. The jackknife technique was used to estimate the robustness of phylogenetic hypotheses. At the interfamilial level, the results suggest the following groupings: [[[(Bucconidae) (Galbulidae)]{(Picidae)[(Capitonidae) (Ramphastidae)]}]]. These results were consistent with hypotheses of familial relationships proposed by two recent cladistic analyses of morphological character complexes (Simpson and Cracraft 1981, Swierczewski and Raikow 1981). Our data challenge the currently accepted monophyly of the Piciformes, however, in much the same way as do DNA-DNA hybridization data. Agreement among independently derived hypotheses of interfamilial relationships suggests confidence in our knowledge of evolutionary patterns among piciform taxa. Hypotheses of intrafamilial relationships, some of which agreed with morphological patterns obtained in other studies, were presented. This study shows that starch-gel electrophoresis may be useful at higher taxonomic levels.",
    url = "https://www.semanticscholar.org/paper/a1c1890db02077eff1558be2f2e8c91bd6cf69fa",
    doi = "10.1093/AUK/104.4.724",
    is_oa = "true",
    number = "4",
    pages = "724-732",
    semanticscholar_citation_count = "35",
    semanticscholar_id = "a1c1890db02077eff1558be2f2e8c91bd6cf69fa",
    volume = "104"
}

@misc{gauthier1987saurischian1,
    author = "Gauthier, J",
    title = "Saurischian monophyly and the origin of birds",
    year = "1987",
    howpublished = "Memoirs of the California Academy of Science, v. 8, p. 1-55",
    note = "talkorigins\_source = {true}; raw\_reference = {Gauthier, J., 1987, Saurischian monophyly and the origin of birds: Memoirs of the California Academy of Science, v. 8, p. 1-55.}"
}

Inter and intrafamilial relationships within the New World Piciformes were examined through an electrophoretic analysis of 20 protein-coding loci (19 of which varied between taxa). One individual from each of 26 species representing 25 genera and 5 families was analyzed; Monotus momota (Coraciiformes, Momotidae) was used as an outgroup. Although levels of genetic differentiation were high (the mean Nei's unbiased distance was 1.07), the data proved useful for phylogenetic inference. The jackknife technique was used to estimate the robustness of phylogenetic hypotheses. At the interfamilial level, the results suggest the following groupings: [[[(Bucconidae) (Galbulidae)]{(Picidae)[(Capitonidae) (Ramphastidae)]}]]. These results were consistent with hypotheses of familial relationships proposed by two recent cladistic analyses of morphological character complexes (Simpson and Cracraft 1981, Swierczewski and Raikow 1981). Our data challenge the currently accepted monophyly of the Piciformes, however, in much the same way as do DNA-DNA hybridization data. Agreement among independently derived hypotheses of interfamilial relationships suggests confidence in our knowledge of evolutionary patterns among piciform taxa. Hypotheses of intrafamilial relationships, some of which agreed with morphological patterns obtained in other studies, were presented. This study shows that starch-gel electrophoresis may be useful at higher taxonomic levels.

@article{lanyon1987genetic,
    author = "Lanyon, Scott M. and Zink, Robert M.",
    title = "Genetic Variation in Piciform Birds: Monophyly and Generic and Familial Relationships",
    year = "1987",
    journal = "The Auk",
    abstract = "Inter and intrafamilial relationships within the New World Piciformes were examined through an electrophoretic analysis of 20 protein-coding loci (19 of which varied between taxa). One individual from each of 26 species representing 25 genera and 5 families was analyzed; Monotus momota (Coraciiformes, Momotidae) was used as an outgroup. Although levels of genetic differentiation were high (the mean Nei's unbiased distance was 1.07), the data proved useful for phylogenetic inference. The jackknife technique was used to estimate the robustness of phylogenetic hypotheses. At the interfamilial level, the results suggest the following groupings: [[[(Bucconidae) (Galbulidae)]{(Picidae)[(Capitonidae) (Ramphastidae)]}]]. These results were consistent with hypotheses of familial relationships proposed by two recent cladistic analyses of morphological character complexes (Simpson and Cracraft 1981, Swierczewski and Raikow 1981). Our data challenge the currently accepted monophyly of the Piciformes, however, in much the same way as do DNA-DNA hybridization data. Agreement among independently derived hypotheses of interfamilial relationships suggests confidence in our knowledge of evolutionary patterns among piciform taxa. Hypotheses of intrafamilial relationships, some of which agreed with morphological patterns obtained in other studies, were presented. This study shows that starch-gel electrophoresis may be useful at higher taxonomic levels.",
    url = "https://doi.org/10.1093/auk/104.4.724",
    doi = "10.1093/auk/104.4.724",
    number = "4",
    pages = "724-732",
    volume = "104"
}

@article{crossref1989the,
    title = "The Origin of Birds",
    year = "1989",
    journal = "The Ballarat Naturalist",
    url = "https://doi.org/10.5962/p.383994",
    doi = "10.5962/p.383994",
    pages = "5-5",
    volume = "(1989:Mar)"
}

@article{doi101127njgpa180199021,
    author = "Sereno, P. and Arcucci, A.",
    title = "The monophyly of crurotarsal archosaurs and the origin of bird and crocodile ankle joints",
    year = "1990",
    journal = "Neues Jahrbuch für Geologie und Paläontologie - Abhandlungen",
    url = "https://www.semanticscholar.org/paper/63f8e112c27231d62beaf709876aacb861a6384f",
    doi = "10.1127/njgpa/180/1990/21",
    is_oa = "true",
    number = "1",
    pages = "21-52",
    semanticscholar_citation_count = "87",
    semanticscholar_id = "63f8e112c27231d62beaf709876aacb861a6384f",
    volume = "180"
}

@incollection{prideaux2004monophyly,
    author = "Prideaux, Gavin J.",
    title = "Monophyly and Origin",
    year = "2004",
    booktitle = "Systematics and Evolution of the Sthenurine Kangaroos",
    url = "https://doi.org/10.1525/california/9780520098459.003.0004",
    doi = "10.1525/california/9780520098459.003.0004",
    pages = "207-250"
}

@article{s2e568f2c09496d3da8d217caa9a6c548e0aa8cdc6,
    author = "Witmer, L.",
    title = "New Aspects of Avian Origins : Roundtable Report",
    year = "2007",
    url = "https://www.semanticscholar.org/paper/e568f2c09496d3da8d217caa9a6c548e0aa8cdc6",
    is_oa = "true",
    semanticscholar_citation_count = "1",
    semanticscholar_id = "e568f2c09496d3da8d217caa9a6c548e0aa8cdc6"
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The proposed nomenclatural system for lamina-bounded fossae adds clarity to descriptions of complex vertebrae and allows these structures to be sourced as character data for phylogenetic analyses. These anatomical terms denote potentially homologous pneumatic structures within Saurischia, but they could be applied to any vertebrate with vertebral laminae that enclose spaces, regardless of their developmental origin or phylogenetic distribution.

@article{doi101371journalpone0017114,
    author = "Wilson, Jeffrey A. and D’Emic, Michael D. and Ikejiri, Takehito and Moacdieh, Emile M. and Whitlock, John A.",
    title = "A Nomenclature for Vertebral Fossae in Sauropods and Other Saurischian Dinosaurs",
    year = "2011",
    journal = "PLoS ONE",
    abstract = "The proposed nomenclatural system for lamina-bounded fossae adds clarity to descriptions of complex vertebrae and allows these structures to be sourced as character data for phylogenetic analyses. These anatomical terms denote potentially homologous pneumatic structures within Saurischia, but they could be applied to any vertebrate with vertebral laminae that enclose spaces, regardless of their developmental origin or phylogenetic distribution.",
    url = "https://doi.org/10.1371/journal.pone.0017114",
    doi = "10.1371/journal.pone.0017114",
    openalex = "W2038699903",
    references = "crossref1976allosaurus, doi101002jez513, doi101002jmor10470, doi101046j10963642200200029x, doi10108002724634199710011027, doi10108002724634199810011115, doi10108002724634199910011178, doi101098rstb19850092, doi101111j109600311988tb00514x, doi101130spe40p1, doi101371journalpone0001230, doi101371journalpone0003303, doi101525california97805202462320010001, doi10167102724634200727127tpasom20co2, doi1023073889325, doi105962p234818, doi105962p234849, openalexw2788234611"
}

@misc{crossref2016the,
    title = "The Origin of Birds",
    year = "2016",
    booktitle = "Avian Evolution",
    url = "https://doi.org/10.1002/9781119020677.ch2",
    doi = "10.1002/9781119020677.ch2",
    pages = "18-42"
}

We studied the phylogeny, biogeography and diversification of suboscine birds in the genus Scytalopus (Rhinocryptidae), a widespread, speciose, and taxonomically challenging group of Neotropical birds. We analyzed nuclear (exons, regions flanking ultraconserved elements) and mitochondrial (ND2) DNA sequence data for a taxonomically and geographically comprehensive sample of specimens collected from Costa Rica to Patagonia and eastern Brazil. We found that Scytalopus is a monophyletic group sister to Eugralla, and consists of three main clades roughly distributed in (1) the Southern Andes, (2) eastern Brazil, and (3) the Tropical Andes and Central America. The clades from the Southern Andes and Eastern Brazil are sister to each other. Despite their confusing overall uniformity in plumage coloration, body shape and overall appearance, rates of species accumulation through time in Scytalopus since the origin of the clade in the Late Miocene are unusually high compared to those of other birds, suggesting rapid non-adaptive diversification in the group which we attribute to their limited dispersal abilities making them speciation-prone and their occurrence in a complex landscape with numerous barriers promoting allopatric differentiation. Divergence times among species and downturns in species accumulation rates in recent times suggest that most speciation events in Scytalopus predate climatic oscillations of the Pleistocene. Our analyses identified various cases of strong genetic structure within species and lack of monophyly of taxa, flagging populations which likely merit additional study to establish their taxonomic status. In particular, detailed analyses of species limits are due in S. parvirostris, S. latrans, S. speluncae, the S. atratus complex, and the Southern Andes clade.

@article{doi101101600775,
    author = "Cadena, C. and Cuervo, Andrés M. and Céspedes, Laura N. and Bravo, Gustavo A. and Krabbe, N. and Schulenberg, T. and Derryberry, Graham E. and Silveira, L. F. and Derryberry, E. and Brumfield, R. T. and Fjeldså, J.",
    title = "Systematics, biogeography, and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds",
    year = "2019",
    journal = "Ornithology",
    abstract = "We studied the phylogeny, biogeography and diversification of suboscine birds in the genus Scytalopus (Rhinocryptidae), a widespread, speciose, and taxonomically challenging group of Neotropical birds. We analyzed nuclear (exons, regions flanking ultraconserved elements) and mitochondrial (ND2) DNA sequence data for a taxonomically and geographically comprehensive sample of specimens collected from Costa Rica to Patagonia and eastern Brazil. We found that Scytalopus is a monophyletic group sister to Eugralla, and consists of three main clades roughly distributed in (1) the Southern Andes, (2) eastern Brazil, and (3) the Tropical Andes and Central America. The clades from the Southern Andes and Eastern Brazil are sister to each other. Despite their confusing overall uniformity in plumage coloration, body shape and overall appearance, rates of species accumulation through time in Scytalopus since the origin of the clade in the Late Miocene are unusually high compared to those of other birds, suggesting rapid non-adaptive diversification in the group which we attribute to their limited dispersal abilities making them speciation-prone and their occurrence in a complex landscape with numerous barriers promoting allopatric differentiation. Divergence times among species and downturns in species accumulation rates in recent times suggest that most speciation events in Scytalopus predate climatic oscillations of the Pleistocene. Our analyses identified various cases of strong genetic structure within species and lack of monophyly of taxa, flagging populations which likely merit additional study to establish their taxonomic status. In particular, detailed analyses of species limits are due in S. parvirostris, S. latrans, S. speluncae, the S. atratus complex, and the Southern Andes clade.",
    url = "https://academic.oup.com/auk/article-pdf/137/2/ukz077/33666749/ukz077.pdf",
    doi = "10.1101/600775",
    is_oa = "true",
    semanticscholar_citation_count = "23",
    semanticscholar_id = "6c6e36136fd1088cb818a8df73282a08a4d6dd59"
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ABSTRACT We studied the phylogeny, biogeography, and diversification of suboscine passerines in the genus Scytalopus (Rhinocryptidae), a widespread, species-rich, and taxonomically challenging group of Neotropical birds. We analyzed nuclear (exons, regions flanking ultraconserved elements) and mitochondrial (ND2) DNA sequence data for a taxonomically and geographically comprehensive sample of specimens collected from Costa Rica to Patagonia and Brazil. We found that Scytalopus is a monophyletic group sister to Eugralla and consists of 3 main clades roughly distributed in (1) the Southern Andes, (2) eastern Brazil, and (3) the Tropical Andes and Central America. The clades from the Southern Andes and eastern Brazil are sister to each other. Despite their confusing uniformity in plumage coloration, body shape, and overall appearance, rates of species accumulation through time in Scytalopus since the origin of the clade in the Late Miocene are unusually high compared with those of other birds, suggesting rapid non-adaptive diversification in the group. We attribute this to their limited dispersal abilities making them speciation-prone and their occurrence in a complex landscape with numerous barriers promoting allopatric differentiation. Divergence times among species and downturns in species accumulation rates in recent times suggest that most speciation events in Scytalopus predate climatic oscillations of the Pleistocene. Our analyses identified various cases of strong genetic structure within species and lack of monophyly of taxa, flagging populations which likely merit additional study to clarify their taxonomic status. In particular, detailed analyses of species limits are due in S. parvirostris, S. latrans, S. speluncae, the S. atratus complex, and the Southern Andes clade.

@article{doi101093aukukz077,
    author = "Cadena, C. and Cuervo, Andrés M. and Céspedes, Laura N. and Bravo, Gustavo A. and Krabbe, N. and Schulenberg, T. and Derryberry, Graham E. and Silveira, L. F. and Derryberry, E. and Brumfield, R. T. and Fjeldså, J.",
    title = "Systematics, biogeography, and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds",
    year = "2020",
    journal = "The Auk",
    abstract = "ABSTRACT We studied the phylogeny, biogeography, and diversification of suboscine passerines in the genus Scytalopus (Rhinocryptidae), a widespread, species-rich, and taxonomically challenging group of Neotropical birds. We analyzed nuclear (exons, regions flanking ultraconserved elements) and mitochondrial (ND2) DNA sequence data for a taxonomically and geographically comprehensive sample of specimens collected from Costa Rica to Patagonia and Brazil. We found that Scytalopus is a monophyletic group sister to Eugralla and consists of 3 main clades roughly distributed in (1) the Southern Andes, (2) eastern Brazil, and (3) the Tropical Andes and Central America. The clades from the Southern Andes and eastern Brazil are sister to each other. Despite their confusing uniformity in plumage coloration, body shape, and overall appearance, rates of species accumulation through time in Scytalopus since the origin of the clade in the Late Miocene are unusually high compared with those of other birds, suggesting rapid non-adaptive diversification in the group. We attribute this to their limited dispersal abilities making them speciation-prone and their occurrence in a complex landscape with numerous barriers promoting allopatric differentiation. Divergence times among species and downturns in species accumulation rates in recent times suggest that most speciation events in Scytalopus predate climatic oscillations of the Pleistocene. Our analyses identified various cases of strong genetic structure within species and lack of monophyly of taxa, flagging populations which likely merit additional study to clarify their taxonomic status. In particular, detailed analyses of species limits are due in S. parvirostris, S. latrans, S. speluncae, the S. atratus complex, and the Southern Andes clade.",
    url = "https://academic.oup.com/auk/article-pdf/137/2/ukz077/33666749/ukz077.pdf",
    doi = "10.1093/auk/ukz077",
    is_oa = "true",
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    semanticscholar_id = "3a0bda6f0f2fbcd40a32bf4f75b2610c70c302b0",
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}

One of the most remarkable features in sauropod dinosaurs relates to their pneumatized skeletons permeated by a bird‐like air sac system. Many studies described the late evolution and diversification of this trait in mid to late Mesozoic forms but few focused on the origin of the invasive respiratory diverticula in sauropodomorphs. Fortunately, it is possible to solve this thanks to the boom of new species described in the last decade as well as the broad accessibility of new technologies. Here we analyze the unaysaurid sauropodomorph Macrocollum itaquii from the Late Triassic (early Norian) of southern Brazil using micro‐computed tomography. We describe the chronologically oldest and phylogenetically earliest unambiguous evidence of an invasive air sac system in a dinosaur. Surprisingly, this species presented a unique pattern of pneumatization in non‐sauropod sauropodomorphs, with pneumatic foramina in posterior cervical and anterior dorsal vertebrae. This suggests that patterns of pneumatization were not cladistically consistent prior to the arrival of Jurassic eusauropods. Additionally, we describe the protocamerae tissue, a new type of pneumatic tissue with properties of both camellae and camerae. This reverts the previous hypothesis which stated that the skeletal pneumatization first evolved into camarae, and derived into delicate trabecular arrangements. This tissue is evidence of thin camellate‐like tissue developing into larger chambers. Finally, Macrocollum is an example of the gradual evolution of skeletal tissues responding to the fastly specializing Respiratory System of saurischian dinosaurs.

@article{doi101002ar25209,
    author = "Aureliano, T. and Ghilardi, A. and Müller, R. and Kerber, L. and Fernandes, M. and Ricardi-Branco, F. and Wedel, M.",
    title = "The origin of an invasive air sac system in sauropodomorph dinosaurs",
    year = "2023",
    journal = "The Anatomical Record",
    abstract = "One of the most remarkable features in sauropod dinosaurs relates to their pneumatized skeletons permeated by a bird‐like air sac system. Many studies described the late evolution and diversification of this trait in mid to late Mesozoic forms but few focused on the origin of the invasive respiratory diverticula in sauropodomorphs. Fortunately, it is possible to solve this thanks to the boom of new species described in the last decade as well as the broad accessibility of new technologies. Here we analyze the unaysaurid sauropodomorph Macrocollum itaquii from the Late Triassic (early Norian) of southern Brazil using micro‐computed tomography. We describe the chronologically oldest and phylogenetically earliest unambiguous evidence of an invasive air sac system in a dinosaur. Surprisingly, this species presented a unique pattern of pneumatization in non‐sauropod sauropodomorphs, with pneumatic foramina in posterior cervical and anterior dorsal vertebrae. This suggests that patterns of pneumatization were not cladistically consistent prior to the arrival of Jurassic eusauropods. Additionally, we describe the protocamerae tissue, a new type of pneumatic tissue with properties of both camellae and camerae. This reverts the previous hypothesis which stated that the skeletal pneumatization first evolved into camarae, and derived into delicate trabecular arrangements. This tissue is evidence of thin camellate‐like tissue developing into larger chambers. Finally, Macrocollum is an example of the gradual evolution of skeletal tissues responding to the fastly specializing Respiratory System of saurischian dinosaurs.",
    url = "https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ar.25209",
    doi = "10.1002/ar.25209",
    is_oa = "true",
    number = "4",
    pages = "1084-1092",
    semanticscholar_citation_count = "13",
    semanticscholar_id = "67c27ddb9ea80818b40988561771f551fdeb8023",
    volume = "307"
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The remarkable morphological diversity and species abundance of teleost fishes offer a valuable resource for understanding vertebrate evolution. In phase I of the Fish10K project, genomes of 110 teleost species were sequenced and assembled, filling gaps in 3 previously unrepresented orders, and integrated with existing data to generate a 464 species whole-genome alignment spanning all teleost orders-the largest such resource beyond mammals and birds. Comparative analyses reveal distinctive genomic features, including progressive genome compaction with shortened intron lengths relative to non-teleost ray-finned fishes. Analysis of the transposable element (TE) landscape suggests a potential association between TE expansion in teleost genomes and different habitats, as well as the uniqueness of teleosts' DNA-dominated transposon composition among vertebrates. Genome-wide phylogenetic analyses refute the widely accepted monophyly of "Siluriphysi" hypothesis and support the hypothesis of a single origin of electroreception followed by secondary loss in Characiformes. A refined evolutionary timeline of teleosts by whole-genome alignment resource placed teleosts at ∼253 million years ago, predating the Permian-Triassic extinction, and delineates three diversification phases punctuated by mass extinctions, challenging continuous post-Cretaceous-Palaeogene acceleration models. This study establishes a large-scale genomic database and a foundational whole-genome alignment resource, advancing insights into the landscape of teleost genomic architecture and macroevolution.

@article{doi101016jxinn2025101177,
    author = "Song, Yue and Yuan, Zengbao and Fang, Chengchi and Zhang, Suyu and Yang, Liandong and Hu, Mingliang and Seim, Inge and Liu, Shanshan and Tian, Xiaolin and Wang, Cheng and Zhang, Yaolei and Pan, Zhaohui and Qu, Qingming and Liu, Hongyue and Li, Yuanning and Pan, Luyuan and Zhu, Chenglong and Yang, Hengjia and Chen, Xiao and Zhang, Mengqi and Hou, G. and Liu, Meiru and Wang, Jiahao and Liu, Qun and Gan, Xiaoni and Zeng, Honghui and Xu, Wenjie and Feng, Chenguang and Wang, Mengjun and Zhou, Zhuocheng and He, Song and Liu, Chenglong and Yu, Mengjun and Li, Hanbo and Liang, Jian and Zhang, He and Li, Yongxin and Lee, Simon Ming-Yuen and Sun, Yonghua and Qiu, Qiang and Liu, Xin and Kristiansen, Karsten and Wang, Wen and Wang, Jian and Zhu, Min and Yang, Huanming and Chen, Songlin and Gui, Jianfang and Chen, Yiyu and Zhang, Guojie and Xu, Xun and Wang, Kun and Fan, Guangyi and He, Shunping",
    title = "A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape.",
    year = "2025",
    journal = "Innovation (Cambridge (Mass.))",
    abstract = {The remarkable morphological diversity and species abundance of teleost fishes offer a valuable resource for understanding vertebrate evolution. In phase I of the Fish10K project, genomes of 110 teleost species were sequenced and assembled, filling gaps in 3 previously unrepresented orders, and integrated with existing data to generate a 464 species whole-genome alignment spanning all teleost orders-the largest such resource beyond mammals and birds. Comparative analyses reveal distinctive genomic features, including progressive genome compaction with shortened intron lengths relative to non-teleost ray-finned fishes. Analysis of the transposable element (TE) landscape suggests a potential association between TE expansion in teleost genomes and different habitats, as well as the uniqueness of teleosts' DNA-dominated transposon composition among vertebrates. Genome-wide phylogenetic analyses refute the widely accepted monophyly of "Siluriphysi" hypothesis and support the hypothesis of a single origin of electroreception followed by secondary loss in Characiformes. A refined evolutionary timeline of teleosts by whole-genome alignment resource placed teleosts at ∼253 million years ago, predating the Permian-Triassic extinction, and delineates three diversification phases punctuated by mass extinctions, challenging continuous post-Cretaceous-Palaeogene acceleration models. This study establishes a large-scale genomic database and a foundational whole-genome alignment resource, advancing insights into the landscape of teleost genomic architecture and macroevolution.},
    url = "https://www.semanticscholar.org/paper/5435c4e71880224ebb1458a87db8ff83f16fb711",
    doi = "10.1016/j.xinn.2025.101177",
    is_oa = "true",
    number = "3",
    pages = "101177",
    semanticscholar_citation_count = "3",
    semanticscholar_id = "5435c4e71880224ebb1458a87db8ff83f16fb711",
    volume = "7"
}