Complexity of avian evolution revealed by family-level genomes

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions 1 – 3 . Here we address these issues by...

Full description

Saved in:
Bibliographic Details
Published inNature (London) Vol. 629; no. 8013; pp. 851 - 860
Main Authors Stiller, Josefin, Feng, Shaohong, Chowdhury, Al-Aabid, Rivas-González, Iker, Duchêne, David A., Fang, Qi, Deng, Yuan, Kozlov, Alexey, Stamatakis, Alexandros, Claramunt, Santiago, Nguyen, Jacqueline M. T., Ho, Simon Y. W., Faircloth, Brant C., Haag, Julia, Houde, Peter, Cracraft, Joel, Balaban, Metin, Mai, Uyen, Chen, Guangji, Gao, Rongsheng, Zhou, Chengran, Xie, Yulong, Huang, Zijian, Cao, Zhen, Yan, Zhi, Ogilvie, Huw A., Nakhleh, Luay, Lindow, Bent, Morel, Benoit, Fjeldså, Jon, Hosner, Peter A., da Fonseca, Rute R., Petersen, Bent, Tobias, Joseph A., Székely, Tamás, Kennedy, Jonathan David, Reeve, Andrew Hart, Liker, Andras, Stervander, Martin, Antunes, Agostinho, Tietze, Dieter Thomas, Bertelsen, Mads F., Lei, Fumin, Rahbek, Carsten, Graves, Gary R., Schierup, Mikkel H., Warnow, Tandy, Braun, Edward L., Gilbert, M. Thomas P., Jarvis, Erich D., Mirarab, Siavash, Zhang, Guojie
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 23.05.2024
Subjects
631/181/735
631/181/757
631/181/759
631/208/182
631/208/212/2304
Humanities and Social Sciences
multidisciplinary
Science
Science (multidisciplinary)
Online AccessGet full text

Cover

Abstract Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions 1 – 3 . Here we address these issues by analysing the genomes of 363 bird species 4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous–Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies. Using intergenic regions and coalescent methods to analyse the genomes of 363 bird species, the authors present a well-supported tree confirming that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary.
AbstractList Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions 1 – 3 . Here we address these issues by analysing the genomes of 363 bird species 4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous–Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies. Using intergenic regions and coalescent methods to analyse the genomes of 363 bird species, the authors present a well-supported tree confirming that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary.
Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions 1–3 . Here we address these issues by analysing the genomes of 363 bird species 4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous–Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.
Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions . Here we address these issues by analysing the genomes of 363 bird species (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.
Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.
Author Mai, Uyen
Jarvis, Erich D.
Duchêne, David A.
Fjeldså, Jon
Deng, Yuan
Stiller, Josefin
Zhou, Chengran
Ho, Simon Y. W.
Székely, Tamás
Feng, Shaohong
Nakhleh, Luay
Chen, Guangji
Xie, Yulong
Warnow, Tandy
Braun, Edward L.
Cracraft, Joel
Ogilvie, Huw A.
Petersen, Bent
Lindow, Bent
Huang, Zijian
Tietze, Dieter Thomas
Rivas-González, Iker
Stamatakis, Alexandros
Tobias, Joseph A.
Antunes, Agostinho
da Fonseca, Rute R.
Schierup, Mikkel H.
Balaban, Metin
Haag, Julia
Fang, Qi
Nguyen, Jacqueline M. T.
Zhang, Guojie
Reeve, Andrew Hart
Cao, Zhen
Yan, Zhi
Kozlov, Alexey
Graves, Gary R.
Rahbek, Carsten
Mirarab, Siavash
Gao, Rongsheng
Bertelsen, Mads F.
Chowdhury, Al-Aabid
Morel, Benoit
Claramunt, Santiago
Houde, Peter
Kennedy, Jonathan David
Gilbert, M. Thomas P.
Liker, Andras
Faircloth, Brant C.
Hosner, Peter A.
Lei, Fumin
Stervander, Martin
Author_xml – sequence: 1
  givenname: Josefin
  orcidid: 0000-0001-6009-9581
  surname: Stiller
  fullname: Stiller, Josefin
  email: josefin.stiller@bio.ku.dk
  organization: Section for Ecology and Evolution, Department of Biology, University of Copenhagen
– sequence: 2
  givenname: Shaohong
  orcidid: 0000-0002-2462-7348
  surname: Feng
  fullname: Feng, Shaohong
  organization: Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women’s Hospital, Zhejiang University School of Medicine, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Innovation Center of Yangtze River Delta, Zhejiang University
– sequence: 3
  givenname: Al-Aabid
  surname: Chowdhury
  fullname: Chowdhury, Al-Aabid
  organization: School of Life and Environmental Sciences, University of Sydney
– sequence: 4
  givenname: Iker
  orcidid: 0000-0002-0515-0628
  surname: Rivas-González
  fullname: Rivas-González, Iker
  organization: Bioinformatics Research Centre, Aarhus University
– sequence: 5
  givenname: David A.
  orcidid: 0000-0002-5479-1974
  surname: Duchêne
  fullname: Duchêne, David A.
  organization: Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen
– sequence: 6
  givenname: Qi
  orcidid: 0000-0002-9181-8689
  surname: Fang
  fullname: Fang, Qi
  organization: BGI Research
– sequence: 7
  givenname: Yuan
  surname: Deng
  fullname: Deng, Yuan
  organization: BGI Research, BGI Research
– sequence: 8
  givenname: Alexey
  orcidid: 0000-0001-7394-2718
  surname: Kozlov
  fullname: Kozlov, Alexey
  organization: Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies
– sequence: 9
  givenname: Alexandros
  orcidid: 0000-0003-0353-0691
  surname: Stamatakis
  fullname: Stamatakis, Alexandros
  organization: Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Institute of Computer Science, Foundation for Research and Technology Hellas, Institute for Theoretical Informatics, Karlsruhe Institute of Technology
– sequence: 10
  givenname: Santiago
  orcidid: 0000-0002-8926-5974
  surname: Claramunt
  fullname: Claramunt, Santiago
  organization: Department of Ecology and Evolutionary Biology, University of Toronto, Department of Natural History, Royal Ontario Museum
– sequence: 11
  givenname: Jacqueline M. T.
  orcidid: 0000-0002-3076-0006
  surname: Nguyen
  fullname: Nguyen, Jacqueline M. T.
  organization: College of Science and Engineering, Flinders University, Australian Museum Research Institute
– sequence: 12
  givenname: Simon Y. W.
  orcidid: 0000-0002-0361-2307
  surname: Ho
  fullname: Ho, Simon Y. W.
  organization: School of Life and Environmental Sciences, University of Sydney
– sequence: 13
  givenname: Brant C.
  orcidid: 0000-0002-1943-0217
  surname: Faircloth
  fullname: Faircloth, Brant C.
  organization: Department of Biological Sciences and Museum of Natural Science, Louisiana State University
– sequence: 14
  givenname: Julia
  orcidid: 0000-0002-7493-3917
  surname: Haag
  fullname: Haag, Julia
  organization: Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies
– sequence: 15
  givenname: Peter
  orcidid: 0000-0003-4541-5974
  surname: Houde
  fullname: Houde, Peter
  organization: Department of Biology, New Mexico State University
– sequence: 16
  givenname: Joel
  orcidid: 0000-0001-7587-8342
  surname: Cracraft
  fullname: Cracraft, Joel
  organization: Department of Ornithology, American Museum of Natural History
– sequence: 17
  givenname: Metin
  surname: Balaban
  fullname: Balaban, Metin
  organization: Bioinformatics and Systems Biology Graduate Program, University of California San Diego
– sequence: 18
  givenname: Uyen
  surname: Mai
  fullname: Mai, Uyen
  organization: Computer Science and Engineering, University of California San Diego
– sequence: 19
  givenname: Guangji
  orcidid: 0000-0002-9441-1155
  surname: Chen
  fullname: Chen, Guangji
  organization: BGI Research, College of Life Sciences, University of Chinese Academy of Sciences
– sequence: 20
  givenname: Rongsheng
  surname: Gao
  fullname: Gao, Rongsheng
  organization: BGI Research, College of Life Sciences, University of Chinese Academy of Sciences
– sequence: 21
  givenname: Chengran
  orcidid: 0000-0002-9468-5973
  surname: Zhou
  fullname: Zhou, Chengran
  organization: BGI Research
– sequence: 22
  givenname: Yulong
  surname: Xie
  fullname: Xie, Yulong
  organization: Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women’s Hospital, Zhejiang University School of Medicine
– sequence: 23
  givenname: Zijian
  surname: Huang
  fullname: Huang, Zijian
  organization: Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women’s Hospital, Zhejiang University School of Medicine
– sequence: 24
  givenname: Zhen
  surname: Cao
  fullname: Cao, Zhen
  organization: Department of Computer Science, Rice University
– sequence: 25
  givenname: Zhi
  orcidid: 0000-0003-2433-5553
  surname: Yan
  fullname: Yan, Zhi
  organization: Department of Computer Science, Rice University
– sequence: 26
  givenname: Huw A.
  orcidid: 0000-0003-1589-6885
  surname: Ogilvie
  fullname: Ogilvie, Huw A.
  organization: Department of Computer Science, Rice University
– sequence: 27
  givenname: Luay
  orcidid: 0000-0003-3288-6769
  surname: Nakhleh
  fullname: Nakhleh, Luay
  organization: Department of Computer Science, Rice University
– sequence: 28
  givenname: Bent
  orcidid: 0000-0002-1864-4221
  surname: Lindow
  fullname: Lindow, Bent
  organization: Natural History Museum Denmark, University of Copenhagen
– sequence: 29
  givenname: Benoit
  surname: Morel
  fullname: Morel, Benoit
  organization: Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Institute of Computer Science, Foundation for Research and Technology Hellas
– sequence: 30
  givenname: Jon
  orcidid: 0000-0003-0790-3600
  surname: Fjeldså
  fullname: Fjeldså, Jon
  organization: Natural History Museum Denmark, University of Copenhagen
– sequence: 31
  givenname: Peter A.
  orcidid: 0000-0001-7499-6224
  surname: Hosner
  fullname: Hosner, Peter A.
  organization: Natural History Museum Denmark, University of Copenhagen, Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen
– sequence: 32
  givenname: Rute R.
  orcidid: 0000-0002-2805-4698
  surname: da Fonseca
  fullname: da Fonseca, Rute R.
  organization: Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen
– sequence: 33
  givenname: Bent
  orcidid: 0000-0002-2472-8317
  surname: Petersen
  fullname: Petersen, Bent
  organization: Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University
– sequence: 34
  givenname: Joseph A.
  orcidid: 0000-0003-2429-6179
  surname: Tobias
  fullname: Tobias, Joseph A.
  organization: Department of Life Sciences, Imperial College London, Silwood Park
– sequence: 35
  givenname: Tamás
  orcidid: 0000-0003-2093-0056
  surname: Székely
  fullname: Székely, Tamás
  organization: Milner Centre for Evolution, University of Bath, ELKH-DE Reproductive Strategies Research Group, University of Debrecen
– sequence: 36
  givenname: Jonathan David
  surname: Kennedy
  fullname: Kennedy, Jonathan David
  organization: Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen
– sequence: 37
  givenname: Andrew Hart
  orcidid: 0000-0001-5233-6030
  surname: Reeve
  fullname: Reeve, Andrew Hart
  organization: Natural History Museum Denmark, University of Copenhagen
– sequence: 38
  givenname: Andras
  surname: Liker
  fullname: Liker, Andras
  organization: HUN-REN-PE Evolutionary Ecology Research Group, University of Pannonia, Behavioural Ecology Research Group, Center for Natural Sciences, University of Pannonia
– sequence: 39
  givenname: Martin
  orcidid: 0000-0002-6139-7828
  surname: Stervander
  fullname: Stervander, Martin
  organization: Bird Group, Natural History Museum
– sequence: 40
  givenname: Agostinho
  orcidid: 0000-0002-1328-1732
  surname: Antunes
  fullname: Antunes, Agostinho
  organization: CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Department of Biology, Faculty of Sciences, University of Porto
– sequence: 41
  givenname: Dieter Thomas
  orcidid: 0000-0001-6868-227X
  surname: Tietze
  fullname: Tietze, Dieter Thomas
  organization: NABU
– sequence: 42
  givenname: Mads F.
  surname: Bertelsen
  fullname: Bertelsen, Mads F.
  organization: Centre for Zoo and Wild Animal Health, Copenhagen Zoo
– sequence: 43
  givenname: Fumin
  orcidid: 0000-0001-9920-8167
  surname: Lei
  fullname: Lei, Fumin
  organization: Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, College of Life Science, University of Chinese Academy of Sciences
– sequence: 44
  givenname: Carsten
  orcidid: 0000-0003-4585-0300
  surname: Rahbek
  fullname: Rahbek, Carsten
  organization: Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Institute of Ecology, Peking University, Danish Institute for Advanced Study, University of Southern Denmark
– sequence: 45
  givenname: Gary R.
  orcidid: 0000-0003-1406-5246
  surname: Graves
  fullname: Graves, Gary R.
  organization: Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution
– sequence: 46
  givenname: Mikkel H.
  orcidid: 0000-0002-5028-1790
  surname: Schierup
  fullname: Schierup, Mikkel H.
  organization: Bioinformatics Research Centre, Aarhus University
– sequence: 47
  givenname: Tandy
  surname: Warnow
  fullname: Warnow, Tandy
  organization: University of Illinois Urbana-Champaign
– sequence: 48
  givenname: Edward L.
  orcidid: 0000-0003-1643-5212
  surname: Braun
  fullname: Braun, Edward L.
  organization: Department of Biology, University of Florida
– sequence: 49
  givenname: M. Thomas P.
  orcidid: 0000-0002-5805-7195
  surname: Gilbert
  fullname: Gilbert, M. Thomas P.
  organization: Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, University Museum, NTNU
– sequence: 50
  givenname: Erich D.
  surname: Jarvis
  fullname: Jarvis, Erich D.
  organization: Vertebrate Genome Lab, The Rockefeller University, Howard Hughes Medical Institute
– sequence: 51
  givenname: Siavash
  orcidid: 0000-0001-5410-1518
  surname: Mirarab
  fullname: Mirarab, Siavash
  email: smirarabbaygi@ucsd.edu
  organization: University of California, San Diego
– sequence: 52
  givenname: Guojie
  orcidid: 0000-0001-6860-1521
  surname: Zhang
  fullname: Zhang, Guojie
  email: guojiezhang@zju.edu.cn
  organization: Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women’s Hospital, Zhejiang University School of Medicine, Innovation Center of Yangtze River Delta, Zhejiang University, BGI Research, Villum Center for Biodiversity Genomics, Department of Biology, University of Copenhagen
BackLink https://www.ncbi.nlm.nih.gov/pubmed/38560995$$D View this record in MEDLINE/PubMed
BookMark eNp9UU1v1DAQtVArum35AxxQjlwM49hxnAsIrfiSKvVCz9bEO1lcOfZiJyv235NlWwQcOhdL4_cxeu-SncUUibGXAt4IkOZtUaIxmkOtOLSyllw8YyuhWs2VNu0ZWwHUhoOR-oJdlnIPAI1o1XN2IU2joeuaFXu3TuMu0E8_Hao0VLj3GCvapzBPPsUq054w0KbqD9WAow8HHpZVqLYU00jlmp0PGAq9eHiv2N2nj9_WX_jN7eev6w83HFULEx-0g8Y41UvnYNMPnd40negapFZiR93gAMkNNUKtEZfThABnBt3XSKSR5BV7f9Ldzf1IG0dxyhjsLvsR88Em9Pbfn-i_223aW3EcJdSi8PpBIacfM5XJjr44CgEjpblYCVIIqaQRC_TV32Z_XB5TWwDmBHA5lZJpsM5PeAxs8fbBCrDHguypILsUZH8XZI_a9X_UR_UnSfJEKgs4binb-zTnuAT-FOsX-TekmA
CitedBy_id crossref_primary_10_1016_j_conb_2025_102993
crossref_primary_10_1093_molbev_msae146
crossref_primary_10_1080_14772019_2024_2356086
crossref_primary_10_1098_rstb_2023_0421
crossref_primary_10_1002_jmor_21710
crossref_primary_10_1007_s10814_024_09206_5
crossref_primary_10_1098_rsbl_2024_0596
crossref_primary_10_1016_j_cell_2024_10_026
crossref_primary_10_1080_08912963_2024_2418895
crossref_primary_10_1186_s13039_024_00696_y
crossref_primary_10_1126_science_ads0215
crossref_primary_10_1038_s41467_025_56201_5
crossref_primary_10_1093_molbev_msae214
crossref_primary_10_1111_syen_12669
crossref_primary_10_3390_ani14192790
crossref_primary_10_1002_jmv_70247
crossref_primary_10_3390_biology13080643
crossref_primary_10_1093_biolinnean_blae070
crossref_primary_10_1038_s41577_024_01083_9
crossref_primary_10_1016_j_actatropica_2024_107411
crossref_primary_10_1093_gbe_evae138
crossref_primary_10_1093_sysbio_syae052
crossref_primary_10_3390_ijms26031167
crossref_primary_10_1093_gbe_evae211
crossref_primary_10_1002_tax_13308
crossref_primary_10_1093_molbev_msae264
crossref_primary_10_1073_pnas_2401106122
crossref_primary_10_1186_s12864_024_10899_7
crossref_primary_10_3390_ijms252312654
crossref_primary_10_1007_s00114_025_01977_1
crossref_primary_10_1038_s41586_025_08777_7
crossref_primary_10_1038_s41598_024_70018_0
crossref_primary_10_1098_rstb_2023_0439
crossref_primary_10_1126_science_adk9688
crossref_primary_10_3390_biology13070478
crossref_primary_10_1016_j_vprsr_2024_101118
crossref_primary_10_1126_sciadv_adp0114
crossref_primary_10_1073_pnas_2412448121
crossref_primary_10_1002_spp2_1611
crossref_primary_10_3389_fgene_2024_1414074
crossref_primary_10_1016_j_conb_2024_102965
crossref_primary_10_1146_annurev_animal_030424_074906
crossref_primary_10_1038_s41467_024_47501_3
crossref_primary_10_1146_annurev_genet_111523_101929
crossref_primary_10_1080_02724634_2024_2400252
crossref_primary_10_1038_d41586_024_04153_z
crossref_primary_10_1111_1749_4877_12870
crossref_primary_10_3389_fetho_2025_1520935
crossref_primary_10_1073_pnas_2405887121
Cites_doi 10.1016/S0169-5347(03)00017-X
10.1089/cmb.2014.0156
10.1093/molbev/msaa015
10.1080/10635150490445779
10.1371/journal.pone.0054848
10.1093/bioinformatics/btq243
10.1089/cmb.2009.0179
10.1371/journal.pbio.1002224
10.1093/molbev/msj024
10.1111/2041-210X.13977
10.1093/molbev/msx092
10.1093/sysbio/syw018
10.1038/522034d
10.1126/science.aaz6970
10.1093/bioinformatics/btr597
10.7717/peerj.6399
10.1126/science.aab1578
10.1080/10635150490522232
10.1080/10635150600755453
10.1016/j.ympev.2018.01.019
10.1093/sysbio/syx064
10.3390/genes9030123
10.1038/s41586-020-2873-9
10.1038/nature15697
10.3390/d12040164
10.1093/molbev/msac254
10.1186/1471-2156-11-11
10.1093/sysbio/syab052
10.1126/science.1230492
10.1111/j.1420-9101.2010.02029.x
10.1093/sysbio/syu020
10.3390/birds2010001
10.1038/nature03154
10.3389/fgene.2019.01049
10.1093/oxfordjournals.molbev.a025892
10.1139/z01-204
10.1126/science.1253451
10.1038/s41586-020-2871-y
10.1093/molbev/msu300
10.1093/sysbio/syr107
10.1080/10635150600697358
10.1007/BF00379994
10.1093/bioinformatics/btv646
10.1093/bioinformatics/btz305
10.4137/EBO.S9657
10.1126/science.abn4409
10.1093/bib/bbr014
10.1093/nar/gkf436
10.1093/gbe/evx147
10.1093/bioinformatics/btw108
10.1016/j.tig.2006.02.003
10.1371/journal.pbio.1000602
10.1146/annurev-ecolsys-012121-095340
10.1016/j.avrs.2022.100027
10.1111/j.2041-210X.2011.00169.x
10.1093/sysbio/syw030
10.1038/ncomms12709
10.1038/44766
10.1073/pnas.1423041112
10.1126/science.1157704
10.1016/j.ympev.2015.10.027
10.1126/sciadv.1501005
10.1093/bioinformatics/bty839
10.1093/molbev/msaa191
10.1371/journal.pone.0163962
10.1093/molbev/msz189
10.1080/10635150290102339
10.1093/molbev/msq089
10.1111/zsc.12213
10.1126/science.aab1062
10.1093/molbev/msw079
10.1038/s41586-021-04341-1
10.1038/nature21074
10.1007/BF00897326
10.1093/molbev/msj124
10.1093/bioinformatics/btu181
10.1093/sysbio/syz019
10.1111/bij.12765
10.1093/bioinformatics/btt128
10.1093/gbe/evac129
10.1093/sysbio/syab075
10.1073/pnas.2319696121
10.1186/s12864-018-4620-2
10.1093/molbev/msm088
10.1371/journal.pone.0182238
10.1016/j.cub.2020.03.060
10.1038/381226a0
10.1093/sysbio/syu005
10.1093/sysbio/syx041
10.3390/genes9030132
10.1073/pnas.1813206116
10.1111/ele.13898
10.1101/2022.10.21.513146
10.1007/978-3-030-16477-5_6
10.17894/ucph.85624f66-c8e5-4b89-8e8a-fe984ca89e4a
10.1007/978-3-030-87645-6
10.1093/bioinformatics/btz211
10.1038/s41586-019-1693-2
10.5061/dryad.fbg79cnw7
10.1073/pnas.2319506121
10.5524/101041
ContentType Journal Article
Copyright This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2024
2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.
Copyright_xml – notice: This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2024
– notice: 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.
DBID C6C
AAYXX
CITATION
NPM
7X8
5PM
DOI 10.1038/s41586-024-07323-1
DatabaseName Springer Nature OA Free Journals
CrossRef
PubMed
MEDLINE - Academic
PubMed Central (Full Participant titles)
DatabaseTitle CrossRef
PubMed
MEDLINE - Academic
DatabaseTitleList

CrossRef
PubMed
MEDLINE - Academic
Database_xml – sequence: 1
  dbid: C6C
  name: Springer Nature OA Free Journals
  url: http://www.springeropen.com/
  sourceTypes: Publisher
– sequence: 2
  dbid: NPM
  name: PubMed
  url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  sourceTypes: Index Database
DeliveryMethod fulltext_linktorsrc
Discipline Sciences (General)
Physics
EISSN 1476-4687
EndPage 860
ExternalDocumentID PMC11111414
38560995
10_1038_s41586_024_07323_1
Genre Journal Article
GroupedDBID ---
--Z
-DZ
-ET
-~X
.55
.CO
.XZ
07C
0R~
123
186
1OL
29M
2KS
39C
53G
5RE
6TJ
70F
7RV
85S
8WZ
97F
A6W
A7Z
AAEEF
AAHBH
AAHTB
AAIKC
AAKAB
AAMNW
AASDW
AAYEP
AAYZH
AAZLF
ABDQB
ABFSI
ABIVO
ABJNI
ABLJU
ABOCM
ABPEJ
ABPPZ
ABWJO
ABZEH
ACBEA
ACBWK
ACGFO
ACGFS
ACGOD
ACIWK
ACKOT
ACMJI
ACNCT
ACPRK
ACWUS
ADBBV
ADFRT
ADUKH
AENEX
AFBBN
AFFNX
AFLOW
AFRAH
AFSHS
AGAYW
AGHSJ
AGHTU
AGOIJ
AGSOS
AHMBA
AHSBF
AIDUJ
ALFFA
ALIPV
ALMA_UNASSIGNED_HOLDINGS
AMTXH
ARAPS
ARMCB
ASPBG
ATCPS
ATWCN
AVWKF
AXYYD
AZFZN
BENPR
BHPHI
BIN
BKKNO
C6C
CJ0
CS3
DU5
E.-
E.L
EAP
EBS
EE.
EPS
EXGXG
F5P
FAC
FEDTE
FQGFK
FSGXE
HCIFZ
HG6
HVGLF
HZ~
IAO
ICQ
IEA
IEP
IGS
IH2
IHR
INH
IOF
IPY
KOO
L7B
LGEZI
LOTEE
LSO
M0K
M2O
M7P
N9A
NADUK
NEPJS
NXXTH
O9-
OBC
ODYON
OES
OHH
OMK
OVD
P2P
PKN
PV9
RND
RNS
RNT
RNTTT
RXW
SC5
SHXYY
SIXXV
SJN
SNYQT
SOJ
TAE
TAOOD
TBHMF
TDRGL
TEORI
TN5
TSG
TWZ
U5U
UIG
UKR
UMD
UQL
VQA
VVN
WH7
X7M
XIH
XKW
XZL
Y6R
YAE
YCJ
YFH
YIF
YIN
YJ6
YNT
YOC
YQT
YR2
YR5
YXB
YZZ
Z5M
ZCA
~02
~88
~KM
1VR
2XV
41X
7X2
7X7
7XC
88E
88I
8AF
8AO
8C1
8CJ
8FE
8FG
8FH
8FI
8FJ
8G5
8R4
8R5
97L
AARCD
AAYXX
ABFSG
ABJCF
ABUWG
ACMFV
ACSTC
AEUYN
AEZWR
AFANA
AFHIU
AFKRA
AHWEU
AIXLP
ALPWD
ATHPR
AZQEC
BBNVY
BCU
BEC
BGLVJ
BKEYQ
BKSAR
BPHCQ
BVXVI
CCPQU
CITATION
D1I
D1J
D1K
DWQXO
EMH
EX3
FYUFA
GNUQQ
GUQSH
HMCUK
INR
ISR
K6-
KB.
L6V
LK5
LK8
M1P
M2M
M2P
M7R
M7S
NAPCQ
NFIDA
P62
PATMY
PCBAR
PDBOC
PHGZM
PHGZT
PQQKQ
PROAC
PSQYO
PSYQQ
PTHSS
PYCSY
Q2X
R05
S0X
SJFOW
UKHRP
WOW
~7V
NPM
PJZUB
PPXIY
PQGLB
7X8
5PM
AFKWF
TUS
ID FETCH-LOGICAL-a470t-f6c058c4b3cc0dbf96d59195ae73a9e9fc0aecf2a026aa609110c8f6b2aee6ae3
IEDL.DBID C6C
ISSN 0028-0836
1476-4687
IngestDate Thu Aug 21 18:35:03 EDT 2025
Fri Jul 11 09:44:44 EDT 2025
Mon Jul 21 06:07:16 EDT 2025
Thu Apr 24 23:11:33 EDT 2025
Tue Jul 01 02:58:53 EDT 2025
Fri Feb 21 02:39:35 EST 2025
IsDoiOpenAccess true
IsOpenAccess true
IsPeerReviewed true
IsScholarly true
Issue 8013
Language English
License 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
LinkModel DirectLink
MergedId FETCHMERGED-LOGICAL-a470t-f6c058c4b3cc0dbf96d59195ae73a9e9fc0aecf2a026aa609110c8f6b2aee6ae3
Notes ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ORCID 0000-0001-5233-6030
0000-0002-8926-5974
0000-0002-0515-0628
0000-0001-7394-2718
0000-0002-5479-1974
0000-0001-6009-9581
0000-0001-6868-227X
0000-0002-9441-1155
0000-0003-1406-5246
0000-0002-1864-4221
0000-0003-1643-5212
0000-0002-9181-8689
0000-0002-9468-5973
0000-0003-4541-5974
0000-0002-6139-7828
0000-0003-0353-0691
0000-0003-1589-6885
0000-0001-7587-8342
0000-0003-2429-6179
0000-0002-5805-7195
0000-0002-2472-8317
0000-0003-2093-0056
0000-0002-5028-1790
0000-0002-3076-0006
0000-0002-2462-7348
0000-0001-9920-8167
0000-0003-0790-3600
0000-0001-6860-1521
0000-0002-0361-2307
0000-0001-5410-1518
0000-0003-3288-6769
0000-0002-2805-4698
0000-0002-1943-0217
0000-0001-7499-6224
0000-0002-1328-1732
0000-0002-7493-3917
0000-0003-2433-5553
0000-0003-4585-0300
OpenAccessLink https://www.nature.com/articles/s41586-024-07323-1
PMID 38560995
PQID 3031134381
PQPubID 23479
PageCount 10
ParticipantIDs pubmedcentral_primary_oai_pubmedcentral_nih_gov_11111414
proquest_miscellaneous_3031134381
pubmed_primary_38560995
crossref_citationtrail_10_1038_s41586_024_07323_1
crossref_primary_10_1038_s41586_024_07323_1
springer_journals_10_1038_s41586_024_07323_1
ProviderPackageCode CITATION
AAYXX
PublicationCentury 2000
PublicationDate 2024-05-23
PublicationDateYYYYMMDD 2024-05-23
PublicationDate_xml – month: 05
  year: 2024
  text: 2024-05-23
  day: 23
PublicationDecade 2020
PublicationPlace London
PublicationPlace_xml – name: London
– name: England
PublicationSubtitle International weekly journal of science
PublicationTitle Nature (London)
PublicationTitleAbbrev Nature
PublicationTitleAlternate Nature
PublicationYear 2024
Publisher Nature Publishing Group UK
Publisher_xml – name: Nature Publishing Group UK
References Slack (CR79) 2006; 23
Springer, Gatesy (CR53) 2018; 9
Zhang (CR28) 2015; 522
Chen, Liang, Zhang (CR29) 2017; 9
Iwaniuk, Nelson (CR98) 2002; 80
CR34
CR33
Kozlov, Darriba, Flouri, Morel, Stamatakis (CR61) 2019; 35
Rivas-González (CR90) 2023; 380
Revell (CR96) 2012; 3
Mai, Sayyari, Mirarab (CR71) 2017; 12
Harvey (CR37) 2020; 370
Thorne, Kishino, Painter (CR78) 1998; 15
Nguyen, Schmidt, von Haeseler, Minh (CR62) 2015; 32
CR48
Jeffroy, Brinkmann, Delsuc, Philippe (CR7) 2006; 22
Dos Reis, Zhu, Yang (CR81) 2014; 63
Bravo (CR10) 2019; 7
Foster (CR87) 2004; 53
Plummer, Best, Cowles, Vines (CR102) 2006; 6
Feduccia (CR21) 2003; 18
Nabhan, Sarkar (CR40) 2012; 13
Mitchell, Cooper, Phillips (CR17) 2015; 349
Sangster (CR50) 2022; 13
Kuhl (CR3) 2021; 38
Feng (CR4) 2020; 587
Mendes, Hahn (CR91) 2016; 65
Reddy (CR12) 2017; 66
Haag, Höhler, Bettisworth, Stamatakis (CR84) 2022; 39
Parham (CR72) 2012; 61
Tobias (CR94) 2022; 25
Sayyari, Mirarab (CR66) 2016; 33
Pick (CR43) 2010; 27
Hedtke, Townsend, Hillis (CR27) 2006; 55
Álvarez-Carretero (CR69) 2022; 602
Prum (CR2) 2015; 526
Lozano-Fernandez (CR42) 2022; 14
Solís-Lemus, Yang, Ané (CR36) 2016; 65
Katoh, Misawa, Kuma, Miyata (CR56) 2002; 30
Mirarab (CR54) 2015; 22
Duchêne, Mather, Van Der Wal, Ho (CR89) 2022; 71
Junier, Zdobnov (CR64) 2010; 26
Braun, Kimball (CR13) 2021; 2
Berv, Field (CR47) 2018; 67
Western, Ssemakula (CR46) 1982; 54
Sayyari, Whitfield, Mirarab (CR67) 2018; 122
Yang (CR77) 2007; 24
(CR85) 2004; 432
Pagel (CR93) 1999; 401
Anisimova, Gascuel (CR63) 2006; 55
CR65
Oliveros (CR24) 2019; 116
Hickey, Paten, Earl, Zerbino, Haussler (CR52) 2013; 29
Mai, Mirarab (CR55) 2018; 19
Walker, Smith, Hodel, Moyroud (CR92) 2022; 71
Suh, Smeds, Ellegren (CR32) 2015; 13
Yang, Rannala (CR80) 2006; 23
Renne (CR19) 2013; 339
Suh (CR14) 2016; 45
CR76
Wu (CR11) 2024; 121
Faircloth (CR58) 2016; 32
Sayyari, Mirarab (CR35) 2018; 9
Stekhoven, Bühlmann (CR99) 2012; 28
CR6
Hedges, Parker, Sibley, Kumar (CR20) 1996; 381
Armstrong (CR51) 2020; 587
Pattengale, Alipour, Bininda-Emonds, Moret, Stamatakis (CR68) 2010; 17
CR9
Ho, Ané (CR95) 2014; 63
Heath, Hedtke, Hillis (CR41) 2008; 46
Zwickl, Hillis (CR26) 2002; 51
Elferink, van As, Veenendaal, Crooijmans, Groenen (CR86) 2010; 11
Claramunt, Cracraft (CR23) 2015; 1
Cooney (CR104) 2017; 542
Mirarab, Nakhleh, Warnow (CR31) 2021; 52
Cracraft (CR18) 2015; 349
Bogdanowicz, Giaro, Wróbel (CR82) 2012; 8
Pennell (CR103) 2014; 30
Ksepka (CR49) 2020; 30
Claramunt (CR73) 2022; 13
CR15
Morel, Kozlov, Stamatakis (CR59) 2019; 35
Darriba (CR60) 2020; 37
CR97
Philippe (CR8) 2011; 9
Minh (CR70) 2020; 37
Katoh, Standley (CR57) 2016; 32
Marshall (CR74) 2019; 10
Hinchliff (CR5) 2015; 112
Pagel, Meade, Barker (CR101) 2004; 53
Jarvis (CR1) 2014; 346
McCormack (CR25) 2013; 8
Yoder (CR45) 2010; 23
Smaers, Mongle, Kandler (CR100) 2016; 118
Moyle (CR38) 2016; 7
Strauss, Sadler (CR75) 1989; 21
Hackett (CR16) 2008; 320
Edwards (CR30) 2016; 94
CR22
CR105
Houde, Braun, Zhou (CR44) 2020; 12
Shen, Le, Li, Hu (CR83) 2016; 11
Cloutier (CR39) 2019; 68
CR108
Duchêne, Duchêne, Ho (CR88) 2017; 34
CR106
CR107
A Suh (7323_CR32) 2015; 13
7323_CR9
E Sayyari (7323_CR35) 2018; 9
RG Moyle (7323_CR38) 2016; 7
JL Thorne (7323_CR78) 1998; 15
TA Heath (7323_CR41) 2008; 46
J Armstrong (7323_CR51) 2020; 587
7323_CR6
ND Pattengale (7323_CR68) 2010; 17
JF Walker (7323_CR92) 2022; 71
7323_CR33
7323_CR34
MW Pennell (7323_CR103) 2014; 30
W Shen (7323_CR83) 2016; 11
International Chicken Genome Sequencing Consortium. (7323_CR85) 2004; 432
MG Harvey (7323_CR37) 2020; 370
S Mirarab (7323_CR54) 2015; 22
SM Hedtke (7323_CR27) 2006; 55
L-T Nguyen (7323_CR62) 2015; 32
A Cloutier (7323_CR39) 2019; 68
D Western (7323_CR46) 1982; 54
U Mai (7323_CR71) 2017; 12
JB Smaers (7323_CR100) 2016; 118
E Sayyari (7323_CR66) 2016; 33
CE Hinchliff (7323_CR5) 2015; 112
H Philippe (7323_CR8) 2011; 9
P Houde (7323_CR44) 2020; 12
K Katoh (7323_CR57) 2016; 32
7323_CR22
J Cracraft (7323_CR18) 2015; 349
D Strauss (7323_CR75) 1989; 21
7323_CR97
DT Ksepka (7323_CR49) 2020; 30
A Feduccia (7323_CR21) 2003; 18
S Claramunt (7323_CR73) 2022; 13
KE Slack (7323_CR79) 2006; 23
A Suh (7323_CR14) 2016; 45
LST Ho (7323_CR95) 2014; 63
CR Cooney (7323_CR104) 2017; 542
JS Berv (7323_CR47) 2018; 67
7323_CR15
GA Bravo (7323_CR10) 2019; 7
G Sangster (7323_CR50) 2022; 13
EL Braun (7323_CR13) 2021; 2
B Morel (7323_CR59) 2019; 35
BC Faircloth (7323_CR58) 2016; 32
G Hickey (7323_CR52) 2013; 29
O Jeffroy (7323_CR7) 2006; 22
LJ Revell (7323_CR96) 2012; 3
DJ Zwickl (7323_CR26) 2002; 51
DA Duchêne (7323_CR89) 2022; 71
RO Prum (7323_CR2) 2015; 526
SJ Hackett (7323_CR16) 2008; 320
S Wu (7323_CR11) 2024; 121
E Sayyari (7323_CR67) 2018; 122
SV Edwards (7323_CR30) 2016; 94
S Mirarab (7323_CR31) 2021; 52
7323_CR76
U Mai (7323_CR55) 2018; 19
SB Hedges (7323_CR20) 1996; 381
JE McCormack (7323_CR25) 2013; 8
D Bogdanowicz (7323_CR82) 2012; 8
AM Kozlov (7323_CR61) 2019; 35
S Claramunt (7323_CR23) 2015; 1
JB Yoder (7323_CR45) 2010; 23
S Álvarez-Carretero (7323_CR69) 2022; 602
7323_CR105
7323_CR106
7323_CR107
S Reddy (7323_CR12) 2017; 66
FK Mendes (7323_CR91) 2016; 65
7323_CR65
J Lozano-Fernandez (7323_CR42) 2022; 14
7323_CR108
S Feng (7323_CR4) 2020; 587
D Darriba (7323_CR60) 2020; 37
Z Yang (7323_CR80) 2006; 23
K Katoh (7323_CR56) 2002; 30
J Haag (7323_CR84) 2022; 39
PG Foster (7323_CR87) 2004; 53
M Plummer (7323_CR102) 2006; 6
JA Tobias (7323_CR94) 2022; 25
AR Nabhan (7323_CR40) 2012; 13
BQ Minh (7323_CR70) 2020; 37
G Zhang (7323_CR28) 2015; 522
CR Marshall (7323_CR74) 2019; 10
MG Elferink (7323_CR86) 2010; 11
KS Pick (7323_CR43) 2010; 27
JF Parham (7323_CR72) 2012; 61
CH Oliveros (7323_CR24) 2019; 116
T Junier (7323_CR64) 2010; 26
M Pagel (7323_CR93) 1999; 401
KJ Mitchell (7323_CR17) 2015; 349
M Pagel (7323_CR101) 2004; 53
H Kuhl (7323_CR3) 2021; 38
MS Springer (7323_CR53) 2018; 9
M Dos Reis (7323_CR81) 2014; 63
M Anisimova (7323_CR63) 2006; 55
I Rivas-González (7323_CR90) 2023; 380
AN Iwaniuk (7323_CR98) 2002; 80
PR Renne (7323_CR19) 2013; 339
M-Y Chen (7323_CR29) 2017; 9
DJ Stekhoven (7323_CR99) 2012; 28
C Solís-Lemus (7323_CR36) 2016; 65
ED Jarvis (7323_CR1) 2014; 346
7323_CR48
Z Yang (7323_CR77) 2007; 24
DA Duchêne (7323_CR88) 2017; 34
References_xml – volume: 18
  start-page: 172
  year: 2003
  end-page: 176
  ident: CR21
  article-title: ‘Big bang’ for tertiary birds?
  publication-title: Trends Ecol. Evol.
  doi: 10.1016/S0169-5347(03)00017-X
– ident: CR22
– volume: 22
  start-page: 377
  year: 2015
  end-page: 386
  ident: CR54
  article-title: PASTA: ultra-large multiple sequence alignment for nucleotide and amino-acid sequences
  publication-title: J. Comput. Biol.
  doi: 10.1089/cmb.2014.0156
– ident: CR97
– volume: 37
  start-page: 1530
  year: 2020
  end-page: 1534
  ident: CR70
  article-title: IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msaa015
– volume: 53
  start-page: 485
  year: 2004
  end-page: 495
  ident: CR87
  article-title: Modeling compositional heterogeneity
  publication-title: Syst. Biol.
  doi: 10.1080/10635150490445779
– volume: 8
  start-page: e54848
  year: 2013
  ident: CR25
  article-title: A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing
  publication-title: PLoS ONE
  doi: 10.1371/journal.pone.0054848
– volume: 26
  start-page: 1669
  year: 2010
  end-page: 1670
  ident: CR64
  article-title: The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btq243
– volume: 17
  start-page: 337
  year: 2010
  end-page: 354
  ident: CR68
  article-title: How many bootstrap replicates are necessary?
  publication-title: J. Comput. Biol.
  doi: 10.1089/cmb.2009.0179
– ident: CR106
– volume: 13
  start-page: e1002224
  year: 2015
  ident: CR32
  article-title: The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds
  publication-title: PLoS Biol.
  doi: 10.1371/journal.pbio.1002224
– volume: 23
  start-page: 212
  year: 2006
  end-page: 226
  ident: CR80
  article-title: Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msj024
– volume: 13
  start-page: 2331
  year: 2022
  end-page: 2338
  ident: CR73
  article-title: CladeDate: calibration information generator for divergence time estimation
  publication-title: Methods Ecol. Evol.
  doi: 10.1111/2041-210X.13977
– volume: 34
  start-page: 1529
  year: 2017
  end-page: 1534
  ident: CR88
  article-title: New statistical criteria detect phylogenetic bias caused by compositional heterogeneity
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msx092
– volume: 65
  start-page: 711
  year: 2016
  end-page: 721
  ident: CR91
  article-title: Gene tree discordance causes apparent substitution rate variation
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syw018
– volume: 522
  start-page: 34
  year: 2015
  ident: CR28
  article-title: Genomics: bird sequencing project takes off
  publication-title: Nature
  doi: 10.1038/522034d
– volume: 370
  start-page: 1343
  year: 2020
  end-page: 1348
  ident: CR37
  article-title: The evolution of a tropical biodiversity hotspot
  publication-title: Science
  doi: 10.1126/science.aaz6970
– volume: 28
  start-page: 112
  year: 2012
  end-page: 118
  ident: CR99
  article-title: MissForest–non-parametric missing value imputation for mixed-type data
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btr597
– volume: 7
  start-page: e6399
  year: 2019
  ident: CR10
  article-title: Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
  publication-title: PeerJ
  doi: 10.7717/peerj.6399
– volume: 349
  start-page: 1460
  year: 2015
  ident: CR18
  article-title: Response to Comment on ‘Whole-genome analyses resolve early branches in the tree of life of modern birds’
  publication-title: Science
  doi: 10.1126/science.aab1578
– volume: 53
  start-page: 673
  year: 2004
  end-page: 684
  ident: CR101
  article-title: Bayesian estimation of ancestral character states on phylogenies
  publication-title: Syst. Biol.
  doi: 10.1080/10635150490522232
– volume: 55
  start-page: 539
  year: 2006
  end-page: 552
  ident: CR63
  article-title: Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative
  publication-title: Syst. Biol.
  doi: 10.1080/10635150600755453
– volume: 122
  start-page: 110
  year: 2018
  end-page: 115
  ident: CR67
  article-title: DiscoVista: interpretable visualizations of gene tree discordance
  publication-title: Mol. Phylogenet. Evol.
  doi: 10.1016/j.ympev.2018.01.019
– volume: 67
  start-page: 1
  year: 2018
  end-page: 13
  ident: CR47
  article-title: Genomic signature of an avian Lilliput effect across the K-Pg extinction
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syx064
– volume: 9
  start-page: 123
  year: 2018
  ident: CR53
  article-title: Delimiting coalescence genes (C-genes) in phylogenomic data sets
  publication-title: Genes
  doi: 10.3390/genes9030123
– volume: 587
  start-page: 252
  year: 2020
  end-page: 257
  ident: CR4
  article-title: Dense sampling of bird diversity increases power of comparative genomics
  publication-title: Nature
  doi: 10.1038/s41586-020-2873-9
– volume: 526
  start-page: 569
  year: 2015
  end-page: 573
  ident: CR2
  article-title: A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
  publication-title: Nature
  doi: 10.1038/nature15697
– volume: 12
  start-page: 164
  year: 2020
  ident: CR44
  article-title: Deep-time demographic inference suggests ecological release as driver of neoavian adaptive radiation
  publication-title: Diversity
  doi: 10.3390/d12040164
– volume: 39
  start-page: msac254
  year: 2022
  ident: CR84
  article-title: From easy to hopeless-predicting the difficulty of phylogenetic analyses
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msac254
– volume: 11
  year: 2010
  ident: CR86
  article-title: Regional differences in recombination hotspots between two chicken populations
  publication-title: BMC Genet.
  doi: 10.1186/1471-2156-11-11
– volume: 71
  start-page: 943
  year: 2022
  end-page: 958
  ident: CR92
  article-title: Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic data sets
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syab052
– volume: 339
  start-page: 684
  year: 2013
  end-page: 687
  ident: CR19
  article-title: Time scales of critical events around the Cretaceous-Paleogene boundary
  publication-title: Science
  doi: 10.1126/science.1230492
– volume: 23
  start-page: 1581
  year: 2010
  end-page: 1596
  ident: CR45
  article-title: Ecological opportunity and the origin of adaptive radiations
  publication-title: J. Evol. Biol.
  doi: 10.1111/j.1420-9101.2010.02029.x
– volume: 63
  start-page: 555
  year: 2014
  end-page: 565
  ident: CR81
  article-title: The impact of the rate prior on Bayesian estimation of divergence times with multiple loci
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syu020
– ident: CR33
– volume: 2
  start-page: 1
  year: 2021
  end-page: 22
  ident: CR13
  article-title: Data types and the phylogeny of Neoaves
  publication-title: Birds
  doi: 10.3390/birds2010001
– volume: 432
  start-page: 695
  year: 2004
  end-page: 716
  ident: CR85
  article-title: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
  publication-title: Nature
  doi: 10.1038/nature03154
– ident: CR6
– volume: 10
  start-page: 1049
  year: 2019
  ident: CR74
  article-title: Using the fossil record to evaluate timetree timescales
  publication-title: Front. Genet.
  doi: 10.3389/fgene.2019.01049
– volume: 46
  start-page: 239
  year: 2008
  end-page: 257
  ident: CR41
  article-title: Taxon sampling and the accuracy of phylogenetic analyses
  publication-title: J. Syst. Evol.
– volume: 15
  start-page: 1647
  year: 1998
  end-page: 1657
  ident: CR78
  article-title: Estimating the rate of evolution of the rate of molecular evolution
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/oxfordjournals.molbev.a025892
– volume: 80
  start-page: 16
  year: 2002
  end-page: 23
  ident: CR98
  article-title: Can endocranial volume be used as an estimate of brain size in birds?
  publication-title: Can. J. Zool.
  doi: 10.1139/z01-204
– ident: CR108
– volume: 346
  start-page: 1320
  year: 2014
  end-page: 1331
  ident: CR1
  article-title: Whole-genome analyses resolve early branches in the tree of life of modern birds
  publication-title: Science
  doi: 10.1126/science.1253451
– volume: 587
  start-page: 246
  year: 2020
  end-page: 251
  ident: CR51
  article-title: Progressive Cactus is a multiple-genome aligner for the thousand-genome era
  publication-title: Nature
  doi: 10.1038/s41586-020-2871-y
– volume: 32
  start-page: 268
  year: 2015
  end-page: 274
  ident: CR62
  article-title: IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msu300
– volume: 61
  start-page: 346
  year: 2012
  end-page: 359
  ident: CR72
  article-title: Best practices for justifying fossil calibrations
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syr107
– volume: 55
  start-page: 522
  year: 2006
  end-page: 529
  ident: CR27
  article-title: Resolution of phylogenetic conflict in large data sets by increased taxon sampling
  publication-title: Syst. Biol.
  doi: 10.1080/10635150600697358
– volume: 54
  start-page: 281
  year: 1982
  end-page: 290
  ident: CR46
  article-title: Life history patterns in birds and mammals and their evolutionary interpretation
  publication-title: Oecologia
  doi: 10.1007/BF00379994
– volume: 32
  start-page: 786
  year: 2016
  end-page: 788
  ident: CR58
  article-title: PHYLUCE is a software package for the analysis of conserved genomic loci
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btv646
– volume: 35
  start-page: 4453
  year: 2019
  end-page: 4455
  ident: CR61
  article-title: RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btz305
– volume: 8
  start-page: EBO.S9657
  year: 2012
  ident: CR82
  article-title: TreeCmp: comparison of trees in polynomial time
  publication-title: Evol. Bioinform. Online
  doi: 10.4137/EBO.S9657
– volume: 380
  start-page: eabn4409
  year: 2023
  ident: CR90
  article-title: Pervasive incomplete lineage sorting illuminates speciation and selection in primates
  publication-title: Science
  doi: 10.1126/science.abn4409
– volume: 13
  start-page: 122
  year: 2012
  end-page: 134
  ident: CR40
  article-title: The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
  publication-title: Brief. Bioinform.
  doi: 10.1093/bib/bbr014
– volume: 30
  start-page: 3059
  year: 2002
  end-page: 3066
  ident: CR56
  article-title: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
  publication-title: Nucleic Acids Res.
  doi: 10.1093/nar/gkf436
– volume: 9
  start-page: 1998
  year: 2017
  end-page: 2012
  ident: CR29
  article-title: Phylogenomic resolution of the phylogeny of laurasiatherian mammals: exploring phylogenetic signals within coding and noncoding sequences
  publication-title: Genome Biol. Evol.
  doi: 10.1093/gbe/evx147
– volume: 32
  start-page: 1933
  year: 2016
  end-page: 1942
  ident: CR57
  article-title: A simple method to control over-alignment in the MAFFT multiple sequence alignment program
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btw108
– volume: 22
  start-page: 225
  year: 2006
  end-page: 231
  ident: CR7
  article-title: Phylogenomics: the beginning of incongruence?
  publication-title: Trends Genet.
  doi: 10.1016/j.tig.2006.02.003
– volume: 9
  start-page: e1000602
  year: 2011
  ident: CR8
  article-title: Resolving difficult phylogenetic questions: why more sequences are not enough
  publication-title: PLoS Biol.
  doi: 10.1371/journal.pbio.1000602
– volume: 52
  start-page: 247
  year: 2021
  end-page: 268
  ident: CR31
  article-title: Multispecies coalescent: theory and applications in phylogenetics
  publication-title: Annu. Rev. Ecol. Evol. Syst.
  doi: 10.1146/annurev-ecolsys-012121-095340
– volume: 13
  year: 2022
  ident: CR50
  article-title: Phylogenetic definitions for 25 higher-level clade names of birds
  publication-title: Avian Res.
  doi: 10.1016/j.avrs.2022.100027
– volume: 3
  start-page: 217
  year: 2012
  end-page: 223
  ident: CR96
  article-title: phytools: An R package for phylogenetic comparative biology (and other things)
  publication-title: Methods Ecol. Evol.
  doi: 10.1111/j.2041-210X.2011.00169.x
– volume: 65
  start-page: 843
  year: 2016
  end-page: 851
  ident: CR36
  article-title: Inconsistency of species tree methods under gene flow
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syw030
– volume: 7
  year: 2016
  ident: CR38
  article-title: Tectonic collision and uplift of Wallacea triggered the global songbird radiation
  publication-title: Nat. Commun.
  doi: 10.1038/ncomms12709
– volume: 401
  start-page: 877
  year: 1999
  end-page: 884
  ident: CR93
  article-title: Inferring the historical patterns of biological evolution
  publication-title: Nature
  doi: 10.1038/44766
– volume: 112
  start-page: 12764
  year: 2015
  end-page: 12769
  ident: CR5
  article-title: Synthesis of phylogeny and taxonomy into a comprehensive tree of life
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1423041112
– volume: 320
  start-page: 1763
  year: 2008
  end-page: 1768
  ident: CR16
  article-title: A phylogenomic study of birds reveals their evolutionary history
  publication-title: Science
  doi: 10.1126/science.1157704
– volume: 94
  start-page: 447
  year: 2016
  end-page: 462
  ident: CR30
  article-title: Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics
  publication-title: Mol. Phylogenet. Evol.
  doi: 10.1016/j.ympev.2015.10.027
– ident: CR15
– volume: 1
  start-page: e1501005
  year: 2015
  ident: CR23
  article-title: A new time tree reveals Earth history’s imprint on the evolution of modern birds
  publication-title: Sci. Adv.
  doi: 10.1126/sciadv.1501005
– volume: 35
  start-page: 1771
  year: 2019
  end-page: 1773
  ident: CR59
  article-title: ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bty839
– volume: 38
  start-page: 108
  year: 2021
  end-page: 127
  ident: CR3
  article-title: An unbiased molecular approach using 3’-UTRs resolves the avian family-level Tree of Life
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msaa191
– ident: CR9
– volume: 11
  start-page: e0163962
  year: 2016
  ident: CR83
  article-title: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  publication-title: PLoS ONE
  doi: 10.1371/journal.pone.0163962
– volume: 37
  start-page: 291
  year: 2020
  end-page: 294
  ident: CR60
  article-title: ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msz189
– volume: 51
  start-page: 588
  year: 2002
  end-page: 598
  ident: CR26
  article-title: Increased taxon sampling greatly reduces phylogenetic error
  publication-title: Syst. Biol.
  doi: 10.1080/10635150290102339
– ident: CR105
– volume: 27
  start-page: 1983
  year: 2010
  end-page: 1987
  ident: CR43
  article-title: Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msq089
– volume: 45
  start-page: 50
  year: 2016
  end-page: 62
  ident: CR14
  article-title: The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves
  publication-title: Zool. Scr.
  doi: 10.1111/zsc.12213
– volume: 349
  start-page: 1460
  year: 2015
  ident: CR17
  article-title: Comment on ‘Whole-genome analyses resolve early branches in the tree of life of modern birds’
  publication-title: Science
  doi: 10.1126/science.aab1062
– volume: 33
  start-page: 1654
  year: 2016
  end-page: 1668
  ident: CR66
  article-title: Fast coalescent-based computation of local branch support from quartet frequencies
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msw079
– volume: 602
  start-page: 263
  year: 2022
  end-page: 267
  ident: CR69
  article-title: A species-level timeline of mammal evolution integrating phylogenomic data
  publication-title: Nature
  doi: 10.1038/s41586-021-04341-1
– volume: 542
  start-page: 344
  year: 2017
  end-page: 347
  ident: CR104
  article-title: Mega-evolutionary dynamics of the adaptive radiation of birds
  publication-title: Nature
  doi: 10.1038/nature21074
– volume: 21
  start-page: 411
  year: 1989
  end-page: 427
  ident: CR75
  article-title: Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges
  publication-title: Math. Geol.
  doi: 10.1007/BF00897326
– volume: 23
  start-page: 1144
  year: 2006
  end-page: 1155
  ident: CR79
  article-title: Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msj124
– volume: 30
  start-page: 2216
  year: 2014
  end-page: 2218
  ident: CR103
  article-title: geiger v2.0: An expanded suite of methods for fitting macroevolutionary models to phylogenetic trees
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btu181
– volume: 68
  start-page: 937
  year: 2019
  end-page: 955
  ident: CR39
  article-title: Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syz019
– volume: 118
  start-page: 78
  year: 2016
  end-page: 94
  ident: CR100
  article-title: A multiple variance Brownian motion framework for estimating variable rates and inferring ancestral states
  publication-title: Biol. J. Linn. Soc. Lond.
  doi: 10.1111/bij.12765
– volume: 29
  start-page: 1341
  year: 2013
  end-page: 1342
  ident: CR52
  article-title: HAL: a hierarchical format for storing and analyzing multiple genome alignments
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btt128
– volume: 14
  start-page: evac129
  year: 2022
  ident: CR42
  article-title: A practical guide to design and assess a phylogenomic study
  publication-title: Genome Biol. Evol.
  doi: 10.1093/gbe/evac129
– volume: 71
  start-page: 676
  year: 2022
  end-page: 689
  ident: CR89
  article-title: Excluding loci with substitution saturation improves inferences from phylogenomic data
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syab075
– ident: CR48
– volume: 6
  start-page: 7
  year: 2006
  end-page: 11
  ident: CR102
  article-title: CODA: convergence diagnosis and output analysis for MCMC
  publication-title: Rnews
– volume: 121
  start-page: e2319696121
  year: 2024
  ident: CR11
  article-title: Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.2319696121
– ident: CR65
– volume: 19
  year: 2018
  ident: CR55
  article-title: TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees
  publication-title: BMC Genomics
  doi: 10.1186/s12864-018-4620-2
– volume: 24
  start-page: 1586
  year: 2007
  end-page: 1591
  ident: CR77
  article-title: PAML 4: phylogenetic analysis by maximum likelihood
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msm088
– volume: 12
  start-page: e0182238
  year: 2017
  ident: CR71
  article-title: Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction
  publication-title: PLoS ONE
  doi: 10.1371/journal.pone.0182238
– volume: 30
  start-page: 2026
  year: 2020
  end-page: 2036
  ident: CR49
  article-title: Tempo and pattern of avian brain size evolution
  publication-title: Curr. Biol.
  doi: 10.1016/j.cub.2020.03.060
– volume: 381
  start-page: 226
  year: 1996
  end-page: 229
  ident: CR20
  article-title: Continental breakup and the ordinal diversification of birds and mammals
  publication-title: Nature
  doi: 10.1038/381226a0
– ident: CR34
– ident: CR76
– volume: 63
  start-page: 397
  year: 2014
  end-page: 408
  ident: CR95
  article-title: A linear-time algorithm for Gaussian and non-Gaussian trait evolution models
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syu005
– ident: CR107
– volume: 66
  start-page: 857
  year: 2017
  end-page: 879
  ident: CR12
  article-title: Why do phylogenomic data sets yield conflicting trees? Data type influences the avian Tree of Life more than taxon sampling
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syx041
– volume: 9
  start-page: 132
  year: 2018
  ident: CR35
  article-title: Testing for polytomies in phylogenetic species trees using quartet frequencies
  publication-title: Genes
  doi: 10.3390/genes9030132
– volume: 116
  start-page: 7916
  year: 2019
  end-page: 7925
  ident: CR24
  article-title: Earth history and the passerine superradiation
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1813206116
– volume: 25
  start-page: 581
  year: 2022
  end-page: 597
  ident: CR94
  article-title: AVONET: morphological, ecological and geographical data for all birds
  publication-title: Ecol. Lett.
  doi: 10.1111/ele.13898
– volume: 9
  start-page: e1000602
  year: 2011
  ident: 7323_CR8
  publication-title: PLoS Biol.
  doi: 10.1371/journal.pbio.1000602
– volume: 370
  start-page: 1343
  year: 2020
  ident: 7323_CR37
  publication-title: Science
  doi: 10.1126/science.aaz6970
– volume: 112
  start-page: 12764
  year: 2015
  ident: 7323_CR5
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1423041112
– volume: 65
  start-page: 711
  year: 2016
  ident: 7323_CR91
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syw018
– volume: 71
  start-page: 676
  year: 2022
  ident: 7323_CR89
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syab075
– volume: 13
  start-page: 122
  year: 2012
  ident: 7323_CR40
  publication-title: Brief. Bioinform.
  doi: 10.1093/bib/bbr014
– volume: 320
  start-page: 1763
  year: 2008
  ident: 7323_CR16
  publication-title: Science
  doi: 10.1126/science.1157704
– volume: 37
  start-page: 291
  year: 2020
  ident: 7323_CR60
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msz189
– volume: 71
  start-page: 943
  year: 2022
  ident: 7323_CR92
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syab052
– volume: 24
  start-page: 1586
  year: 2007
  ident: 7323_CR77
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msm088
– volume: 14
  start-page: evac129
  year: 2022
  ident: 7323_CR42
  publication-title: Genome Biol. Evol.
  doi: 10.1093/gbe/evac129
– volume: 46
  start-page: 239
  year: 2008
  ident: 7323_CR41
  publication-title: J. Syst. Evol.
– volume: 9
  start-page: 123
  year: 2018
  ident: 7323_CR53
  publication-title: Genes
  doi: 10.3390/genes9030123
– volume: 116
  start-page: 7916
  year: 2019
  ident: 7323_CR24
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1813206116
– ident: 7323_CR76
– volume: 6
  start-page: 7
  year: 2006
  ident: 7323_CR102
  publication-title: Rnews
– volume: 7
  year: 2016
  ident: 7323_CR38
  publication-title: Nat. Commun.
  doi: 10.1038/ncomms12709
– volume: 30
  start-page: 2216
  year: 2014
  ident: 7323_CR103
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btu181
– volume: 63
  start-page: 555
  year: 2014
  ident: 7323_CR81
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syu020
– volume: 53
  start-page: 673
  year: 2004
  ident: 7323_CR101
  publication-title: Syst. Biol.
  doi: 10.1080/10635150490522232
– volume: 38
  start-page: 108
  year: 2021
  ident: 7323_CR3
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msaa191
– ident: 7323_CR33
– volume: 27
  start-page: 1983
  year: 2010
  ident: 7323_CR43
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msq089
– volume: 65
  start-page: 843
  year: 2016
  ident: 7323_CR36
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syw030
– volume: 3
  start-page: 217
  year: 2012
  ident: 7323_CR96
  publication-title: Methods Ecol. Evol.
  doi: 10.1111/j.2041-210X.2011.00169.x
– volume: 17
  start-page: 337
  year: 2010
  ident: 7323_CR68
  publication-title: J. Comput. Biol.
  doi: 10.1089/cmb.2009.0179
– volume: 7
  start-page: e6399
  year: 2019
  ident: 7323_CR10
  publication-title: PeerJ
  doi: 10.7717/peerj.6399
– volume: 34
  start-page: 1529
  year: 2017
  ident: 7323_CR88
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msx092
– volume: 22
  start-page: 225
  year: 2006
  ident: 7323_CR7
  publication-title: Trends Genet.
  doi: 10.1016/j.tig.2006.02.003
– volume: 55
  start-page: 539
  year: 2006
  ident: 7323_CR63
  publication-title: Syst. Biol.
  doi: 10.1080/10635150600755453
– ident: 7323_CR48
  doi: 10.1101/2022.10.21.513146
– volume: 13
  year: 2022
  ident: 7323_CR50
  publication-title: Avian Res.
  doi: 10.1016/j.avrs.2022.100027
– volume: 61
  start-page: 346
  year: 2012
  ident: 7323_CR72
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syr107
– volume: 33
  start-page: 1654
  year: 2016
  ident: 7323_CR66
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msw079
– volume: 67
  start-page: 1
  year: 2018
  ident: 7323_CR47
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syx064
– volume: 15
  start-page: 1647
  year: 1998
  ident: 7323_CR78
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/oxfordjournals.molbev.a025892
– volume: 22
  start-page: 377
  year: 2015
  ident: 7323_CR54
  publication-title: J. Comput. Biol.
  doi: 10.1089/cmb.2014.0156
– ident: 7323_CR15
  doi: 10.1007/978-3-030-16477-5_6
– volume: 26
  start-page: 1669
  year: 2010
  ident: 7323_CR64
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btq243
– volume: 380
  start-page: eabn4409
  year: 2023
  ident: 7323_CR90
  publication-title: Science
  doi: 10.1126/science.abn4409
– ident: 7323_CR105
  doi: 10.17894/ucph.85624f66-c8e5-4b89-8e8a-fe984ca89e4a
– volume: 346
  start-page: 1320
  year: 2014
  ident: 7323_CR1
  publication-title: Science
  doi: 10.1126/science.1253451
– volume: 23
  start-page: 1144
  year: 2006
  ident: 7323_CR79
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msj124
– volume: 401
  start-page: 877
  year: 1999
  ident: 7323_CR93
  publication-title: Nature
  doi: 10.1038/44766
– volume: 63
  start-page: 397
  year: 2014
  ident: 7323_CR95
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syu005
– ident: 7323_CR22
  doi: 10.1007/978-3-030-87645-6
– ident: 7323_CR65
  doi: 10.1093/bioinformatics/btz211
– volume: 55
  start-page: 522
  year: 2006
  ident: 7323_CR27
  publication-title: Syst. Biol.
  doi: 10.1080/10635150600697358
– volume: 13
  start-page: 2331
  year: 2022
  ident: 7323_CR73
  publication-title: Methods Ecol. Evol.
  doi: 10.1111/2041-210X.13977
– volume: 432
  start-page: 695
  year: 2004
  ident: 7323_CR85
  publication-title: Nature
  doi: 10.1038/nature03154
– volume: 2
  start-page: 1
  year: 2021
  ident: 7323_CR13
  publication-title: Birds
  doi: 10.3390/birds2010001
– volume: 52
  start-page: 247
  year: 2021
  ident: 7323_CR31
  publication-title: Annu. Rev. Ecol. Evol. Syst.
  doi: 10.1146/annurev-ecolsys-012121-095340
– volume: 30
  start-page: 2026
  year: 2020
  ident: 7323_CR49
  publication-title: Curr. Biol.
  doi: 10.1016/j.cub.2020.03.060
– volume: 21
  start-page: 411
  year: 1989
  ident: 7323_CR75
  publication-title: Math. Geol.
  doi: 10.1007/BF00897326
– volume: 13
  start-page: e1002224
  year: 2015
  ident: 7323_CR32
  publication-title: PLoS Biol.
  doi: 10.1371/journal.pbio.1002224
– volume: 349
  start-page: 1460
  year: 2015
  ident: 7323_CR18
  publication-title: Science
  doi: 10.1126/science.aab1578
– volume: 35
  start-page: 1771
  year: 2019
  ident: 7323_CR59
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bty839
– volume: 9
  start-page: 1998
  year: 2017
  ident: 7323_CR29
  publication-title: Genome Biol. Evol.
  doi: 10.1093/gbe/evx147
– ident: 7323_CR6
  doi: 10.1038/s41586-019-1693-2
– volume: 11
  start-page: e0163962
  year: 2016
  ident: 7323_CR83
  publication-title: PLoS ONE
  doi: 10.1371/journal.pone.0163962
– volume: 32
  start-page: 268
  year: 2015
  ident: 7323_CR62
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msu300
– volume: 10
  start-page: 1049
  year: 2019
  ident: 7323_CR74
  publication-title: Front. Genet.
  doi: 10.3389/fgene.2019.01049
– ident: 7323_CR106
– volume: 35
  start-page: 4453
  year: 2019
  ident: 7323_CR61
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btz305
– volume: 54
  start-page: 281
  year: 1982
  ident: 7323_CR46
  publication-title: Oecologia
  doi: 10.1007/BF00379994
– volume: 80
  start-page: 16
  year: 2002
  ident: 7323_CR98
  publication-title: Can. J. Zool.
  doi: 10.1139/z01-204
– volume: 53
  start-page: 485
  year: 2004
  ident: 7323_CR87
  publication-title: Syst. Biol.
  doi: 10.1080/10635150490445779
– volume: 381
  start-page: 226
  year: 1996
  ident: 7323_CR20
  publication-title: Nature
  doi: 10.1038/381226a0
– volume: 45
  start-page: 50
  year: 2016
  ident: 7323_CR14
  publication-title: Zool. Scr.
  doi: 10.1111/zsc.12213
– ident: 7323_CR9
– volume: 122
  start-page: 110
  year: 2018
  ident: 7323_CR67
  publication-title: Mol. Phylogenet. Evol.
  doi: 10.1016/j.ympev.2018.01.019
– volume: 9
  start-page: 132
  year: 2018
  ident: 7323_CR35
  publication-title: Genes
  doi: 10.3390/genes9030132
– volume: 602
  start-page: 263
  year: 2022
  ident: 7323_CR69
  publication-title: Nature
  doi: 10.1038/s41586-021-04341-1
– volume: 11
  year: 2010
  ident: 7323_CR86
  publication-title: BMC Genet.
  doi: 10.1186/1471-2156-11-11
– volume: 587
  start-page: 252
  year: 2020
  ident: 7323_CR4
  publication-title: Nature
  doi: 10.1038/s41586-020-2873-9
– volume: 349
  start-page: 1460
  year: 2015
  ident: 7323_CR17
  publication-title: Science
  doi: 10.1126/science.aab1062
– volume: 32
  start-page: 1933
  year: 2016
  ident: 7323_CR57
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btw108
– volume: 68
  start-page: 937
  year: 2019
  ident: 7323_CR39
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syz019
– volume: 66
  start-page: 857
  year: 2017
  ident: 7323_CR12
  publication-title: Syst. Biol.
  doi: 10.1093/sysbio/syx041
– volume: 542
  start-page: 344
  year: 2017
  ident: 7323_CR104
  publication-title: Nature
  doi: 10.1038/nature21074
– volume: 12
  start-page: e0182238
  year: 2017
  ident: 7323_CR71
  publication-title: PLoS ONE
  doi: 10.1371/journal.pone.0182238
– ident: 7323_CR97
  doi: 10.5061/dryad.fbg79cnw7
– volume: 522
  start-page: 34
  year: 2015
  ident: 7323_CR28
  publication-title: Nature
  doi: 10.1038/522034d
– volume: 18
  start-page: 172
  year: 2003
  ident: 7323_CR21
  publication-title: Trends Ecol. Evol.
  doi: 10.1016/S0169-5347(03)00017-X
– ident: 7323_CR34
  doi: 10.1073/pnas.2319506121
– volume: 1
  start-page: e1501005
  year: 2015
  ident: 7323_CR23
  publication-title: Sci. Adv.
  doi: 10.1126/sciadv.1501005
– volume: 339
  start-page: 684
  year: 2013
  ident: 7323_CR19
  publication-title: Science
  doi: 10.1126/science.1230492
– volume: 39
  start-page: msac254
  year: 2022
  ident: 7323_CR84
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msac254
– ident: 7323_CR108
– volume: 29
  start-page: 1341
  year: 2013
  ident: 7323_CR52
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btt128
– volume: 30
  start-page: 3059
  year: 2002
  ident: 7323_CR56
  publication-title: Nucleic Acids Res.
  doi: 10.1093/nar/gkf436
– volume: 12
  start-page: 164
  year: 2020
  ident: 7323_CR44
  publication-title: Diversity
  doi: 10.3390/d12040164
– volume: 32
  start-page: 786
  year: 2016
  ident: 7323_CR58
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btv646
– volume: 8
  start-page: e54848
  year: 2013
  ident: 7323_CR25
  publication-title: PLoS ONE
  doi: 10.1371/journal.pone.0054848
– volume: 25
  start-page: 581
  year: 2022
  ident: 7323_CR94
  publication-title: Ecol. Lett.
  doi: 10.1111/ele.13898
– volume: 94
  start-page: 447
  year: 2016
  ident: 7323_CR30
  publication-title: Mol. Phylogenet. Evol.
  doi: 10.1016/j.ympev.2015.10.027
– volume: 28
  start-page: 112
  year: 2012
  ident: 7323_CR99
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btr597
– volume: 118
  start-page: 78
  year: 2016
  ident: 7323_CR100
  publication-title: Biol. J. Linn. Soc. Lond.
  doi: 10.1111/bij.12765
– volume: 121
  start-page: e2319696121
  year: 2024
  ident: 7323_CR11
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.2319696121
– volume: 37
  start-page: 1530
  year: 2020
  ident: 7323_CR70
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msaa015
– ident: 7323_CR107
  doi: 10.5524/101041
– volume: 23
  start-page: 212
  year: 2006
  ident: 7323_CR80
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msj024
– volume: 51
  start-page: 588
  year: 2002
  ident: 7323_CR26
  publication-title: Syst. Biol.
  doi: 10.1080/10635150290102339
– volume: 19
  year: 2018
  ident: 7323_CR55
  publication-title: BMC Genomics
  doi: 10.1186/s12864-018-4620-2
– volume: 8
  start-page: EBO.S9657
  year: 2012
  ident: 7323_CR82
  publication-title: Evol. Bioinform. Online
  doi: 10.4137/EBO.S9657
– volume: 587
  start-page: 246
  year: 2020
  ident: 7323_CR51
  publication-title: Nature
  doi: 10.1038/s41586-020-2871-y
– volume: 526
  start-page: 569
  year: 2015
  ident: 7323_CR2
  publication-title: Nature
  doi: 10.1038/nature15697
– volume: 23
  start-page: 1581
  year: 2010
  ident: 7323_CR45
  publication-title: J. Evol. Biol.
  doi: 10.1111/j.1420-9101.2010.02029.x
SSID ssj0005174
Score 2.675683
Snippet Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have...
SourceID pubmedcentral
proquest
pubmed
crossref
springer
SourceType Open Access Repository
Aggregation Database
Index Database
Enrichment Source
Publisher
StartPage 851
SubjectTerms 631/181/735
631/181/757
631/181/759
631/208/182
631/208/212/2304
Humanities and Social Sciences
multidisciplinary
Science
Science (multidisciplinary)
Title Complexity of avian evolution revealed by family-level genomes
URI https://link.springer.com/article/10.1038/s41586-024-07323-1
https://www.ncbi.nlm.nih.gov/pubmed/38560995
https://www.proquest.com/docview/3031134381
https://pubmed.ncbi.nlm.nih.gov/PMC11111414
Volume 629
hasFullText 1
inHoldings 1
isFullTextHit
isPrint
link http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3fSxwxEB6sUuiLVG3r2fZIoQ-WNjS_djf7IujhVfogUhTuLWSzE1rQPXFPwf--SXb3ymkRfMnLJiHMTDIzO1--AHwOx36NqOpgvF6GBIVn1JaSU1cozzwKX3doi9P85EL9nGWzNRDDXZgE2k-UlumYHtBh39vgaHSEyyoajFJIGjKejUjdHhOuST75B-t4wLzcX5RhUv9njlVn9CjCfAyUfFAtTU5o-ho2--iRHHbr3YI1bLbhZUJxunYbtvqd2pL9nk76yw4cxC0faS8X92Tuib0LBkHwrjc5EimcgpOoSXVPur8d9DICiUhkb73C9g1cTI_PJye0fzWBWlWwBfW5Y5l2qpLOsbryZV5nJS8zi4W0JZbeMYvOCxuyL2vzEC9w5rTPK2ERc4vyLaw38wZ3gVS1y7BwUlr0ShTMMhS50K7SzGpEPgI-iM-4nlI8vmxxaVJpW2rTidwEkZskchPGfF2Oue4INZ7s_WnQigl2H4sZtsH5bWuC6-VcRoKyEbzrtLScT-oQx5VlNgK9or9lh8ipvfql-fM7cWtHD8IVVyP4Nqja9Lu6fWKde8_r_h5eiWSGGRXyA6wvbm7xYwhuFtUYXhSzIrR6wmM7_TGGjaPj07Nf42TnfwEWZPZm
linkProvider Springer Nature
linkToHtml http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1bSxwxFD6IRdoXqfa29mIKfWhpQ3ObTOalUBZl21qfFHwLmcwJLeisOKvgvzfJzGxZLYLPcxLCOV9yTiZfvgB8iMt-g6iaCN4g4waFF9RVklNfqsACitD0bItDPTtWP0-KkzUQ412YTNrPkpZ5mR7ZYV-7mGhMossqGkEpJI07nkex1tYJyVM9_UfruKW8PFyUYdL8p4_VZHSnwrxLlLx1WpqT0P5T2ByqR_K9H-8WrGG7DRuZxem7bdgaZmpHPg5y0p-ewbc05ZPs5eKazANxVxEQBK8GyJEk4RSTREPqa9L_7aCniUhEknrrGXbP4Xh_72g6o8OrCdSpki1o0J4Vxqtaes-aOlS6KSpeFQ5L6SqsgmcOfRAu7r6c07Fe4MyboGvhELVD-QLW23mLr4DUjS-w9FI6DEqUzDEUWhhfG-YMIp8AH91n_SApnl62OLX5aFsa27vcRpfb7HIb23xetjnvBTXutX4_RsVG3KfDDNfi_LKzMfVyLpNA2QRe9lFa9idNrOOqqpiAWYnf0iBpaq9-af_-ydraKYNwxdUEvoyhtsOs7u4Z587DzHfh8ezo94E9-HH46zU8ERmSBRXyDawvLi7xbSx0FvW7jOwb1FP1IQ
linkToPdf http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1baxQxFD7UitIXsfXSrbcUfFA0mNtkMi-CrC61LcUHC30LmcwJCu1s6WwL_fcmmZmVbaXg8yQhnPPlnJPJly8Ab2PYbxBVE8EbZNyg8IK6SnLqSxVYQBGanm1xpPeO1f5JcbIGerwLk0n7WdIyh-mRHfapi4nGJLqsohGUQtIYYZpwD-7HepslKtdUT_9SO26oLw-XZZg0_xhnNSHdqjJvkyVvnJjmRDR7DI-GCpJ86ee8CWvYbsGDzOT03RZsDqu1I-8GSen3T-BzWvZJ-nJxTeaBuKsICoJXA-xIknGKiaIh9TXp_3jQ00QmIknB9Qy7p3A8-_ZzukeHlxOoUyVb0KA9K4xXtfSeNXWodFNUvCocltJVWAXPHPogXNyBOadjzcCZN0HXwiFqh_IZrLfzFreB1I0vsPRSOgxKlMwxFFoYXxvmDCKfAB_NZ_0gK55etzi1-XhbGtub3EaT22xyG_t8WPY570U17my9O3rFRuynAw3X4vyyszH9ci6TSNkEnvdeWo4nTazlqqqYgFnx37JB0tVe_dL-_pX1tVMW4YqrCXwcXW2Hld3dMc-d_2v-Bh7--Dqzh9-PDl7AhsiILKiQL2F9cXGJr2Kts6hfZ2D_AVwZ9io
openUrl ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Complexity+of+avian+evolution+revealed+by+family-level+genomes&rft.jtitle=Nature+%28London%29&rft.au=Stiller%2C+Josefin&rft.au=Feng%2C+Shaohong&rft.au=Chowdhury%2C+Al-Aabid&rft.au=Rivas-Gonz%C3%A1lez%2C+Iker&rft.date=2024-05-23&rft.pub=Nature+Publishing+Group+UK&rft.issn=0028-0836&rft.eissn=1476-4687&rft.volume=629&rft.issue=8013&rft.spage=851&rft.epage=860&rft_id=info:doi/10.1038%2Fs41586-024-07323-1&rft_id=info%3Apmid%2F38560995&rft.externalDocID=PMC11111414
thumbnail_l http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0028-0836&client=summon
thumbnail_m http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0028-0836&client=summon
thumbnail_s http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0028-0836&client=summon