Cited by 928Evolution and Paleontology StudiesPaleontology and Evolutionary BiologyGenomics and Phylogenetic Studies

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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

Prum, Richard O., Berv, Jacob S., Dornburg, Alex, Field, Daniel J., Townsend, Jeffrey P., Lemmon, Emily Moriarty, Lemmon, Alan R.·2016·Nature

DOI 10.1038/nature19417

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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
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“The theoretical framework of Darwinian classification, perfected in the 20 century thanks to the technology of genomic sequencing, has led to a comprehensive phylogeny of the class of birds (Aves) based on the notion of last common ancestor [20].”
Background
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Background
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Visual field shape and foraging ecology in diurnal raptors
Potier, S., Duriez, O., Cunningham, G. B., Bonhomme, V., O'Rourke, C. T., Fernández‐Juricic, E., & Bonadonna, F. (2018) · Journal of Experimental Biology · doi:10.1242/jeb.177295 · Cited by 41
“Among diurnal raptors, Accipitriformes are a monophyletic order (Prum et al., 2015), including eagles, vultures, and hawks, which forage using mainly visual cues (Jones et al., 2007).”
Background
All iguana families with the exception of basilisks share sex chromosomes
Altmanová, M., Rovatsos, M., Pokorná, M., Veselý, M., Wagner, F., & Kratochvíl, L. (2017) · Zoology · doi:10.1016/j.zool.2017.11.007 · Cited by 33
Evidence for a prealternate molt-migration in the Rufous Hummingbird and its implications for the evolution of molts in Apodiformes
Sieburth, D., & Pyle, P. (2018) · The Auk · doi:10.1642/auk-17-231.1 · Cited by 34
“…than a first prealternate molt (for discussion on assigning first-cycle molts within the simple alternate molt strategy, see Pyle 2008, Howell and Pyle 2015, Johnson and Wolfe 2018), despite the fact that it appears to be very similar in timing, location, and extent to the definitive…”
Background
Evidence for mtDNA capture in the jacamar Galbula leucogastra/chalcothorax species-complex and insights on the evolution of white-sand ecosystems in the Amazon basin
Ferreira, M., Fernandes, A. M., Aleixo, A. L. P., Antonelli, A., Olsson, U., Bates, J. M., Cracraft, J. L., & RIBAS, C. C. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.07.007 · Cited by 32
Evolution of avian egg shape: underlying mechanisms and the importance of taxonomic scale
Stoddard, M. C., Sheard, C., Akkaynak, D., Yong, E. H., Mahadevan, L., & Tobias, J. A. (2019) · Ibis · doi:10.1111/ibi.12755 · Cited by 33
Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering Bird
Jaiswal, S. K., Gupta, A., Saxena, R., K., V., Sharma, A. K., Mittal, P., Roy, A., Shafer, A. B. A., Vijay, N., & Sharma, V. K. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00392 · Cited by 31
Convergent genomic signatures of flight loss in birds suggest a switch of main fuel
Pan, S., Lin, Y., Liu, Q., Duan, J., Lin, Z., Wang, Y., Wang, X., Lam, S. M., Zou, Z., Shui, G., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10682-3 · Cited by 36
Quantifying shape and ecology in avian pedal claws: The relationship between the bony core and keratinous sheath
Hedrick, B. P., Cordero, S. A., Zanno, L. E., Noto, C. R., & Dodson, P. (2019) · Ecology and Evolution · doi:10.1002/ece3.5507 · Cited by 35
A comprehensive phylogeny and taxonomic evaluation of the waxbills (Aves: Estrildidae)
Olsson, U., & Alström, P. (2020) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2020.106757 · Cited by 35
PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R
Dornburg, A., Fisk, J. N., Tamagnan, J. A., & Townsend, J. P. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0837-3 · Cited by 33
“1 Phylogenetic informativeness profiles generated in PhyInformR based on a selection of 60 loci from [3] for ( a ) all loci; ( b ) a user defined partition of “ fast ” versus “ slow ” rates of nucleotide substitution, with the upper 10% of the rate distribution selected as “ fast ” higher…”
BackgroundMethodInfluentialSelf-citation
Distinct developmental pathways underlie independent losses of flight in ratites
Faux, C. M., & Field, D. J. (2017) · Biology Letters · doi:10.1098/rsbl.2017.0234 · Cited by 35
Self-citation
A well-preserved new mid-paleocene penguin (Aves, Sphenisciformes) from the Waipara Greensand in New Zealand
Mayr, G., Pietri, V. L. D., Love, L., Mannering, A. A., & Scofield, R. P. (2017) · Journal of Vertebrate Paleontology · doi:10.1080/02724634.2017.1398169 · Cited by 36
“We consider this character likely to be plesiomorphic, because it is also present in Sequiwaimanu and occurs in Procellariiformes, the extant sister taxon of penguins (e.g., Hackett et al., 2008; Prum et al., 2015).”
Background
Analyses of phenotypic differentiations among South Georgian Diving Petrel (Pelecanoides georgicus) populations reveal an undescribed and highly endangered species from New Zealand
Fischer, J. H., Debski, I., Miskelly, C. M., Bost, C., Fromant, A., Tennyson, A. J. D., Tessler, J., Cole, R., Hiscock, J. H., Taylor, G. A., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0197766 · Cited by 34
Frequent Retroviral Gene Co-option during the Evolution of Vertebrates
Wang, J., & Han, G. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa180 · Cited by 35
Widespread Evolution of Molecular Resistance to Snake Venom α-Neurotoxins in Vertebrates
Khan, M. A., Dashevsky, D., Kerkkamp, H. M. I., Kordiš, D., Bakker, M., Wouters, R. M., van Thiel, J., den Brouw, B. O., Vonk, F. J., Kini, R. M., et al. (2020) · Toxins · doi:10.3390/toxins12100638 · Cited by 35
Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction
Klein, C. G., Pisani, D., Field, D. J., Lakin, R. J., Wills, M. A., & Longrich, N. R. (2021) · Nature Communications · doi:10.1038/s41467-021-25136-y · Cited by 35
Self-citation
Multiple Evolutionary Origins of Ubiquitous Cu2+ and Zn2+ Binding in the S100 Protein Family
Wheeler, L. C., Donor, M. T., Prell, J. S., & Harms, M. J. (2016) · PLoS ONE · doi:10.1371/journal.pone.0164740 · Cited by 35
Detecting ancient codispersals and host shifts by double dating of host and parasite phylogenies: Application in proctophyllodid feather mites associated with passerine birds
Klimov, P. B., Mironov, S. V., & OConnor, B. M. (2017) · Evolution · doi:10.1111/evo.13309 · Cited by 35
Multiple IgH Isotypes Including IgD, Subclasses of IgM, and IgY Are Expressed in the Common Ancestors of Modern Birds
Han, B., Yuan, H., Wang, T., Li, B., Ma, L., Yu, S., Huang, T., Li, Y., Fang, D., Chen, X., et al. (2016) · The Journal of Immunology · doi:10.4049/jimmunol.1600307 · Cited by 34
“To address this question, we analyzed the IgH isotypes expressed in the Emu (Dromaius novaehollandiae), another primitive bird species, which is thought to have diverged from the ostrich ∼50 million years ago (41).”
Ancient mitochondrial genomes clarify the evolutionary history of New Zealand’s enigmatic acanthisittid wrens
Mitchell, K. J., Wood, J. R., Llamas, B., McLenachan, P. A., Kardailsky, O., Scofield, R. P., Worthy, T. H., & Cooper, A. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.05.038 · Cited by 33
“13 recent studies (Claramunt and Cracraft, 2015; Jarvis et al., 2014; Prum et al., 2015).”
BackgroundMethodResultInfluential
Evolution of iris colour in relation to cavity nesting and parental care in passerine birds
Davidson, G. L., Thornton, A., & Clayton, N. S. (2017) · Biology Letters · doi:10.1098/rsbl.2016.0783 · Cited by 32
“Nodes in this tree are supported by a recently published phylogeny [13].”
Background
Avian brains: Insights from development, behaviors and evolution
Nomura, T., & Izawa, E. (2017) · Development Growth & Differentiation · doi:10.1111/dgd.12362 · Cited by 34
“Living birds are classified into several cladistic groups (Hackett et al. 2008; Jarvis et al. 2014; Prum et al. 2015).”
Background
Parasitaemia data and molecular characterization of Haemoproteus catharti from New World vultures (Cathartidae) reveals a novel clade of Haemosporida
Yabsley, M. J., Vanstreels, R. E. T., Martinsen, E. S., Wickson, A. G., Holland, A. E., Hernandez, S. M., Thompson, A. T., Perkins, S. L., West, C. J., Bryan, A. L., et al. (2018) · Malaria Journal · doi:10.1186/s12936-017-2165-5 · Cited by 34
“should be placed in its own order, Cathartiformes [38], being most closely related to hawks and eagles [39].”
Background
Mitochondrial Genomes from New Zealand’s Extinct Adzebills (Aves: Aptornithidae: Aptornis) Support a Sister-Taxon Relationship with the Afro-Madagascan Sarothruridae
Boast, A. P., Chapman, B., Herrera, M. B., Worthy, T. H., Scofield, R. P., Tennyson, A. J. D., Houde, P., Bunce, M., Cooper, A., & Mitchell, K. J. (2019) · Diversity · doi:10.3390/d11020024 · Cited by 32
Evolution of green lacewings (Neuroptera: Chrysopidae): an anchored phylogenomics approach
Winterton, S. L., Gillung, J. P., Garzón‐Orduña, I. J., Badano, D., Breitkreuz, L. C. V., Duelli, P., Engel, M. S., Liu, X., Machado, R. J. P., Mansell, M. W., et al. (2019) · Systematic Entomology · doi:10.1111/syen.12347 · Cited by 33
Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise
Prost, S., Armstrong, E. E., Nylander, J. A. A., Thomas, G. W. C., Suh, A., Petersen, B., Dalén, L., Benz, B. W., Blom, M. P. K., Palkopoulou, E., et al. (2019) · GigaScience · doi:10.1093/gigascience/giz003 · Cited by 34
Feeding in Birds: Thriving in Terrestrial, Aquatic, and Aerial Niches
Rico‐Guevara, A., Sustaita, D., Gussekloo, S. W. S., Olsen, A. M., Bright, J. A., Corbin, C. E., & Dudley, R. (2019) · Fascinating life sciences · doi:10.1007/978-3-030-13739-7_17 · Cited by 33
Total-Evidence Framework Reveals Complex Morphological Evolution in Nightbirds (Strisores)
Chen, A., White, N. D., Benson, R., Braun, M. J., & Field, D. J. (2019) · Diversity · doi:10.3390/d11090143 · Cited by 35
Self-citation

Authors: Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R.
Affiliations: Yale University (US)
ORCID: Prum, Richard O.
Berv, Jacob S.
Dornburg, Alex
Field, Daniel J.
Townsend, Jeffrey P.
Lemmon, Emily Moriarty
Lemmon, Alan R.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2016-06
Volume: 534
Issue: 7607
Pages: S7-S8
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature19417
OpenAlex: W4231969088
Cited by: 928
References: 7
Citations by year: 2026: 1 · 2025: 4 · 2024: 6 · 2023: 13 · 2022: 10 · 2021: 152 · 2020: 170 · 2019: 159 · 2018: 147 · 2017: 164 · 2016: 94
FWCI: 156.34
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
Topics: Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
Physical Sciences › Earth and Planetary Sciences › Paleontology › Paleontology and Evolutionary Biology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: avian phylogeny, Neoaves, anchored hybrid enrichment, nuclear loci, avian evolution, hoatzin, waterbirds, landbirds, divergence time estimation, dinosaur systematics

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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

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