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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Paleogene Fossil Birds
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Taxon sampling and the accuracy of phylogenetic analyses
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Statistical Methods in Molecular Evolution
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The Origin and Evolution of Birds
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Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era
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Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference
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Range of motion in the avian wing is strongly associated with flight behavior and body mass
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Tropical secondary forest regeneration conserves high levels of avian phylogenetic diversity
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“Recent studies have proposed different theories for the deep evolutionary relationships between the major avian clades (Jarvis et al., 2014; Prum et al., 2015), revising the non-passerine relationships and suggesting a younger age of passerines.”
Background
Dinosaur origin of egg color: oviraptors laid blue-green eggs
Wiemann, J., Yang, T.-R., Sander, P. N., Schneider, M., Engeser, M., Kath‐Schorr, S., Müller, C. E., & Sander, P. M. (2017) · PeerJ · doi:10.7717/peerj.3706 · Cited by 65
“The presence of neognath birds in the 464 Late Cretaceous implies that paleognath birds already diverged at this point (based on avian 465 phylogeny by Prum et al., 2015).”
Anchored phylogenomics illuminates the skipper butterfly tree of life
Toussaint, E. F. A., Breinholt, J. W., Earl, C., WARREN, A. D., Brower, A. V. Z., Yago, M., Dexter, K. M., Espeland, M., Pierce, N. E., Lohman, D. J., et al. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1216-z · Cited by 65
“[5] used AHE to sequence 259 loci and infer a novel and robust time-tree for birds, highlighting the power of the approach to shed light on ancient avian divergences that could not be resolved with 19 loci [6].”
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Uva, V., Päckert, M., Cibois, A., Fumagalli, L., & Roulin, A. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.03.013 · Cited by 64
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The Vav GEF Family: An Evolutionary and Functional Perspective
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More on the Best Evolutionary Rate for Phylogenetic Analysis
Klopfstein, S., Massingham, T., & Goldman, N. (2017) · Systematic Biology · doi:10.1093/sysbio/syx051 · Cited by 58
“An alternative interpretation has been suggested for PI profiles which examines the shape of the PI curves in a qualitative way (Townsend and Leuenberger 2011; Prum et al. 2015); we have not examined this approach here.”
BackgroundMethodInfluential
More than eating dirt: a review of avian geophagy
Downs, C. T., Bredin, I. P., & Wragg, P. D. (2019) · African Zoology · doi:10.1080/15627020.2019.1570335 · Cited by 60
A comparative analysis of the dopaminergic innervation of the executive caudal nidopallium in pigeon, chicken, zebra finch, and carrion crow
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“…linear mixed effects (LME) models in the MATLAB statistical toolbox (v2015b, MathWorks, Natick, MA, USA) with continuous factors body mass (M ), leg length index, posture index and a random effect based on phylogenetic classification at the order or infraclass level (Table 1) (Prum et al., 2015).”
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“However, at higher taxonomic levels there is debate based around different technique of classification (Livezey and Zusi, 2007; Hackett et al., 2008; Jetz et al., 2012; Jarvis et al., 2014; Prum et al., 2015) and so deeper evolutionary affinities are not always certain.”
Background
Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements
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“By probing resolution probabilities over different hypothetical internode lengths, this approach accounts for uncertainty in the guide tree, which may contain errors in topology or branch lengths but is assumed in PI analyses to represent the ‘true’ tree (Prum et al., 2015).”
BackgroundMethodInfluential
Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data
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“Whole genome analyses have recently been used to unravel the phylogenetic relations between the major bird orders (Jarvis et al., 2014; Prum et al., 2015), but our study presents one of the first phylogenomic analyses of a group of closely related bird species (DaCosta and Sorenson, 2016; Nater et…”
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“2015), the neoavian radiation (e.g., Jarvis et al. 2014; Prum et al. 2015), and the relationships among lineages at the origin of land plants (e.”
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How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)
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“To identify loci with duplications and to discern between potential loci copies, orthologous sequences were determined following Prum et al. (2015) and Buddenhagen et al. (2016).”
BackgroundMethodInfluentialSelf-citation
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“Reads were assembled using a quasi de novo approach described by Prum et al. (2015) and Hamilton et al. (2016).”
MethodSelf-citation
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“of tumor heterogeneity, thus enhancing our understanding of the complexity of HCC [5, 8].”
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A stem anseriform from the early Palaeocene of Antarctica provides new key evidence in the early evolution of waterfowl
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A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the torrent frogs, genus Amolops (Anura: Ranidae)
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Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensationPreprint
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“Unresolved phylogenetic relationships are often attributed to ancient, rapid diversification of lineages (e.g. in birds; Jarvis et al., 2014; Prum et al., 2015; Suh, 2016).”
Background
Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets
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Novikova, P. Y., Brennan, I. G., Booker, W. W., Mahony, M. J., Doughty, P., Lemmon, A. R., Lemmon, E. M., Roberts, J. D., Yant, L. J., de Peer, Y. V., et al. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008769 · Cited by 54
Self-citation
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“This finding is consistent with other studies (e.g., Prum et al. 2015) that have reported higher bootstrap percentages for methods when individual gene segments are not binned through local or global concatalescence (Gatesy and Springer 2013) to mitigate gene tree reconstruction errors.”
Result
Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches
Rodríguez, A., Burgon, J. D., Lyra, M. L., Irisarri, I., Baurain, D., Blaustein, L., Göçmen, B., Künzel, S., Mable, B. K., Nolte, A. W., et al. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.07.009 · Cited by 56
“, the transcribed RNA; RNAseq), are more affordable and are increasingly being used to obtain markers that are representative of the nucleotide diversity across the genome (e.g., Emerson et al., 2010; Lemmon et al., 2012; Prum et al., 2015; Wen et al., 2015).”
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Self-citation
Two new genera of songbirds represent endemic radiations from the Shola Sky Islands of the Western Ghats, India
Robin, V. V., Vishnudas, C. K., Gupta, P., Rheindt, F. E., Hooper, D. M., Ramakrishnan, U., & Reddy, S. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-0882-6 · Cited by 52
Squamate Conserved Loci (Sq CL ): A unified set of conserved loci for phylogenomics and population genetics of squamate reptiles
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Patterns of skeletal integration in birds reveal that adaptation of element shapes enables coordinated evolution between anatomical modules
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Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements
Chen, D., Hosner, P. A., Dittmann, D. L., O’Neill, J. P., Birks, S. M., Braun, E. L., & Kimball, R. T. (2021) · BMC Ecology and Evolution · doi:10.1186/s12862-021-01935-1 · Cited by 52
Fifty-ninth Supplement to the American Ornithological Society'sCheck-list of North American Birds
Chesser, R. T., Burns, K. J., Cicero, C., Dunn, J. L., Kratter, A. W., Lovette, I. J., Rasmussen, P. C., Remsen, J. V., Stotz, D. F., Winger, B. M., et al. (2018) · The Auk · doi:10.1642/auk-18-62.1 · Cited by 47
The dynamics of introgression across an avian radiation
Singhal, S., Derryberry, G. E., Bravo, G. A., Derryberry, E. P., Brumfield, R. T., & Harvey, M. G. (2021) · Evolution Letters · doi:10.1002/evl3.256 · Cited by 48
Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
Dutoit, L., Vijay, N., Mugal, C. F., Bossu, C. M., Burri, R., Wolf, J. B. W., & Ellegren, H. (2017) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2016.2756 · Cited by 47
On the taxonomic composition and phylogenetic affinities of the recently proposed clade Vegaviidae Agnolín et al., 2017 ‒ neornithine birds from the Upper Cretaceous of the Southern Hemisphere
Mayr, G., Pietri, V. L. D., Scofield, R. P., & Worthy, T. H. (2018) · Cretaceous Research · doi:10.1016/j.cretres.2018.02.013 · Cited by 49
Genome sequences identify three families of Coleoptera as morphologically derived click beetles (Elateridae)
Kusy, D., Motyka, M., Boček, M., Vogler, A. P., & Bocák, L. (2018) · Scientific Reports · doi:10.1038/s41598-018-35328-0 · Cited by 54
Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships
Prasanna, A. N., Gerber, D., Kijpornyongpan, T., Aime, M. C., Doyle, V. P., & Nagy, L. G. (2019) · Systematic Biology · doi:10.1093/sysbio/syz029 · Cited by 46
Multi-locus phylogenetic inference among New World vultures (Aves: Cathartidae)
Johnson, J. A., Brown, J. W., Fuchs, J., & Mindell, D. P. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.08.025 · Cited by 54
Evolutionary Associations of Endosymbiotic Ciliates Shed Light on the Timing of the Marsupial–Placental Split
Vďačný, P. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy071 · Cited by 50
“2009); 3) a minimum bound of 65 Ma was associated with the node leading to Aviisotricha hoazini which lives exclusively in the crop of Opisthocomus hoazin, representing the most ancient bird lineage (Prum et al. 2015); 4) minimum and maximum bounds of 5.”
BackgroundInfluential
In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus)
Domingos, F. M. C. B., Colli, G. R., Lemmon, A. R., Lemmon, E. M., & Beheregaray, L. B. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.12.009 · Cited by 49
“Indexed libraries were pooled in equal quantities ( 12–16 samples per pool), and enrichments were performed on each pool via an Agilent Custom SureSelect kit (Agilent Technologies, Inc.), designed for use in amniotes (Prum et al., 2015; Ruane et al., 2015; Tucker et al., 2016).”
MethodSelf-citation
No evidence for the ‘rate‐of‐living’ theory across the tetrapod tree of life
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An introduction to plant phylogenomics with a focus on palms
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“This has become a preferred method in many taxonomic groups because of the power to identify hundreds of variable loci (e.g. Faircloth et al., 2012; Lemmon, Emme & Lemmon, 2012; McCormack et al., 2012; Prum et al., 2015).”
Method
New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset
Dornburg, A., Townsend, J. P., Brooks, W. R., Spriggs, E. L., Eytan, R. I., Moore, J. A., Wainwright, P. C., Lemmon, A. R., Lemmon, E. M., & Near, T. J. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.02.017 · Cited by 46
Self-citation
Cladistics
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Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New Technology)
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Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi
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“…resolve species-and genus-level relationships among much of this radiation despite its rapid timeframe evolutionary divergence in rapid radiations are often difﬁcult to resolve (Prum et al. 2016; Suh 2016; Moreira andSchrago2018),andalthoughsaturationmayplayless similarchallengesfortheirresolution.”
Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae
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Phylogeny of a cosmopolitan family of morphologically conserved trapdoor spiders (Mygalomorphae, Ctenizidae) using Anchored Hybrid Enrichment, with a description of the family, Halonoproctidae Pocock 1901
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What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data?
Tamashiro, R. A., White, N. D., Braun, M. J., Faircloth, B. C., Braun, E. L., & Kimball, R. T. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.10.008 · Cited by 47
Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness
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Computational modelling of muscle fibre operating ranges in the hindlimb of a small ground bird (Eudromia elegans), with implications for modelling locomotion in extinct species
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Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: Phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences
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High-throughput sequencing for algal systematics
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“HTS data has resolved challenging phylogenies and classification issues for plants (Ma et al., 2014; Lu et al., 2015), animals (Finstermeier et al., 2012; Prum et al., 2015) and protists (Cavalier-Smith et al., 2015; Kang et al., 2017).”
Background
Simultaneous radiation of bird and mammal lice following the K-Pg boundary
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Melanosome diversity and convergence in the evolution of iridescent avian feathers-Implications for paleocolor reconstruction
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Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota)
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HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing
Dupuis, J. R., Bremer, F. T., Kauwe, A. N., Jose, M. S., Leblanc, L., Rubinoff, D., & Geib, S. M. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12783 · Cited by 50
“…Faircloth, Glenn, Braun, & Kimball, 2016; e.g., Lem-mon et al., 2012; McCormack et al., 2012); however, data sets sampling 100 – 200 specimens have also been generated (e.g., Branstetter, Danforth, et al., 2017; Branstetter, Je (cid:1) sovnik, et al., 2017; Moyle et al., 2016; Prum et al., 2015).”
Resource predictability and specialization in avian malaria parasites
Svensson‐Coelho, M., Loiselle, B. A., Blake, J. G., & Ricklefs, R. E. (2016) · Molecular Ecology · doi:10.1111/mec.13758 · Cited by 43
“Birds, primarily suboscines (Passeriformes, suborder Tyranni), were sampled in January and March, typically a drier period, between 2001 and 2010 at the Tiputini Biodiversity Station (hereafter ‘Tiputini’), Orellana Province, Ecuador (0°380S, 76°080W).”
MethodInfluential
Recalcitrant deep and shallow nodes in Aristolochia (Aristolochiaceae) illuminated using anchored hybrid enrichment
Wanke, S., Mendoza, C. G., Müller, S., Guillén, A. P., Neinhuis, C., Lemmon, A. R., Lemmon, E. M., & Samain, M. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.05.014 · Cited by 44
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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