A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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The similarity of neuronal scaling rules between songbirds and parrots is not too surprising, considering their close phylogenetic relationship.
“The similarity of neuronal scaling rules between songbirds and parrots is not too surprising, considering their close phylogenetic relationship (48–51).”
From Birds have primate-like numbers of neurons in the forebrain (2016) · cites this paper as [51]
Cites
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“…tree are roughly following that of the OneZoom project [40] with modifications based on more specific research; for example, the branching order within the birds is according to Prum et al. [41] Examples of the seed alignments generated as part of the aforementioned pipeline can be observed in Fig.”
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BackgroundPhylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
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“…phylogenies (Lemmon et al. 2012; McCormack et al. 2013a; Pyron et al. 2014; Smith et al. 2014; Brandley et al. 2015; Eytan et al. 2015; Prum et al. 2015; Ruane et al. 2015; Hamilton et al. 2016; Peloso et al. 2016; Young et al. 2016), the results obtained here indicate that more data…”
BackgroundResultInfluentialSelf-citationProjected losses of global mammal and bird ecological strategies
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Self-citationGlobal loss of avian evolutionary uniqueness in urban areas
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Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites
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“Assuming concomitant diversification, we used the onset of the adaptive radiation of Neoaves (69–67 mya) (Jarvis et al., 2014; Prum et al., 2015; Claramunt and Cracraft, 2015) as the age for the eAHBV-FRY root, thus allowing for dating the other branching points in the virus tree.”
InfluentialResolving the backbone of the Brassicaceae phylogeny for investigating trait diversity
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“Furthermore, this timeframe is consistent with molecular estimates for the origin of modern birds using avian mitochondrial genomes and targeted next-generation DNA sequencing (Pacheco, Battistuzzi, Lentino, et al. 2011; Prum et al. 2015).”
A fly in a tube: Macroevolutionary expectations for integrated phenotypes
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“Although the phylogenetic position of many species remains unresolved [14], deep phylogenetic relationships are relatively well-known for some lineages, thus constituting “ backbone ” working phylogenies for different groups of organisms such as flowering plants [15] and birds [16, 17].”
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Ticks parasitised feathered dinosaurs as revealed by Cretaceous amber assemblages
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Phylogenomic Evidence Overturns Current Conceptions of Social Evolution in Wasps (Vespidae)
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“Recent time-calibrated phylogenies for birds showed the age of Neoaves to also be close to the KPB (Jarvis et al. 2014; Claramunt and Cracraft 2015; Prum et al. 2015), with rapid post-KPB divergence represented by a hard polytomy (Suh 2016).”
BackgroundDietrich, C. H., Allen, J. M., Lemmon, A. R., Lemmon, E. M., Takiya, D. M., Evangelista, O., Walden, K. K. O., Grady, P. G. S., & Johnson, K. P. (2017) · Insect Systematics and Diversity · doi:10.1093/isd/ixx003 · Cited by 161 · see citing works
Self-citationGlobal trade‐offs of functional redundancy and functional dispersion for birds and mammals
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Feeding ecology is the primary driver of beak shape diversification in waterfowl
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Bayesian molecular dating: opening up the black box
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“For example, in a recent bird phylogeny that included representatives of every order (Prum et al., 2015), the order Opisthocomiformes had 100% of tips sampled (because the sole species, hoatzin, was included) while the species-rich Passeriformes had fewer than 1% of its tips sampled (because 44…”
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Self-citationA Phylogenomic Supertree of Birds
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Self-citationTempo and Pattern of Avian Brain Size Evolution
Ksepka, D. T., Balanoff, A. M., Smith, N., Bever, G. S., Bhullar, B.-A. S., Bourdon, E., Braun, E. L., Burleigh, J. G., Clarke, J. A., Colbert, M. W., et al. (2020) · Current Biology · doi:10.1016/j.cub.2020.03.060 · Cited by 143 · see citing works
Self-citationEmbracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
Bravo, G. A., Antonelli, A., Bacon, C. D., Bartoszek, K., Blom, M. P. K., Huynh, S., Jones, G., Knowles, L. L., Lamichhaney, S., Marcussen, T., et al. (2019) · PeerJ · doi:10.7717/peerj.6399 · Cited by 143 · see citing works
Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes
Li, Y., Zhang-hai, L., Schuiteman, A., Chase, M. W., Li, J., Huang, W., Hidayat, A., Wu, S., & Jin, X. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.106540 · Cited by 140 · see citing works
Tetrapods on the EDGE: Overcoming data limitations to identify phylogenetic conservation priorities
Gumbs, R., Gray, C. L., Wearn, O. R., & Owen, N. (2018) · PLoS ONE · doi:10.1371/journal.pone.0194680 · Cited by 138 · see citing works
Late Cretaceous neornithine from Europe illuminates the origins of crown birds
Field, D. J., Benito, J., Chen, A., Jagt, J. W. M., & Ksepka, D. T. (2020) · Nature · doi:10.1038/s41586-020-2096-0 · Cited by 141 · see citing works
Self-citationPhylogenomics from low‐coverage whole‐genome sequencing
Zhang, F., Ding, Y., Zhu, C., Zhou, X. Y., Orr, M. C., Scheu, S., & Luan, Y. (2019) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.13145 · Cited by 140 · see citing works
“In recent years, these techniques have been successfully used to addressed a wide variety of questions in systematic and evolutionary biology (Fernández et al., 2018; Misof et al., 2014; Oakley, Wolfe, Lindgren, & Zaharoff, 2012; Prum et al., 2015; Young et al., 2016).”
MethodResolving Cypriniformes relationships using an anchored enrichment approach
Stout, C. C., Tan, M., Lemmon, A. R., Lemmon, E. M., & Armbruster, J. W. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0819-5 · Cited by 138 · see citing works
“[44] and the 135 loci identified as Fugu-Danio single-copy orthologs by Li [43].”
BackgroundMethodResultInfluentialSelf-citationNear-complete phylogeny and taxonomic revision of the world’s babblers (Aves: Passeriformes)
Cai, T., Cibois, A., Alström, P., Moyle, R. G., Kennedy, J. D., Shao, S., Zhang, R., Irestedt, M., Ericson, P. G. P., Gelang, M., et al. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.10.010 · Cited by 137 · see citing works
Dietary niche and the evolution of cranial morphology in birds
Felice, R. N., Tobias, J. A., Pigot, A. L., & Goswami, A. (2019) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2018.2677 · Cited by 137 · see citing works
Global patterns of interaction specialization in bird–flower networks
Zanata, T. B., Dalsgaard, B., Passos, F. C., Cotton, P. A., Roper, J. J., Maruyama, P. K., Fischer, E. A., Schleuning, M., González, A. M. M., Vizentin‐Bugoni, J., et al. (2017) · Journal of Biogeography · doi:10.1111/jbi.13045 · Cited by 134 · see citing works
“These three families contain most of the specialized nectar-feeding bird species, and are an example of convergent evolution, as they have independently evolved adaptations associated with nectarivory (Prum et al., 2015).”
BackgroundPhylogenomic Data Yield New and Robust Insights into the Phylogeny and Evolution of Weevils
Shin, S., Clarke, D., Lemmon, A. R., Lemmon, E. M., Aitken, A. L., Haddad, S., Farrell, B. D., Marvaldi, A. E., Oberprieler, R. G., & McKenna, D. D. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx324 · Cited by 133 · see citing works
Self-citationFeather arrays are patterned by interacting signalling and cell density waves
Ho, W., Freem, L. J., Zhao, D., Painter, K. J., Woolley, T. E., Gaffney, E. A., McGrew, M. J., Tzika, A. C., Milinkovitch, M. C., Schneider, P., et al. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000132 · Cited by 133 · see citing works
A phenology of the evolution of endothermy in birds and mammals
Lovegrove, B. G. (2016) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12280 · Cited by 133 · see citing works
“…Ruta et al., 2013), mammaliaforms (Bi et al., 2014; Meng, 2014; Luo et al., 2015), mammals (O’Leary et al., 2013), archosaurs (Brusatte et al., 2010a,b; Nesbitt, 2011), non-avian dinosaurs (including theropods) (Carrano, Benson & Sampson, 2012; Benson et al., 2014), and birds (Prum et al., 2015).”
The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves
Suh, A. (2016) · Zoologica Scripta · doi:10.1111/zsc.12213 · Cited by 134 · see citing works
“…relationships have only been discovered through analysis of hundreds or thousands of unlinked nuclear loci, such as Phaethontimorphae (sunbittern + tropicbirds), the turaco/bustard clade and the sandgrouse/mesite clade (McCormack et al. 2013; Jarvis et al. 2014; Prum et al. 2015; Suh et al. 2015).”
BackgroundMethodResultInfluentialGenomic Signature of an Avian Lilliput Effect across the K-Pg Extinction
Berv, J. S., & Field, D. J. (2017) · Systematic Biology · doi:10.1093/sysbio/syx064 · Cited by 129 · see citing works
Self-citationKlaus, K. V., & Matzke, N. J. (2019) · Systematic Biology · doi:10.1093/sysbio/syz034 · Cited by 126 · see citing works
Young, A. D., Lemmon, A. R., Skevington, J. H., Mengual, X., Ståhls, G., Reemer, M., Jordaens, K., Kelso, S., Lemmon, E. M., Hauser, M., et al. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0714-0 · Cited by 130 · see citing works
Self-citationMarki, P. Z., Jønsson, K. A., Irestedt, M., Nguyen, J. M. T., Rahbek, C., & Fjeldså, J. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.12.021 · Cited by 127 · see citing works
Cloutier, A., Sackton, T. B., Grayson, P., Clamp, M. E., Baker, A. J., & Edwards, S. V. (2019) · Systematic Biology · doi:10.1093/sysbio/syz019 · Cited by 126 · see citing works
“…et al. 2013; note that moa sequences were absent from these analyses), or to a clade containing emu, cassowary, and kiwi (Haddrath and Baker 2012, Prum et al. 2015), with the same data sometimes producing conflicting results under different analysis regimes (e.g. Harshman et al. 2008, Smith et…”
BackgroundMethodResultInfluentialMosaic genome evolution in a recent and rapid avian radiation
Stryjewski, K. F., & Sorenson, M. D. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0364-7 · Cited by 119 · see citing works
The functions of vocal learning in parrots
Bradbury, J., & Balsby, T. (2016) · Behavioral Ecology and Sociobiology · doi:10.1007/s00265-016-2068-4 · Cited by 144 · see citing works
“Parrots apparently emerged in the Paleocene, and most major lineages were present by the end of the Eocene (Wright et al. 2008; Schweizer et al. 2010, 2011; Jarvis et al. 2014; Prum et al. 2015; see Toft and Wright (2015) for an excellent review of parrot phylogeny).”
BackgroundBayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes
Matschiner, M., Musilová, Z., Barth, J. M. I., Starostová, Z., Salzburger, W., Steel, M., & Bouckaert, R. (2016) · Systematic Biology · doi:10.1093/sysbio/syw076 · Cited by 119 · see citing works
“Presumably as a consequence of these difficulties, node dating has remained popular despite its drawbacks, and was applied in all recent phylogenomic time-tree analyses of groups above the order level (dos Reis et al. 2015; Prum et al. 2015; Fernández et al. 2016).”
BackgroundAnderson, S. R., & Wiens, J. J. (2017) · Evolution · doi:10.1111/evo.13284 · Cited by 116 · see citing works
“Higher-level bird phylogeny has been contentious in recent studies (e.g., Jarvis et al. 2014; Prum et al. 2015), but we do explore alternative trees in this group, and these recent phylogenomic trees did not contain sufficient species sampling to allow their use here.”
BackgroundBhullar, B., Hanson, M., Fabbri, M., Pritchard, A., Bever, G., & Hoffman, E. (2016) · Integrative and Comparative Biology · doi:10.1093/icb/icw069 · Cited by 90 · see citing works
“Recent molecular phylogenetic work has dated the origin of Aves to between 70 and 75 million years ago (Prum et al. 2015b).”
BackgroundVoskamp, A., Baker, D. J., Stephens, P. A., Valdes, P. J., & Willis, S. G. (2017) · Journal of Biogeography · doi:10.1111/jbi.12916 · Cited by 117 · see citing works
“Recent amendments demonstrate the rapid advances in this field (Jarvis et al., 2014; Prum et al., 2015; Rocha et al., 2015).”
BackgroundTapping the woodpecker tree for evolutionary insight
Shakya, S. B., Fuchs, J., Pons, J., & Sheldon, F. H. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.09.005 · Cited by 116 · see citing works
“Although the phylogenetic position of the woodpecker family within birds as a whole–along with its closest relatives, the honeyguides (Indicatoridae) and barbets (Capitonidae, sensu lato)–is now well-established (Hackett et al., 2008; Jarvis et al., 2014; Prum et al., 2015), the relationships of many taxa within the f…”
BackgroundMethodKuntner, M., Hamilton, C. A., Cheng, R., Gregorič, M., Lupše, N., Lokovšek, T., Lemmon, E. M., Lemmon, A. R., Agnarsson, I., Coddington, J. A., et al. (2018) · Systematic Biology · doi:10.1093/sysbio/syy082 · Cited by 116 · see citing works
Self-citationGasc, C., Peyretaillade, É., & Peyret, P. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw309 · Cited by 112 · see citing works
“(119) reconstructed the phylogeny of 198 living bird species, revealing some erroneous relationships in the previously established phylogeny and identifying many new clades.”
BackgroundChiarenza, A. A., Mannion, P. D., Lunt, D. J., Farnsworth, A., Jones, L. A., Kelland, S.-J., & Allison, P. A. (2019) · Nature Communications · doi:10.1038/s41467-019-08997-2 · Cited by 114 · see citing works
Kriebel, R., Drew, B. T., Drummond, C. P., González‐Gallegos, J. G., Celep, F., Mahdjoub, M. M., Rose, J. P., Xiang, C., Hu, G., Walker, J. B., et al. (2019) · American Journal of Botany · doi:10.1002/ajb2.1268 · Cited by 114 · see citing works
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
- Venue
- Nature
- Published
- 2016-06
- Volume
- 534
- Issue
- 7607
- Pages
- S7-S8
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- 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 · 2015: 7
- 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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