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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 (48–51).”
From Birds have primate-like numbers of neurons in the forebrain (2016) · cites this paper as [51]
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“Nevertheless, the community has adopted MLBS as a standard way of estimating support using ILS-based summary methods; most biological studies using summary methods rely on site-only or site/gene MLBS (e.g., Song et al. 2012; Jarvis et al. 2014; Wickett et al. 2014; Prum et al. 2015).”
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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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“For example, there is considerable phylogenetic discordance at the base of the Neoaves, ormodern birds [79–81].”
BackgroundInfluentialBirds have primate-like numbers of neurons in the forebrain
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Dense sampling of bird diversity increases power of comparative genomics
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Species’ traits influenced their response to recent climate change
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Earth history and the passerine superradiation
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Self-citationA new time tree reveals Earth history’s imprint on the evolution of modern birds
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Cytochrome P450 diversity in the tree of life
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Mega-evolutionary dynamics of the adaptive radiation of birds
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Global elevational diversity and diversification of birds
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Self-citationSpider phylogenomics: untangling the Spider Tree of Life
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“Recent advances in sequencing technologies have made it possible to obtain very large phylogenetic data sets by using methods such as sequence capture (Faircloth et al. 2012; Prum et al. 2015; Hosner et al. 2016), transcriptome sequencing (Misof et al.”
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“In addition, targeted next-generation DNA sequencing identified 198 bird species based on genomic sequence data [199,200].”
BackgroundSo many genes, so little time: A practical approach to divergence-time estimation in the genomic era
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“And while these datasets have been used for divergence-time estimation [16, 17], their overall utility for divergence-time analyses has not been fully examined.”
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“In each case the host tree topologies used were the most up-to-date available in the literature [40] [41] [42] [43] [44] .”
MethodDevelopmental origins of mosaic evolution in the avian cranium
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“In contrast, Columbaves and Coraciiformes tend to evolve slowly in all modules.”
BackgroundMethodResultInfluentialGenome-wide interrogation advances resolution of recalcitrant groups in the tree of life
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Mammal madness: is the mammal tree of life not yet resolved?
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The shapes of bird beaks are highly controlled by nondietary factors
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“…in resolving challenging short internal nodes in phylogenetic trees by providing millions of nucleotides and thousands of unlinked loci suitable for analyses (Faircloth et al. 2012; Lemmon EM and Lemmon AR 2013; McCormack and Faircloth 2013; Jarvis et al. 2014; Misof et al. 2014; Prum et al. 2015).”
BackgroundInfluentialTectonic collision and uplift of Wallacea triggered the global songbird radiation
Moyle, R. G., Oliveros, C. H., Andersen, M. J., Hosner, P. A., Benz, B. W., Manthey, J. D., Travers, S. L., Brown, R. M., & Faircloth, B. C. (2016) · Nature Communications · doi:10.1038/ncomms12709 · Cited by 240
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Avian egg shape: Form, function, and evolution
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Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary
Alfaro, M. E., Faircloth, B. C., Harrington, R. C., Sorenson, L., Friedman, M., Thacker, C. E., Oliveros, C. H., Černý, D., & Near, T. J. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0494-6 · Cited by 206
“24 presents a topology with multiple points of disagreement among these lineages including: (1) the relative position of gobiarians and syngnatharians + pelagiarians; (2) the relationship between labrids and other percomorph lineages; (3) the sister group of the centrarchiforms; and (4) the position of Serranoidei and…”
BackgroundPhylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
Hime, P. M., Lemmon, A. R., Lemmon, E. C. M., Prendini, E., Brown, J. M., Thomson, R. C., Kratovil, J. D., Noonan, B. P., Pyron, R. A., Peloso, P. L. V., et al. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa034 · Cited by 219
Self-citationExceptional continental record of biotic recovery after the Cretaceous–Paleogene mass extinction
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An Unbiased Molecular Approach Using 3′-UTRs Resolves the Avian Family-Level Tree of Life
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A biologist’s guide to Bayesian phylogenetic analysis
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Next-generation biology: Sequencing and data analysis approaches for non-model organisms
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“In phylogenetic studies this is particularly important, as inadequate taxon sampling introduces artifacts such as long branch attraction (e.g. (Prum et al., 2015)).”
BackgroundThe challenge of biased evidence in conservation
Christie, A. P., Amano, T., Martin, P. A., Petrovan, S. O., Shackelford, G. E., Simmons, B. I., Smith, R. K., Williams, D. R., Wordley, C. F. R., & Sutherland, W. J. (2021) · Conservation Biology · doi:10.1111/cobi.13577 · Cited by 202
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“…and more recent timescales, thus illuminating those that are most closely associated with periods of rapid diversification (Zhou et al. 2012; Andersen et al. 2015), evolutionary stasis (Alfaro et al. 2009, Liu et al. 2014), or high rates of extinction (Prum et al. 2015; Zhang et al. 2016).”
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“And when one genomic study reveals a slightly different resolution of relationships than another, we should not jump wholesale to new conclusions about the direction of evolution for key traits (e.g., Prum et al. 2015 vs. Jarvis et al. 2014).”
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“S1, S2 and S3) as previously described [16].”
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Self-citationBreinholt, J. W., Earl, C., Lemmon, A. R., Lemmon, E. M., Xiao, L., & Kawahara, A. Y. (2017) · Systematic Biology · doi:10.1093/sysbio/syx048 · Cited by 189
“…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
Cooke, R., Eigenbrod, F., & Bates, A. E. (2019) · Nature Communications · doi:10.1038/s41467-019-10284-z · Cited by 191
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“, PrumD6, 200 taxa, and 259 genes [Prum et al. 2015]), large numbers of genes (e.”
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Self-citationGlobal loss of avian evolutionary uniqueness in urban areas
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Evolution of bird genomes—a transposon's‐eye view
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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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“, 2016), and is widely used in metazoan phylogenomics (e.g. Faircloth et al., 2015; Prum et al., 2016; Alfaro et al., 2018; Espeland et al., 2018).”
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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 163
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
Kimball, R. T., Oliveros, C. H., Wang, N., White, N. D., Barker, F. K., Field, D. J., Ksepka, D. T., Chesser, R. T., Moyle, R. G., Braun, M. J., et al. (2019) · Diversity · doi:10.3390/d11070109 · Cited by 148
Self-citationTempo and Pattern of Avian Brain Size Evolution
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Self-citationEmbracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
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Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes
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Tetrapods on the EDGE: Overcoming data limitations to identify phylogenetic conservation priorities
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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 149
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 144
“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
“[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
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 139
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 132
“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 134
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 141
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 143
“…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 137
“…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 135
Self-citationKlaus, K. V., & Matzke, N. J. (2019) · Systematic Biology · doi:10.1093/sysbio/syz034 · Cited by 130
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 134
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 125
Cloutier, A., Sackton, T. B., Grayson, P., Clamp, M., Baker, A. J., & Edwards, S. V. (2019) · Systematic Biology · doi:10.1093/sysbio/syz019 · Cited by 124
“…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 123
The functions of vocal learning in parrots
Bradbury, J. W., & Balsby, T. J. S. (2016) · Behavioral Ecology and Sociobiology · doi:10.1007/s00265-016-2068-4 · Cited by 122
“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 122
“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 118
“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.-A. S., Hanson, M., Fabbri, M., Pritchard, A. C., Bever, G. S., & Hoffman, E. A. (2016) · Integrative and Comparative Biology · doi:10.1093/icb/icw069 · Cited by 113
“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 118
“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
“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 120
Self-citationGasc, C., Peyretaillade, É., & Peyret, P. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw309 · Cited by 119
“(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 116
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 116
Self-citation
Metadata
- 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
- 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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