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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“I omitted owl sequences derived from transcriptomes, removed stop codons and sites with dubious homology (ESM, Dataset S1), and assumed the topology from Prum et al. (2015).”
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“As an MLGO input phylogenetic tree for the eight birds plus ostrich, we took as a basis the tree shown in Figure 1 that was derived from the comprehensive [36] phylogeny for the class Aves.”
Method
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Statistical binning leads to profound model violation due to gene tree error incurred by trying to avoid gene tree error
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“However, the latter scenario seems unlikely, because doves diversified in the Cenozoic (Steadman 2008; Prum et al. 2015), making vicariance an unlikely explanation.”
Background
Evolutionary Footprints of Short Tandem Repeats in Avian Promoters
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“The turkey and chicken have a similar genomic composition to each other, regardless of their deep divergent splits (around 20 ~ 40 MYA).”
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“Well-resolved sequence-based phylogenetic analyses (e.g. Ericson et al., 2006; Hackett et al., 2008; Prum et al., 2015) offer a new perspective on aspects of the evolutionary history of birds, of which the divergence times of the major clades and their areas of origin are among the most obvious.”
BackgroundMethod
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“The cladogram is based on Prum et al. (2015).”
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“The modern avian body plan emerged across a stem lineage whose total length easily exceeds 100 million years [Prum et al., 2015].”
Background
A simple strategy for recovering ultraconserved elements, exons, and introns from low coverage shotgun sequencing of museum specimens: Placement of the partridge genus Tropicoperdix within the galliformes
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“As with mammals, the bird record also supports rapid diversification around the K-Pg transition Frontiers of Biogeography 2021, 13.1, e48678 © the authors, CC-BY 4.0 license 6 (Jarvis et al. 2014, Claramunt and Cracraft 2015, Prum et al. 2015, Kimball et al. 2019).”
BackgroundInfluential
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Calibrations from the Fossil Record
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“6 (Rambaut et al. 2013), the effective sampling sizes (ESSs) were computed.”
Method

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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