A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.

Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence...

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Autores principales: John E McCormack, Michael G Harvey, Brant C Faircloth, Nicholas G Crawford, Travis C Glenn, Robb T Brumfield
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Publicado: Public Library of Science (PLoS) 2013
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Acceso en línea:https://doaj.org/article/e86430a2e23a4bdb80567f66f11b4684
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spelling oai:doaj.org-article:e86430a2e23a4bdb80567f66f11b46842021-11-18T07:59:41ZA phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.1932-620310.1371/journal.pone.0054848https://doaj.org/article/e86430a2e23a4bdb80567f66f11b46842013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23382987/?tool=EBIhttps://doaj.org/toc/1932-6203Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.John E McCormackMichael G HarveyBrant C FairclothNicholas G CrawfordTravis C GlennRobb T BrumfieldPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 1, p e54848 (2013)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
John E McCormack
Michael G Harvey
Brant C Faircloth
Nicholas G Crawford
Travis C Glenn
Robb T Brumfield
A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.
description Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.
format article
author John E McCormack
Michael G Harvey
Brant C Faircloth
Nicholas G Crawford
Travis C Glenn
Robb T Brumfield
author_facet John E McCormack
Michael G Harvey
Brant C Faircloth
Nicholas G Crawford
Travis C Glenn
Robb T Brumfield
author_sort John E McCormack
title A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.
title_short A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.
title_full A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.
title_fullStr A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.
title_full_unstemmed A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.
title_sort phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.
publisher Public Library of Science (PLoS)
publishDate 2013
url https://doaj.org/article/e86430a2e23a4bdb80567f66f11b4684
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