Phylogenomic analyses data of the avian phylogenomics project

GigaScience
Erich D JarvisAvian Phylogenomics Consortium

Abstract

Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses. Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescen...Continue Reading

Associated Datasets

Apr 22, 2014·The Avian Genome ConsortiumE Jarvis
Apr 22, 2014·C LiThe Avian Genome Consortium
Apr 22, 2014·The Avian Genome ConsortiumJ. Wang
Apr 22, 2014·The Avian Genome ConsortiumG Zhang
Apr 22, 2014·The Avian Genome ConsortiumMTP Gilbert
Apr 22, 2014·G ZhangMTP Gilbert
May 8, 2014·B LiG Zhang
Apr 22, 2014·The Avian Genome ConsortiumMTP Gilbert

References

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Dec 14, 2004·Nature·UNKNOWN International Chicken Genome Sequencing Consortium
Jul 8, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ari Löytynoja, Nick Goldman
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Dec 17, 2014·Genome Biology and Evolution·Alexander SuhJürgen Schmitz
Feb 12, 2015·GigaScience·Guojie ZhangUNKNOWN Avian Genome Consortium

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Citations

Feb 27, 2016·Molecular Biology and Evolution·Kassian KobertAlexandros Stamatakis
Jul 23, 2015·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Daniela H Palmer, Marcus R Kronforst
Apr 22, 2015·Current Biology : CB·Krystyna Nadachowska-BrzyskaHans Ellegren
Feb 28, 2015·Genome Biology·Lél EöryDavid W Burt
Jan 23, 2019·Molecular Biology and Evolution·Claudia C Weber, Simon Whelan
Feb 15, 2019·Genome Biology·Shahab SarmashghiSiavash Mirarab
May 5, 2020·Molecular Biology and Evolution·Bui Quang MinhRobert Lanfear
Jul 3, 2020·Evolution; International Journal of Organic Evolution·Shuo WangCheng-Ming Chuong
Sep 1, 2016·BMC Genomics·Andrew S MasonDavid W Burt
May 6, 2020·Cytogenetic and Genome Research·Tiago M DegrandiRicardo J Gunski
Feb 23, 2019·Molecular Phylogenetics and Evolution·Richard H Adams, Todd A Castoe

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Datasets Mentioned

BETA
PRJNA237821

Software Mentioned

R GPL
ENSEMBL
MP
ExaML
EST
phylip
SATé
Newick
PRANK
MULTIZ

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