Phylogenomic analyses data of the avian phylogenomics project

Erich D Jarvis; Siavash Mirarab; Andre J Aberer; Bo Li; Peter Houde; Cai Li; Simon Y. W. Ho; Brant C. Faircloth; Benoit Nabholz; Jason T. Howard; Alexander Suh; Claudia C. Weber; Rute Andreia Rodrigues da Fonseca; Luis Alonso Alfaro Nuñez; Nitish Narula; Liang Liu; Dave Burt; Hans Ellegren; Scott V. Edwards; Alexandros Stamatakis; David P. Mindell; Joel Cracraft; Edward L. Braun; Tandy Warnow; Jun Wang; M. Thomas P. Gilbert; Guojie Zhang

doi:10.1186/s13742-014-0038-1

Phylogenomic analyses data of the avian phylogenomics project

Erich D Jarvis, Siavash Mirarab, Andre J Aberer, Bo Li, Peter Houde, Cai Li, Simon Y. W. Ho, Brant C. Faircloth, Benoit Nabholz, Jason T. Howard, Alexander Suh, Claudia C. Weber, Rute Andreia Rodrigues da Fonseca, Luis Alonso Alfaro Nuñez, Nitish Narula, Liang Liu, Dave Burt, Hans Ellegren, Scott V. Edwards, Alexandros StamatakisDavid P. Mindell, Joel Cracraft, Edward L. Braun, Tandy Warnow, Jun Wang, M. Thomas P. Gilbert, Guojie Zhang

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Abstract

BACKGROUND: 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.

FINDINGS: 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 coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence.

CONCLUSIONS: The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.

Original language	English
Article number	4
Journal	GigaScience
Volume	4
Number of pages	9
ISSN	2047-217X
DOIs	https://doi.org/10.1186/s13742-014-0038-1
Publication status	Published - 12 Feb 2015

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Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., Suh, A., Weber, C. C., Rodrigues da Fonseca, R. A., Alfaro Nuñez, L. A., Narula, N., Liu, L., Burt, D., Ellegren, H., Edwards, S. V., ... Zhang, G. (2015). Phylogenomic analyses data of the avian phylogenomics project. GigaScience, 4, [4]. https://doi.org/10.1186/s13742-014-0038-1

Jarvis, ED, Mirarab, S, Aberer, AJ, Li, B, Houde, P, Li, C, Ho, SYW, Faircloth, BC, Nabholz, B, Howard, JT, Suh, A, Weber, CC, Rodrigues da Fonseca, RA, Alfaro Nuñez, LA, Narula, N, Liu, L, Burt, D, Ellegren, H, Edwards, SV, Stamatakis, A, Mindell, DP, Cracraft, J, Braun, EL, Warnow, T, Wang, J, Gilbert, MTP & Zhang, G 2015, 'Phylogenomic analyses data of the avian phylogenomics project', GigaScience, vol. 4, 4. https://doi.org/10.1186/s13742-014-0038-1

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title = "Phylogenomic analyses data of the avian phylogenomics project",

abstract = "BACKGROUND: 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.FINDINGS: 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 coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence.CONCLUSIONS: The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.",

author = "Jarvis, {Erich D} and Siavash Mirarab and Aberer, {Andre J} and Bo Li and Peter Houde and Cai Li and Ho, {Simon Y. W.} and Faircloth, {Brant C.} and Benoit Nabholz and Howard, {Jason T.} and Alexander Suh and Weber, {Claudia C.} and {Rodrigues da Fonseca}, {Rute Andreia} and {Alfaro Nu{\~n}ez}, {Luis Alonso} and Nitish Narula and Liang Liu and Dave Burt and Hans Ellegren and Edwards, {Scott V.} and Alexandros Stamatakis and Mindell, {David P.} and Joel Cracraft and Braun, {Edward L.} and Tandy Warnow and Jun Wang and Gilbert, {M. Thomas P.} and Guojie Zhang",

year = "2015",

month = feb,

day = "12",

doi = "10.1186/s13742-014-0038-1",

language = "English",

volume = "4",

journal = "GigaScience",

issn = "2047-217X",

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TY - JOUR

T1 - Phylogenomic analyses data of the avian phylogenomics project

AU - Jarvis, Erich D

AU - Mirarab, Siavash

AU - Aberer, Andre J

AU - Li, Bo

AU - Houde, Peter

AU - Li, Cai

AU - Ho, Simon Y. W.

AU - Faircloth, Brant C.

AU - Nabholz, Benoit

AU - Howard, Jason T.

AU - Suh, Alexander

AU - Weber, Claudia C.

AU - Rodrigues da Fonseca, Rute Andreia

AU - Alfaro Nuñez, Luis Alonso

AU - Narula, Nitish

AU - Liu, Liang

AU - Burt, Dave

AU - Ellegren, Hans

AU - Edwards, Scott V.

AU - Stamatakis, Alexandros

AU - Mindell, David P.

AU - Cracraft, Joel

AU - Braun, Edward L.

AU - Warnow, Tandy

AU - Wang, Jun

AU - Gilbert, M. Thomas P.

AU - Zhang, Guojie

PY - 2015/2/12

Y1 - 2015/2/12

N2 - BACKGROUND: 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.FINDINGS: 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 coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence.CONCLUSIONS: The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.

AB - BACKGROUND: 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.FINDINGS: 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 coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence.CONCLUSIONS: The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.

U2 - 10.1186/s13742-014-0038-1

DO - 10.1186/s13742-014-0038-1

M3 - Journal article

C2 - 25741440

SN - 2047-217X

VL - 4

JO - GigaScience

JF - GigaScience

M1 - 4

ER -

Phylogenomic analyses data of the avian phylogenomics project

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