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Phylogenomic analyses data of the avian phylogenomics project

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 th... Full description

Journal Title: GigaScience 2015, Vol.4 (1), p.4-4
Main Author: Jarvis, Erich D
Other Authors: Mirarab, Siavash , Aberer, Andre J , Li, Bo , Houde, Peter , Li, Cai , Ho, Simon Y W , Faircloth, Brant C , Nabholz, Benoit , Howard, Jason T , Suh, Alexander , Weber, Claudia C , da Fonseca, Rute R , Alfaro-Núñez, Alonzo , Narula, Nitish , Liu, Liang , Burt, Dave , Ellegren, Hans , Edwards, Scott V , Stamatakis, Alexandros , Mindell, David P , Cracraft, Joel , Braun, Edward L , Warnow, Tandy , Jun, Wang , Gilbert, M Thomas Pius , Zhang, Guojie
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: United States: Oxford University Press
ID: ISSN: 2047-217X
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recordid: cdi_swepub_primary_oai_DiVA_org_uu_271607
title: Phylogenomic analyses data of the avian phylogenomics project
format: Article
creator:
  • Jarvis, Erich D
  • Mirarab, Siavash
  • Aberer, Andre J
  • Li, Bo
  • Houde, Peter
  • Li, Cai
  • Ho, Simon Y W
  • Faircloth, Brant C
  • Nabholz, Benoit
  • Howard, Jason T
  • Suh, Alexander
  • Weber, Claudia C
  • da Fonseca, Rute R
  • Alfaro-Núñez, Alonzo
  • Narula, Nitish
  • Liu, Liang
  • Burt, Dave
  • Ellegren, Hans
  • Edwards, Scott V
  • Stamatakis, Alexandros
  • Mindell, David P
  • Cracraft, Joel
  • Braun, Edward L
  • Warnow, Tandy
  • Jun, Wang
  • Gilbert, M Thomas Pius
  • Zhang, Guojie
subjects:
  • Algorithms
  • Amino acids
  • Analysis
  • Animal genetics
  • Animals
  • avian genome
  • Avian genomes
  • Biodiversity
  • Biological Sciences
  • Biologiska vetenskaper
  • Birds
  • Birds - classification
  • Birds - genetics
  • Classification - methods
  • Data Note
  • DNA - chemistry
  • DNA Transposable Elements
  • Evolution
  • Evolutionary Biology
  • Evolutionsbiologi
  • Gene trees
  • Genes
  • Genome
  • Genomes
  • Genomics
  • Indels
  • Life Sciences
  • Natural Sciences
  • Naturvetenskap
  • Phylogenetics
  • phylogenomic
  • Phylogenomics
  • Phylogeny
  • Populations
  • Populations and Evolution
  • Sequence Alignment
  • Sequence alignments
  • Species tree
  • Systematics
  • Systematics, Phylogenetics and taxonomy
  • taxonomy
  • transposable element
  • Transposable elements
  • Transposons
ispartof: GigaScience, 2015, Vol.4 (1), p.4-4
description: 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 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. 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.
language: eng
source:
identifier: ISSN: 2047-217X
fulltext: no_fulltext
issn:
  • 2047-217X
  • 2047-217X
url: Link


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titlePhylogenomic analyses data of the avian phylogenomics project
creatorJarvis, Erich D ; Mirarab, Siavash ; Aberer, Andre J ; Li, Bo ; Houde, Peter ; Li, Cai ; Ho, Simon Y W ; Faircloth, Brant C ; Nabholz, Benoit ; Howard, Jason T ; Suh, Alexander ; Weber, Claudia C ; da Fonseca, Rute R ; Alfaro-Núñez, Alonzo ; Narula, Nitish ; Liu, Liang ; Burt, Dave ; Ellegren, Hans ; Edwards, Scott V ; Stamatakis, Alexandros ; Mindell, David P ; Cracraft, Joel ; Braun, Edward L ; Warnow, Tandy ; Jun, Wang ; Gilbert, M Thomas Pius ; Zhang, Guojie
creatorcontribJarvis, Erich D ; Mirarab, Siavash ; Aberer, Andre J ; Li, Bo ; Houde, Peter ; Li, Cai ; Ho, Simon Y W ; Faircloth, Brant C ; Nabholz, Benoit ; Howard, Jason T ; Suh, Alexander ; Weber, Claudia C ; da Fonseca, Rute R ; Alfaro-Núñez, Alonzo ; Narula, Nitish ; Liu, Liang ; Burt, Dave ; Ellegren, Hans ; Edwards, Scott V ; Stamatakis, Alexandros ; Mindell, David P ; Cracraft, Joel ; Braun, Edward L ; Warnow, Tandy ; Jun, Wang ; Gilbert, M Thomas Pius ; Zhang, Guojie ; Avian Phylogenomics Consortium ; The Avian Phylogenomics Consortium
descriptionDetermining 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 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. 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.
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0ISSN: 2047-217X
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2DOI: 10.1186/s13742-014-0038-1
3PMID: 25741440
languageeng
publisherUnited States: Oxford University Press
subjectAlgorithms ; Amino acids ; Analysis ; Animal genetics ; Animals ; avian genome ; Avian genomes ; Biodiversity ; Biological Sciences ; Biologiska vetenskaper ; Birds ; Birds - classification ; Birds - genetics ; Classification - methods ; Data Note ; DNA - chemistry ; DNA Transposable Elements ; Evolution ; Evolutionary Biology ; Evolutionsbiologi ; Gene trees ; Genes ; Genome ; Genomes ; Genomics ; Indels ; Life Sciences ; Natural Sciences ; Naturvetenskap ; Phylogenetics ; phylogenomic ; Phylogenomics ; Phylogeny ; Populations ; Populations and Evolution ; Sequence Alignment ; Sequence alignments ; Species tree ; Systematics ; Systematics, Phylogenetics and taxonomy ; taxonomy ; transposable element ; Transposable elements ; Transposons
ispartofGigaScience, 2015, Vol.4 (1), p.4-4
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7Faircloth, Brant C
8Nabholz, Benoit
9Howard, Jason T
10Suh, Alexander
11Weber, Claudia C
12da Fonseca, Rute R
13Alfaro-Núñez, Alonzo
14Narula, Nitish
15Liu, Liang
16Burt, Dave
17Ellegren, Hans
18Edwards, Scott V
19Stamatakis, Alexandros
20Mindell, David P
21Cracraft, Joel
22Braun, Edward L
23Warnow, Tandy
24Jun, Wang
25Gilbert, M Thomas Pius
26Zhang, Guojie
27Avian Phylogenomics Consortium
28The Avian Phylogenomics Consortium
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0Phylogenomic analyses data of the avian phylogenomics project
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descriptionDetermining 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 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. 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.
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1Amino acids
2Analysis
3Animal genetics
4Animals
5avian genome
6Avian genomes
7Biodiversity
8Biological Sciences
9Biologiska vetenskaper
10Birds
11Birds - classification
12Birds - genetics
13Classification - methods
14Data Note
15DNA - chemistry
16DNA Transposable Elements
17Evolution
18Evolutionary Biology
19Evolutionsbiologi
20Gene trees
21Genes
22Genome
23Genomes
24Genomics
25Indels
26Life Sciences
27Natural Sciences
28Naturvetenskap
29Phylogenetics
30phylogenomic
31Phylogenomics
32Phylogeny
33Populations
34Populations and Evolution
35Sequence Alignment
36Sequence alignments
37Species tree
38Systematics
39Systematics, Phylogenetics and taxonomy
40taxonomy
41transposable element
42Transposable elements
43Transposons
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titlePhylogenomic analyses data of the avian phylogenomics project
authorJarvis, Erich D ; Mirarab, Siavash ; Aberer, Andre J ; Li, Bo ; Houde, Peter ; Li, Cai ; Ho, Simon Y W ; Faircloth, Brant C ; Nabholz, Benoit ; Howard, Jason T ; Suh, Alexander ; Weber, Claudia C ; da Fonseca, Rute R ; Alfaro-Núñez, Alonzo ; Narula, Nitish ; Liu, Liang ; Burt, Dave ; Ellegren, Hans ; Edwards, Scott V ; Stamatakis, Alexandros ; Mindell, David P ; Cracraft, Joel ; Braun, Edward L ; Warnow, Tandy ; Jun, Wang ; Gilbert, M Thomas Pius ; Zhang, Guojie
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1Amino acids
2Analysis
3Animal genetics
4Animals
5avian genome
6Avian genomes
7Biodiversity
8Biological Sciences
9Biologiska vetenskaper
10Birds
11Birds - classification
12Birds - genetics
13Classification - methods
14Data Note
15DNA - chemistry
16DNA Transposable Elements
17Evolution
18Evolutionary Biology
19Evolutionsbiologi
20Gene trees
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24Genomics
25Indels
26Life Sciences
27Natural Sciences
28Naturvetenskap
29Phylogenetics
30phylogenomic
31Phylogenomics
32Phylogeny
33Populations
34Populations and Evolution
35Sequence Alignment
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37Species tree
38Systematics
39Systematics, Phylogenetics and taxonomy
40taxonomy
41transposable element
42Transposable elements
43Transposons
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8Nabholz, Benoit
9Howard, Jason T
10Suh, Alexander
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abstractDetermining 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 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. 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.
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