WFRF:(Ho Simon Y. W.)
Sökning: WFRF:(Ho Simon Y. W.) > Phylogenomic analys...
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| Fältnamn | Indikatorer | Metadata |
|---|---|---|
| 000 | 04920naa a22009493a 4500 | |
| 001 | 22017806 | |
| 003 | SE-LIBR | |
| 005 | 20171201151322.0 | |
| 007 | cr|||||||||||| | |
| 008 | 171201s2015 sw |||| o |||| ||eng c | |
| 024 | 7 | a http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-2716072 uri |
| 024 | 7 | a urn:nbn:se:uu:diva-2716072 urn |
| 024 | 7 | a 10.1186/s13742-014-0038-12 doi |
| 040 | a S | |
| 041 | 0 | a eng |
| 042 | 9 EPLK | |
| 100 | 1 | a Jarvis, Erich D.4 aut |
| 245 | 1 0 | a Phylogenomic analyses data of the avian phylogenomics projecth [Elektronisk resurs] |
| 260 | c 2015 | |
| 500 | a Published | |
| 506 | 0 | a gratis |
| 520 | a 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. | |
| 650 | 7 | a Natural Sciences2 hsv |
| 650 | 7 | a Biological Sciences2 hsv |
| 650 | 7 | a Evolutionary Biology2 hsv |
| 650 | 7 | a Naturvetenskap2 hsv0 264446 |
| 650 | 7 | a Biologiska vetenskaper2 hsv |
| 650 | 7 | a Evolutionsbiologi2 hsv |
| 653 | 0 | a Avian genomes |
| 653 | 0 | a Phylogenomics |
| 653 | 0 | a Sequence alignments |
| 653 | 0 | a Species tree |
| 653 | 0 | a Gene trees |
| 653 | 0 | a Indels |
| 653 | 0 | a Transposable elements |
| 700 | 1 | a Mirarab, Siavash4 aut |
| 700 | 1 | a Aberer, Andre J.4 aut |
| 700 | 1 | a Li, Bo4 aut |
| 700 | 1 | a Houde, Peter4 aut |
| 700 | 1 | a Li, Cai4 aut |
| 700 | 1 | a Ho, Simon Y. W.4 aut |
| 700 | 1 | a Faircloth, Brant C.4 aut |
| 700 | 1 | a Nabholz, Benoit4 aut |
| 700 | 1 | a Howard, Jason T.4 aut |
| 700 | 1 | a Suh, Alexander4 aut |
| 700 | 1 | a Weber, Claudia C.4 aut |
| 700 | 1 | a da Fonseca, Rute R.4 aut |
| 700 | 1 | a Alfaro-Nunez, Alonzo4 aut |
| 700 | 1 | a Narula, Nitish4 aut |
| 700 | 1 | a Liu, Liang4 aut |
| 700 | 1 | a Burt, Dave4 aut |
| 700 | 1 | a Ellegren, Hans4 aut |
| 700 | 1 | a Edwards, Scott V.4 aut |
| 700 | 1 | a Stamatakis, Alexandros4 aut |
| 700 | 1 | a Mindell, David P.4 aut |
| 700 | 1 | a Cracraft, Joel4 aut |
| 700 | 1 | a Braun, Edward L.4 aut |
| 700 | 1 | a Warnow, Tandy4 aut |
| 700 | 1 | a Jun, Wang4 aut |
| 700 | 1 | a Gilbert, M. Thomas Pius4 aut |
| 700 | 1 | a Zhang, Guojie4 aut |
| 710 | 1 2 | a Uppsala universitetb Teknisk-naturvetenskapliga vetenskapsområdet4 pbl |
| 772 | 1 8 | i channel recordw 19753896 |
| 773 | 0 8 | i Värdpublikationt GigaScienceg 4x 2047-217X |
| 856 | 4 0 | u http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-271607 |
| 856 | 4 0 | u http://dx.doi.org/10.1186/s13742-014-0038-1 |
| 856 | 4 0 | u http://uu.diva-portal.org/smash/get/diva2:892896/FULLTEXT01 |
| 950 | k | 6 650a Atomerw hu Naturvetenskap |
| 950 | k | 6 650a Experimentw hu Naturvetenskap |
| 950 | k | 6 650a Fysikw hu Naturvetenskap |
| 950 | k | 6 650a Kemiw hu Naturvetenskap |
| 950 | k | 6 650a Kloningw hu Naturvetenskap |
| 950 | k | 6 650a Laboratorierw hu Naturvetenskap |
| 950 | k | 6 650a Marinbiologiw hu Naturvetenskap |
| 950 | k | 6 650a Matematikw hu Naturvetenskap |
| 950 | k | 6 650a Medicinska experimentw hu Naturvetenskap |
| 950 | k | 6 650a Tyngdlagenw hu Naturvetenskap |
| 950 | k | 6 650a Utvecklingsläraw hu Naturvetenskap |
| 841 | 5 APISa x ab 171201||0000|||||001||||||000000e 1 | |
| 024 | 7 | 5 APISa urn:nbn:se:uu:diva-2716072 urn |
| 852 | 5 APISb APIS | |
| 856 | 4 0 | 5 APISu http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-271607 |
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