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Phylogenomic analyses data of the avian phylogenomics project
- 作者:Erich D Jarvis (1)
Siavash Mirarab (2) Andre J Aberer (3) Bo Li (4) (5) (6) Peter Houde (7) Cai Li (4) (6) Simon Y W Ho (8) Brant C Faircloth (10) (9) Benoit Nabholz (11) Jason T Howard (1) Alexander Suh (12) Claudia C Weber (12) Rute R da Fonseca (6) Alonzo Alfaro-N煤帽ez (6) Nitish Narula (13) (7) Liang Liu (14) Dave Burt (15) Hans Ellegren (12) Scott V Edwards (16) Alexandros Stamatakis (17) (3) David P Mindell (18) Joel Cracraft (19) Edward L Braun (20) Tandy Warnow (2) Wang Jun (21) (22) (23) (24) (4) M Thomas Pius Gilbert (25) (6) Guojie Zhang (26) (4) The Avian Phylogenomics Consortium
1. Department of Neurobiology ; Howard Hughes Medical Institute and Duke University Medical Center ; Durham ; NC ; 27710 ; USA 2. Department of Computer Science ; The University of Texas at Austin ; Austin ; TX ; 78712 ; USA 3. Scientific Computing Group ; Heidelberg Institute for Theoretical Studies ; Heidelberg ; Germany 4. China National GeneBank ; BGI-Shenzhen ; Shenzhen ; 518083 ; China 5. College of Medicine and Forensics ; Xi鈥檃n Jiaotong University ; Xi鈥檃n ; 710061 ; China 6. Centre for GeoGenetics ; Natural History Museum of Denmark ; University of Copenhagen ; 脴ster Voldgade 5-7 ; 1350 ; Copenhagen ; Denmark 7. Department of Biology ; New Mexico State University ; Las Cruces ; NM ; 88003 ; USA 8. School of Biological Sciences ; University of Sydney ; Sydney ; NSW ; 2006 ; Australia 10. Department of Biological Sciences ; Louisiana State University ; Baton Rouge ; LA ; 70803 ; USA 9. Department of Ecology and Evolutionary Biology ; University of California Los Angeles ; Los Angeles ; CA ; 90095 ; USA 11. CNRS UMR 5554 ; Institut des Sciences de l鈥橢volution de Montpellier ; Universit茅 Montpellier II ; Montpellier ; France 12. Department of Evolutionary Biology ; Uppsala University ; SE-752 36 ; Uppsala ; Sweden 13. Biodiversity and Biocomplexity Unit ; Okinawa Institute of Science and Technology Onna-son ; Okinawa ; 904-0495 ; Japan 14. Department of Statistics and Institute of Bioinformatics ; University of Georgia ; Athens ; 30602 ; USA 15. Department of Genomics and Genetics ; The Roslin Institute and Royal (Dick) School of Veterinary Studies ; University of Edinburgh ; Easter Bush Campus ; Midlothian ; EH25 9RG ; UK 16. Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology ; Harvard University ; Cambridge ; MA ; USA 17. Institute of Theoretical Informatics ; Department of Informatics ; Karlsruhe Institute of Technology ; D- 76131 ; Karlsruhe ; Germany 18. Department of Biochemistry & Biophysics ; University of California ; San Francisco ; CA ; 94158 ; USA 19. Department of Ornithology ; American Museum of Natural History ; New York ; NY ; 10024 ; USA 20. Department of Biology and Genetics Institute ; University of Florida ; Gainesville ; FL ; 32611 ; USA 21. Department of Biology ; University of Copenhagen ; Ole Maal酶es Vej 5 ; 2200 ; Copenhagen ; Denmark 22. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders ; King Abdulaziz University ; Jeddah ; 21589 ; Saudi Arabia 23. Macau University of Science and Technology ; Avenida Wai long ; Taipa ; Macau ; 999078 ; China 24. Department of Medicine ; University of Hong Kong ; Hong Kong ; Hong Kong 25. Trace and Environmental DNA Laboratory Department of Environment and Agriculture ; Curtin University ; Perth ; WA ; 6102 ; Australia 26. Centre for Social Evolution ; Department of Biology ; Universitetsparken 15 ; University of Copenhagen ; DK-2100 ; Copenhagen ; Denmark
- 关键词:Avian genomes ; Phylogenomics ; Sequence alignments ; Species tree ; Gene trees ; Indels ; Transposable elements
- 刊名:GigaScience
- 出版年:2015
- 出版时间:December 2015
- 年:2015
- 卷:4
- 期:1
- 全文大小:937 KB
- 参考文献:1. Jarvis, ED, Mirarab, S, Aberer, AJ, Li, B, Houde, P, Li, C (2014) Whole genome analyses resolve the early branches in the tree of life of modern birds. Science 346: pp. 1320-31 3451" target="_blank" title="It opens in new window">CrossRef
2. Zhang, G, Li, C, Li, Q, Li, B, Larkin, DM, Lee, C (2014) Comparative genomics reveal insights into avian genome evolution and adaption. Science 346: pp. 1311-20 385" target="_blank" title="It opens in new window">CrossRef 3. A Stamatakis, AJ Aberer. Novel parallelization schemes for large-scale likelihood-based phylogenetic inference. IEEE 27th International Symposium on Parallel and Distributed Processing, 1195鈥?204. 2013 4. Mirarab, S, Bayzid, MS, Boussau, B, Warnow, T (2014) Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science 346: pp. 1-9 3" target="_blank" title="It opens in new window">CrossRef 5. J Cracraft, in The Howard and Moore Complete Checklist of the Birds of the World, E. C. Dickinson, J. V. Remsen, Eds. Eastbourne, U.K.: Aves Press; 2013. pp. xxi-xliii 6. Dickinson, EC, Remsen, JV (2013) Eds. The Howard and Moore Complete Checklist of Birds of the World, Aves Press 7. Gill, F, Wright, M (2006) Birds of the World: Recommended English Names. Princeton University Press, Princeton, N.J. 8. Hillier, LW, Miller, W, Birney, E, Warren, W, Hardison, RD, Ponting, CP (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: pp. 695-716 38/nature03154" target="_blank" title="It opens in new window">CrossRef 9. Warren, WC, Clayton, DF, Ellegren, H, Arnold, AP, Hillier, LW, K眉nstner, A (2010) The genome of a songbird. Nature 464: pp. 757-62 38/nature08819" target="_blank" title="It opens in new window">CrossRef 10. Faircloth, BC, McCormack, JE, Crawford, NG, Harvey, MG, Brumfield, RT, Glenn, TC (2012) Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst Biol 61: pp. 717-26 3/sysbio/sys004" target="_blank" title="It opens in new window">CrossRef 11. McCormack, JE, Faircloth, BC, Crawford, NG, Gowaty, PA, Brumfield, RT, Glenn, TC (2012) Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res 22: pp. 746-54 CrossRef 12. Dimitrieva, S, Bucher, P (2013) UCNEbase鈥揳 database of ultraconserved non-coding elements and genomic regulatory blocks. Nucleic Acids Res 41: pp. D101-9 3/nar/gks1092" target="_blank" title="It opens in new window">CrossRef 13. Harris, RS (2007) Improved pairwise alignment of genomic DNA. Ph.D. Thesis. 14. Blanchette, M, Faircloth, BC, Crawford, NG, Gowaty, PA, Brumfield, RT, Glenn, TC (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14: pp. 708-15 33104" target="_blank" title="It opens in new window">CrossRef 15. Simmons, MP, Ochoterena, H (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 49: pp. 369-81 3/sysbio/49.2.369" target="_blank" title="It opens in new window">CrossRef 16. D. P. Liitle. 2xread: a simple indel coding tool. Program distributed by the author . 2005. http://www.nybg.org/files/scientists/2xread.html. 17. Young, ND, Healy, J (2003) GapCoder automates the use of indel characters in phylogenetic analysis. BMC Bioinformatics 4: pp. 6 CrossRef 18. Katoh, K, Toh, H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: pp. 286-98 3/bib/bbn013" target="_blank" title="It opens in new window">CrossRef 19. Suh, A, Paus, M, Kiefmann, M, Churakov, G, Franke, FA, Brosius, J (2011) Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds. Nat Commun 2: pp. 443 38/ncomms1448" target="_blank" title="It opens in new window">CrossRef 20. Suh, A, Kriegs, JO, Donnellan, S, Brosius, J, Schmitz, J (2012) A universal method for the study of CR1 retroposons in nonmodel bird genomes. Mol Biol Evol 29: pp. 2899-903 3/molbev/mss124" target="_blank" title="It opens in new window">CrossRef 21. Suh, A, Churakov, G, Ramakodi, MP, Platt, RN 2nd, Jurka, J, Kojima, KK, Caballero, J (2015) Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biol. Evol 7: pp. 205-217 3/gbe/evu256" target="_blank" title="It opens in new window">CrossRef 22. Liu, K, Warnow, TJ, Holder, MT, Nelesen, SM, Yu, J, Stamatakis, AP (2012) SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Syst Biol 61: pp. 90-106 3/sysbio/syr095" target="_blank" title="It opens in new window">CrossRef 23. Liu, K, Raghavan, S, Nelesen, S, Linder, CR, Warnow, T (2009) Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324: pp. 1561-4 3" target="_blank" title="It opens in new window">CrossRef 24. L枚ytynoja, A, Goldman, N (2005) An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci U S A 102: pp. 10557-62 3/pnas.0409137102" target="_blank" title="It opens in new window">CrossRef 25. Zhang G, Li B, Li C, Gilbert MTP, Jarvis ED, Wang J. The Avian genome Consortium, Wang J: Comparative genomic data of the Avian Phylogenomics Project. GigaSci Database 2014, http://dx.doi.org/10.5524/101000 26. Jarvis ED, Mirarab S, Aberer A, Houde P, Li C, Ho S, et al. Phylogenomic analyses data of the avian phylogenomics project. GigaScience Database. 2014. http://dx.doi.org/10.5524/101041
- 刊物主题:Bioinformatics; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Proteomics; Data Mining and Knowledge Discovery;
- 出版者:BioMed Central
- ISSN:2047-217X
文摘
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.
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