학술논문
Dense sampling of bird diversity increases power of comparative genomics
Document Type
article
Author
Feng, Shaohong; Stiller, Josefin; Deng, Yuan; Armstrong, Joel; Fang, Qi; Reeve, Andrew Hart; Xie, Duo; Chen, Guangji; Guo, Chunxue; Faircloth, Brant C; Petersen, Bent; Wang, Zongji; Zhou, Qi; Diekhans, Mark; Chen, Wanjun; Andreu-Sánchez, Sergio; Margaryan, Ashot; Howard, Jason Travis; Parent, Carole; Pacheco, George; Sinding, Mikkel-Holger S; Puetz, Lara; Cavill, Emily; Ribeiro, Ângela M; Eckhart, Leopold; Fjeldså, Jon; Hosner, Peter A; Brumfield, Robb T; Christidis, Les; Bertelsen, Mads F; Sicheritz-Ponten, Thomas; Tietze, Dieter Thomas; Robertson, Bruce C; Song, Gang; Borgia, Gerald; Claramunt, Santiago; Lovette, Irby J; Cowen, Saul J; Njoroge, Peter; Dumbacher, John Philip; Ryder, Oliver A; Fuchs, Jérôme; Bunce, Michael; Burt, David W; Cracraft, Joel; Meng, Guanliang; Hackett, Shannon J; Ryan, Peter G; Jønsson, Knud Andreas; Jamieson, Ian G; da Fonseca, Rute R; Braun, Edward L; Houde, Peter; Mirarab, Siavash; Suh, Alexander; Hansson, Bengt; Ponnikas, Suvi; Sigeman, Hanna; Stervander, Martin; Frandsen, Paul B; van der Zwan, Henriette; van der Sluis, Rencia; Visser, Carina; Balakrishnan, Christopher N; Clark, Andrew G; Fitzpatrick, John W; Bowman, Reed; Chen, Nancy; Cloutier, Alison; Sackton, Timothy B; Edwards, Scott V; Foote, Dustin J; Shakya, Subir B; Sheldon, Frederick H; Vignal, Alain; Soares, André ER; Shapiro, Beth; González-Solís, Jacob; Ferrer-Obiol, Joan; Rozas, Julio; Riutort, Marta; Tigano, Anna; Friesen, Vicki; Dalén, Love; Urrutia, Araxi O; Székely, Tamás; Liu, Yang; Campana, Michael G; Corvelo, André; Fleischer, Robert C; Rutherford, Kim M; Gemmell, Neil J; Dussex, Nicolas; Mouritsen, Henrik; Thiele, Nadine; Delmore, Kira; Liedvogel, Miriam; Franke, Andre; Hoeppner, Marc P; Krone, Oliver
Source
Nature. 587(7833)
Subject
Language
Abstract
Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.