Dense sampling of bird diversity increases power of comparative genomics

作者：Shaohong Feng, Josefin Stiller, Yuan Deng, J. Armstrong, Qi Fang, A. H. Reeve, Duo Xie, Guangji Chen, Chunxue Guo, B. Faircloth, Bent Petersen, Zongji Wang, Qi Zhou, M. Diekhans, Wanjun Chen, S. Andreu-Sánchez, A. Margaryan, Jason T. Howard, Carole Parent, George Pacheco, Mikkel‐Holger S. Sinding, Lara C. Puetz, Emily L. Cavill, Ângela M. Ribeiro, L. Eckhart, J. Fjeldså, P. Hosner, R. T. Brumfield, L. Christidis, M. Bertelsen, Thomas Sicheritz-Pontén, D. Tietze, B. Robertson, G. Song, G. Borgia, Santiago Claramunt, I. Lovette, S. Cowen, P. Njoroge, J. Dumbacher, O. Ryder, Jérôme Fuchs, M. Bunce, D. Burt, J. Cracraft, Guanliang Meng, S. Hackett, P. Ryan, K. Jønsson, I. Jamieson, R. D. da Fonseca, E. Braun, P. Houde, S. Mirarab, Alexander Suh, B. Hansson, Suvi Ponnikas, Hanna Sigeman, Martin Stervander, P. Frandsen, H. van der Zwan, R. van der Sluis, C. Visser, C. N. Balakrishnan, A. Clark, J. Fitzpatrick, R. Bowman, Nancy Chen, A. Cloutier, Timothy B Sackton, S. Edwards, Dustin J. Foote, Subir B. Shakya, F. Sheldon, A. Vignal, André E. R. Soares, B. Shapiro, J. González‐Solís, Joan Ferrer-Obiol, J. Rozas, M. Riutort, Anna Tigano, V. Friesen, L. Dalén, Araxi O. Urrutia, T. Székely, Yang Liu, M. G. Campana, A. Corvelo, R. Fleischer, Kim M. Rutherford, N. Gemmell, N. Dussex, H. Mouritsen, N. Thiele, K. Delmore, M. Liedvogel, A. Franke, Marc P. Hoeppner, O. Krone, Adam M. Fudickar, Borja Milá, E. Ketterson, A. Fidler, Guillermo Friis, Á. M. Parody-Merino, P. Battley, M. Cox, N. C. Lima, F. Prosdocimi, T. Parchman, B. Schlinger, Bette A. Loiselle, J. Blake, H. C. Lim, L. Day, Matthew J. Fuxjager, Maude W. Baldwin, M. Braun, Morgan E. Wirthlin, R. Dikow, T. Ryder, G. Camenisch, L. Keller, Jeffrey M. DaCosta, M. Hauber, Matthew I. M. Louder, Christopher C. Witt, J. McGuire, J. Mudge, Libby C. Megna, Matthew D. Carling, Biao Wang, Scott A. Taylor, Glaucia Del‐Rio, A. Aleixo, A. T. Vasconcelos, C. Mello, J. Weir, D. Haussler, Qiye Li, Huanming Yang, Jian Wang, F. Lei, C. Rahbek, M. Gilbert, G. Graves, E. Jarvis, Benedict Paten, Guojie Zhang · 发表于：Nature · 年份：2020 · DOI：10.1038/s41586-020-2873-9 · 被引用次数：370 · 研究领域：Medicine、Geography

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. A dataset of the genomes of 363 species from the Bird 10,00...