Dense sampling of bird diversity increases power of comparative genomics
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Feng, Shaohong | Stiller, Josefin | Deng, Yuan | Armstrong, Joel | Fang, Qi | Reeve, Andrew Hart | Xie, Duo | Chen, Guangji | Guo, Chunxue | Faircloth, Brant | 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 | Puetz, Lara | Cavill, Emily | Ribeiro, Ângela | Eckhart, Leopold | Fjeldså, Jon | Hosner, Peter | Brumfield, Robb | Christidis, Les | Bertelsen, Mads | Sicheritz-Ponten, Thomas | Tietze, Dieter Thomas | Robertson, Bruce | Song, Gang | Borgia, Gerald | Claramunt, Santiago | Lovette, Irby | Cowen, Saul | Njoroge, Peter | Dumbacher, John Philip | Ryder, Oliver | Fuchs, Jérôme | Bunce, Michael | Burt, David | Cracraft, Joel | Meng, Guanliang | Hackett, Shannon | Ryan, Peter | Jønsson, Knud Andreas | Jamieson, Ian | da Fonseca, Rute | Braun, Edward | Houde, Peter | Mirarab, Siavash | Suh, Alexander | Hansson, Bengt | Ponnikas, Suvi | Sigeman, Hanna | Stervander, Martin | Frandsen, Paul | van Der Zwan, Henriette | van Der Sluis, Rencia | Visser, Carina | Balakrishnan, Christopher | Clark, Andrew | Fitzpatrick, John | Bowman, Reed | Chen, Nancy | Cloutier, Alison | Sackton, Timothy | Edwards, Scott | Foote, Dustin | Shakya, Subir | Sheldon, Frederick | Vignal, Alain | Soares, André | Shapiro, Beth | González-Solís, Jacob | Ferrer-Obiol, Joan | Rozas, Julio | Riutort, Marta | Tigano, Anna | Friesen, Vicki | Dalén, Love | Urrutia, Araxi | Székely, Tamás | Liu, Yang | Campana, Michael | Corvelo, André | Fleischer, Robert | Rutherford, Kim | Gemmell, Neil | Dussex, Nicolas | Mouritsen, Henrik | Thiele, Nadine | Delmore, Kira | Liedvogel, Miriam | Franke, Andre | Hoeppner, Marc | Krone, Oliver | Fudickar, Adam | Milá, Borja | Ketterson, Ellen | Fidler, Andrew Eric | Friis, Guillermo | Parody-Merino, Ángela | Battley, Phil | Cox, Murray | Lima, Nicholas Costa Barroso | Prosdocimi, Francisco | Parchman, Thomas Lee | Schlinger, Barney | Loiselle, Bette | Blake, John | Lim, Haw Chuan | Day, Lainy | Fuxjager, Matthew | Baldwin, Maude | Braun, Michael | Wirthlin, Morgan | Dikow, Rebecca | Ryder, T. Brandt | Camenisch, Glauco | Keller, Lukas | Dacosta, Jeffrey | Hauber, Mark | Louder, Matthew | Witt, Christopher | Mcguire, Jimmy | Mudge, Joann | Megna, Libby | Carling, Matthew | Wang, Biao | Taylor, Scott | Del-Rio, Glaucia | Aleixo, Alexandre | Vasconcelos, Ana Tereza Ribeiro | Mello, Claudio | Weir, Jason | Haussler, David | Li, Qiye | Yang, Huanming | Wang, Jian | Lei, Fumin | Rahbek, Carsten | Gilbert, M. Thomas P. | Graves, Gary | Jarvis, Erich | Paten, Benedict | Zhang, Guojie
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CCSD ; Nature Publishing Group -
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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 confdently 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-specifc variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will ofer new perspectives on evolutionary processes in cross-species comparative analyses and assist in eforts to conserve species.
