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  • Dense sampling of bird diversity increases power of comparative genomics
    Feng, Shaohong; Stiller, Josefin; Deng, Yuan; Armstrong, Joel; Fang, Qi; Xie, Duo; Chen, Guangji; Guo, Chunxue; Petersen, Bent; Wang, Zongji; Zhou, Qi; Diekhans, Mark; Chen, Wanjun; Andreu-Sánchez, Sergio; Margaryan, Ashot; Howard, Jason Travis; Parent, Carole; Sinding, Mikkel-Holger S; Cavill, Emily; Ribeiro, Ângela M; Eckhart, Leopold; Hosner, Peter A; Brumfield, Robb T; Christidis, Les; Bertelsen, Mads F; Tietze, Dieter Thomas; Song, Gang; Lovette, Irby J; Dumbacher, John Philip; Bunce, Michael; Burt, David W; Cracraft, Joel; Meng, Guanliang; Hackett, Shannon J; Ryan, Peter G; Jamieson, Ian G; da Fonseca, Rute R; Braun, Edward L; Mirarab, Siavash; Suh, Alexander; Ponnikas, Suvi; 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; Edwards, Scott V; Foote, Dustin J; Shakya, Subir B; Vignal, Alain; González-Solís, Jacob; Ferrer-Obiol, Joan; Rozas, Julio; Friesen, Vicki; Urrutia, Araxi O; Székely, Tamás; Liu, Yang; Campana, Michael G; Fleischer, Robert C; Rutherford, Kim M; Dussex, Nicolas; Delmore, Kira; Liedvogel, Miriam; Franke, Andre; Krone, Oliver; Fudickar, Adam M; Milá, Borja; Ketterson, Ellen D; Parody-Merino, Ángela M; Battley, Phil F; Cox, Murray P; Lima, Nicholas Costa Barroso; Parchman, Thomas Lee; Schlinger, Barney A; Loiselle, Bette A; Blake, John G; Fuxjager, Matthew J; Baldwin, Maude W; Braun, Michael J; Wirthlin, Morgan; Camenisch, Glauco; Keller, Lukas F; DaCosta, Jeffrey M; Hauber, Mark E; Carling, Matthew D; Del-Rio, Glaucia; Aleixo, Alexandre; Vasconcelos, Ana Tereza Ribeiro; Weir, Jason T; Haussler, David; Yang, Huanming; Rahbek, Carsten; Gilbert, M Thomas P; Graves, Gary R; Jarvis, Erich D; Paten, Benedict

    Nature (London), 11/2020, Letnik: 587, Številka: 7833
    Journal Article

    Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity . Sparse taxon sampling has previously been proposed to confound phylogenetic inference , 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.

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