Dense sampling of bird diversity increases power of comparative genomics

• Published in: Nature (London) Vol. 587; no. 7833; pp. 252 - 257
• Main Authors: Feng, Shaohong, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, 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, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Eckhart, Leopold, Christidis, Les, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Song, Gang, Borgia, Gerald, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Ryder, Oliver A., Fuchs, Jérôme, Bunce, Michael, Burt, David W., Cracraft, Joel, Hackett, Shannon J., Jamieson, Ian G., Braun, Edward L., Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Cloutier, Alison, Sackton, Timothy B., Shakya, Subir B., Sheldon, Frederick H., Soares, André E. R., Shapiro, Beth, González-Solís, Jacob, Rozas, Julio, Riutort, Marta, Dalén, Love, Urrutia, Araxi O., Székely, Tamás, Liu, Yang, Campana, Michael G., Corvelo, André, Fleischer, Robert C., Rutherford, Kim M., Dussex, Nicolas, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Ketterson, Ellen D., Fidler, Andrew Eric, Parody-Merino, Ángela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Parchman, Thomas Lee, Blake, John G., Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Keller, Lukas F., Hauber, Mark E., Louder, Matthew I. M., McGuire, Jimmy A., Mudge, Joann, Wang, Biao, Taylor, Scott A., Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Weir, Jason T., Li, Qiye, Yang, Huanming, Wang, Jian, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, Zhang, Guojie
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 12.11.2020; Nature Publishing Group
• Subjects: 45/22; 45/23; 45/77; 631/181/2474; 631/208/212/748; Alignment; Animal biology; Animal genetics; Animals; Biodiversity; Biologi; Biological Sciences; Birds; Birds - classification; Birds - genetics; Chelonia mydas; Chickens - genetics; Comparative analysis; Comparative studies; Conservation; Conservation of Natural Resources; Consumer goods; Datasets as Topic; Deoxyribonucleic acid; Diversity of life; DNA; Endangered & extinct species; Evolutionary Biology; Evolutionsbiologi; Finches - genetics; Gene expression; Gene sequencing; Genetics; Genome - genetics; Genomes; Genomics; Genomics - methods; Genomics - standards; Humanities and Social Sciences; Humans; Life Sciences; Livets mångfald; multidisciplinary; Natural Sciences; Naturvetenskap; Phylogenetics; Phylogeny; Pipelines; Sampling; Science; Science (multidisciplinary); Selection, Genetic - genetics; Synteny - genetics; Systematics, Phylogenetics and taxonomy; Vertebrate Zoology; Whole genome sequencing; Wildlife conservation; Sampling Methods; génomique; genomics; échantillonnage
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/s41586-020-2873-9

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity 1 – 4 . Sparse taxon sampling has previously been proposed to confound phylogenetic inference 5 , 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 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.