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1. Author Correction: Dense sampling of bird diversity increases power of comparative genomics

Author

M. Thomas P. Gilbert, Alexandre Aleixo, Bent O. Petersen, Subir B. Shakya, Marta Riutort, Marc P. Hoeppner, Emily Cavill, Hanna Sigeman, Nadine Thiele, John G. Blake, Libby C. Megna, Andrew G. Clark, Christopher C. Witt, Santiago Claramunt, Shaohong Feng, John P. Dumbacher, Beth Shapiro, Love Dalén, Bruce C. Robertson, David Haussler, Ashot Margaryan, Alain Vignal, Shannon J. Hackett, Glauco Camenisch, Joel Armstrong, Joann Mudge, Michael Bunce, Paul B. Frandsen, Joan Ferrer-Obiol, Mikkel-Holger S. Sinding, Saul J. Cowen, Phil F. Battley, Borja Milá, Ángela M. Parody-Merino, Wanjun Chen, Rencia van der Sluis, Glaucia Del-Rio, Jason T. Howard, Sergio Andreu-Sánchez, Carole A. Parent, Ângela M. Ribeiro, Erich D. Jarvis, Rute R. da Fonseca, Duo Xie, Qi Fang, Ana Tereza Ribeiro de Vasconcelos, Yang Liu, Reed Bowman, Rebecca B. Dikow, Irby J. Lovette, Chunxue Guo, Claudio V. Mello, Andrew Hart Reeve, Dieter Thomas Tietze, Guanliang Meng, André E. R. Soares, Guangji Chen, Joel Cracraft, Mads F. Bertelsen, Michael J. Braun, Thomas L. Parchman, Mark E. Hauber, Miriam Liedvogel, Knud A. Jønsson, Tamás Székely, Gang Song, Gary R. Graves, David W. Burt, Adam M. Fudickar, Jérôme Fuchs, Oliver A. Ryder, John W. Fitzpatrick, Benedict Paten, Morgan Wirthlin, Peter Houde, Neil J. Gemmell, Bengt Hansson, Oliver Krone, Brant C. Faircloth, Carsten Rahbek, Andrew E. Fidler, André Corvelo, Vicki L. Friesen, Martin Stervander, Les Christidis, Siavash Mirarab, T. Brandt Ryder, Jason T. Weir, Michael G. Campana, Lara Puetz, Qi Zhou, Matthew I. M. Louder, Anna Tigano, Scott V. Edwards, Matthew J. Fuxjager, Fumin Lei, Robert C. Fleischer, Henriette van der Zwan, Francisco Prosdocimi, Jeffrey M. DaCosta, Peter Njoroge, Nancy F. Chen, Leopold Eckhart, Zongji Wang, Yuan Deng, Lainy B. Day, Jon Fjeldså, Carina Visser, Robb T. Brumfield, Scott A. Taylor, Josefin Stiller, Peter A. Hosner, Qiye Li, Barney A. Schlinger, Jimmy A. McGuire, Kira E. Delmore, Julio Rozas, Haw Chuan Lim, Alexander Suh, Murray P. Cox, Henrik Mouritsen, Christopher N. Balakrishnan, George Pacheco, Lukas F. Keller, Jian Wang, Thomas Sicheritz-Pontén, Frederick H. Sheldon, Biao Wang, Bette A. Loiselle, Ellen D. Ketterson, Ian G. Jamieson, Edward L. Braun, Nicolas Dussex, Mark Diekhans, Maude W. Baldwin, Peter G. Ryan, Nicholas Costa Barroso Lima, Gerald Borgia, Huanming Yang, Guillermo Friis, Suvi Ponnikas, Timothy B. Sackton, Alison Cloutier, Matthew D. Carling, Andre Franke, Dustin J. Foote, Kim Rutherford, Jacob González-Solís, Araxi O. Urrutia, and Guojie Zhang

Subjects
0301 basic medicine, Conservation of Natural Resources, Genome, Multidisciplinary, Comparative genomics, Published Erratum, Datasets as Topic, Sampling (statistics), Genomics, Synteny, Evolutionary genetics, Birds, 03 medical and health sciences, 030104 developmental biology, Geography, Statistics, Animals, Humans, Table (landform), Finches, Selection, Genetic, Author Correction, Chickens, Phylogeny
Abstract

In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.

Published
2021
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2. Dense sampling of bird diversity increases power of comparative genomics.

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, and Pacheco, George

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. 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. [ABSTRACT FROM AUTHOR]

Published
2020
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