Dense sampling of bird diversity increases power of comparative genomics.
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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 363genomes from 92.4% of bird families-including 267newly sequenced genomes produced for phaseII of the Bird 10,000Genomes (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.
Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q. i., Reeve, A. H., ... Zhang, G.
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191
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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 C||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||Ribeiro, Ângela M||Eckhart, Leopold||Fjeldså, Jon||Hosner, Peter A||Brumfield, Robb T||Christidis, Les||Bertelsen, Mads F||Sicheritz-Ponten, Thomas||Tietze, Dieter Thomas||Robertson, Bruce C||Song, Gang||Borgia, Gerald||Claramunt, Santiago||Lovette, Irby J||Cowen, Saul J||Njoroge, Peter||Dumbacher, John Philip||Ryder, Oliver A||Fuchs, Jérôme||Bunce, Michael||Burt, David W||Cracraft, Joel||Meng, Guanliang||Hackett, Shannon J||Ryan, Peter G||Jønsson, Knud Andreas||Jamieson, Ian G||da Fonseca, Rute R||Braun, Edward L||Houde, Peter||Mirarab, Siavash||Suh, Alexander||Hansson, Bengt||Ponnikas, Suvi||Sigeman, Hanna||Stervander, Martin||Frandsen, Paul B||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||Sackton, Timothy B||Edwards, Scott V||Foote, Dustin J||Shakya, Subir B||Sheldon, Frederick H||Vignal, Alain||Soares, André ER||Shapiro, Beth||González-Solís, Jacob||Ferrer-Obiol, Joan||Rozas, Julio||Riutort, Marta||Tigano, Anna||Friesen, Vicki||Dalén, Love||Urrutia, Araxi O||Székely, Tamás||Liu, Yang||Campana, Michael G||Corvelo, André||Fleischer, Robert C||Rutherford, Kim M||Gemmell, Neil J||Dussex, Nicolas||Mouritsen, Henrik||Thiele, Nadine||Delmore, Kira||Liedvogel, Miriam||Franke, Andre||Hoeppner, Marc P||Krone, Oliver||Fudickar, Adam M||Milá, Borja||Ketterson, Ellen D||Fidler, Andrew Eric||Friis, Guillermo||Parody-Merino, Ángela M||Battley, Phil F||Cox, Murray P||Lima, Nicholas Costa Barroso||Prosdocimi, Francisco||Parchman, Thomas Lee||Schlinger, Barney A||Loiselle, Bette A||Blake, John G||Lim, Haw Chuan||Day, Lainy B||Fuxjager, Matthew J||Baldwin, Maude W||Braun, Michael J||Wirthlin, Morgan||Dikow, Rebecca B||Ryder, T Brandt||Camenisch, Glauco||Keller, Lukas F||DaCosta, Jeffrey M||Hauber, Mark E||Louder, Matthew IM||Witt, Christopher C||McGuire, Jimmy A||Mudge, Joann||Megna, Libby C||Carling, Matthew D||Wang, Biao||Taylor, Scott A||Del-Rio, Glaucia||Aleixo, Alexandre||Vasconcelos, Ana Tereza Ribeiro||Mello, Claudio V||Weir, Jason T||Haussler, David||Li, Qiye||Yang, Huanming||Wang, Jian||Lei, Fumin||Rahbek, Carsten||Gilbert, M Thomas P||Graves, Gary R||Jarvis, Erich D||Paten, Benedict||Zhang, Guojie
