(174) Densely sampling genomes across the diversity of birds increases power of comparative genomics analyses. Nature 587: 252–257
Feng, S., J.Stiller, Y.Deng, J.Armstrong, Q.Fang, A.H.Reeve, D.Xie, G.Chen, C.Guo, B.C.Faircloth, B.Petersen, Z.Wang, Q.Zhou, M.Diekhans, W.Chen, S.Andreu-Sánchez, A.Margaryan, J.T.Howard, C.Parent, G.Pacheco, M.S.Sinding, L.Puetz, E.Cavill, Â.M.Ribeiro, L.Eckhart, J.Fjeldså, P.A.Hosner, R.T.Brumfield, L.Christidis, M.F.Bertelsen, T.Sicheritz-Ponten, D.T.Tietze, B.C.Robertson, G.Song, G.Borgia, S.Claramunt, I.J.Lovette, S.J.Cowen, P.Njoroge, J.P.Dumbacher, O.A.Ryder, J.Fuchs, M.Bunce, D.W.Burt, J.Cracraft, G.Meng, S.J.Hackett, P.G. Ryan, K.A.Jønsson, I.G.Jamieson, R.R. da Fonseca, E.L.Braun, P.Houde, S.Mirarab, A.Suh, B.Hansson, S.Ponnikas, H.Sigeman, M.Stervander, P.B.Frandsen, H. van der Zwan, R. van der Sluis, C.Visser, C.N.Balakrishnan, A.G.Clark, J.W.Fitzpatrick, R.Bowman, N.Chen, A.Cloutier, T.B.Sackton, S.V.Edwards, D.J.Foote, S.B.Shakya, F.H.Sheldon, A.Vignal, A.E.R.Soares, B.Shapiro, J.González-Solís, J.Ferrer-Obiol, J.Rozas, M.Riutort, A.Tigano, V.Friesen, L.Dalén, A.O.Urrutia, T.Székely, Y.Liu, M.G.Campana, A.Corvelo, R.C.Fleischer, K.M.Rutherford, N.J.Gemmell, N.Dussex, H.Mouritsen, N.Thiele, K.Delmore, M.Liedvogel, A.Franke, M.P.Hoeppner, O.Krone, A.M.Fudickar, B.Milá, E.D.Ketterson, A.E.Fidler, G.Friis, Á.M.Parody-Merino, P.F.Battley, M.P.Cox, N.C.B.Lima, F.Prosdocimi, T.L.Parchman, B.A.Schlinger, B.A.Loiselle, J.G.Blake, H.C.Lim, L.B.Day, M.J.Fuxjager, M.W.Baldwin, M.J.Braun, M.Wirthlin, R.B.Dikow, T.B.Ryder, G.Camenisch, L.F.Keller, J.M.DaCosta, M.E.Hauber, M.I.M.Louder, C.C.Witt, J.A.McGuire, J.Mudge, L.C.Megna, M.D.Carling, B.Wang, S.A.Taylor, G.Del-Rio, A.Aleixo, A.T.R.Vasconcelos, C.V.Mello, J.T.Weir, D.Haussler, Q.Li, H.Yang, J.Wang, F.Lei, C.Rahbek, M.TP.Gilbert, G.R.Graves, E.D.Jarvis, B.Paten & G.Zhang (2020)
Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity. 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.