Dense sampling of bird diversity increases power of comparative genomics
- Feng, S.
- Stiller, J.
- Deng, Y.
- Armstrong, J.
- Fang, Q.
- Reeve, A.
- Xie, D.
- Chen, G.
- Guo, C.
- Faircloth, B.
- Petersen, B.
- Wang, Z.
- Zhou, Q.
- Diekhans, M.
- Chen, W.
- Andreu-Sánchez, S.
- Margaryan, A.
- Howard, J.
- Parent, C.
- Pacheco, G.
- Sinding, M.
- Puetz, L.
- Cavill, E.
- Ribeiro, Â.
- Eckhart, L.
- Fjeldså, J.
- Hosner, P.
- Brumfield, R.
- Christidis, L.
- Bertelsen, M.
- Sicheritz-Ponten, T.
- Tietze, D.
- Robertson, B.
- Song, G.
- Borgia, G.
- Claramunt, S.
- Lovette, I.
- Cowen, S.
- Njoroge, P.
- Dumbacher, J.
- Ryder, O.
- Fuchs, J.
- Bunce, M.
- Burt, D.
- Cracraft, J.
- Meng, G.
- Hackett, S.
- Ryan, P.
- Jønsson, K.
- Jamieson, I.
- da Fonseca, R.
- Braun, E.
- Houde, P.
- Mirarab, S.
- Suh, A.
- Hansson, B.
- Ponnikas, S.
- Sigeman, H.
- Stervander, M.
- Frandsen, P.
- van der Zwan, H.
- van der Sluis, R.
- Visser, C.
- Balakrishnan, C.
- Clark, A.
- Fitzpatrick, J.
- Bowman, R.
- Chen, N.
- Cloutier, A.
- Sackton, T.
- Edwards, S.
- Foote, D.
- Shakya, S.
- Sheldon, F.
- Vignal, A.
- Soares, A.
- Shapiro, B.
- González-Solís, J.
- Ferrer-Obiol, J.
- Rozas, J.
- Riutort, M.
- Tigano, A.
- Friesen, V.
- Dalén, L.
- Urrutia, A.
- Székely, T.
- Liu, Y.
- Campana, M.
- Corvelo, A.
- Fleischer, R.
- Rutherford, K.
- Gemmell, N.
- Dussex, N.
- Mouritsen, H.
- Thiele, N.
- Delmore, K.
- Liedvogel, M.
- Franke, A.
- Hoeppner, M.
- Krone, O.
- Fudickar, A.
- Milá, B.
- Ketterson, E.
- Fidler, A.
- Friis, G.
- Parody-Merino, Á.
- Battley, P.
- Cox, M.
- Lima, N.
- Prosdocimi, F.
- Parchman, T.
- Schlinger, B.
- Loiselle, B.
- Blake, J.
- Lim, H.
- Day, L.
- Fuxjager, M.
- Baldwin, M.
- Braun, M.
- Wirthlin, M.
- Dikow, R.
- Ryder, T.
- Camenisch, G.
- Keller, L.
- DaCosta, J.
- Hauber, M.
- Louder, M.
- Witt, C.
- McGuire, J.
- Mudge, J.
- Megna, L.
- Carling, M.
- Wang, B.
- Taylor, S.
- Del-Rio, G.
- Aleixo, A.
- Vasconcelos, A.
- Mello, C.
- Weir, J.
- Haussler, D.
- Li, Q.
- Yang, H.
- Wang, J.
- Lei, F.
- Rahbek, C.
- Gilbert, M.
- Graves, G.
- Jarvis, E.
- authors, B.
DOIAbstract
Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1,2,3,4. 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 re...
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