Shaohong Feng, China National Genebank
Josefin Stiller, Københavns Universitet
Yuan Deng, China National Genebank
Joel Armstrong, University of California, Santa Cruz
Qi Fang, China National Genebank
Andrew Hart Reeve, Københavns Universitet
Duo Xie, China National Genebank
Guangji Chen, China National Genebank
Chunxue Guo, China National Genebank
Brant C. Faircloth, Louisiana State University
Bent Petersen, Asian Institute of Medicine, Science & Technology
Zongji Wang, China National Genebank
Qi Zhou, Life Sciences Institute, Zhejiang University
Mark Diekhans, University of California, Santa Cruz
Wanjun Chen, China National Genebank
Sergio Andreu-Sánchez, Københavns Universitet
Ashot Margaryan, University of Copenhagen, Faculty of Health Sciences
Jason Travis Howard, Novogene
Carole Parent, Duke University Medical Center
George Pacheco, University of Copenhagen, Faculty of Health Sciences
Mikkel Holger S. Sinding, University of Copenhagen, Faculty of Health Sciences
Lara Puetz, University of Copenhagen, Faculty of Health Sciences
Emily Cavill, University of Copenhagen, Faculty of Health Sciences
Ângela M. Ribeiro, Københavns Universitet
Leopold Eckhart, Medizinische Universitat Wien
Jon Fjeldså, Københavns Universitet
Peter A. Hosner, Københavns Universitet
Robb T. Brumfield, Louisiana State University
Les Christidis, Southern Cross University
Mads F. Bertelsen, Copenhagen Zoo
Thomas Sicheritz-Ponten, Asian Institute of Medicine, Science & Technology
Dieter Thomas Tietze, Universität Hamburg
Bruce C. Robertson, University of Otago
Gang Song, Chinese Academy of Sciences

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© 2020, The Author(s). 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.

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