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Dense sampling of bird diversity increases power of comparative genomics

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Delmore,  Kira
Max Planck Research Group Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Liedvogel,  Miriam
Max Planck Research Group Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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s41586-020-2873-9.pdf
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Citation

Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Reeve, A. H., et al. (2020). Dense sampling of bird diversity increases power of comparative genomics. Nature, 587(7833), 252-257. doi:10.1038/s41586-020-2873-9.


Cite as: http://hdl.handle.net/21.11116/0000-0007-9CAE-6
Abstract
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 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.