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Dense sampling of bird diversity increases power of comparative genomics
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2020 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 587, no 7833Article in journal (Refereed) Published
Abstract [en]

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), 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. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

Place, publisher, year, edition, pages
2020. Vol. 587, no 7833
National Category
Evolutionary Biology
Research subject
Diversity of life
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URN: urn:nbn:se:nrm:diva-4089DOI: 10.1038/s41586-020-2873-9OAI: oai:DiVA.org:nrm-4089DiVA, id: diva2:1511422
Available from: 2020-12-18 Created: 2020-12-18 Last updated: 2020-12-18Bibliographically approved

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Dalen, LoveDussex, Nicolas
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