Dense sampling of bird diversity increases power of comparative genomics

Research output: Contribution to journalArticle

Abstract

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. © 2020, The Author(s).

Details

Authors
Organisations
External organisations
  • China National Genebank
  • University of California, Santa Cruz
  • University of Oregon
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Evolutionary Biology

Keywords

  • bird, genetic analysis, genome, genomics, phylogenetics, sampling, article, comparative genomics, comparative study, nonhuman, pipeline
Original languageEnglish
Pages (from-to)252-257
Number of pages6
JournalNature
Volume587
Issue number7833
Publication statusPublished - 2020
Publication categoryResearch
Peer-reviewedYes