Dense sampling of bird diversity increases power of comparative genomics

Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterising biodiversity1–4. Sparse taxon sampling has been proposed to confound phylogenetic inference5 and captures only a fraction of the genomic diversity. Here, we report a significant step towards 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. This largest eukaryotic comparative genome dataset to date is used with a novel pipeline leveraging a reference-free whole-genome alignment to identify orthologous regions in greater numbers than previously possible and to recognise genomic novelties in particular bird lineages. The densely sampled alignment provided the first single base-pair map of selection, more than doubled the fraction of bases confidently predicted to be under conservation, and revealed extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can unveil more shared and lineage-specific variation, and improve the dissection of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist species conservation efforts.