Dense sampling of bird diversity increases power of comparative genomics

Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift


title = "Dense sampling of bird diversity increases power of comparative genomics",
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. {\textcopyright} 2020, The Author(s).",
keywords = "bird, genetic analysis, genome, genomics, phylogenetics, sampling, article, comparative genomics, comparative study, nonhuman, pipeline",
author = "S. Feng and Bengt Hansson and Suvi Ponnikas and Hanna Sigeman and Martin Stervander and B. Paten and G. Zhang and {et al.}",
year = "2020",
doi = "10.1038/s41586-020-2873-9",
language = "English",
volume = "587",
pages = "252--257",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7833",