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Published (Version of record)CC BY V4.0, Open
Published (Version of record)CC BY V4.0, Open
Journal article
Dense sampling of bird diversity increases power of comparative genomics
Nature, Vol.587(7833), pp.252-257
2020
PMID: 33177665
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Source: InCites
Abstract
Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity. Sparse taxon sampling has previously been proposed to confound phylogenetic inference, 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.
Details
- Title
- Dense sampling of bird diversity increases power of comparative genomics
- Creators
- Shaohong Feng (Author) - BGI ShenzhenJosefin Stiller - University of CopenhagenYuan Deng (Author) - BGI ShenzhenJoel Armstrong (Author)Qi Fang (Author) - University of CopenhagenAndrew Hart Reeve (Author) - IT University of CopenhagenDuo Xie (Author) - Graduate University of Chinese Academy of SciencesGuangji Chen (Author) - Graduate University of Chinese Academy of SciencesGuo Chunxue (Author) - China National GenebankLeslie Christidis (Author) - Southern Cross University
- Publication Details
- Nature, Vol.587(7833), pp.252-257
- Publisher
- Nature Publishing Group
- Identifiers
- 991012893898802368
- Copyright
- Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
- Academic Unit
- Faculty of Science and Engineering; School of Environment, Science and Engineering; Graduate School
- Language
- English
- Resource Type
- Journal article