Dense sampling of bird diversity increases power of comparative genomics
Feng, S. ; Hansson, Bengt LU
; Ponnikas, Suvi
LU
; Sigeman, Hanna
LU
; Stervander, Martin
LU
; Paten, B.
and Zhang, G.
(2020)
In Nature
587(7833).
p.252-257
- 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... (More)
- 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). (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/01dd0a45-f3df-4f18-a0d6-7cff35bd27b4
- author
- Feng, S.
; Hansson, Bengt
LU
; Ponnikas, Suvi
LU
; Sigeman, Hanna
LU
; Stervander, Martin
LU
; Paten, B.
and Zhang, G.
- author collaboration
- organization
- publishing date
- 2020
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- bird, genetic analysis, genome, genomics, phylogenetics, sampling, article, comparative genomics, comparative study, nonhuman, pipeline
- in
- Nature
- volume
- 587
- issue
- 7833
- pages
- 6 pages
- publisher
- Nature Publishing Group
- external identifiers
-
- scopus:85095836366
- pmid:33177665
- ISSN
- 0028-0836
- DOI
- 10.1038/s41586-020-2873-9
- language
- English
- LU publication?
- yes
- id
- 01dd0a45-f3df-4f18-a0d6-7cff35bd27b4
- alternative location
- https://www.scopus.com/inward/record.uri?eid=2-s2.0-85095836366&doi=10.1038%2fs41586-020-2873-9&partnerID=40&md5=a98b88533e28fb690eb0200760b565fd
- date added to LUP
- 2020-11-24 13:00:49
- date last changed
- 2022-04-26 22:05:14
@article{01dd0a45-f3df-4f18-a0d6-7cff35bd27b4,
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).}},
author = {{Feng, S. and Hansson, Bengt and Ponnikas, Suvi and Sigeman, Hanna and Stervander, Martin and Paten, B. and Zhang, G.}},
issn = {{0028-0836}},
keywords = {{bird; genetic analysis; genome; genomics; phylogenetics; sampling; article; comparative genomics; comparative study; nonhuman; pipeline}},
language = {{eng}},
number = {{7833}},
pages = {{252--257}},
publisher = {{Nature Publishing Group}},
series = {{Nature}},
title = {{Dense sampling of bird diversity increases power of comparative genomics}},
url = {{http://dx.doi.org/10.1038/s41586-020-2873-9}},
doi = {{10.1038/s41586-020-2873-9}},
volume = {{587}},
year = {{2020}},
}