Dense sampling of bird diversity increases power of comparative genomics

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Dense sampling of bird diversity increases power of comparative genomics. / Feng, S.; Hansson, Bengt; Ponnikas, Suvi; Sigeman, Hanna; Stervander, Martin; Paten, B.; Zhang, G.; et al.

I: Nature, Vol. 587, Nr. 7833, 2020, s. 252-257.

Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

Harvard

Feng, S, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Paten, B, Zhang, G & et al. 2020, 'Dense sampling of bird diversity increases power of comparative genomics', Nature, vol. 587, nr. 7833, s. 252-257. https://doi.org/10.1038/s41586-020-2873-9

APA

Feng, S., Hansson, B., Ponnikas, S., Sigeman, H., Stervander, M., Paten, B., Zhang, G., & et al. (2020). Dense sampling of bird diversity increases power of comparative genomics. Nature, 587(7833), 252-257. https://doi.org/10.1038/s41586-020-2873-9

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MLA

Vancouver

Author

Feng, S. ; Hansson, Bengt ; Ponnikas, Suvi ; Sigeman, Hanna ; Stervander, Martin ; Paten, B. ; Zhang, G. ; et al. / Dense sampling of bird diversity increases power of comparative genomics. I: Nature. 2020 ; Vol. 587, Nr. 7833. s. 252-257.

RIS

TY - JOUR

T1 - Dense sampling of bird diversity increases power of comparative genomics

AU - Feng, S.

AU - Hansson, Bengt

AU - Ponnikas, Suvi

AU - Sigeman, Hanna

AU - Stervander, Martin

AU - Paten, B.

AU - Zhang, G.

AU - et al.

PY - 2020

Y1 - 2020

N2 - 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).

AB - 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).

KW - bird

KW - genetic analysis

KW - genome

KW - genomics

KW - phylogenetics

KW - sampling

KW - article

KW - comparative genomics

KW - comparative study

KW - nonhuman

KW - pipeline

U2 - 10.1038/s41586-020-2873-9

DO - 10.1038/s41586-020-2873-9

M3 - Article

C2 - 33177665

VL - 587

SP - 252

EP - 257

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7833

ER -