MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

A Abyzov

A Alexa

A Conesa

A Hussain

AJ Iafrate

AJ Sharp

AJ Vilella

AR Boyko

AR Quinlan

B Guo

BE Deagle

C Eizaguirre

Christophe Eizaguirre

CL McGrath

CL Peichel

D Bryant

D Juan

D Tautz

DE Cook

DH Huson

DJ Turner

DR Schrider

DR Zerbino

E Gazave

E Proux

Erich Bornberg-Bauer

FA Kondrashov

FC Jones

Frédéric J. J. Chain

G Gibson

G Orti

GC Conant

GH Perry

GM Cooper

H Kehrer-Sawatzki

H Li

Irene E. Samonte

J Sebat

JA Fawcett

Jianzhi Zhang

JJ Emerson

JK Colbourne

JO Korbel

K Chen

K Khalturin

K Ye

KJ Lipinski

KJ Livak

KM Teshima

KM Wegner

L Xu

LC Hsing

LR Saraiva

M Hiraiwa

M Long

M Lynch

M Milinski

M Roesti

MA DePristo

Mahesh Panchal

Manfred Milinski

Martin Kalbe

Monika Stoll

N Ghanem

P Danecek

P Flicek

P Sjödin

PA Hohenlohe

PGD Feulner

PH Sudmant

Philine G. D. Feulner

PM Kim

R Redon

RC Iskow

S Moretti

S Sawyer

SF Altschul

SH Williamson

SM Waszak

SR Browning

T Marques-Bonet

T Rausch

TD Schmittgen

Thorsten B. H. Reusch

Tobias L. Lenz

V Guryev

V Katju

V Ranwez

X Huang

Y Hashiguchi

Y Zheng

YE Zhang

PLoS Genetics

English

PubMed

Duplicate genes emerge as copy-number variations (CNVs) at the population level, and remain copy-number polymorphic until they are fixed or lost. The successful establishment of such structural polymorphisms in the genome plays an important role in evolution by promoting genetic diversity, complexity and innovation. To characterize the early evolutionary stages of duplicate genes and their potential adaptive benefits, we combine comparative genomics with population genomics analyses to evaluate the distribution and impact of CNVs across natural populations of an ecogenomic model, the three-spined stickleback. With whole genome sequences of 66 individuals from populations inhabiting three distinct habitats, we find that CNVs generally occur at low frequencies and are often only found in one of the 11 populations surveyed. A subset of CNVs, however, displays copy-number differentiation between populations, showing elevated within-population frequencies consistent with local adaptation. By comparing teleost genomes to identify lineagespecific genes and duplications in sticklebacks, we highlight rampant gene content differences among individuals in which over 30% of young duplicate genes are CNVs. These CNV genes are evolving rapidly at the molecular level and are enriched with functional categories associated with environmental interactions, depicting the dynamic early copy-number polymorphic stage of genes during population differentiation

Chain, F.

Feulner, P.

Panchal, M.

Eizaguirre, C.

Samonte, I.

Kalbe, M.

Lenz, T.

Stoll, M.

Bornberg-Bauer, E.

Milinski, M.

Reusch, T.

MPG.PuRe

Extensive copy-number variation of young genes across stickleback populations

Chain, FJJ

Feulner, PGD

Panchal, M

Eizaguirre, C

Samonte, IE

Kalbe, M

Lenz, TL

Stoll, M

Bornberg-Bauer, E

Milinski, M

Reusch, TBH

Queen Mary Research Online

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Extensive Copy-Number Variation of Young Genes across Stickleback Populations

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

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