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PMID: 20195501 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags.

PLoS genetics ·Vol. 6 ·No. 2 ·2010-02-26 ·Pages e1000862

Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA

Abstract

Next-generation sequencing technology provides novel opportunities for gathering genome-scale sequence data in natural populations, laying the empirical foundation for the evolving field of population genomics. Here we conducted a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback (Gasterosteus aculeatus). We used Illumina-sequenced RAD tags to identify and type over 45,000 single nucleotide polymorphisms (SNPs) in each of 100 individuals from two oceanic and three freshwater populations. Overall estimates of genetic diversity and differentiation among populations confirm the biogeographic hypothesis that large panmictic oceanic populations have repeatedly given rise to phenotypically divergent freshwater populations. Genomic regions exhibiting signatures of both balancing and divergent selection were remarkably consistent across multiple, independently derived populations, indicating that replicate parallel phenotypic evolution in stickleback may be occurring through extensive, parallel genetic evolution at a genome-wide scale. Some of these genomic regions co-localize with previously identified QTL for stickleback phenotypic variation identified using laboratory mapping crosses. In addition, we have identified several novel regions showing parallel differentiation across independent populations. Annotation of these regions revealed numerous genes that are candidates for stickleback phenotypic evolution and will form the basis of future genetic analyses in this and other organisms. This study represents the first high-density SNP-based genome scan of genetic diversity and differentiation for populations of threespine stickleback in the wild. These data illustrate the complementary nature of laboratory crosses and population genomic scans by confirming the adaptive significance of previously identified genomic regions, elucidating the particular evolutionary and demographic history of such regions in natural populations, and identifying new genomic regions and candidate genes of evolutionary significance.

MeSH Terms
Adaptation, Physiological/genetics Alleles Animals Base Sequence DNA/genetics Fresh Water Gene Frequency Genetic Linkage Genetic Variation Genome/genetics Geography Metagenomics/methods Polymorphism, Single Nucleotide/genetics Population Dynamics Restriction Mapping/methods Seawater Selection, Genetic Sequence Analysis, DNA/methods Smegmamorpha/genetics Water-Electrolyte Balance/genetics
Chemicals
DNA
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Hohenlohe Paul A
Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon, United States of America.
Bassham Susan
Etter Paul D
Stiffler Nicholas
Johnson Eric A
Cresko William A
Conflict of Interest

The authors have declared that no competing interests exist.

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Article Info
Journal
PLoS genetics
Abbr.
PLoS Genet
ISSN
1553-7404
DOI
10.1371/journal.pgen.1000862
Published
2010-02-26
Epub
2010-00-26
Pages
e1000862
Language
English
Region
United States
NLM ID
101239074
PMCID
PMC2829049
Subset
IM
Grants
NIGMS NIH HHS · F32 GM078949 · United States
NIGMS NIH HHS · R24 GM079486 · United States
NIGMS NIH HHS · 1R24GM079486-01A1 · United States
External Links
PubMed source DOI: 10.1371/journal.pgen.1000862 PMC Full Text View journal details
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