Article

Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes.

Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
Philosophical Transactions of The Royal Society B Biological Sciences (impact factor: 6.4). 02/2012; 367(1587):395-408. DOI:10.1098/rstb.2011.0245 pp.395-408
Source: PubMed

ABSTRACT Population genomic studies are beginning to provide a more comprehensive view of dynamic genome-scale processes in evolution. Patterns of genomic architecture, such as genomic islands of increased divergence, may be important for adaptive population differentiation and speciation. We used next-generation sequencing data to examine the patterns of local and long-distance linkage disequilibrium (LD) across oceanic and freshwater populations of threespine stickleback, a useful model for studies of evolution and speciation. We looked for associations between LD and signatures of divergent selection, and assessed the role of recombination rate variation in generating LD patterns. As predicted under the traditional biogeographic model of unidirectional gene flow from ancestral oceanic to derived freshwater stickleback populations, we found extensive local and long-distance LD in fresh water. Surprisingly, oceanic populations showed similar patterns of elevated LD, notably between large genomic regions previously implicated in adaptation to fresh water. These results support an alternative biogeographic model for the stickleback radiation, one of a metapopulation with appreciable bi-directional gene flow combined with strong divergent selection between oceanic and freshwater populations. As predicted by theory, these processes can maintain LD within and among genomic islands of divergence. These findings suggest that the genomic architecture in oceanic stickleback populations may provide a mechanism for the rapid re-assembly and evolution of multi-locus genotypes in newly colonized freshwater habitats, and may help explain genetic mapping of parallel phenotypic variation to similar loci across independent freshwater populations.

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Keywords

adaptive population differentiation
 
ancestral oceanic
 
appreciable bi-directional gene flow
 
colonized freshwater habitats
 
comprehensive view
 
divergent selection
 
dynamic genome-scale processes
 
fresh water
 
freshwater populations
 
genomic islands
 
large genomic regions
 
long-distance linkage disequilibrium
 
next-generation sequencing data
 
oceanic stickleback populations
 
Population genomic studies
 
rapid re-assembly
 
results support
 
stickleback radiation
 
strong divergent selection
 
threespine stickleback