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

Area of Science:

• Population genomics
• Evolutionary biology
• Genetics

Background:

• Next-generation sequencing enables genome-scale data collection in natural populations.
• Population genomics is a rapidly advancing field.
• Threespine stickleback (Gasterosteus aculeatus) are a model organism for studying adaptation.

Purpose of the Study:

• To conduct a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback.
• To identify genomic regions under selection and candidate genes associated with phenotypic evolution.
• To investigate the extent of parallel genetic evolution across independently derived populations.

Main Methods:

• Used Illumina-sequenced RAD tags to identify and genotype over 45,000 single nucleotide polymorphisms (SNPs).
• Analyzed 100 individuals from two oceanic and three freshwater populations.
• Performed genome scans to assess genetic diversity and differentiation.

Main Results:

• Confirmed that large oceanic populations repeatedly gave rise to divergent freshwater populations.
• Identified genomic regions with signatures of balancing and divergent selection consistently across multiple populations.
• Found that these regions co-localize with previously identified quantitative trait loci (QTL) for phenotypic variation.
• Discovered novel regions showing parallel differentiation and identified candidate genes for phenotypic evolution.

Conclusions:

• Replicate parallel phenotypic evolution in stickleback likely occurs through extensive, parallel genetic evolution at a genome-wide scale.
• This study confirms the adaptive significance of previously identified genomic regions and identifies new ones.
• The findings highlight the complementary power of laboratory crosses and population genomic scans for understanding evolution in natural populations.