Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

By Paul A Hohenlohe, S. Bassham, Paul D. Etter, Nicholas Stiffler, Eric A. Johnson, W. Cresko. PLoS Genetics, 2010

1,454 citations recorded by the source corpus.

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.

Subfields: Education

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Citations in the corpus

The impact of global climate change on genetic diversity within populations and species (2013, background): “Such approaches are particularly effective for species with a sequenced genome (Hohenlohe et al. 2010; Tollrian & Leese 2010).”
Applications of next generation sequencing in molecular ecology of non-model organisms (2011, methodology): “, 2007) and sticklebacks (Gasterosteus; Hohenlohe et al., 2010) are becoming important genetic models (Mitchell-Olds et al.”
Genomics and the future of conservation genetics (2010, background): “New genomic tools also allow anonymous markers to be assayed across the genome to identify local adaptation; for example, Hohenlohe et al.(66) sampled 100 threespine stickleback individuals across 5 populations in Alaska.”
Identifying targets and agents of selection: innovative methods to evaluate the processes that contribute to local adaptation (2017, methodology): “These methods have also been effectively combined with mapping approaches to identify causal genes under broadQTL,whichwould otherwise take years to resolve via positional cloning (Stinchcombe &Hoekstra 2008; Hohenlohe et al. 2010; Wright et al. 2015; Gould, Chen & Lowry 2017).”
Ecological genetics of invasive alien species (2011, background): “…the RAD-tag method (Baird et al. 2008) allows an unprecedented number of genetic markers to be characterised and typed, offering a powerful means to identify loci contributing to adaptation during invasions (see Hohenlohe et al. 2010 for a recent application and Stapley et al. 2010 for a review).”
Species Delimitation using Genome-Wide SNP Data (2013, methodology): “The program ustacks then uses a maximum likelihood algorithm to determine haplotypes for each individual (Hohenlohe et al. 2010).”
A practical guide to environmental association analysis in landscape genomics (2015, background): “Population genomics (reviewed in Hohenlohe et al. 2010b) and quantitative genetics (Stinchcombe & Hoekstra 2008) use genotypic and phenotypic information, respectively, alone to identify adaptive genetic variation.”
Stacks: an analysis tool set for population genomics (2013, methodology): “The study of nearly complete genetic information in numerous individuals drawn from scores of populations is now rapidly becoming a reality (Storz 2005; Bonin 2008; Hohenlohe et al. 2010a, 2012a; Stapley et al. 2010).”
Inferring Phylogenies from RAD Sequence Data (2012, methodology): “[13] used the method to conduct population genomic analysis of natural populations of threespine stickleback (G.”
Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences (2011, methodology): “At each nucleotide position in a locus, Stacks adapts the single-nucleotide, diploid genotyping method described by (Hohenlohe et al. 2010).”