Data from: Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach

In recent years, the explosion of affordable next generation sequencing
technology has provided an unprecedented opportunity to conduct
genome-wide studies of adaptive evolution in organisms previously lacking
extensive genomic resources. Here, we characterise genome-wide patterns of
variability and differentiation using pooled DNA from eight populations of
the nine-spined stickleback (Pungitius pungitius L.) from marine, lake and
pond environments. We developed a novel genome complexity reduction
protocol, defined as paired-end double restriction-site associated DNA (PE
dRAD), to maximise read coverage at sequenced locations. This allowed us
to identify over 114,000 short consensus sequences and 15,000 SNPs
throughout the genome. A total of 6,834 SNPs mapped to a single position
on the related three-spined stickleback genome, allowing the detection of
genomic regions affected by divergent and balancing selection, both
between species and between freshwater and marine populations of the
nine-spined stickleback. Gene ontology (GO) analysis revealed 15 genomic
regions with elevated diversity, enriched for genes involved in functions
including immunity, chemical stimulus response, lipid metabolism and
signalling pathways. Comparisons of marine and freshwater populations
identified nine regions with elevated differentiation related to kidney
development, immunity and MAP kinase pathways. In addition, our analysis
revealed that a large proportion of the identified SNPs mapping to LG XII
are likely to represent alternative alleles from divergent X and Y
chromosomes, rather than true autosomal markers following Mendelian
segregation. Our work demonstrates how population-wide sequencing and
combining inter- and intra-specific RAD analysis can uncover genome-wide
patterns of differentiation and adaptations in a non-model species.