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Abstract

Since the end of the Pleistocene, the three-spined stickleback (Gasterosteus aculeatus) has
repeatedly colonized and adapted to various freshwater habitats probably originating from
ancestral marine populations. Standing genetic variation and the underlying genomic
architecture both have been speculated to contribute to recent adaptive radiations of
sticklebacks. Here, we expand on the current genomic resources of this fish by providing
extensive genome-wide variation data from six individuals from a marine (North Sea)
stickleback population. Using next-generation sequencing and a combination of pairedend
and mate-pair libraries, we detected a wide size range of genetic variation. Among the
six individuals, we found more than 7% of the genome is polymorphic, consisting of
2 599 111 SNPs, 233 464 indels and structural variation (SV) (>50 bp) such as 1054 copynumber
variable regions (deletions and duplications) and 48 inversions. Many of these
polymorphisms affect gene and coding sequences. Based on SNP diversity, we determined
outlier regions concordant with signatures expected under adaptive evolution. As some of
these outliers overlap with pronounced regions of copy-number variation, we propose the
consideration of such SV when analysing SNP data from re-sequencing approaches. We
further discuss the value of this resource on genome-wide variation for further investigation
upon the relative contribution of standing variation on the parallel evolution of
sticklebacks and the importance of the genomic architecture in adaptive radiation.