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Background  Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail  Littorina saxatilis.  First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the  Littorina  genome draft. Secondly, we performed a genome-wide comparison of four closely related  Littorina  species:  L. fabalis ,  L. compressa ,  L. arcana  and  L. saxatilis  and of populations of  L. saxatilis  found in Spain, Britain and Sweden. Finally, we tested whether we could identify genetic variation underlying “Crab” and “Wave” ecotypes of  L. saxatilis.Results  We could reliably detect copy number variations, deletions and high sequence divergence (i.e. above 3%), but not single nucleotide polymorphisms. The overall hybridization pattern and number of significantly diverged genes were in close agreement with earlier phylogenetic reconstructions based on single genes. The trichotomy of  L. arcana ,  L. compressa  and  L. saxatilis  could not be resolved and we argue that these divergence events have occurred recently and very close in time. We found evidence for high levels of segmental duplication in the  Littorina  genome (10% of the transcripts represented on the array and up to 23% of the analyzed genomic fragments); duplicated genes and regions were mostly the same in all analyzed species. Finally, this method discriminated geographically distant populations of  L. saxatilis , but we did not detect any significant genome divergence associated with ecotypes of  L. saxatilis.Conclusions  The present study provides new information on the sensitivity and the potential use of oligonucleotide arrays for genotyping of non-model organisms. Applying this method to  Littorina  species yields insights into genome evolution following the recent species radiation and supports earlier single-gene based phylogenies. Genetic differentiation of  L. saxatilis  ecotypes was not detected in this study, despite pronounced innate phenotypic differences. The reason may be that these differences are due to single-nucleotide polymorphisms.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-687) contains supplementary material, which is available to authorized users.

Species and gene divergence in Littorina snails detected by array comparative genomic hybridization