Habitat-associated Genomic Variation in a Wall Lizard from an Oceanic Island

The lizard Teira dugesii exhibits morphological divergence between beach and inland habitats in the face of gene flow, within the volcanic island of Madeira, Portugal. Here, we analyzed genomic data obtained by genotyping-by-sequencing, which provided 16,378 single nucleotide polymorphisms (SNPs) from 94 individuals sampled from 15 sites across Madeira. Ancient within-island divergence in allopatry appears to have mediated divergence in similar species within other Atlantic islands, but this hypothesis was not supported for T. dugesii. Across all samples, a total of 168 SNPs were classified as statistical outliers using pcadapt and OutFLANK. Redundancy analysis (RDA) revealed that 17 of these outliers were associated with beach/inland habitats. The SNPs were located within 16 sequence tags and 15 of these were homologous with sequences in a 31 Mb region on chromosome 3 of a reference wall lizard genome (the remaining tag could not be associated with any chromosome). We further investigated outliers through contingency analyses of allele frequencies at each of four pairs of adjacent beach–inland sites. The majority of the outliers detected by the RDA were confirmed at two pairs of these matched sites. These analyses also suggested some parallel divergence at different localities. Six other outliers were associated with site elevation, four of which were located on chromosome 5 of the reference genome. Our study lends support to a previous hypothesis that divergent selection between gray shingle beaches and inland regions overcomes gene flow and leads to the observed morphological divergence between populations in these adjacent habitats.