Genomic identification of conservation areas amid lineage divergence and admixture in a threatened island gecko

Abstract Background Identification of ancient evolutionary lineages and areas of natural admixture can have important implications for conservation policies aimed at preserving biodiversity in the face of existential threats. The island gecko Tarentola boettgeri is potentially threatened by the introduced California kingsnake ( Lampropeltis californiae ) within the relatively small oceanic island (1532 km 2 ) of Gran Canaria, Canary Islands, Spain. Results A 1.9-Gb T. boettgeri genome was assembled de novo from PacBio HiFi reads. Sequences obtained by genotyping-by-sequencing (GBS) were aligned to this reference and provided over 440,000 SNPs from 134 geckos obtained from 40 sample sites (Fig. 1). Analyses of ancestry coefficients supported five genomic groups within Gran Canaria plus two additional groups from the other parts of its range, namely the Canary Island of El Hierro and the Selvagens archipelago. Phylogenomic and divergence time analyses of both GBS sequences and SNPs revealed lineage divergence within Gran Canaria, starting 1.5–2.9 Ma, and also between-island divergence due to subsequent colonization of both the Selvagens and El Hierro around 1 Ma. The latter two colonization events occurred from distinct lineages that had originated in the NW and the W of Gran Canaria, respectively. Lineage divergence within Gran Canaria appears to have been followed by secondary contact and admixture, likely starting in the Late Pleistocene around 20–110 Ka ago. Individuals with significant mixed ancestry appear to be limited to as little as 5 km either side of contact zones. This facilitates identification of sites containing individuals with negligible mixed ancestry for each of the five ancient lineages. Conclusions The ability to genomically identify five ancient Gran Canarian lineages and geographical areas with ostensibly low mixed ancestry provides a foundation for practical conservation actions—such as selecting sites for creation of snake exclusion areas and/or the acquisition of individuals for ex situ captive breeding. These actions will help conserve the extensive within-island diversity in this species.