Data from: Genome-wide assessment of diversity and divergence among extant Galápagos giant tortoise species

Taking this next step, we used double-digest restriction-site associated DNA sequencing to collect genotypic data at >26,000 single nucleotide polymorphisms (SNPs) for 117 individuals representing all recognized extant Galapagos giant tortoise species. We then quantified genetic diversity, population structure, and compared results to estimates from mitochondrial DNA and microsatellite loci. Our analyses detected 12 genetic lineages concordant with the 11 named species as well as previously described structure within one species, C. becki.

Furthermore, the SNPs provided increased resolution, detecting admixture in four individuals. SNP-based estimates of diversity and differentiation were significantly correlated with those derived from nuclear microsatellite loci and mitochondrial DNA sequences. The SNP toolkit presented here will serve as a resource for advancing efforts to understand tortoise evolution, species radiations, and aid conservation of the Galapagos tortoise species complex.

Usage notes

Miller_et_al_Tortoise_SNPs VCF file containing ddRAD derived SNP genotypes for 117 Galapagos tortoises. Miller_et_al_Tortoise_SNP_PairedMinCov10.vcf.zip