Raw fastq files of 3RAD sequencing for the red-footed tortoise Chelonoidis carbonarius
Wide-ranging species are seldom considered as conservation priorities, yet they have the potential to harbor genetically deeply differentiated units across environments or ecological barriers, including some that warrant taxonomic recognition. Documenting such cryptic genetic diversity is especially important for wide-ranging species that are in decline, as they may comprise a set of even more endangered lineages or species with small distributions. However, studies of wide-ranging species, particularly when they cross political borders, are extremely challenging. One approach to overcoming these challenges is to conduct detailed local analyses in combination with less detailed, range-wide studies. We used this approach with the red-footed tortoise (Chelonoidis carbonarius), a threatened species likely to contain cryptic diversity given its vast range and the distinctive ecoregions that it inhabits. Previous single-gene molecular studies indicated the presence of at least five lineages, two of which occur in different eco-regions separated by the Andes within Colombia. We used a comprehensive genomic analysis to test the hypothesis of cryptic diversity within the single jurisdiction of Colombia. We used a combination of restriction-site-associated DNA sequencing and environmental niche modeling to provide three independent lines of evidence that support the presence of important cryptic diversity that may deserve taxonomic recognition: allopatric reproductive isolation, local adaptation, and ecological divergence. We also provide a fine-scale genetic map with the distribution of conservation units in Colombia. As we complete ongoing range-wide analyses and make taxonomic adjustments, we recommend that the two lineages in Colombia be treated as separate units for conservation purposes.