Data from: Lineage fusion in Galápagos giant tortoises

Although many classic radiations on islands are thought to be the result of repeated lineage splitting, the role of past fusion is rarely known because during these events, purebreds are rapidly replaced by a swarm of admixed individuals. Here we capture lineage fusion in action in a Galápagos giant tortoise species, Chelonoidis becki, from Volcano Wolf (Isabela Island). The long generation time of Galápagos tortoises and dense sampling (~1700 individuals) of genetic and demographic data were integral in detecting and characterizing this phenomenon. In C. becki we identified two genetically distinct, morphologically cryptic lineages. Historical reconstructions show that they colonized Volcano Wolf from Santiago Island in two temporally separated events, the first occurring ~199,000 years ago. Following arrival of the second wave of colonists, both lineages co-existed for ~53,000 years. However, they are now fusing back together, as microsatellite data reveal recent and widespread introgressive hybridization. Consistent with evolutionary theory, pre-zygotic isolation is weakest in the most recent colonizers. Forward-in-time projections predict rapid extinction of the older lineage, with negligible potential for genetic rescue. This study provides a rare example of reticulate evolution in action, and underscores the power of population genetics for understanding the past, present and future.