Complete mitogenomes of ancient Caribbean Guinea pigs (Cavia porcellus)

Abstract The domestic guinea pig ( Cavia porcellus ) was translocated from South America to several Caribbean islands sometime after 500 CE. Identifying the timing and routes of guinea pig translocation can provide a proxy for human interaction in the region. A recent investigation of aDNA of Caribbean guinea pig remains, based on sequences from short regions of the mitochondrial D-loop and cytochrome B regions, suggested a Colombian origin and single introduction of guinea pigs to the Caribbean. Here, we present the first complete mitogenome sequences for three ancient guinea pigs from Puerto Rico, Antigua and Carriacou, as well as for a modern Puerto Rican specimen, which allow us to clarify and expand upon the results of the earlier study. Complete mitogenome sequences indicate that there are at least two different mitochondrial DNA haplotypes in the ancient Caribbean guinea pigs, suggesting two distinct ancient introductions and a modern reintroduction of guinea pigs to Puerto Rico. Our results demonstrate the value of Next Generation Sequencing and the analysis of complete mitogenome sequences to investigate genetic variation and translocation of guinea pigs into the Caribbean.