Molecular diversity among domestic guinea-pigs (Cavia porcellus) and their close phylogenetic relationship with the Andean wild species Cavia tschudii

To investigate the origin and diversity of domestic guinea-pigs Cavia porcellus (Linnaeus, 1758; Rodentia, Caviidae), we sequenced the mitochondrial cytochrome b gene of 12 domestic and 10 wild specimens from six species, including the two presumed as ancestral to the domestic one: Cavia tschudii and Cavia aperea. All maximum parsimony and maximum likelihood analyses grouped C. porcellus with C. tschudii (mean K2P distance = 3.2%); best trees had 609 steps (CI = 0.796; Bremer support Index (SI) = 28), and a -Ln = 4419.52, with 100% and 97% bootstrap support respectively. This clade, supported by three substitutions and 96% bootstrap, is also obtained in the cladistic analysis of corresponding amino acids. When the C. aperea node was forced to join C. porcellus, these trees were consistently longer, less likely and robust, and with less defining characters than the optimal one. All C. porcellus sequences also clustered in a node defined by 15 substitutions. The sub-node containing animals from city markets, pet shops and laboratories was characterized by four substitutions (one non-silent, SI = 7, and 91% bootstrap). Some South American C. porcellus, called "criollos" (creoles) by local breeders, were more diverse. Probably, a particular clade from southern Peru and Chile may represent a pre-Columbian lineage. Mean K2P distance between C. tschudii and C. aperea was rather large, 7.7%. Cavia appeared as a robust node (100% bootstrap). These results indicate that C. tschudii is the species most closely related to C. porcellus