In Bolivian Andean Highlands, mixed husbandry and breeding of llama and alpacas take place in some productive systems, where hybridization events may occur, thus generating fertile hybrids (huarizos). Alpacas, llamas and huarizos of two highly genetically diversed productive systems, Ulla Ulla and Catacora, have been analyzed, and then contrasted with theoretical hybrid populations. Lower values of genetic differentiation (Fst=0.026) were displayed between alpacas and llamas from Catacora than Ulla Ulla's (Fst=0.065), and huarizos from both productive systems seemed to be more related to alpacas. Admixture analysis allowed identifying hybrids in both alpaca and llama populations of both productive systems. When compared actual populations with theoretical hybrid populations, hybrid individuals displayed different levels of introgression, which, according to NEWHYBRIDS results and estimated membership coefficient values (q), can be inferred as they are related to different generations of interbreeding. In general, the Catacora productive system seems to be more affected by introgression events.
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