Genetic diversity and population structure of Bolivian alpacas

Abstract

We have examined the genetic diversity and population structure of 149 Bolivian alpacas from eight different locations in Bolivia. The analysis of 22 microsatellite loci revealed high levels of genetic diversity, similar to the results reported in other alpaca populations. This high genetic variability was sustained by the identification of a total of 258 alleles; we identified between 4 and 18 alleles per locus with high levels of observed heterozygosity that ranged from 0.611 to 0.696. The inbreeding coefficients (Fis) were positive and significantly different from zero for all of the populations except for Turco. The genetic differentiation between populations (Fst) was low to moderate with pair-wise Fst estimates ranging from 0.008 for the Curahuara–Cosapa pair, to 0.077 for the Poopó–Ayopaya and Poopó–Ulla Ulla pairs. The analysis of molecular variance (AMOVA) indicated that the total variability observed between different populations was 3.86%, whereas 96.14% of the variation was found within the populations. The population structure analysis revealed that the eight studied populations could be assigned to five differentiated clusters. In agreement with the factorial analysis of correspondence, and supported through a bootstrapping analysis to adjust for differences in population sample size, this analysis suggested a genetic isolation of the Poopó population and the influence of the Turco population on the populations linked to the Cochabamba and the Pacajes-Sajama alpaquero systems. The Ulla Ulla population showed a clear subdivision into two clusters; in addition, these two clusters had an influence on the Challapata population and less impact on the rest of the populations. The Cosapa, Lagunas and Curahuara populations showed a clear common genetic background, whereas the Ayopaya population was influenced by the five defined clusters. Despite some sampling limitations and the need of confirming the results reported here through larger datasets, overall, this study provides the first survey of the genetic diversity in Bolivian alpaca populations, which may be of great value for the development of appropriate breeding strategies for these populations.