Abstract
The domestication of wild vicuña and guanaco by early pre-Inca cultures is an iconic example of wildlife management and domestication in the Americas. Although domestic llamas and alpacas were clearly selected for key, yet distinct, phenotypic traits, the relative patterns and direction of selection and domestication have not been confirmed using genetic approaches. However, the detailed archaeological records from the region suggest that domestication was a process carried out under significant control and planning, which would have facilitated coordinated and thus extremely effective selective pressure to achieve and maintain desired phenotypic traits. Here we link patterns of sequence variation in two well-characterised genes coding for colour variation in vertebrates and interpret the results in the context of domestication in guanacos and vicuñas. We hypothesise that colour variation in wild populations of guanacos and vicunas were strongly selected against. In contrast, variation in coat colour variation in alpaca was strongly selected for and became rapidly fixed in alpacas. In contrast, coat colour variants in llamas were of less economic value, and thus were under less selective pressure. We report for the first time the full sequence of MC1R and 3 exons of ASIP in 171 wild specimens from throughout their distribution and which represented a range of commonly observed colour patterns. We found a significant difference in the number of non-synonymous substitutions, but not synonymous substitutions among wild and domestics species. The genetic variation in MC1R and ASIP did not differentiate alpaca from llama due to the high degree of reciprocal introgression, but the combination of 11 substitutions are sufficient to distinguish domestic from wild animals. Although there is gene flow among domestic and wild species, most of the non-synonymous variation in MC1R and ASIP was not observed in wild species, presumably because these substitutions and the associated colour phenotypes are not effectively transmitted back into wild populations. Therefore, this set of substitutions unequivocally differentiates wild from domestic animals, which will have important practical application in forensic cases involving the poaching of wild vicuñas and guanacos. These markers will also assist in identifying and studying archaeological remains pre- and post-domestication.
Highlights
The first attempts at domestication coincided with the origins of agriculture some 10,000 years ago
A > G) that have not been previously reported in alpacas or llamas but which are present in vicuñas and alpacas
Archaeological records suggest that the domestication of llamas and alpacas involved very active and directed management practises
Summary
The first attempts at domestication coincided with the origins of agriculture some 10,000 years ago. More or less simultaneously in several locations of the world, a change from nomadic hunting-gathering to more-sedentary agricultural economies took place, which had a profound impact of human societies and the environment (Gepts and Papa, 2002). Once agricultural societies became more established, their domesticated plants and animals often spread from their original centres of domestication. The transition from hunting and gathering to agriculture was a revolutionary inflexion point for humankind, helping support dramatic increases in human population sizes in South America, as in the rest of the world, and facilitating the emergence of modern societies (Larson and Burger, 2013; Goldberg et al, 2016). The most iconic examples occurred in the Andean high plateau, where the llama (Lama glama) was raised primarily as a pack animal and for its fibre and the alpaca (Vicugna pacos) was domesticated from the vicuña for its fine fibre
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