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. 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. We found a significant difference in the number of non-synonymous substitutions, but not synonymous substitutions among wild and domestics species. 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. In contrast, coat colour variants in llamas were of less economic value, and thus were under less selective pressure. In contrast, variation in coat colour variation in alpaca was strongly selected for and became rapidly fixed in alpacas. We hypothesise that colour variation in wild populations of guanacos and vicunas were strongly selected against. 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. 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. 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. The domestication of wild vicuña and guanaco by early pre-Inca cultures is an iconic example of wildlife management and domestication in the Americas. 6School of Biosciences, Cardiff University, Cardiff, United Kingdom.5Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, United States.4Departamento de Zoología, Universidad de Concepción, Concepción, Chile.3Doctorado en Ciencias, Mención Ecología y Evolución, Instituto de Ciencias Ambientales & Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.2Departamento de Ciencias Básicas, Universidad Santo Tomas, Iquique, Chile.1Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile.Marín 1*, Romina Rivera 1,2, Valeria Varas 3, Jorge Cortés 1,4, Ana Agapito 1, Ana Chero 1, Alexandra Chávez 1, Warren E.

Guanaco vs alpaca vs llama