Abstract Selective breeding of the guanaco and vicuna indisputably led to the domestic llama and alpaca. However, the place, time and process of domestication remain poorly documented, exacerbated by increased evidence of historic and recent introgression among both domestic populations, especially those involving alpaca. Here, we report the first comprehensive assessment of patterns of microsatellite variation of 13 polymorphic microsatellites in 797 individuals representing 4 species and 2 subspecies to estimate historic and ongoing patterns of gene flow. Our results confirm that llamas were domesticated almost exclusively from the northern subspecies of guanaco (Lama guanicoe cacsilensis), but cluster analyses did not support previous findings that alpacas are solely derived from the northern subspecies of vicuna (Vicugna mensalis), with some more-recent admixture with southern populations. We also confirmed continued gene flow between llama and alpaca, and found evidence for crosses between presumably feral llamas and guanacos in northern Chile. Our results highlight the need to develop and test more-accurate markers and tools for assessing the genetic heritage of individuals, to link phenotypic variation with genetic ancestry, and to conserve historic patterns of unique variation among both the wild and domestic populations.

中文翻译：

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南美骆驼科动物杂交威胁物种完整性

摘要 原驼和骆马的选择性育种无可争议地导致了家养美洲驼和羊驼。然而，驯化的地点、时间和过程仍然没有得到很好的记录，而且越来越多的证据表明历史和最近两种家养种群，尤其是那些涉及羊驼的种群之间的基因渗入，加剧了这种情况。在这里，我们报告了对代表 4 个物种和 2 个亚种的 797 个个体中 13 个多态性微卫星的微卫星变异模式的首次综合评估，以估计基因流的历史和持续模式。我们的结果证实，美洲驼几乎完全是从原驼的北部亚种（Lama guanicoe cacsilensis）驯化而来，但聚类分析并不支持先前的发现，即羊驼完全来自于骆马的北部亚种（Vicugna mensalis），最近与南方人口混合。我们还证实了美洲驼和羊驼之间的持续基因流动，并发现了智利北部可能是野生美洲驼和原驼之间杂交的证据。我们的结果强调需要开发和测试更准确的标记和工具来评估个体的遗传遗产，将表型变异与遗传祖先联系起来，并保护野生和家养种群之间独特变异的历史模式。