Background Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alpaca genome, and resequence seven individuals of all four species to better understand domestication and introgression between the llama and alpaca. Results Phylogenomic analysis confirms that the llama was domesticated from the guanaco and the alpaca from the vicuña. Introgression was much higher in the alpaca genome (36%) than the llama (5%) and could be dated close to the time of the Spanish conquest, approximately 500 years ago. Introgression patterns are at their most variable on the X-chromosome of the alpaca, featuring 53 genes known to have deleterious X-linked phenotypes in humans. Strong genome-wide introgression signatures include olfactory receptor complexes into both species, hypertension resistance into alpaca, and fleece/fiber traits into llama. Genomic signatures of domestication in the llama include male reproductive traits, while in alpaca feature fleece characteristics, olfaction-related and hypoxia adaptation traits. Expression analysis of the introgressed region that is syntenic to human HSA4q21, a gene cluster previously associated with hypertension in humans under hypoxic conditions, shows a previously undocumented role for PRDM8 downregulation as a potential transcriptional regulation mechanism, analogous to that previously reported at high altitude for hypoxia-inducible factor 1α. Conclusions The unprecedented introgression signatures within both domestic camelid genomes may reflect post-conquest changes in agriculture and the breakdown of traditional management practices.

中文翻译：

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美洲驼和羊驼的驯化和后西班牙征服进化的基因组分析

背景尽管美洲驼和羊驼在区域经济中具有重要意义并且在全球范围内越来越多地被饲养，但人们对美洲驼和羊驼的起源和进化仍然知之甚少。在这里，我们报告了美洲驼、原驼和骆马（它们假定的野生祖先）的参考基因组，将它们与已发表的羊驼基因组进行比较，并对所有四个物种的七个个体进行重新测序，以更好地了解美洲驼和羊驼之间的驯化和基因渗入。结果 系统发育分析证实美洲驼是从原驼驯化而来，而羊驼则是从骆马驯化而来。羊驼基因组中的基因渗入 (36%) 比美洲驼 (5%) 高得多，并且可以追溯到大约 500 年前西班牙征服时期。基因渗入模式在羊驼的 X 染色体上变化最大，具有 53 个已知在人类中具有有害 X 连锁表型的基因。强大的全基因组基因渗入特征包括两个物种的嗅觉受体复合物、羊驼的高血压抗性和美洲驼的羊毛/纤维特性。美洲驼驯化的基因组特征包括雄性生殖特征，而羊驼则具有羊毛特征、嗅觉相关和缺氧适应特征。与人类 HSA4q21 同线的基因渗入区域的表达分析表明，PRDM8 下调作为潜在的转录调节机制，具有先前未记录的作用，类似于先前在高海拔地区报道的缺氧诱导因子1α。