Abstract
BackgroundDespite 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.ResultsPhylogenomic 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.ConclusionsThe unprecedented introgression signatures within both domestic camelid genomes may reflect post-conquest changes in agriculture and the breakdown of traditional management practices.
Highlights
Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood
While confirming that the genera Lama and Vicugna are valid and separated 2–3 Millions of years ago (MYA), have documented extensive hybridization among modern domestic South American camelids (SACs), with microsatellite and mitochondrial DNA analysis suggesting that the llama is descended from the guanaco and the alpaca is descended from the vicuña, and the alpaca has been reclassified from Lama pacos to Vicuna pacos [4, 5]
Resequencing Genomes were sequenced to 129x, 108x, and 102x coverage for L. guanicoe, V. vicugna, and L. glama, respectively (Additional file 1: Supplementary Text 1a, b and Additional file 1: Table S1); all these genomes were assembled by SOAPdenovo [9] and featuring contig and scaffold N50 lengths of 91.6 kb and 14.6 Mb for L. guanicoe, 91.1 kb and 6.15 Mb for V. vicugna, and 44.1 kb and 3.2 Mb for L. glama (Additional file 1: Table S2ac)
Summary
Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. South and Central America encompasses one of the most important cradles of domestication, giving rise to key crop plants and domesticated animals including turkey, guinea pig, and the region’s key domestic herbivores, the llama and alpaca [1] These South American camelids (SACs) attained central importance in the economy of the Andean region, with the llama used as a pack animal, facilitating the expansion of the Inca Empire [2], and the alpaca selected to produce some of the world’s finest wool [3]. A genomic perspective on this problem is urgently needed, because previous analysis used a few neutral genetic markers, representing only a very small fraction of the genome, and was incapable of accurately assessing genetic diversity, genomic regions under selection and systematically evaluating genomewide introgression in wild and domestic forms
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