Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca

Abstract

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.

Ancient DNA reveals the lost domestication history of South American camelids in Northern Chile and across the Andes

“…In particular, Fan et al (2020) timed the hybridization history between South American camelids and found evidence for a post-colonial hybridization, and not an ancient one, thereby suggesting that the bulk of the taxonomic uncertainty driven by this process affects modern samples. Moreover, although rare, hybridization between llamas and guanacos (i.e.…”

“…Consequently, the results presented here advocate for efforts to be made to attempt sequencing the Y-chromosome of ancient samples that may further help unravelling this hybridization history. In the absence of Y-chromosome sequences, efforts to obtain ancient nuclear DNA sequences discriminating between the four species would also help understanding the patterns of hybridization as indicated with modern samples by Fan et al, 2020. However, despite advances in the field of ancient DNA, it still remains very challenging to obtain nuclear data from ancient samples, due to the fragmentary nature of the DNA on these samples and the low endogenous content and, so far, it has not been possible to be obtained from ancient South American camelid samples (Lindahl, 1993;Collins et al, 2002;Bollongino et al, 2008;Pruvost, 2007;Shapiro & Hofreiter, 2012). In fact, the hybrid samples (i.e.…”

Polimorfismos de nucleótido simple (PNSs) del gen MC1R en alpacas negras y marrones

“…Los genes MC1R (receptor 1 de melanocortina) y ASIP (proteína de señalización agouti) son los principales genes que intervienen en la síntesis y distribución de eumelanina y feomelanina en el vellón de alpacas (Feeley & Munyard 2009, Cieslak et al 2011, Marín et al 2018, pero en otros animales se han descrito más de 150 genes asociados a la expresión del color (Montoliu et al 2011). Estudios moleculares sugieren que la domesticación de la vicuña se inició hace 6000 -7000 años en los andes centrales del Perú, siendo la alpaca descendiente de la vicuña (Kadwell et al 2001, Gentry et al 2004, Fan et al 2020. Posteriormente la selección de alpacas por su vellón blanco favoreció la fijación de alelos específicos en los genes MC1R y ASIP (Marín et al 2018).…”

Ancient DNA Reveals the Lost Domestication History of South American Camelids in Northern Chile and Across the Andes

“…Others support the concomitant domestication of guanacos and vicuñas into llamas and alpacas. Finally, efforts using whole genome sequencing suggest support for the hypothesis that llama derived from guanaco and alpaca derived from vicuña (Stanley et al, 1994;Kadwell et al, 2001;Wheeler et al,2006;Marín et al, 2007a, Fan et al, 2020. Although some of these problems may be addressed using ancient DNA samples, such material is scarce for SACs with only four complete mitochondrial genomes from two different species currently available, three llamas dated to around 700 yr BP from Isla Mocha in Southern Chile (Westbury et al, 2016) and one vicuña dated between 3200-2400 yr BP, from Tulán 54 (Diaz-Maroto et al, 2018).…”