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

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  • Ruiwen Fan, Shanxi Agricultural University
  • ,
  • Zhongru Gu, Chinese Academy of Sciences, University of Chinese Academy of Sciences
  • ,
  • Xuanmin Guang, BGI Genomics
  • ,
  • Juan Carlos Marín, UNIVERSIDAD DEL BIO-BIO
  • ,
  • Valeria Varas, Universidad Austral de Chile
  • ,
  • Benito A González, University of Chile, Santiago, Chile
  • ,
  • Jane C Wheeler, University of Lima
  • ,
  • Yafei Hu, BGI Genomics
  • ,
  • Erli Li, BGI Genomics
  • ,
  • Xiaohui Sun, BGI Genomics
  • ,
  • Xukui Yang, BGI Genomics
  • ,
  • Chi Zhang, BGI Genomics
  • ,
  • Wenjun Gao, Shanxi Agricultural University
  • ,
  • Junping He, Shanxi Agricultural University
  • ,
  • Kasper Munch
  • Russel Corbett-Detig, University of California, Santa Cruz
  • ,
  • Mario Barbato, Universita Cattolica del Sacro Cuore
  • ,
  • Shengkai Pan, Chinese Academy of Sciences
  • ,
  • Xiangjiang Zhan, Chinese Academy of Sciences
  • ,
  • Michael W Bruford, Cardiff University, Chinese Academy of Sciences
  • ,
  • Changsheng Dong, Shanxi Agricultural University

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.

Original languageEnglish
Article number159
JournalGenome Biology
Volume21
ISSN1474-7596
DOIs
Publication statusPublished - Jul 2020

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