Hybrid Origin of Alpaca ( Vicugna pacos ) During Domestication of Camelids in the Mid‐Holocene

ABSTRACT Alpaca ( Vicugna pacos ) is a large camelid that originated in South America. However, its evolutionary origin is debated, with hypotheses suggesting domestication from vicuña ( V. vicugna ) or guanaco ( Lama guanicoe ) or descent from extinct wild species with introgression from these two camelids. We show by means of phylogenetic, population and demographic genomic analyses, that the alpaca is a homoploid hybrid species that originated following hybridization between vicuña and the ancestor of wild guanaco and domesticated llama ( L. glama ). This event occurred during the mid‐Holocene (~6.3 thousand years ago [Ka]) and shortly before the two Lama species diverged from each other (~5.9 Ka). Following its origin, the alpaca occasionally interbred with both llama and vicuña with recent gene flow and introgression. In addition, we identify alleles of many genes in alpaca that are derived alternately from its two parents. In combination, these alleles may have contributed to the reproductive isolation of the alpaca from its parents due to their effects on body size and sperm development, respectively. While attempting to domesticate camelids in South America, it is likely that humans may have retained hybrid offspring that exhibited preferred traits from both parents. This selective retention, along with the alternately inheriting highly diverged genes, may have led to the establishment of a new homoploid hybrid species in the case of alpaca, as sexual reproduction was restored through iterative evolution.