Gene flow in domestic camelids across different production systems in Bolivia: Insights from mitochondrial D-loop and Y-chromosome DBY gene

Llama (Lama glama) and alpaca (Vicugna pacos) farming in the Bolivian highlands in mixed camelid herds can lead to crossbreeding and introgression, particularly affecting alpacas. This genetic exchange has important implications for camelid phylogeny and production traits, including fiber and meat quality. To investigate patterns of gene flow, we analyzed sex-specific markers (mitochondrial D-loop and Y-chromosome DBY gene) in llamas, alpacas, and hybrids from three Bolivian production systems: Catacora, Ulla Ulla, and Curahuara de Carangas. We included sequences from vicu & ntilde;as and guanacos and identified 37 mitochondrial D-loop haplotypes, as well as three Y-chromosomal DBY haplotypes, revealing significant asymmetric introgression. Mitochondrial DNA analysis showed that 6.7 % of llamas and 53.3 % of alpacas carried introgressed haplotypes, indicating extensive maternal gene flow. In contrast, Y-chromosome introgression was lower (<5 %, all from Curahuara de Carangas). Population structure analysis of the D-loop fragment revealedregional differences, with the highest FST (0.307) observed between llamas and alpacas in Curahuara. In contrast, no differentiation (FST = 0) was observed in Catacora. These findings highlight a female-biased introgression pattern, with gene flow predominantly from female llamas to male alpacas. The asymmetry between maternal and paternal introgression, which varies across production systems, likely reflects historical hybridization and breeding practices favoring conspecific males. Our results underscore the impact of long-term gene flow and human-mediated practices on the genetic structure of domestic camelids, offering critical insights for conservation and breeding programs aimed at preserving the genetic integrity of Andean camelid populations.