Assessment of Ex Situ Conservation Strategies for the Preservation of Domestic South American Camels in Southern Peru: Insights from Mitochondrial DNA Analysis

Southern Peru is home to the largest population of alpacas and the second-largest population of llamas. For many rural families, breeding these animals is vital. Recently, breeding communities have faced several challenges, including restricted market access, climate change, a reduction in coloured individuals, and pasture degradation, which hinder trading and genetic improvement efforts. This study examines the D-loop region of mitochondrial DNA to assess the genetic maternal diversity of alpacas and llamas. It also evaluates this alongside the preservation initiatives of the Quimsachata ex situ germplasm bank, which aims to sustain both phenotypic and genetic diversity while advancing breeding technologies. Our analysis identified 55 maternal haplotypes with 41 variation sites, indicating significant genetic diversity ( h ≈ 0.8–0.9) and low differentiation ( Fst = 0.01–0.05) within these populations. This finding is particularly noteworthy when compared to the maternal haplotypes of domestic and wild South American camelids (SAC) in other areas of South America. We did not observe any recent demographic shifts in population structure. Additionally, our research uncovers two genetic maternal clusters among alpacas and llamas, suggesting their ancestral connections to vicunas and guanacos, with indications of crossbreeding, particularly among alpacas, which show a closer lineage to guanaco-llamas. The Quimsachata bank currently safeguards a significant diversity of maternal heritage in alpacas and llamas within this region. The monitoring and protection of these resources is crucial for the economic advancement of Andean communities and can help promote genetic programmes aimed at enhancing sustainable productivity.