Comparing genetic diversity and demographic history in co-distributed wild South American camelids

Vicunas and guanacos are two species of wild South American camelids that are key ruminants in the ecosystems where they occur. Although closely related, these species feature differing ecologies and life history characters, which are expected to influence both their genetic diversity and population differentiation at different spatial scales. Here, using mitochondrial and microsatellite genetic markers, we show that vicuna display lower genetic diversity within populations than guanaco but exhibit more structure across their Peruvian range, which may reflect a combination of natural genetic differentiation linked to geographic isolation and recent anthropogenic population declines. Coalescent-based demographic analyses indicate that both species have passed through a strong bottleneck, reducing their effective population sizes from over 20,000 to less than 1000 individuals. For vicuna, this bottleneck is inferred to have taken place similar to 3300 years ago, but to have occurred more recently for guanaco at similar to 2000 years ago. These inferred dates are considerably later than the onset of domestication (when the alpaca was domesticated from the vicuna while the llama was domesticated from the guanaco), coinciding instead with a major human population expansion following the mid-Holocene cold period. As importantly, they imply earlier declines than the well-documented Spanish conquest, where major mass mortality events were recorded for Andean human and camelid populations. We argue that underlying species' differences and recent demographic perturbations have influenced genetic diversity in modern vicuna and guanaco populations, and these processes should be carefully evaluated in the development and implementation of management strategies for these important genetic resources.