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

Vicuñas 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 vicuña
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 1,000 individuals. For vicuña this bottleneck is
inferred to have taken place ~3,300 years ago, but to have occurred more
recently for guanaco at ~2,000 years ago. These inferred dates are
considerably later than the onset of domestication (when the alpaca was
domesticated from the vicuña 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 vicuña and
guanaco populations, and these processes should be carefully evaluated in
the development and implementation of management strategies for these
important genetic resources.