South America has four camelids: two wild, the guanaco and the vicuña, and two domestic, the llama and the alpaca. The traditional assumption paired llama with guanaco and alpaca with guanaco as well, or left the alpaca's ancestry vague. Mitochondrial and microsatellite work found the alpaca's closest wild relative to be the vicuña, the smaller, finer-fleeced highland species.
Centuries of crossbreeding had obscured this. After the Spanish conquest, Andean camelid herds were heavily disrupted and llama-alpaca hybridisation became widespread, so a large share of modern alpacas carry llama mitochondrial DNA. Disentangling the signal required sampling and analysis that separated introgressed lineages from the ancestral one.
The finding has a practical edge. Vicuña fibre is among the finest animal fibres known, and the coarsening of alpaca fleece over recent centuries is attributable in part to llama introgression. Breeding programmes aimed at recovering fineness are, in effect, trying to reverse a post-conquest genetic accident rather than to invent something new.