Using modern and ancient DNA from tuco-tuco teeth found in the two caves, Stanford graduate student Yvonne Chan, lead author of the PLoS Genetics study, mapped the rodent population through time. Her results show that over the last 10,000 years, the once dominant colonial tuco-tuco, C. sociabilis, was gradually crowded out of the northern cave area by a larger species of tuco-tuco, C. haigi. Around 3,000 years ago, C. sociabilis disappeared entirely from the northern cave site. At the same time, the genetic diversity of C. sociabilis in the southern cave declined precipitously.
''When you talk about genetic variation being lost, you need to really reduce [the population] to a small number of individuals,'' Chan says.
By fitting modern and ancient DNA data into a standard population genetics model, Chan was able to pinpoint the drastic decline of C. sociabilis to about 2,600 years ago, when the population was likely reduced to less than 300 individuals. When a population becomes that small, it loses much of its genetic diversity-a phenomenon known as a genetic bottleneck. Chan thinks that a volcanic eruption known to have occurred in the Andes roughly 3,000 years ago, combined with environmental change and competition from the larger species of tuco-tuco, likely caused the die-off.
Most genetic studies rely entirely on modern DNA to estimate historical population size, but Hadly and Chan's technique provides much more detailed information. ''You can't get the bottleneck time or the bottleneck size without both modern and ancient DNA,'' Chan explains.