Bayesian Estimation of the Timing and Severity of a Population Bottleneck from Ancient DNA

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Abstract
In this first application of the approximate Bayesian computation approach using the serial coalescent, we demonstrated the estimation of historical demographic parameters from ancient DNA. We estimated the timing and severity of a population bottleneck in an endemic subterranean rodent, Ctenomys sociabilis, over the last 10,000 y from two cave sites in northern Patagonia, Argentina. Understanding population bottlenecks is important in both conservation and evolutionary biology. Conservation implications include the maintenance of genetic variation, inbreeding, fixation of mildly deleterious alleles, and loss of adaptive potential. Evolutionary processes are impacted because of the influence of small populations in founder effects and speciation. We found a decrease from a female effective population size of 95,231 to less than 300 females at 2,890 y before present: a 99.7% decline. Our study demonstrates the persistence of a species depauperate in genetic diversity for at least 2,000 y and has implications for modes of speciation in the incredibly diverse rodent genus Ctenomys. Our approach shows promise for determining demographic parameters for other species with ancient and historic samples and demonstrates the power of such an approach using ancient DNA. Modern genetic variation can be used to reconstruct past events in a population's history, such as severe population declines (population bottlenecks). However, ancient DNA has the potential to improve our ability to estimate the timing and severity of such events, increasing our understanding of their causes and consequences. The authors apply a method for estimating historical demography, approximate Bayesian computation, to modern and ancient genetic variation sampled over the last 10,000 y, in order to estimate the timing and severity of a population bottleneck in an endemic Patagonian rodent. Their method shows promise for determining demographic parameters for other species with ancient and historic samples and demonstrates the power of such an approach using ancient DNA.