Detecting bottlenecks – University of Copenhagen

GeoGenetics > News > Detecting bottlenecks

21 March 2012

Detecting bottlenecks

In a recent paper published in Molecular Biology and Evolution, researchers at the Centre for GeoGenetics show that many previous studies on historic population genetics may not be able to reliably detect ancient population structure changes.

In the past, many animal populations may have decreased in size following epidemic outbreaks, food shortage, or major shifts in environmental conditions. These so-called population demographic bottlenecks will likely leave a trace in the genomes of the organisms.

By performing millions of simulations, the researchers found that when they used DNA from the mitochondria - the most commonly used marker for population genetic studies - they were only able to detect ancient population bottlenecks that were extremely severe.

Difficult but not impossible to detect

More subtile demographic shifts, or shifts that lasted only for a limited time period before the population fully recovered, appeared extremely difficult to detect, even when large sequence datasets could be made available. In striking contrast, using genetic markers from the nuclear genome - so-called SNPs - had a much higher power to detect relatively subtle bottlenecks and highly dynamic demographic histories.

The extraction of ancient DNA molecules is in most of the cases a destructive procedure. The simulation framework developped in this study offers the opportunity to test upfront the number of samples and the amount of sequence information needed in order to maximize our ability to infer past population demographic shifts.

These results will have a strong impact on experimental designs of future studies on ancient population genetics, and will contribute to limit damage to precious fossil collections.