Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure

Area of Science:

• Population genetics
• Evolutionary biology
• Bioinformatics

Background:

• Natural populations are often genetically subdivided but frequently analyzed as single, panmictic units.
• Inferences of past demographic changes (e.g., population size fluctuations) from genetic data often rely on the assumption of a non-subdivided population.
• Recent immigration can mimic signals of demographic bottlenecks, potentially leading to erroneous conclusions about population history.

Purpose of the Study:

• To develop and validate a method for distinguishing between demographic size changes and population subdivision in genetic diversity data.
• To contrast scenarios of a panmictic population with size changes against a recently subdivided population using a finite island model.
• To prevent misinterpretation of genetic signals by accurately identifying population structure.

Main Methods:

• Utilized an Approximate Bayesian Computation (ABC) approach for model selection.
• Simulated genetic diversity patterns under two alternative models: a panmictic population with size changes and a subdivided population (finite island model).
• Applied the model choice procedure to genetic data from chimpanzee (Pan troglodytes) populations.

Main Results:

• Simulations demonstrated high accuracy (up to 95%) in correctly identifying samples from subdivided populations across a wide parameter range.
• The developed ABC method effectively differentiates between demographic history scenarios.
• Conclusive evidence was found supporting spatial subdivision in Western and Eastern chimpanzee populations.

Conclusions:

• The study highlights the critical importance of considering population subdivision when inferring demographic history from genetic data.
• The developed Approximate Bayesian Computation (ABC) model choice procedure provides a robust tool for distinguishing population subdivision from demographic size changes.
• Genetic data from chimpanzees strongly suggest a spatially subdivided population structure between Western and Eastern groups, rather than a single panmictic population experiencing size changes.