PSMC

PSMC infers historical effective population size trajectories from diploid whole-genome sequence data using the Pairwise Sequentially Markovian Coalescent to reconstruct past demographic dynamics.

Key Features:

• Whole Genome Analysis: Utilizes complete diploid genome sequences to reconstruct historical population sizes.
• Fewer Assumptions: Requires fewer assumptions about population size fluctuations than traditional demographic models.
• Temporal Resolution: Infers demographic histories across broad timescales, approximately 10,000 to 1,000,000 years ago.

Scientific Applications:

• Population Bottlenecks: Identifies and characterizes bottlenecks, for example severe bottlenecks reported in European and Chinese populations between 10–60 thousand years ago and a milder, earlier recovery in African populations.
• Effective Population Size: Detects periods of elevated effective population size, such as increases observed between 60–250 thousand years ago across human populations, potentially reflecting population substructure.
• Genetic Differentiation: Provides timing estimates for genetic differentiation among modern humans, suggesting initiation around 100–120 thousand years ago with continued genetic exchange until roughly 20–40 thousand years ago.

Methodology:

Analyzes patterns of genetic variation across diploid genomes and applies the pairwise sequentially Markovian coalescent model to estimate historical changes in effective population size.