MSMC

MSMC infers historical population sizes and gene flow from multiple genome sequences using the Multiple Sequentially Markovian Coalescent (MSMC) model.

Key Features:

• Modeling Ancestral Relationships: Models ancestral relationships under recombination and mutation to analyze genetic variation across samples.
• Temporal Resolution: Extends temporal resolution of population genetic inference into more recent periods beyond ~20,000–30,000 years ago.
• Coalescent Analysis: Focuses on the first coalescence event between any two individuals within a sample to reconstruct demography and gene flow patterns.

Scientific Applications:

• Population History Reconstruction: Reconstructs genetic separations and bottlenecks across global populations, including evidence that the divergence of non-African ancestors from Yoruban ancestors predates 50,000 years ago.
• Recent Human History: Resolves recent demographic events as recent as ~2,000 years ago, including the bottleneck associated with the peopling of the Americas and separations within Africa, East Asia, and Europe.

Methodology:

Analyzes observed mutation patterns across multiple genomes, models ancestral relationships under recombination and mutation, and infers demographic history by focusing on first coalescence events between pairs of individuals.