MEAdmix

MEAdmix estimates admixture proportions and genetic drift from DNA sequence and microsatellite data using a coalescent-based estimator that accounts for mutations occurring since the admixture event.

Key Features:

• Coalescent-Based Estimation: Evaluates the entire genealogy of sampled genes and uses the numbers of segregating sites in DNA sequence samples rather than relying solely on allele-frequency summaries.
• Incorporation of Molecular Information: Utilizes molecular markers such as microsatellites and DNA sequences to accommodate scenarios with post-admixture mutation.
• Joint Estimation of Parameters: Facilitates joint estimation of admixture time, divergence time, population size, and mutation rate within the admixture model.
• Improved Accuracy for Ancient Admixture Events: Comparative analyses with simulated data indicate generally better estimates of admixture proportions than previous molecular estimators when parental populations are not highly differentiated, and reasonably accurate estimates of other parameters.
• Fortran Implementation: Provided as a Fortran program for the described computations.

Scientific Applications:

• Hybrid population analysis: Inference of genetic contributions from ancestral populations in hybrid or admixed populations.
• Ancient admixture studies: Estimation of admixture proportions and related parameters in cases where admixture events precede substantial mutation.
• Evolutionary biology and population genetics: Joint inference of demographic and mutational parameters relevant to evolutionary and population-genetic studies.
• Human mtDNA analysis: Applied to human mitochondrial DNA (mtDNA) sequence data for admixture and parameter estimation.

Methodology:

Implements a coalescent-based estimator that evaluates entire genealogies and uses numbers of segregating sites to jointly estimate admixture time, divergence time, population size, and mutation rate; implemented in Fortran.