admixturegraph

admixturegraph constructs and fits admixture graphs to model divergence and gene flow among populations and to test demographic hypotheses using genetic data.

Key Features:

• Graph construction and visualization: Constructs admixture graphs that represent divergence and merging events among populations and provides visualization of graph structure.
• Parameter fitting: Fits graph parameters such as edge lengths and admixture proportions to observed genetic data using statistical methods.
• Statistical testing and comparison: Extracts equations from admixture graphs and compares them to f-statistics, including evaluation of predicted versus observed signs of f_4-statistics.
• Goodness-of-fit evaluation: Visualizes and assesses goodness of fit between alternative admixture graphs to identify models that better explain the data.
• Implementation: Implemented as an R package for integration with R-based bioinformatics workflows.

Scientific Applications:

• Demographic reconstruction: Reconstructs complex demographic histories involving multiple populations and admixture events.
• Gene flow investigation: Tests and quantifies historical gene flow events that have shaped current genetic diversity.
• Model comparison: Compares alternative historical scenarios to determine which admixture graphs are consistent with empirical f-statistics.

Methodology:

Implemented as an R package; fits graph parameters (edge lengths and admixture proportions) to observed genetic data using statistical methods; extracts equations from graphs and compares them to f-statistics (including f_4-statistics) to evaluate model consistency; and visualizes and assesses goodness of fit between graphs.