alder

alder detects and dates population admixture by analyzing weighted linkage disequilibrium (LD) decay as a function of genetic distance to infer admixture timing and mixture proportions.

Key Features:

• Weighted LD Statistic: Introduces a weighted LD statistic that infers mixture proportions and dates admixture events with fewer constraints on reference populations.
• Three-Population Test for Admixture: Implements an LD-based three-population test to identify admixture scenarios that formal tests may miss.
• Phylogenetic Relationship Analysis: Compares weighted LD curves obtained using a suite of reference populations to reveal phylogenetic relationships among groups.
• Improved Computation and Fitting: Incorporates enhancements to the computation and fitting of weighted LD curves to increase robustness and speed.

Scientific Applications:

• Investigate Historical Admixture Events: Infer timing and proportions of gene flow underlying historical admixture events that shaped genetic landscapes.
• Study Population History: Applied to Human Genome Diversity Project (HGDP) populations, including Central African Pygmies, Sardinians, and Japanese, to elucidate population histories.
• Validate Simulations: Methods and inferences validated through simulations to assess reliability and accuracy.

Methodology:

Analyzes patterns of linkage disequilibrium and leverages the exponential decay of LD with genetic distance using a weighted LD statistic, an LD-based three-population test, comparison of weighted LD curves across reference populations, and enhanced computation and fitting of weighted LD curves, with validation via simulations.