PCAdmix

PCAdmix estimates local ancestry along chromosomes using principal components analysis on phased haplotypes to characterize ancestry tracts and infer migration history.

Key Features:

• Principal Components Analysis on phased haplotypes: Utilizes PCA on phased haplotypes to assign local ancestry at locus-level resolution.
• Chromosome-by-chromosome analysis: Processes genetic data separately for each chromosome to produce locus-specific ancestry assignments.
• Migrant-tract identification: Implements a principal component–based analysis tailored to identify migrant tracts from multiple ancestral populations.
• Input data: Leverages dense genome-wide SNP genotyping array data for ancestry characterization.
• Maximum likelihood dating: Applies a maximum likelihood dating method based on the distribution of migrant tracts to estimate timing of migrations.

Scientific Applications:

• Population-history inference: Assigns local ancestry to haplotypes to dissect complex population histories and migration patterns.
• North African population analysis: Applied to North African datasets to reveal a gradient of Maghrebi ancestry increasing from east to west.
• Detection of multi-source gene flow: Identified gene flow from the Near East, Europe, sub-Saharan Africa, and a back-to-Africa migration >12,000 years ago.
• Fine-scale migration dating: Dated specific migrations into Morocco (~1,200 years ago) and Egypt (~750 years ago) from western African and Nilotic origins, respectively.

Methodology:

Performs PCA on phased haplotypes chromosome-by-chromosome using dense genome-wide SNP genotyping array data to assign local ancestry and identify migrant tracts, and applies a maximum likelihood dating method based on the distribution of migrant tracts.