ChromoPainter

ChromoPainter reconstructs individual haplotypes and quantifies shared ancestry by "chromosome painting" to infer population structure and date admixture events.

Key Features:

• Haplotype Reconstruction: Reconstructs individual haplotypes by copying DNA segments from other individuals in the dataset to capture patterns of haplotype similarity.
• Coancestry Matrix Generation: Summarizes painting results into a coancestry matrix that encodes donor–recipient relationships and ancestral sharing among individuals.
• Integration with PCA and STRUCTURE: When markers are treated as independent, the coancestry matrix captures nearly all information used by PCA and STRUCTURE, and for markers in linkage disequilibrium it aggregates information across successive markers to enhance fine-scale structure detection.
• Model-Based Population Identification: Implements an efficient model-based method on the coancestry matrix to identify discrete populations, with improved interpretability and sensitivity to subtle structure and gains in speed and separability relative to some clustering algorithms.

Scientific Applications:

• Population Structure Analysis: Reveals broad- and fine-scale population structure across continental, regional, local, and familial levels (e.g., Human Genome Diversity Panel analysis identified 226 populations among 938 individuals using 641,000 markers).
• Admixture Dating: Dates admixture events by analyzing patterns of haplotype similarity and inferred recombination events.
• Data Summarization for fineSTRUCTURE: Produces summarized coancestry input compatible with fineSTRUCTURE for clustering and visualization of population structure.

Methodology:

Performs chromosome painting by reconstructing each recipient chromosome as a mosaic of donor segments from other individuals, summarizes painting into a coancestry matrix, aggregates information across successive markers in linkage disequilibrium when applicable, and applies a model-based clustering method on the coancestry matrix; admixture dating uses patterns of haplotype similarity and recombination.