Estimating the time since admixture from phased and unphased molecular data

Area of Science:

• Population Genetics
• Genomics
• Evolutionary Biology

Background:

• Admixture events break down genomic blocks of contiguous ancestry.
• Recombination creates a 'molecular clock' for dating admixture, but existing theory is limited.
• Previous methods relied on regularly spaced markers and phased data.

Purpose of the Study:

• To extend the theory of genomic block breakdown and 'junctions' using the ancestral recombination graph.
• To develop a new framework for inferring admixture time from unphased genetic data.
• To improve the accuracy of admixture dating, especially for smaller populations and ancient events.

Main Methods:

• Developed an extension to junction theory applicable to any marker distribution using the ancestral recombination graph.
• Created a novel framework for admixture time inference using unphased genetic data.
• Validated methods on simulated data and applied them to empirical datasets (yeast, swordtail fish, Populus trees).

Main Results:

• The extended theory accurately predicts the expected number of junctions for diverse marker distributions.
• The new framework demonstrates improved accuracy in admixture time inference compared to previous methods.
• Enhanced accuracy was particularly notable for smaller population sizes and more ancient admixture events.

Conclusions:

• The developed methods provide a more robust and accurate approach to dating admixture events.
• The framework's ability to handle unphased data broadens its applicability in population genetics research.
• The study successfully demonstrates the practical utility of the new methods across different species.