PT  - JOURNAL ARTICLE
AU  - Alisa Sedghifar
AU  - Yaniv Brandvain
AU  - Peter Ralph
AU  - Graham Coop
TI  - The Spatial Mixing of Genomes in Secondary Contact Zones
AID  - 10.1101/016337
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 016337
4099  - http://biorxiv.org/content/early/2015/03/13/016337.short
4100  - http://biorxiv.org/content/early/2015/03/13/016337.full
AB  - Recent genomic studies have highlighted the important role of admixture in shaping genome-wide patterns of diversity. Past admixture leaves a population genomic signature of linkage disequilibrium (LD), reflecting the mixing of parental chromosomes by segregation and recombination. The extent of this LD can be used to infer the timing of admixture. However, the results of inference can depend strongly on the assumed demographic model. Here, we introduce a theoretical framework for modeling patterns of LD in a geographic contact zone where two differentiated populations are diffusing back together. We derive expressions for the expected LD and admixture tract lengths across geographic space as a function of the age of the contact zone and the dispersal distance of individuals. We develop an approach to infer age of contact zones using population genomic data from multiple spatially sampled populations by fitting our model to the decay of LD with recombination distance. We use our approach to explore the fit of a geographic contact zone model to three human population genomic datasets from populations along the Indonesian archipelago, populations in Central Asia and populations in India.