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Peruvian Population Genomics: Unraveling the Genetic Landscape and Admixture Dynamics of Urban Populations

Borda, V.; Caceres, O.; Sanchez, C.; Padilla, C.; Veliz-Otani, D.; Mendes, M.; Silva-Carvalho, C.; Alvin, I.; Maron, B. A.; Gouveia, M. H.; Peruvian Genome Project Consortium, ; Tarazona-Santos, E.; Guio, H.; O'Connor, T. D.

2025-04-16 genetics
10.1101/2025.04.10.648256 bioRxiv
Show abstract

Latin American populations exhibit high genetic and phenotypic diversity shaped by complex admixture histories, yet remain underrepresented in genomic research. Here, we analyze genome-wide data from 432 urban individuals across 13 regions of Peru, including 346 newly genotyped from the Peruvian Genome Project. We revealed fine-scale population structure and demographic patterns shaped by both ancient and recent events. Indigenous American ancestries in urban individuals trace back to ancient north-south interactions consisted with archaeological records, while admixture events occurring within the last 8-10 generations involved sources already admixed between distinct ancestral lineages. Identity-by-descent analyses reveal sustained gene flow in southern Peru, while effective population size trends highlight demographic stability in Lima over the past 25 generations. Sex-biased admixture patterns suggest Indigenous ancestry contribution preferentially mediated by females. These findings offer a comprehensive view of Perus genetic heritage, advancing our understanding of human genetic diversity and historical demographic processes in Latin America.

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