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bioRxiv · 10.1101/2025.04.10.648256

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.
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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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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. Peruvian Population Genomics: Unraveling the Genetic Landscape and Admixture Dynamics of Urban Populations. https://doi.org/10.1101/2025.04.10.648256

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