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Genetic History of Latin America: Fine-scale population structure, sub-continental ancestry and phenotypic diversity

Chacon Duque, Juan Camilo; (2018) Genetic History of Latin America: Fine-scale population structure, sub-continental ancestry and phenotypic diversity. Doctoral thesis (Ph.D), UCL (University College London). Green open access

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Abstract

The history of Latin America involved extensive genetic admixture, particularly between Native Americans, Europeans and Africans. Although these conti-nental contributions to the genetic make-up of the region have been explored previously with genetic data, more precise information about sub-continental contributions has proven elusive. Applying new haplotype-based approaches to ~600,000 SNPs in ~7,000 Latin Americans from Brazil, Chile, Colombia, Mexico and Peru, this PhD thesis provides a comprehensive analysis of the sub-continental ancestry and demographic history of Latin America at a resolu-tion not previously achieved. Furthermore, using measurements on sampled individuals' physical appearances, I explore the impact of this fine-scale genet-ic structure on phenotypic variation across Latin America. To achieve these aims, I use a novel haplotype-based statistical technique that I compare to previously published haplotype-based and allele-frequency-based methods, using real data and simulations mimicking Latin American admixture. I show that this new approach provides a substantial increase in accuracy, al-lowing more precise inference about ancestral components at both regional and individual levels. Strikingly, Native American ancestry across Latin Ameri-ca mirrors the geographic locations of present-day Native groups. Furthermore, non-Native ancestries match to precise areas within the Iberian Peninsula and elsewhere, consistent with historical records detailing migrations and highlight-ing previously unseen ancestry sources. For the first time in single-sampled individuals, I date the timings of these non-Native Post-Columbian genetic contributions, including newly identified recent contributions related to East Asia. Finally, I show how this sub-continental ancestral reconstruction corre-lates with variation in pigmentation and facial features in Latin Americans, un-earthing new associations that could not be found with available techniques. Overall, I demonstrate how increasing the robustness and accuracy of fine-scale genetic structure analysis allows a comprehensive picture of the histori-cal and biological diversity of Latin America, highlighting the impact of regional genetic variation on human phenotypic diversity.

Type: Thesis (Doctoral)
Qualification: Ph.D
Title: Genetic History of Latin America: Fine-scale population structure, sub-continental ancestry and phenotypic diversity
Event: UCL (University College London)
Open access status: An open access version is available from UCL Discovery
Language: English
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
URI: https://discovery.ucl.ac.uk/id/eprint/10045516
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