Genome-wide patterns of selection in pre- and post-European contact Caribbean populations Restricted; Files Only

Abstract

In recent years, the study of human population genetics has opened up the possibility to reconstruct ancestral and physiological changes from a biological perspective. Supplementing historical and cultural analyses, the use of ancient and modern genomes can improve our understanding of complex turning points in human history. Beginning in the late 15th century in the Americas, colonization acted as a powerful selective pressure on the genomes of Indigenous populations due to the rapid influx of novel pathogens, shifting labor and agricultural practices, and a population wipeout. In this study, recent methods from the field of computational genomics will be applied to pre- and post-contact Caribbean populations to examine ancestral cluster components, visualize demographic history, and investigate positive selection on genes involved with a multitude of functions. Demographic analyses were conducted using principal components analysis, maximum likelihood trees, and model-based cluster analysis to estimate population substructure. Following demographic analysis, allele frequency-based selection scans were performed to identify gene candidates for positive selection. In the ancient cohort’s selection scan, variants associated with genes coding for proteins involved in skin pigmentation lightening and tumor suppressor pathways exhibited signs of positive selection. Moreover, in the contemporary Caribbean cohort, polymorphisms associated with a number of genes linked to DNA repair, maintenance of genomic and cellular stability, immune system regulation, and immune cell development and activation showed positive selection signals. Given the colonial history of the Caribbean islands, as well as the complex pattern of migration and admixture between Indigenous American, European, and African populations, it is expected that genes related to cell repair, genomic stability, and immune regulation exhibit signs of positive selection in the modern Caribbean cohort. Taken together, the results of the demographic analyses and selection scans, alongside a review of the relevant literature, supports a more holistic understanding of post-colonial Caribbean legacies and the lasting impact of European colonization on contemporary populations in the region.

Table of Contents

Table of Contents

Introduction......................................................................................................................................1

Literature Review.............................................................................................................................4

        The pre-Columbian period and the immunological history of the Caribbean.......................4

        Post-contact Caribbean: Genetic and social legacies...........................................................7

        Human population genetics....................................................................................................9

        Previous ancient genomic research in Caribbean population history.................................10

        Broader applications, implications, and ethics....................................................................12

Methods..........................................................................................................................................15

        Principal Component Analysis (PCA)..................................................................................15

        Ancestry clustering...............................................................................................................15

        Ancestry clustering for maximum likelihood trees...............................................................16

        Selection scans......................................................................................................................17

Results............................................................................................................................................19

        Demographic analyses.........................................................................................................19

        Selection scans......................................................................................................................23

Discussion......................................................................................................................................28

Conclusion.....................................................................................................................................35

References......................................................................................................................................37

Supplemental Information.............................................................................................................43

        Table S1. Information about ancient Caribbean population cohort....................................43

        Table S2. Information about modern Caribbean population cohort....................................44

        Table S3. Outgroup samples utilized from the SGDP dataset..............................................46

        Table S4. Outgroup samples utilized for the natural selection scans..................................47

        Figure S1. Scope cluster analysis visualizations with K=2–8.............................................48

        Figure S2. Highest likelihood TreeMix scenarios for m=0-3 migration events...................49

        Table S5. Top 30 annotated SNPs from selection scan on ancient Caribbean cohort.........50

        Table S6. Top 30 annotated SNPs from selection scan on modern Caribbean cohort........51

        

Figures

Figure 1. Demographic analyses....................................................................................................21

Figure 2. Maximum likelihood trees generated by TreeMix.........................................................22

Figure 3. Selection scans................................................................................................................27

Tables

Table 1. SNPs of interest under high probability of selection.......................................................26

About this Honors Thesis

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School	Emory College
Department	Anthropology
Degree	B.S.
Submission	Honors Thesis
Language	English
Research Field	Biology, Genetics Caribbean Studies Anthropology, Physical
Keyword	Colonization Genomics
Committee Chair / Thesis Advisor	John Lindo, Emory University
Committee Members	Dietrich Stout, Emory University Kristin Phillips, Emory University Sophie Joseph, Emory University

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