Genomic Analysis and Natural Selection Scan of Mexican Mayan and Indigenous Populations Open Access

Abstract

In recent years, the field of human population genetics has increased the possibilities of reconstructing human histories. Using modern and ancient DNA, this kind of analysis can complement archaeological and historical accounts of a population history. In this study, human population genetics methods will be applied to a population of Maya and similar indigenous communities in Mexico. The objectives of such study were two-fold. First, the mating patterns and migration history of the Maya, in relation to other groups in the Americas, were reconstructed. Second, a natural selection scan of the Maya population was done to analyze specific markers of natural selection in this population. Having obtained nuclear genomic data for this population of interest from previously published studies, the Mayan nuclear genomes were compared to a set of 55 ancient and modern nuclear reference genomes from North, Central, and South America to answer these objectives. This comparison was done through computational analysis by employing principal component analysis (PCA) and the population branch statistic (PBS). To answer the first objective, the results of the PCA supported the idea that the Maya of Mexico mated with groups in both northern and southern America, creating a spectrum of genetic similarity that correlates to geography. To answer the second objective regarding natural selection, the genes with the highest PBS scores from the natural selection scan were analyzed. Several of these genes were associated with calcium regulation, brain development, olfactory receptors, and the nervous system (RNU5F-1, CDH18, OR52Z1, ROBO2, RAPGEF2, CNTN4, CAMK2D, CRBN). The functional correlations for certain genes are connected to a multitude of functions, including but not limited to fetal adrenal gland and muscle trunk cells; adipose cells; muscle and skeletal tissue; primary T cells in blood; brain cells; neuronal progenitor cells; and mesoderm, ectoderm, and endoderm cultured cells. By analyzing the genes specifically selected for in the Maya population, the history of this population can be reconstructed. Overall, these results broaden our knowledge of the landscape in which the modern Mayan population evolved over their thousands of years of history.

Table of Contents

I. Introduction......................................................................................................................1

II. Literature Review.............................................................................................................3

Overview of Mayan Civilization...........................................................................................3

Modern Maya Today.............................................................................................................6

Human Population Genetics..............................................................................................10

Previous Genomic Work in Mayan Population History and Demography..........................13

Broader Applications and Cultural Implications...............................................................18

III. Methods.......................................................................................................................22

Objectives..........................................................................................................................22

Reference Genomes...........................................................................................................23

Analyses............................................................................................................................25

IV. Results.........................................................................................................................26

Principal Component Analysis (PCA)...............................................................................26

Natural Selection Scan .....................................................................................................27

V. Discussion.....................................................................................................................35

VI. Conclusion...................................................................................................................39

VII. References..................................................................................................................41

Tables

1: Variant associations with disease among twelve modern Mayan individuals................19

2: List of all populations used in downstream analyses.....................................................25

3: Genes with highest signal of natural selection for Mexican Maya.................................31

4: Genes with highest signal of natural selection for Aymara............................................33

Figures

1: Timeline of ancient Mayan civilization, 1800 BC – 1500 AD...........................................4

2: The coalescent model describing branching of a given population over time................12

3: PCA of reference populations.........................................................................................27

4: Manhattan plot of Population Branch Statistic (PBS) scores

with Mexican Maya as the target population......................................................................28

5: Manhattan plot of Population Branch Statistic (PBS) scores

with Aymara as the target population.................................................................................29

About this Honors Thesis

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School	Emory College
Department	Anthropology
Degree	B.S.
Submission	Honors Thesis
Language	English
Research Field	Biology, Bioinformatics Biology, Genetics Anthropology, Physical
Keyword	Central America Biological anthropology Population Genetics DNA
Committee Chair / Thesis Advisor	Lindo, John, Emory University
Committee Members	Hadley, Craig, Emory University Pachon, Helena, Emory University

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