An aDNA Approach to Investigating Post-Admixture Selection in Mexico: Assessing the (Immuno)Genetic Consequences of European Colonization 公开
Warn, Jack (Spring 2024)
Published
Abstract
The development and advancement of ancient DNA technologies have opened up new possibilities in recent years to gain insight into past demographic histories, population movements, and to understand the various evolutionary processes that have led to the modern day. The onset of European colonization in the 15th century marked a significant turning point in the history of the Americas and the world. The emergence of the trans-Atlantic slave trade was accompanied by the interchange of populations previously geographically isolated and genetically distinct from each other. With this increased contact between populations, various pathogens were introduced to certain populations of Indigenous Americans which, when combined with warfare and slavery, caused devastating population collapse. As such, modern genomic methods have the potential to illustrate how post-admixture selection shaped our evolution, particularly with respect to genes regulating the immune system and response. However, whole-genome data for Latin American and Indigenous American populations are drastically underrepresented in genomics research. This not only stifles biological discovery, but makes our knowledge disproportionately relevant to populations of European descent, thereby corrupting understandings of health and genetics.
Recently, 12 whole-genome ancient samples were discovered in Mexico. including 4 high-coverage (>1x) samples. With these samples, there is a potential to further understanding of evolutionary histories in the region. By sequencing the recently-discovered genomes of ancient Mexican individuals alongside modern Mexican samples, we hope to identify several gene pathways and proteins that have been affected as a result of European colonization in Mexico. Moreover, it is our goal that these findings can be useful in understanding not only how post-admixture selection in this context shaped the modern population, but also in directing population health interventions in the region.
Using computational genomic methods, modern and ancient Mexican genomes will be analyzed for signals of selection, with particular focus on genes affecting the immune system and human health. Utilizing a combination of demographic analyses and selection scans, the study aims to achieve a deeper understanding of the processes of evolution that have shaped the contemporary Mexican population.
Table of Contents
Table of Contents
Introduction......................................................................................................................................1
Literature Review.............................................................................................................................2
Ancient samples and pre-contact Mexico.............................................................................2
Demographic history of Mexico...........................................................................................3
Genetics and health…………..............................................................................................5
Immunogenetic histories......................................................................................................7
Similar studies......................................................................................................................8
Genomics as a clinical intervention and biological implications.......................................11
Limitations.........................................................................................................................12
Methods..........................................................................................................................................13
Data processing.................................................................................................................13
Demographic analyses.......................................................................................................14
Genome-wide selection scan…...…....................................................................................16
Results............................................................................................................................................17
Demographic analyses.......................................................................................................17
Selection scan.....................................................................................................................22
Discussion......................................................................................................................................30
References......................................................................................................................................33
Supplemental Information.............................................................................................................37
Table S1. List of immune-related SNPs.............................................................................37
Table S2: Variants with health-related gTEX eQTL hits...................................................38
Table S3. List of samples referenced by study……………...............................................39
Table S4. List of high-coverage (>1x) ancient samples…………….................................42
Figure S1. Map of high-coverage ancient samples............................................................43
Figure S2. Illustration of NFKB pathway…………………………………….................43
Figure S3. Illustration of Dendritic Cell function…………………………….................44
Figure S4. Manhattan Plot of PBS Results…………………………..……….................45
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An aDNA Approach to Investigating Post-Admixture Selection in Mexico: Assessing the (Immuno)Genetic Consequences of European Colonization () | 2024-05-02 11:22:12 -0400 |
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