|
" Characterizing the Natural Genetic and Epigenetic Diversity of Human Populations "
Gopalan, Shyamalika
Henn, Brenna M.
| Document Type
|
:
|
Latin Dissertation
|
| Language of Document
|
:
|
English
|
| Record Number
|
:
|
1052476
|
| Doc. No
|
:
|
TL51593
|
| Main Entry
|
:
|
Gopalan, Shyamalika
|
| Title & Author
|
:
|
Characterizing the Natural Genetic and Epigenetic Diversity of Human Populations\ Gopalan, ShyamalikaHenn, Brenna M.
|
| College
|
:
|
State University of New York at Stony Brook
|
| Date
|
:
|
2019
|
| Degree
|
:
|
Ph.D.
|
| student score
|
:
|
2019
|
| Note
|
:
|
176 p.
|
| Abstract
|
:
|
Patterns of genetic diversity are shaped by both demographic history and natural selection, and underlie much of the observed phenotypic variation in our species. An additional factor in determining phenotypic variation is epigenetics – broadly, a suite of chemical modifications to the primary DNA sequence that control which are involved in controlling the function of specific parts of the genome. In particular, it has been shown that patterns of DNA methylation have been shown to shift in response to certain environmental exposures as well as intrinsic factors like aging and disease. I analyze genome-wide patterns of change in DNA methylation with increasing age in sub-Saharan Africans and show that certain sites in the genome can serve as accurate biomarkers of chronological age even across highly diverse human populations. I also identify genetic variants may influence baseline levels of DNA methylation at certain age-associated sites in the genome. I characterize patterns of DNA methylation and age in human bone in order to develop the first statistical method of estimating age from skeletal remains for forensic purposes. To this end, I generated a dataset of genome-wide DNA methylation from bone samples collected from body donation programs and leveraged existing bone datasets, derived from living donors, to statistically identify strong biomarkers of age in this tissue type. In this dissertation, I also analyze genetic data from the Chabu, a population of isolated hunter-gatherers from southwest Ethiopia to understand their recent demographic history. By integrating genetic data from across eastern Africa, I show that the Chabu are genetically distinct from all nearby populations, and show a genetic affinity to an ancient individual who predated the arrival of agriculture to this region. My results strongly suggest that the Chabu are direct descendants of earlier populations of local hunter-gatherers. By analyzing patterns of relatedness within the population, I also show that the Chabu have experienced a precipitous decline in effective population size (Ne) over the past 50 generations, mirroring the demographic history of other hunter-gatherer populations in eastern Africa. Finally, I also review the extensive literature surrounding archaic introgression and ancient DNA for a non-specialist audience, providing a resource that aims to facilitate the engagement of scientists of various disciplines with this burgeoning field. In this dissertation, I present several projects that together link several topics at the forefront of human genetics today, from epigenetics to ancient DNA to the increased inclusion of natural genetic diversity.
|
| Descriptor
|
:
|
Aging
|
|
|
:
|
Forensic anthropology
|
|
|
:
|
Genetics
|
| Added Entry
|
:
|
Henn, Brenna M.
|
| Added Entry
|
:
|
State University of New York at Stony Brook
|
| |