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Quantitative Biosciences Thesis Proposal
Open to the community
Aaron Pfennig
School of Biological Sciences
Georgia Institute of Technology
Theoretical and empirical population genetics of admixture and introgression
Friday, September 2, 2022
11:00 am Eastern Time
EBB Krone - Children's Healthcare of Atlanta Seminar Room (room #1005)
Zoom Link: https://gatech.zoom.us/j/97879627092
Thesis Advisor:
Dr. Joseph Lachance
School of Biological Sciences
Georgia Institute of Technology
Committee Members:
Dr. Annalise Paaby
School of Biological Sciences
Georgia Institute of Technology
Dr. Patrick McGrath
School of Biological Sciences
Georgia Institute of Technology
Dr. I. King Jordan
School of Biological Sciences
Georgia Institute of Technology
Summary:
Admixture and introgression are central components of human evolution. Large-scale
movements of people have allowed gene flow between previously isolated extant populations,
creating admixed populations (e.g., African-Americans). In addition, historically anatomically
modern humans interbred with archaic hominins on multiple occasions, i.e., with Neanderthals
and Denisovans. For these reasons, admixture and introgression are crucial sources of human
genetic variation. Thus, improving our understanding of the role and implications of admixture
and introgression during human evolution will be invaluable to human health in the era of
precision medicine.
In the first part of this thesis proposal, I aim to explore population genetics models for estimating
magnitudes of sex-biased admixture from X chromosomal and autosomal ancestry proportions. I
evaluate their robustness to noisy data and violations of demographic assumptions using a
sensitivity analysis and forward simulations. Knowing the confounding effects of population
structure will help to improve the interpretability of such models. To further improve the
interpretability of such models, I also describe an approach for obtaining confidence intervals for
sex bias estimates.
In the second part, I propose a theoretical population genetics model that accounts for fitness
effects that can arise from the heterogeneous background in hybrid genomes. I aim to examine
the impact of such fitness effects on the evolutionary dynamics of an unlinked introgressed
marker allele. Specifically, I derive expressions for the fixation probability of an introgressed
allele using diffusion approximations and branching processes.
Lastly, I propose to study the legacy of archaic introgression in African Americans. A s
Neanderthal interbreeding occurred in Eurasia, many archaic alleles were only recently
(re-)exposed to human-specific alleles in genomes of African-Americans, allowing us to study
the dynamics in real-time. Therefore, studying introgressed DNA in African-American genomes
allows testing whether archaic variants are still selected against and what their phenotypic
effects are in African-Americans, among others.
