WeissSarah_Spring_2023.pdf
- Author (aut): Weiss, Sarah
- Thesis director: Pfeifer, Susanne
- Committee member: Versoza, Cyril
- Contributor (ctb): Barrett, The Honors College
- Contributor (ctb): School of Art
- Contributor (ctb): School of Life Sciences
Previous recombination rate estimation studies in rhesus macaques have been mostly restricted to a singular approach (e.g., using microsatellite loci). Here, we employ a bilateral method in estimating recombination rates—pedigree-based and linkage-disequilibrium-based—from whole-genome data of rhesus macaques to estimate CO and NCO recombination events and to compare contemporary and historical rates of recombination.
Recombination is the process of exchange between maternal and paternal chromosomal segments which gives rise to new allele combinations in the offspring. The rate of recombination refers to the chances that such crossing over events will take place. Recombination is an especially important process for driving genetic diversity and therefore evolution. However, the specifics of the factors affecting the recombination frequency and how the rate itself can evolve have not been the focus of many studies in the past. The purpose of this study was to utilize sequenced genomes of parent-offspring trios of Rhesus Macaque to create a high quality dataset from which a direct, sex-specific, estimate of recombination rate can be calculated for the species.
Levels of nucleotide diversity vary greatly across the genomes of most species owing to multiple factors. These include variation in the underlying mutation rates, as well as the effects of both direct and linked selection. Fundamental to interpreting the relative importance of these forces is the common observation of a strong positive correlation between nucleotide diversity and recombination rate. While indeed observed in humans, the interpretation of this pattern has been difficult in the absence of high-quality polymorphism data and recombination maps in closely related species. Here, we characterize genetic features driving nucleotide diversity in Western chimpanzees using a recently generated whole genome polymorphism data set. Our results suggest that recombination rate is the primary predictor of nucleotide variation with a strongly positive correlation. In addition, telomeric distance, regional GC-content, and regional CpG-island content are strongly negatively correlated with variation. These results are compared with humans, with both similarities and differences interpreted in the light of the estimated effective population sizes of the two species as well as their strongly differing recent demographic histories.