Date of Award

Spring 5-15-2017

Author's School

Graduate School of Arts and Sciences

Author's Department


Degree Name

Doctor of Philosophy (PhD)

Degree Type



Hybridization is increasingly recognized as a common, important process shaping the evolution of organisms including humans. Across hybrid zones, the genomes of incipient species are mixed and recombined through hybridization and backcrossing, creating conditions ideal for evaluating the actions of natural selection on gene variants in novel genomic contexts. This dissertation aims to increase our understanding of hybridization using a Zambian baboon study system in which two species, Kinda baboons (Papio kindae) and grayfoot baboons (Papio griseipes), hybridize despite exhibiting pronounced differences in body size and behavior. Using genome-wide genotypic data prepared using double-digest RADseq, I scan for genomic regions under selection in these species and in their hybrids.Because a large section of the hybrid zone contains groups unhabituated to human presence, I develop a new method for noninvasive genomic-scale genotyping from feces. I demonstrate that an enrichment procedure using methyl-CpG-binding-domain proteins to preferentially capture densely CpG-methylated mammalian DNA effectively partitions baboon host DNA from contaminating bacterial DNA, yielding efficient sequencing of target genomic DNA. Comparisons of same-animal double-digest RADseq libraries demonstrate high concordance between feces-derived and blood-derived genotypes.By scanning genome-wide data for regions with significant levels of differentiation between Kinda and grayfoot baboon populations, I identify candidate genes under selection in the two species. I find evidence for selection on genes and biological pathways that underlie differences in body size between the parental species. One pathway exhibiting significantly elevated differentiation was the JAK/STAT signaling pathway, which notably serves an important role in mediating the effects of cytokine signals on processes including epiphyseal chondrocyte proliferation essential for bone growth.Analysis of hybrids reveals that Kinda and grayfoot baboons form a relatively wide cline in the Kafue river valley in central Zambia. Comparison of autosomal ancestry patterns to mitochondrial-DNA and Y-chromosome ancestry patterns reveals that the Kinda baboon Y chromosome has introgressed extensively across the species barrier relative to both the mitochondrial genome and the remainder of the nuclear genome. The JAK/STAT signaling pathway exhibits restricted introgression, suggesting a role in barriers to reproduction possibly due to the unusually high or low body size sexual dimorphism between male grayfoot x female Kinda and male Kinda x female grayfoot baboon mating partners. The toll-like receptor pathway exhibits enhanced introgression, suggesting adaptive introgression of pathogen defenses. Finally, the sperm tail gene ODF2 exhibits enhanced introgression and an advantage of the grayfoot baboon variant. I suggest based on a house mouse analogy that male hybrids may be subjected to reduced sperm quality but that this effect may be mitigated or overcome by the presence of an invading Y chromosome. This effect potentially explains the extreme introgression of the Kinda baboon Y chromosome.


English (en)

Chair and Committee

Jane E. Phillips-Conroy

Committee Members

Amy L. Bauernfeind, Clifford J. Jolly, Allan Larson, Amanda D. Melin,


Permanent URL: https://doi.org/10.7936/K7348HS3