Genomic Analyses of Hybridization and Speciation in Macaques

Abstract

Speciation, the origin of species, is a process fundamental to producing the current diversity of life, and has been a central subject of evolutionary biology for the past century. Hybridization, the mating of individuals from genetically distinct populations, can impede or facilitate a variety of evolutionary processes, including speciation. Genomics, the specialty of genetics focused on analysis of genomes, has recently advanced and thus provides new means to study both these phenomena. Macaques (genus Macaca) are one of the most diverse genera of Old World Monkeys (23 species) and include some of the most widespread primate species. All extant macaque species have originated within the last few millions of years and most have experienced hybridization with other species. Also, many macaque species are widely-studied for medical purposes and thus have abundant genomic resources. Thus, macaques make an excellent model for studying speciation and in particular the effects of hybridization on speciation using genomic data. In this dissertation I describe analyses of this sort that I have conducted. In chapter 1, I introduce the history of the aforementioned concepts. In chapter 2, I show that the bear macaque, Macaca arctoides, a species with mitochondrial and nuclear ancestries tracing to different species, has exhibited intragenomic conflict between genes in these organelles. In chapter 3, I examine genes putatively involved in the genital morphology of this same species, as the genitals of this species are unique amongst macaques and may be one source of reproductive isolation from other species. I find that these genes exhibit increased divergence from other species and genetic diversity within this species as compared to the rest of the genome. In chapter 4, I examine the possibility that reinforcement speciation, selection against hybrids leading to speciation, may have occurred between the rhesus macaque, M. mulatta, and cynomolgus macaque, M. fascicularis, and find a number of genes that may be involved in this process. In chapter 5, I show that software used to calculation genetic diversity and neutrality testing with genomic data is biased by excess amounts of missing data, and try to write software to correct this bias.