A genomic view on the adaptation and diversification of natural populations

Abstract

Earlier studies in evolutionary genetics focused on a few model organisms such as fruit flies or mice that are limited when it comes to answering evolutionary and ecological questions. In contrast, genetic studies of natural populations have now become common and can provide a more realistic understanding of how natural selection, genetic drift, mutation, and gene flow shape the patterns of phenotypic and genetic diversity, as well as adaptation and diversification across a range of environmental conditions. This dissertation illustrates how current genomic tools can be effectively used to (1) study the evolutionary history of species along altitudinal gradients, and (2) understand the genetic basis of adaptive phenotypes in populations inhabiting high-altitude habitats. In the first research paper, we compared whole-genome resequencing data of Eastern honey bee (Apis cerana) populations from high and low altitudes in southwestern China. We identified several regions of the genome that appeared to have been under positive selection in highland bee populations. Candidate loci in these genomic regions included genes related to reproduction and feeding behavior. In the second paper, we generated a transcriptome reference for the Neotropical frogs of the genus Oreobates by sequencing RNA from one individual of the La Paz robber frog (Oreobates cruralis). In the third paper, we used that transcriptome to selectively target and enrich ~18,000 genes across species of Oreobates collected along the Andean Mountains, in South America. We found that highland species have smaller effective populations and accumulate nonsynonymous mutations faster than species sampled at lower altitudes. These mutations can be targeted by natural selection and contribute to the adaptation and differentiation of populations in mountain environments. In the fourth and final paper, we pointed out that genomics has to be integrated with other sources of evidence to understand evolutionary and ecological processes more deeply than was thought in the past.