How recombination alters drift and selection in the genome

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HOW RECOMBINATION ALTERS DRIFT AND SELECTION IN THE GENOME******My research program investigates how the generation and availability of genetic variation interacts with drift and selection to influence evolution. Two fundamental processes generate the variation that fuels evolution: mutation and recombination. Mutation creates new variants, and recombination shuffles mutations into new combinations. During sex, recombination brings together beneficial mutations that have occurred in different individuals, increasing the effectiveness of selection. Similarly, recombination breaks apart nearby beneficial from harmful mutations that would otherwise interfere with the ability of selection to fix the adaptive changes. Interestingly, there is evidence that the rate of recombination varies across the genome. This means that selection in regions of the genome may be more or less effective, depending on the rate of recombination. Surprisingly, there are few studies of recombination rate variation in the genome, primarily because recombination occurs so rarely; less than once in every 10 million sites. Fortunately, the genomic revolution offers the technology needed to observe recombination at the molecular scale. I propose to investigate variation in recombination and its consequences for adaptation in the model alga Chlamydomonas reinhardtii. In my proposal I describe three complementary short-term objectives:******1. I will explore how and why the rate of recombination varies between individuals and across the genome by sequencing the genomes of recombinant lines to identify thousands of recombination events. I will examine what aspects of genome biology best predict the rate of recombination. This work will generate one of the most detailed characterizations of recombination rate variation in any species.******2. I will test whether recombination reduces interference between selected mutations using the fine-scale map of recombination rate variation. I expect that regions with high recombination will adapt more quickly, while regions with low recombination will accumulate harmful mutations. In this framework, I will examine the strength of selection on protein-coding mutations, base composition, and genome size. ******3. I will scan natural genome sequences for islands of genes that control locally adapted traits. Using careful laboratory assays I will link the genes and traits that confer adaption to the local environment and quantify the factors that shape microbial populations in nature.******Only by incorporating direct measurement of recombination and mutation can the work I propose be conducted. This project will provide a comprehensive description of the forces that generate genetic variation, facilitating detailed understanding of how adaptation manifests at the genetic level.