Advancing ancestral graph theory of metacommunities and population genetic theory of polyploids

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Since the work of Darwin and Wallace, the discipline of evolutionary biology has sought to understand the history of life and the mechanisms that underlie the evolutionary process. My research group contributes to the field of evolutionary biology by developing theory in support of these goals. Under my previous Discovery Grant, my group derived a model of the ancestral history of an ecological community that includes the processes of natural selection and species interactions. Over the next five years, we seek to integrate this approach with classic phylogenetic models of historical processes, with the goal of developing a general theory that bridges recent and deep time. This will improve our ability to make inferences across different time scales to understand the processes that have shaped present-day ecological communities. Our model of the ancestral history of an ecological community also has immediate applications. For example, we seek to apply the model to gain insight into the nature of genomic content in prokaryotic microbes. This work will shed light on how horizontal gene transfer shapes genomic content that is shared and unshared among individuals of the same and different species within a prokaryotic community. Another area of application relates to the detection of microbial species within communities. The development of high--throughput DNA sequencing now makes it possible to sequence, in principle, an entire microbial community. Nevertheless, we sometimes fail to sequence DNA from species that are present due to limitations of the technology. We recently derived expectations for patterns of DNA sequence variation when lineages go unsequenced. In this grant, we seek to apply this theory to samples from nature to assess whether lineages have gone undetected. This work will have important implications for reducing uncertainty about the use of environmental DNA in ecological assessments and other research. A second, complementary arm of my research program is addressing long-standing questions about the processes that underlie evolution in polyploid species. An important gap in the literature has been models of selection across multiple regions of a polyploid species' genome. My research group has derived such a model, and we now seek to apply its insights to understand how recombination rates evolve in polyploids, and to identify processes that affect the regression of a polyploid to a lower ploidy state. This work will advance our fundamental knowledge of meiosis, selection and genome evolution in polyploids. My lab group seeks to think broadly and address important gaps in our understanding of evolution. We have ambitious goals for developing fundamental theory in evolutionary biology. The proposed research is expected to make a significant contribution to advancing our basic understanding of nature and our biological heritage.