Dissertation Research: Detecting introgression in the presence of incomplete lineage sorting: phylogenomics and hybridization in Chylismia (Onagraceae)

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A major goal of evolutionary biology has been to use DNA sequences to reconstruct the evolutionary history of relationships among organisms - to reconstruct the tree of life. However, biologists are increasingly aware that many species hybridize, resulting in a 'network' of life. This research introduces a new mathematical model to infer hybridization over the tree of life, and tests the model with DNA data from a group of highly hybridizing evening primrose plants that grow in the harsh habitats of the Sonoran, Mojave and Great Basin deserts. This project also will provide bioinformatics and training and research experience to undergraduates, and produce computer software to detect hybridization events that will be disseminated freely via the Internet.Hybridization is an important evolutionary process in a substantial portion of the tree of life that may act as an evolutionary catalyst by increasing the adaptive variation within lineages. However, inferring hybridization in a phylogenetic context is difficult due to the lack of methods that model evolutionary scenarios involving both incomplete lineage sorting and introgression. This research incorporates both empirical and theoretical work to address the challenges of inferring hybridization and examining its evolutionary significance. The researchers will use next-generation sequencing and genomic datasets to study the evolutionary consequences of introgression and historical biogeography across a homoploid hybrid complex in the plant genus Chylismia (Onagraceae). They also will apply both empirical datasets and simulated datasets to develop and test a novel Bayesian approach for detecting introgression that combines aspects of both phylogenetic and coalescent theory. Finally, they will quantify the genomic structural changes that accompany reticulate evolution and their functional significance in Chylismia using whole chloroplast genomes and markers from across the nuclear genome.