Liming Cai, PhD Candidate
Davis Lab, Department of Organismic and Evolutionary Biology
Topic: Genomic evolution of Malpighiales: duplicated, introgressed, and incompletely-sorted
The application of genomic data to phylogenetic studies have revived hope of resolving recalcitrant relationships but also revealed extensive gene tree heterogeneity. These gene tree variations can shed important light on evolutionary events. Malpighiales are a large and diverse clade that remains one of the thorniest angiosperm nodes to resolve. I will discuss a variety of phylogenomic data sets used to explore the early evolutionary history of this clade. First, using transcriptome data I identified 24 ancient whole genome duplications widely distributed across the order. These events are clustered around the super-greenhouse period during the Paleocene-Eocene Transition (~54 Ma). This finding provide further supporting evidence that polyploidization may be important for surviving periods of global upheaval. Second, I apply a sequence capture data set to examine gene tree–species tree heterogeneity contributing to the recalcitrant relationships in Malpighiales. We developed a novel method to quantify the relative contribution of factors influencing gene tree heterogeneity, including incomplete lineage sorting, gene tree estimation error, and gene flow. We identify that a deep history of gene flow, likely involving a single promiscuous clade, may be the main culprit in our ability to resolve this group. This research highlights the critical need for more sophisticated phylogenetic models that do not strictly enforce a single, bifurcating species tree.