Browsing by Author "Wang, Yaxuan"

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    Computational Methods for Inference of Species/Gene Trees and Trait Evolution
    (2020-12-01) Wang, Yaxuan; Nakhleh, Luay K.
    Phylogenetic trees play a central role in almost all of biology. These trees have emerged as a powerful paradigm in the post-genomic era to elucidate the processes that shaped the evolutionary history. Species trees model how species split and diversify from their most recent common ancestors. Gene trees model how individual recombination-free loci within a set of genomes evolve from the ancestor. Phylogenetic trees also play a significant role in other comparative evolutionary biology studies such as trait evolution. Therefore, deriving accurate phylogenetic trees and developing an appropriate adaptation of the phylogenetic inference methodology to support trait evolution is the major endeavor. The contribution of this thesis comes from three aspects. Firstly, it provides a heuristic framework for species/gene tree co-estimation. By iteratively inferring the species tree and gene tree, the topological inference of phylogenetic trees become accurate and efficient. I implemented the framework in the multispecies coalescent model while it can be applied in various evolutionary models. By taking the advantage of gene tree discordance, this framework is able to derive reliable and efficient phylogenetic inference. Secondly, I presented a novel proposal strategy to improve the scalability of Bayesian sampling estimation by appropriately reducing unnecessary search space. In my thesis, I applied this idea to empower Bayesian sampling approach of phylogenetic inference. More importantly, this idea reveals a feasible direction to fix the poor fixing problem in Bayesian sampling scenarios. Thirdly, adaptive phenotypic convergence is considered as key evidence of convergent evolution However, gene tree discordance can also generate convergent trait patterns. To determine if the horizontal gene transfer plays a role in the trait evolution when the trait is incongruent with the species phylogeny, I presented a statistical factor from the perspective of phylogenomics. I revealed the impact of ignoring the introgression in the phylogenomic and trait evolution analysis. I implemented the methods and models in the publicly available software package PhyloNet. The contributions of my thesis not only empower effective and practical phylogenomic analysis but also reveal the significance of embracing gene heterogeneity in the post-genomic era.
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    Phylogenomic assessment of the role of hybridization and introgression in trait evolution
    (Public Library of Science, 2021) Wang, Yaxuan; Cao, Zhen; Ogilvie, Huw A.; Nakhleh, Luay K.
    Trait evolution among a set of species—a central theme in evolutionary biology—has long been understood and analyzed with respect to a species tree. However, the field of phylogenomics, which has been propelled by advances in sequencing technologies, has ushered in the era of species/gene tree incongruence and, consequently, a more nuanced understanding of trait evolution. For a trait whose states are incongruent with the branching patterns in the species tree, the same state could have arisen independently in different species (homoplasy) or followed the branching patterns of gene trees, incongruent with the species tree (hemiplasy). Another evolutionary process whose extent and significance are better revealed by phylogenomic studies is gene flow between different species. In this work, we present a phylogenomic method for assessing the role of hybridization and introgression in the evolution of polymorphic or monomorphic binary traits. We apply the method to simulated evolutionary scenarios to demonstrate the interplay between the parameters of the evolutionary history and the role of introgression in a binary trait’s evolution (which we call xenoplasy). Very importantly, we demonstrate, including on a biological data set, that inferring a species tree and using it for trait evolution analysis in the presence of gene flow could lead to misleading hypotheses about trait evolution.