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

进化生物学的一个主要目标是利用DNA序列重建生物之间关系的进化史--重建生命之树。然而，生物学家们越来越多地意识到，许多物种进行杂交，形成了一个生命网络。这项研究引入了一种新的数学模型来推断生命树上的杂交，并用一组高度杂交的月见草的DNA数据来测试该模型，这些植物生长在索诺兰、莫哈韦和大盆地沙漠的恶劣生境中。该项目还将为本科生提供生物信息学、培训和研究经验，并制作计算机软件来检测杂交事件，这些事件将通过互联网自由传播。杂交是生命树相当一部分的重要进化过程，它可能通过增加谱系内的适应性变异而起到进化催化剂的作用。然而，在系统发育的背景下推断杂交是困难的，因为缺乏对涉及不完全谱系排序和导入的进化情景进行建模的方法。这项研究结合了经验和理论工作，以解决推断杂交的挑战并检验其进化意义。研究人员将使用下一代测序和基因组数据集来研究渗透和历史生物地理跨植物乳糜属(Onagraceae)同倍体杂交复合体的进化后果。他们还将应用经验数据集和模拟数据集来开发和测试一种新的贝叶斯方法来检测渗透，该方法结合了系统发育和合并理论的各个方面。最后，他们将使用整个叶绿体基因组和整个核基因组的标记来量化伴随着网状进化的基因组结构变化及其在乳糜症中的功能意义。

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.