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

论文研究：在谱系排序不完整的情况下检测基因渗入：Chylismia（Onagraceae）的系统基因组学和杂交

• 批准号: 1601402
• 负责人: Bruce Baldwin
• 金额: $ 2.04万
• 依托单位: University of California-Berkeley
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-07-01 至 2018-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1601402&HistoricalAwards=false
• 关键词: Dissertation; Research; Detecting; introgression; presence

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.

进化生物学的一个主要目标是利用DNA序列来重建生物体之间关系的进化历史-重建生命之树。然而，生物学家越来越意识到，许多物种杂交，形成了一个生命的“网络”。这项研究引入了一个新的数学模型来推断杂交的生命之树，并测试了一组高度杂交的月见报春花植物的DNA数据模型，这些植物生长在索诺兰，莫哈韦和大盆地沙漠的恶劣栖息地。 该项目还将为本科生提供生物信息学和培训及研究经验，并制作检测杂交事件的计算机软件，这些软件将通过互联网免费传播。杂交是生命树中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充当进化催化剂。然而，推断杂交系统发育的背景下是困难的，由于缺乏方法，涉及不完整的谱系排序和基因渗入的进化场景模型。这项研究结合了经验和理论工作，以解决推断杂交和研究其进化意义的挑战。 研究人员将使用下一代测序和基因组数据集来研究植物属Chylismia（Onagraceae）中同源杂交复合体的基因渗入和历史基因组学的进化后果。 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，用于检测结合了系统发育和合并理论的基因渗入。 最后，他们将使用整个叶绿体基因组和来自整个核基因组的标记来量化伴随网状进化的基因组结构变化及其在乳糜中的功能意义。