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.

进化生物学的主要目标是使用DNA序列重建生物之间关系的进化历史 - 重建生命之树。但是，生物学家越来越意识到许多物种杂交，从而导致了“生活网络”。这项研究介绍了一种新的数学模型，以推断生命之树的杂交，并通过一组高度杂交的夜间初月植物的DNA数据测试模型，这些植物在索诺兰，莫哈韦和大盆地沙漠的苛刻栖息地中生长。 该项目还将为大学生提供生物信息学，培训和研究经验，并生产计算机软件来检测杂交事件，这些事件将通过Internet自由分解。杂交是生命之树的大部分进化过程，可以通过增加培养基中的适应性变化来实现生命树的大部分进化过程。然而，由于缺乏模拟涉及不完整谱系分类和渗入的进化场景的方法，因此很难在系统发育环境中推断杂交。这项研究结合了经验和理论工作，以应对推断杂交并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囊肿属（Onagraceae）中同质杂种复合物（Onagraceae）跨同型混合络合物的进化后果。 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型的贝叶斯方法，用于检测结合系统发育和融合理论方面的渗入方法。 最后，他们将使用来自整个核基因组的整个叶绿体基因组和标志物来量化伴随网状进化的基因组结构变化及其在墨西哥的功能意义。