Advancing ancestral graph theory of metacommunities and population genetic theory of polyploids

自从达尔文和华莱士的工作以来，进化生物学这门学科一直试图理解生命的历史和构成进化过程基础的机制。我的研究小组通过发展支持这些目标的理论，为进化生物学领域做出了贡献。在我之前的“发现基金”资助下，我的团队导出了一个生态群落祖先历史的模型，其中包括自然选择和物种相互作用的过程。在接下来的五年里，我们寻求将这种方法与历史过程的经典系统发育模型相结合，目标是建立一个连接近期和深层时间的一般理论。这将提高我们在不同时间尺度上进行推断的能力，从而理解塑造当今生态群落的过程。我们的生态群落祖先历史模型也有直接的应用价值。例如，我们寻求应用该模型来深入了解原核微生物基因组内容的本质。这项工作将阐明水平基因转移如何在原核生物群落中相同和不同物种的个体之间形成共享和不共享的基因组内容。另一个应用领域涉及群落内微生物种类的检测。高通量DNA测序技术的发展使得对整个微生物群落进行测序成为可能。然而，由于技术的限制，我们有时无法对现有物种的DNA进行测序。我们最近得到的期望模式的DNA序列变异当谱系去测序。在这项资助中，我们试图将这一理论应用于自然界的样本，以评估谱系是否未被发现。这项工作将对减少在生态评估和其他研究中使用环境DNA的不确定性具有重要意义。我的研究计划的第二个补充部分是解决关于多倍体物种进化过程的长期问题。文献中的一个重要空白是多倍体物种基因组中多个区域的选择模型。我的研究小组已经推导出了这样一个模型，我们现在寻求应用它的见解来理解多倍体的重组率是如何进化的，并确定影响多倍体向低倍体状态回归的过程。这项工作将推进我们对多倍体减数分裂、选择和基因组进化的基础知识。我的实验室小组试图从更广泛的角度思考，解决我们对进化的理解中的重要空白。我们有发展进化生物学基础理论的宏伟目标。这项拟议的研究有望对增进我们对自然和生物遗产的基本认识作出重大贡献。

Since the work of Darwin and Wallace, the discipline of evolutionary biology has sought to understand the history of life and the mechanisms that underlie the evolutionary process. My research group contributes to the field of evolutionary biology by developing theory in support of these goals. Under my previous Discovery Grant, my group derived a model of the ancestral history of an ecological community that includes the processes of natural selection and species interactions. Over the next five years, we seek to integrate this approach with classic phylogenetic models of historical processes, with the goal of developing a general theory that bridges recent and deep time. This will improve our ability to make inferences across different time scales to understand the processes that have shaped present-day ecological communities. Our model of the ancestral history of an ecological community also has immediate applications. For example, we seek to apply the model to gain insight into the nature of genomic content in prokaryotic microbes. This work will shed light on how horizontal gene transfer shapes genomic content that is shared and unshared among individuals of the same and different species within a prokaryotic community. Another area of application relates to the detection of microbial species within communities. The development of high--throughput DNA sequencing now makes it possible to sequence, in principle, an entire microbial community. Nevertheless, we sometimes fail to sequence DNA from species that are present due to limitations of the technology. We recently derived expectations for patterns of DNA sequence variation when lineages go unsequenced. In this grant, we seek to apply this theory to samples from nature to assess whether lineages have gone undetected. This work will have important implications for reducing uncertainty about the use of environmental DNA in ecological assessments and other research. A second, complementary arm of my research program is addressing long-standing questions about the processes that underlie evolution in polyploid species. An important gap in the literature has been models of selection across multiple regions of a polyploid species' genome. My research group has derived such a model, and we now seek to apply its insights to understand how recombination rates evolve in polyploids, and to identify processes that affect the regression of a polyploid to a lower ploidy state. This work will advance our fundamental knowledge of meiosis, selection and genome evolution in polyploids. My lab group seeks to think broadly and address important gaps in our understanding of evolution. We have ambitious goals for developing fundamental theory in evolutionary biology. The proposed research is expected to make a significant contribution to advancing our basic understanding of nature and our biological heritage.