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

自达尔文和华莱士的工作以来，进化生物学的学科一直试图了解生命的历史和进化过程背后的机制。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中，我的团队得出了一个生态群落的祖先历史模型，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，我们将寻求将这一方法与历史进程的经典系统发育模型相结合，目标是开发一种连接现代和深层时间的一般理论。这将提高我们在不同时间尺度上做出推断的能力，以了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立即得到了应用。例如，我们试图应用该模型来洞察原核微生物基因组内容的性质。这项工作将阐明水平基因转移如何塑造原核生物群落中同一物种和不同物种的个体之间共享和不共享的基因组内容。 另一个应用领域涉及社区内微生物物种的检测。高通量DNA测序的发展现在使原则上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，我们有时无法对存在的物种进行DNA测序。我们最近得出了对血统未测序时DNA序列变异模式的预期。在这笔赠款中，我们试图将这一理论应用于来自大自然的样本，以评估是否有血统没有被发现。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长期存在的关于多倍体物种进化过程的问题。文献中的一个重要空白是多倍体物种基因组的多个区域的选择模型。我的研究小组已经得出了这样一个模型，现在我们试图应用其洞察力来理解多倍体中重组率是如何演变的，并确定影响多倍体退化到较低倍性状态的过程。这项工作将促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广泛思考并解决我们对进化论理解中的重要差距。我们有雄心勃勃的目标，要发展进化生物学的基础理论。预计拟议的研究将对促进我们对自然和我们的生物遗产的基本了解做出重大贡献。

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.