DISSERTATION RESEARCH: Phylogeographic discord in the comparative genomic history of Amazonian birds

物种多样性的产生具有根本性的意义，但引起多样性的因素却知之甚少。众所周知，根据所涉及的物种或物种群的不同，多样化以不同的速度发生，对这种变化的比较研究可以揭示促进多样性的过程。比较系统地理学是在种群水平上研究不同物种的多样性，它使我们能够在物种形成发生的地方观察多样性的差异。本研究的目的是利用比较系统地理学和新的数据生成方法来检测物种间多样化的差异，并分析促进某些物种比其他物种更快多样化的因素。系统地理学将对16种分布相似的亚马逊鸟类进行比较。分散在基因组中的一组新的遗传标记将用于从每个物种的24个个体中生成数据。这些基因序列将从博物馆组织样本中提取，使用一种新的富集感兴趣序列的基因组DNA的方法，然后在下一代测序仪器上进行测序。用于测试模型的新分析工具将使我们能够衡量在推动特定物种多样化方面最重要的过程。通过这种方法产生的大量数据将允许分析比以前分析的更复杂的模型，使我们对促进物种多样性的过程有了新的认识。该项目为路易斯安那州的本科生提供了研究机会，项目的地理范围促进了机构间和国际合作。该研究为下一代测序方法和新的基因组标记集提供了测试，我们的结果将有助于这些方法在其他研究系统中的应用。从我们的工作中获得的新的生物地理和地理遗传数据支持了在亚马逊的保护工作。所有标本、录音、现场工作的观测数据和实验室工作的遗传数据都存放在可公开访问的收集和数据库中。我们认为这些资源对于当前和未来，对亚马逊鸟类和其他系统的纯粹和应用研究都是无价的。

The production of species diversity is of fundamental interest, but the factors that cause diversification are poorly understood. Diversification is known to occur at different rates depending on the species or group of species involved, and comparative study of this variation can reveal the processes that promote diversity. Comparative phylogeography is the study of diversification at the population level within different species, and it allows us to observe differences in diversification at the point where speciation occurs. The goals of this study are to use comparative phylogeography and novel methods of generating data to detect differences in diversification across species, and to analyze the factors that promote faster diversification in some species than in others. Phylogeography will be compared across sixteen Amazonian bird species with similar distributions. A new set of genetic markers scattered across the genome will be used to generate data from 24 individuals of each species. These genetic sequences will be extracted from museum tissue samples using a new method of enriching genomic DNA for sequences of interest, and then sequenced on a next-generation sequencing instrument. New analytical tools for testing models will allow us to measure the processes that are most important in driving the diversification of a given species. The massive amount of data generated by this method will allow for analysis of more complex models than could ever be analyzed previously, giving us new insight into the processes promoting species diversity. This project provides research opportunities for undergraduate students in Louisiana and the geographic scope of the project fosters inter-institutional and international collaborations. The research provides a test of next-generation sequencing methods and a new genomic marker set, and our results will aid in the application of these methods to other study systems. New biogeographic and geographic genetic data from our work support conservation efforts in the Amazon. All specimens, audio recordings, and observational data from our fieldwork and genetic data from our lab work are deposited in publicly accessible collection and databases. We consider these resources invaluable for current and future, pure and applied research on Amazonian birds and other systems.