Collaborative Research: Multilocus phylogenetics and species delimitation using sequence-capture and next-gen sequencing and its application in Adansonia (Malvaceae)

物种是分类学的基本单位，在科学交流和环境政策中发挥着重要作用。 虽然对物种概念的理论理解有了很大的进展，但客观界定物种的方法仍然效率低下。 这项由威斯康星州-麦迪逊大学和爱荷华州州立大学的研究人员进行的研究将开发新的计算工具，使物种划界更有效率。他们的研究还将解决生物学中的一个核心问题：什么是物种？ 这项研究将使用猴面包树属作为这些方法的试验场。猴面包树是马达加斯加、非洲大陆和澳大利亚西北部具有重要文化、生态和经济意义的标志性树木，也是物种界定中出现的许多挑战的缩影。这项工作将培养本科研究人员，K-12教师，研究生和博士后助理在分类学，基因组学和计算统计学的接口，并提供了几个机会，建立国际合作。总之，这项研究将为猴面包树系统学提供新的见解，并提供一个新的框架，以促进物种界定在不同的群体。物种界定包括多种方法，利用遗传，指导分类分组的形态学和其他性状数据（将生物体置于等级嵌套分类群中）和排序（决定分类群相对于从较高水平的树状关系到种群内的网状谱系的过渡的位置）。由于多倍性、基因渗入和/或具有复杂地理形态变异模式的物种，在许多群体中，物种划界仍然具有挑战性。然而，最近的进展，高通量测序技术，促进多位点DNA序列数据的快速采集，并通过新的分析方法，物种水平的分类问题提供了进步的机会。以猴面包树为模型，本研究将开发一种快速有效的实验方案，使用序列捕获技术和下一代测序技术，将允许应用不同的物种划界方法。除了部署现有的分析方法外，研究人员还将扩展贝叶斯系统发生学和系统地理学（BPP）方法，以正式纳入形态学和地理学。此外，他们还将为软件程序BUCKy增加识别数据暗示杂交或基因渗入的能力，这些杂交或基因渗入可以应用于不同的生物群体。

Species are the basic units of taxonomy, playing an important role in scientific communication and environmental policy. While the theoretical understanding of the species concept has advanced greatly, methodologies for the objective delimitation of species remain inefficient. This study by researchers at the University of Wisconsin - Madison and Iowa State University will develop new computational tools to make species delimitation more efficient. Their research will also address a central question in biology: What is a species? This study will use the genus Adansonia (the baobabs) as a testing ground for these methods. Baobabs are iconic trees of great cultural, ecological, and economic importance in Madagascar, continental Africa, and northwestern Australia, and are also a microcosm for many of the challenges that arise in species delimitation. The work will train undergraduate researchers, K-12 teachers, graduate students, and a postdoctoral associate at the interface of taxonomy, genomics, and computational statistics and provide several opportunities to establish international collaboration. Together, this research will provide new insights into Adansonia systematics and provide a new framework to facilitate species delimitation in diverse groups.Species delimitation encompasses diverse methods that use genetic, morphological and other trait data to guide taxonomic grouping (placing organisms in hierarchically nested taxa) and ranking (deciding where taxa sit relative to the transition from tree-like relationships at higher levels to reticulate genealogies within populations). Species delimitation remains challenging in many groups due to polyploidy, introgression, and/or species with complex geographic patterns of morphological variation. However, opportunities for progress are offered by recent advances in high throughput sequencing technologies that facilitate rapid acquisition of multilocus DNA sequence data, and by new analytical methods for species level taxonomic problems. Using baobabs as a model, this study will develop a rapid and efficient experimental protocol using sequence capture technology and next-generation sequencing that will allow the application of different species delimitation methods. In addition to deploying existing analytical methods, the researchers will extend the Bayesian Phylogenetics and Phylogeography (BPP) method to formally incorporate morphology and geography. Further, they will add capability to the software program BUCKy for identifying cases where the data imply hybridization or introgression that could be applied in diverse groups of organisms.