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，在科学传播和环境政策中起着重要作用。虽然对物种概念的理论认识有了很大的进步，但客观界定物种的方法仍然效率低下。威斯康星大学麦迪逊分校和爱荷华州立大学的研究人员进行的这项研究将开发新的计算工具，使物种划分更有效。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？本研究将使用猴面包树属（猴面包树）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，也是物种划分中出现的许多挑战的缩影。这项工作将培养分类学、基因组学和计算统计学领域的本科研究人员、K-12教师、研究生和博士后，并为建立国际合作提供若干机会。本研究将为Adansonia的系统学研究提供新的思路，并为不同类群的物种划分提供新的框架。物种划分包括多种方法，这些方法使用遗传、形态和其他性状数据来指导分类分组（将生物体置于等级嵌套的分类群中）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网状谱系的过渡）。在许多类群中，由于多倍体、渐渗和/或物种具有复杂的地理形态变异模式，物种划分仍然具有挑战性。然而，最近高通量测序技术的进步，促进了多位点DNA序列数据的快速获取，以及物种水平分类问题的新分析方法，提供了取得进展的机会。本研究将以猴面包树为模型，利用序列捕获技术和下一代测序技术，开发一种快速有效的实验方案，从而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育和系统地理学（BPP）方法，将形态学和地理学正式结合起来。此外，他们将增加软件程序BUCKy的功能，以识别数据暗示杂交或基因渗入的情况，这些情况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.