Collaborative Research: Can hundreds of unlinked loci really resolve recent, rapid radiations of plant species?

乳草是北美草原和森林生态系统中常见的多年生植物，具有重要的生态意义。它们是帝王蝶的唯一寄主植物，帝王蝶是一种重要的保护物种。由于马利筋物种在很短的进化时间内多样化，重建它们的进化关系是非常困难的，需要检查大量的遗传变异数据和强大的计算技术。当许多物种在快速演替中形成时，这项研究将有助于开发更准确地确定进化关系的新方法。研究结果将有助于更好地理解乳草与帝王蝶之间的共同进化以及植物防御的进化，并为理解其他以乳草为研究生物的科学研究结果提供一个强有力的进化背景；例如，植物繁殖和基因组进化的研究。该项目将在最新的系统发育和生物信息学方法方面培养博士后和研究生，从而培养下一代系统发育生物学家。这项研究将证明利用下一代测序技术的改进在植物物种水平上解决困难的系统发育问题的可行性。这项工作结合了对核基因组数百个特定区域进行靶向测序的方法，应用于异常大的物种内采样。该项目使用直接从Asclepias基因组和转录组序列中开发的核基因探针，有效靶向768个基因及其大量非编码侧翼区域。系统发育上有用的脱靶序列（例如，完整的叶绿体基因组）也得到了。通过对每个物种取样20个个体，该方法将区分基因树不一致的常见原因：不完整的谱系分类和渐渗。将应用一个分析工作流，该工作流结合了不完整谱系排序的模拟和物种树推理方法的组合，即使在发生渗入时也有效。由于目前的物种树方法受到可同时分析的基因座数量和等位基因数量之间的计算权衡的限制，该项目将评估替代方法的优缺点。大量的基因座样本也将验证目前在Asclepias未被接受的物种的识别。本科生和研究生在基因组学、生物信息学和系统遗传学方面的培训将针对来自代表性不足的群体的参与者。项目成果将通过在科学会议上举办的讲习班、以马利筋生态和进化为重点的K-12教育模块以及在公共植物园举办的示范展览，传播给更广泛的科学界和公众。

Milkweeds (Asclepias) are common and ecologically important perennial plants of North American grassland and forest ecosystems. They are the only host plants of the monarch butterfly, a species of significant conservation concern. Because milkweed species diversified over a short evolutionary time span, reconstructing their evolutionary relationships is exceedingly difficult and requires examination of a large amount of data on genetic variation and powerful computational techniques. This research will contribute to the development of new methods for more accurately determining evolutionary relationships when many species have been formed in rapid succession. The results will have implications for better understanding the coevolution between milkweeds and monarch butterflies and the evolution of plant defense, as well as provide a robust evolutionary context for understanding the results of other scientific studies using milkweeds as study organisms; e.g., research on plant reproduction and genome evolution. The project will train postdoctoral fellows and graduate student in the latest phylogenetic and bioinformatics methods thereby training the next generation of phylogenetic biologists.This research will demonstrate the feasibility of solving difficult phylogenetic problems at the species level in plants by employing improvements in next-generation sequencing techniques. The work combines methods for targeted sequencing of hundreds of specific regions of the nuclear genome applied to unusually large within-species sampling. The project applies nuclear gene probes developed directly from Asclepias genome and transcriptome sequences to effectively target 768 genes and substantial amounts of their non-coding flanking regions. Phylogenetically useful off-target sequences, (e.g., complete chloroplast genomes) are also obtained. By sampling 20 individuals per species, the approach will distinguish common causes of gene tree discordance: incomplete lineage sorting and introgression. An analytic workflow will be applied that incorporates simulation of incomplete lineage sorting and a combination of species tree inference methods that are effective even when introgression has occurred. Because current species tree approaches are constrained by a computational tradeoff between the number of loci and number of alleles that can simultaneously analyzed, the project will evaluate the strengths and weaknesses of alternative methods. The large sample of loci will also validate the recognition of species not currently accepted in Asclepias. Undergraduate and graduate student training in genomics, bioinformatics, and phylogenetics will target participants from underrepresented groups. Project outcomes will reach the broader scientific community and the general public through workshops held at scientific meetings, K-12 education modules focused on milkweed ecology and evolution, and demonstration exhibits at a public botanic garden.