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

合作研究：数百个不相关的位点真的能解决植物物种最近的快速辐射吗？

基本信息

批准号：
1457473
负责人：
Shannon Straub
金额：
$ 33.91万
依托单位：
Hobart and William Smith Colleges
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2015
资助国家：
美国
起止时间：
2015-05-01 至 2021-04-30
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1457473&HistoricalAwards=false
关键词：
Collaborative Research hundreds unlinked loci

项目摘要

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.

乳草（Asclepias）是北美草原和森林生态系统的常见和生态上重要的多年生植物。它们是君主蝴蝶的唯一寄主植物，这是一种重要的保护问题。由于乳草物种在短暂的进化时间范围内多样化，因此重建其进化关系极为困难，需要检查大量有关遗传变异和强大计算技术的数据。这项研究将有助于开发新方法，以更准确地确定许多物种以快速连续形成。结果将对更好地理解乳草和君主蝴蝶之间的共同进化以及植物防御的进化有影响，并提供了一种强大的进化环境，以理解使用牛奶作为研究生物体的其他科学研究的结果；例如，关于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中培训博士后研究员和研究生，从而培训下一代的系统发育生物学家。这项研究将证明，通过在下一代测验中采用改进来解决植物中的物种水平的困难系统发育问题的可行性。该作品结合了用于对异常大型内部采样的数百个核基因组的数百个特定区域进行靶向测序的方法。该项目应用了直接从Asclepias基因组和转录组序列开发的核基因探针，以有效靶向768个基因及其大量非编码侧翼区域。还获得了系统发育有用的脱靶序列（例如，完整的叶绿体基因组）。通过对每个物种的20个人取样，该方法将区分基因树不一致的常见原因：不完全的谱系分类和渗入。将应用一个分析工作流程，其中包含了不完整的谱系排序的模拟和物种树推理方法的组合，即使发生渗入也是有效的。由于当前物种树的方法受到可以同时分析的基因座数量和等位基因数量之间的计算权衡，因此该项目将评估替代方法的优势和劣势。大量基因座样本还将验证对Asclepias当前未接受的物种的识别。基因组学，生物信息学和系统发育学的本科生和研究生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行的研讨会，K-12教育模块上的研讨会来触及更广泛的科学界和公众，该模块的重点是牛奶生态和进化，以及在公共植物园举行的示威展览。