Determinants of amphibian genomic diversity: Integrating traits, phylogeny, and geography

同一物种的个体和种群之间的遗传差异对于生物适应和生存在不断变化的环境中至关重要。因此，调查物种内的基因组变异，并确定哪些因素影响这种变异，是管理野生动物种群和保护生物多样性的重要目标。两栖动物是许多生态系统过程的关键贡献者，但它们是最受威胁的脊椎动物群体之一。它们也缺乏许多基因组变异的比较研究，因为它们拥有庞大而复杂的基因组。该项目将调查影响两栖动物基因组变异的因素，并将产生美国各地抽样的数十种青蛙的新基因组规模数据。更广泛的影响包括培训职业早期学者，包括一名博士后研究员、两名研究生和六名本科生，内容涉及现场采样、基因组测序、生物信息学和统计分析。该项目还将通过在西南生物博物馆存档可搜索的多用途两栖动物标本和组织，为研究基础设施做出贡献。将开发一门新的生物多样性信息学本科课程，通过利用该项目产生的两栖动物基因组数据的合作项目，让学生参与自然历史收藏和生物多样性数据库，提供计算培训，并提供实践研究经验。这项研究解决了遗传多样性决定因素的关键问题，从而促进了对全球生物多样性起源、分布和进化史的了解。两种互补的数据收集方法涵盖了几个影响遗传多样性的复杂因素--生活史和生态特征、系统发育史、种群历史和当前的环境变异--并提供了对这些因素影响物种内多样性的规模的洞察。第一种方法将结合数据再利用、机器学习和系统发育比较方法，使用开放获取的博物馆、特征和遗传序列数据库来识别全球两栖动物遗传多样性的重要预测因素。这些结果将阐明物种特征、系统发育历史和地理范围特征对预测数百个两栖物种遗传多样性的重要性。第二种方法将产生美国40多种青蛙的新的高分辨率基因组规模的数据，并在地理空间内进行战略性抽样，以测试种群历史和当前环境变化对物种内遗传变异的影响的预测。通过整合特征、系统发育和地理，这项研究将揭示两栖动物基因组多样性的决定因素，并建立一个框架，以解决不同分类和空间尺度上的生物多样性这一基本方面。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Genetic differences between individuals and populations of the same species are essential for organisms to adapt and survive in changing environments. Surveying genomic variation within species, and determining what factors influence that variation, are thus important goals for managing wildlife populations and conserving biodiversity. Amphibians are key contributors to many ecosystem processes, but they are one of the most threatened vertebrate groups. They are also lacking from many comparative studies of genomic variation because they have large, complex genomes. This project will investigate the factors that influence genomic variation within amphibians and will produce new genome-scale data for several dozen frog species sampled across the United States. Broader impacts include training early-career scholars including a postdoctoral researcher, two graduate students, and six undergraduate students in field sampling, genomic sequencing, bioinformatics, and statistical analysis. The project will also contribute to research infrastructure by archiving searchable, multi-purpose amphibian specimens and tissues at the Museum of Southwestern Biology for future uses. A new undergraduate course in Biodiversity Informatics will be developed to engage students with natural history collections and biodiversity databases, provide computational training, and offer hands-on research experiences through collaborative projects that leverage the amphibian genomic data produced by the project.This research addresses key questions about the determinants of genetic diversity, thereby advancing knowledge about the origins, distribution, and evolutionary history of global biodiversity. Two complementary approaches to data collection encompass several complex factors that affect genetic diversity – life history and ecological traits, phylogenetic history, population history, and current environmental variation – and provide insights into the scale at which these factors influence diversity within species. The first approach will combine data repurposing, machine learning, and phylogenetic comparative methods to identify important predictors of genetic diversity for global amphibians using open-access museum, trait, and genetic sequence databases. These results will shed light on the importance of species traits, phylogenetic history, and geographic range characteristics for predicting genetic diversity across hundreds of amphibian species. The second approach will produce new high-resolution, genome-scale data for more than 40 frog species in the United States, sampled strategically across geographic space to test predictions about the influence of population history and current environmental variation on genetic variation within species. By integrating traits, phylogeny, and geography, this research will uncover the determinants of amphibian genomic diversity and establish a framework to address this fundamental aspect of biodiversity across different taxonomic and spatial scales.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.