Department of Biology, Radford University, Radford, Virginia, USA.
Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA.
Mol Ecol Resour. 2022 Nov;22(8):2830-2842. doi: 10.1111/1755-0998.13673. Epub 2022 Jul 12.
Patterns of genetic diversity within species contain information the history of that species, including how they have responded to historical climate change and how easily the organism is able to disperse across its habitat. More than 40,000 phylogeographic and population genetic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite these millions of data points, meta-analyses are challenging because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time-consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. To facilitate data repurposing, we created a database (phylogatR) that aggregates data from different sources and conducts automated multiple sequence alignments and data curation to provide users with nearly ready-to-analyse sets of data for thousands of species. Two types of scientific research will be made easier by phylogatR: large meta-analyses of thousands of species that can address classic questions in evolutionary biology and ecology, and student- or citizen- science based investigations that will introduce a broad range of people to the analysis of genetic data. phylogatR enhances the value of existing data via the creation of software and web-based tools that enable these data to be recycled and reanalysed and increase accessibility to big data for research laboratories and classroom instructors with limited computational expertise and resources.
物种内的遗传多样性模式包含了该物种的历史信息，包括它们对历史气候变化的反应方式，以及它们在栖息地中扩散的容易程度。迄今为止，已经发表了超过 40000 项的系统地理学和种群遗传学研究，每个研究都从数百个样本中收集遗传数据。尽管有了这些数百万个数据点，元分析仍然具有挑战性，因为综合数百项研究的结果，这些研究使用不同的方法和分析形式，是一项艰巨且耗时的任务。重新利用现有数据并使用自动化数据分析会更有效率。为了方便数据再利用，我们创建了一个数据库（phylogatR），该数据库聚合了来自不同来源的数据，并进行自动多序列比对和数据管理，为用户提供了数千个物种几乎准备好进行分析的数据集。phylogatR 将使两种类型的科学研究变得更加容易：对数千个物种进行大型元分析，可以解决进化生物学和生态学中的经典问题；以及基于学生或公民科学的调查，将使广泛的人群能够参与到遗传数据分析中。phylogatR 通过创建软件和基于网络的工具来提高现有数据的价值，这些工具可以使这些数据得到再利用和重新分析，并增加了拥有有限计算专业知识和资源的研究实验室和课堂教师对大数据的访问。
