GenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework

GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis.

GenGIS是一款免费开源软件，旨在将生物多样性数据与数字地图以及地理和栖息地信息进行整合。尽管最初开发时聚焦于微生物群落分析和系统地理学研究，但GenGIS目前已被应用于多种数据集的分析。GenGIS的关键特性之一是支持对地理轴进行检验，此类轴可对应于物种迁移路径或影响群落相似性的生态梯度。本文介绍GenGIS 2.0版本，该版本将初代版本引入的线性梯度检验功能进行了扩展，可对所有可能的线性地理轴进行全面检验。GenGIS v2还新增了插件框架，支持开发和使用图形驱动的分析工具包：首批插件包括线性回归与曼特尔检验（Mantel test）的实现、所有样本的α多样性（alpha-diversity）计算（例如香农指数（Shannon Index））以及相似性矩阵的地理可视化。我们还集成了近期发表的生物监测参考条件分析（RCA）方法，该方法通过将观测到的物种丰富度与多样性与预测值进行对比，以判定特定位点是否受到干扰。GenGIS最新版本除支持栅格文件（raster files）外，还支持矢量数据（vector data）。我们通过对澳大利亚袋鼠苹果数据集进行全面梯度分析、使用插件与内嵌统计命令分析人类微生物组样本数据，以及将RCA应用于加拿大大西洋沿岸的样本集，展示了GenGIS的新增特性。GenGIS的发布版本、教程与文档可在http://kiwi.cs.dal.ca/GenGIS 免费获取，源代码托管于https://github.com/beiko-lab/gengis。