EcoPhyloMapper: an R package for integrating geographic ranges, phylogeny, and morphology

1. Spatial patterns of species richness, phylogenetic and morphological diversity are key to answering many questions in ecology and evolution. Across spatial scales, geographic and environmental features, as well as evolutionary history and phenotypic traits, are thought to play roles in shaping both local species communities and regional assemblages. By examining these geographic patterns, it is possible to infer how different axes of biodiversity influence one another, and how their interaction with abiotic factors has led to the spatial distribution of species assemblages – and their attributes – that we observe in the present. Although there has been interest in this area of research for some time, it has recently become more tractable to include multivariate shape data in such analyses. Shape information has the potential to provide a more direct measure of the functional morphology of species as compared to individual trait measurements and might be more relevant to understanding community composition. However, few tools currently exist to explore geographic patterns of both phylogenetic and shape diversity. 2. We present the ecoPhyloMapper R package (epm) that aims to streamline the handling of geographic range polygons or point occurrences and integration of resulting species metacommunities with phylogenetic trees and morphological shape. 3. Geographic maps can be generated that demonstrate spatial patterns in diversity metrics pertaining to phylogenetic similarity, multivariate shape similarity and disparity, and combinations of the two. Patterns of taxonomic, phylogenetic and shape disparity turnover can also be visualized. Biodiversity indices summarized across grid cells can easily be exported to GIS software as well as to other R packages that specialize in community assembly or geospatial statistics. 4. This R package will facilitate the geographic exploration of multivariate shape data in concert with phylogenetic diversity, which will in turn support macroecological research exploring how species assemblages are structured. Further, this R package should prove useful across a wide range of macroecological applications that extend beyond the study of morphology.1. 物种丰富度、系统发育多样性与形态多样性的空间格局，是解答生态学与进化生物学诸多核心问题的关键所在。在不同空间尺度下，地理与环境特征、进化历史以及表型性状，均被认为在塑造本地物种种群与区域集合群落的过程中发挥着重要作用。通过解析此类地理空间格局，我们可以推断不同维度的生物多样性如何相互影响，以及它们与非生物因子的交互作用如何造就了当前我们观测到的物种集合群空间分布格局及其属性特征。尽管该研究领域早已受到学界关注，但直到近期，在相关分析中纳入多变量形状数据才变得更具可行性。相较于单一性状测量手段，形状信息能够更直接地反映物种的功能形态特征，也更有助于理解群落组成机制。然而，目前鲜有工具能够同时探索系统发育多样性与形状多样性的地理空间格局。 2. 本文推出ecoPhyloMapper R包（epm），旨在简化地理分布多边形或物种点出现记录的处理流程，并实现所得物种集合群落与系统发育树、形态形状数据的整合。 3. 该工具可生成地理地图，用以展示与系统发育相似度、多变量形状相似度及歧异度，以及二者组合相关的多样性指标空间格局。同时，还可可视化分类学、系统发育与形状歧异度的群落周转格局。通过网格单元汇总得到的生物多样性指数，可便捷导出至地理信息系统（GIS, Geographic Information System）软件，以及其他专注于群落组装或空间统计的R包中。 4. 本R包将助力多变量形状数据与系统发育多样性的协同地理空间探索，进而支撑围绕物种集合群落构建机制展开的宏生态学研究。此外，该R包的应用场景将不限于形态学研究，可广泛应用于各类宏生态学研究场景。