habCluster: Identifying Geographical Boundary among Intraspecific Units Using Community Detection Algorithm in R

AbstractConservation management for a species generally rests on intraspecific units, while identification of their geographic boundaries is necessary for the implementation. Intraspecific units can be discriminated using population genetic methods, yet an analytical approach is still lacking for detecting their geographic boundaries. Here, based on landscape connectivity, we present a geographical boundary delineation method, habCluster, using community detection algorithm. Community detection is an algorithm in graph theory used to identify clusters of highly connected nodes within a network. We assume that the habitat raster cells with better connections tend to form a continuous habitat patch than the others, thus making the range of an intraspecific unit. The method is tested on grey wolf (Canis lupus) habitat in Europe and on giant panda (Ailuropoda melanoleuca) habitat in China. The habitat suitability for grey wolves and giant pandas were evaluated using species distribution modeling. Each cell in the habitat suitability index (HSI) raster is treated as a node and directly connected with its eight neighbor cells. The edge weight between nodes is the distance between the center of them weighted by the average of their HSI values. We implement habCluster using R programming language with inline C++ code to speed up the computing. The geographical clusters detected were compared with the HSI maps for both species and with the nature reserves for giant panda. We found the boundaries of the clusters delineated using habCluster could serve as a good indicator of habitat patches, and they match generally well with nature reserves in the giant panda case. habCluster can provide spatial analysis basis for conservation management plans such as monitoring, translocation and reintroduction, as well as for population structure research.