DOI: 10.5061/dryad.hmgqnk9hp
title: Spatial patterns of phylogenetic diversity and endemism in the Western Ghats, India: a case study using ancient predatory arthropods

description: The Western Ghats (WG) mountain chain in peninsular India is a global
 biodiversity hotspot, one in which patterns of phylogenetic diversity and
 endemism remain to be documented across taxa. We used a well-characterized
 community of ancient soil predatory arthropods from the WG to understand
 diversity gradients, identify hotspots of endemism and conservation
 importance, and highlight poorly-studied areas with unique biodiversity.
 We compiled an occurrence dataset for 19 species of scolopendrid
 centipedes, which was used to predict areas of habitat suitability using
 bioclimatic and geomorphological variables in Maxent. We used predicted
 distributions and a time-calibrated species phylogeny to calculate
 taxonomic and phylogenetic indices of diversity, endemism and turnover. We
 observed a decreasing latitudinal gradient in taxonomic and phylogenetic
 diversity in the WG, which supports expectations from the latitudinal
 diversity gradient. The southern WG had the highest phylogenetic diversity
 and endemism, and was represented by lineages with long branch lengths as
 observed from relative phylogenetic diversity/endemism. These results
 indicate the persistence of lineages over evolutionary time in the
 southern WG and are consistent with predictions from the southern WG
 refuge hypothesis. The northern WG, despite having low phylogenetic
 diversity, had high values of phylogenetic endemism represented by
 distinct lineages as inferred from relative phylogenetic endemism. The
 distinct endemic lineages in this sub-region might be adapted to life in
 lateritic plateaus characterized by poor soil conditions and high
 seasonality. Sites across an important biogeographic break, the Palghat
 Gap, broadly grouped separately in comparisons of species turnover along
 the WG. The southern WG and Nilgiris, adjoining the Palghat Gap, harbour
 unique centipede communities, where the causal role of climate or
 dispersal barriers in shaping diversity remains to be investigated. Our
 results highlight the need to use phylogeny and distribution data while
 assessing diversity and endemism patterns in the WG.
description: <strong>ReadMe:</strong>
 README_1Sep21.docx: details of each R script (code1 - code8)
 including input and output files <strong>Data
 files:</strong> biasMap.tif - sampling bias
 layer, which is the prediction of a Maxent model which uses all species
 occurrences as presence locations and all the WorldClim layers plus a soil
 type layer as predictors biasBg.csv - coordinates of
 background locations used for Maxent species distribution modeling
 obtained from a sampling bias layer (biasMap.tif)
 gps_9Jun20.csv  - coordinates of occurrence locations used for
 Maxent species distribution modeling
 supp_table_locations - coordinates of occurrence locations used
 for Maxent species distribution modeling (some formatting differences as
 compared to gps_9Jun20.csv in terms of species names), used for plotting
 Figure 1 results_summary_4Apr21.csv - summary of
 results from Maxent species distribution modeling giving indices of model
 transferability and performance, and top two predictor variables in terms
 of permutation importance, used for plotting figures in Appendix
 S2 biodiverse_16Mar21.csv - input site by species
 matrix used as input in Biodiverse 3.1 threegenera.tre
 - phylogenetic tree used for calculations of phylogenetic diversity,
 endemism and turnover  tiplabels.csv - mapping of tip
 labels to species names in threegenera.tre
 threegenera_results_16Mar21.csv - results of diversity and
 endemism indices (taxonomic, phylogenetic, relative phylogenetic)
 calculated in Biodiverse 3.1
 threergenera_struc_randomization_results_16Mar21.csv - results of
 randomizations of diversity and endemism indices obtained in Biodiverse
 3.1 <strong>R scripts:</strong>
 Scripts available
 at https://github.com/bhartidk/centipede_diversity_endemism
 code1-code4, code6-code8 - details of analysis workflow available
 in README_1Sep21.docx code5 - instructions for running
 Biodiverse3.1 GUI