DOI: 10.5061/dryad.hdr7sqvt8
title: Data and code from: The overlooked link between different resource partitioning strategies and plant species richness in tropical alpine ecosystems

description: Species co-existence is based on resource partitioning and modulates
 biodiversity patterns across climates, latitudes, and altitudes. Resource
 partitioning can occur via niche size or separation in the geographic
 range or ecological niche. While resource partitioning promotes
 biodiversity, the impact of different partitioning strategies on species
 richness remains largely unexplored. Study locations: two ecosystems with
 similar climates and ages, the species-rich tropical alpine ecosystem in
 the South American Andes and the more species-poor tropical alpine
 ecosystem in the eastern African mountains. Study time period: present-day
 distribution and climatic conditions, integrating phylogenetic information
 extending back to the last 7 million years maximum. Major taxa studied:
 Six lineages from the Asterales; three in each ecosystem, respectively. We
 test whether geographic range and climatic niche partitioning strategies
 may explain differences in species richness between the two ecosystems. We
 combine phylogenomic data with occurrence records and estimate metrics of
 size and overlap for climatic niche and geographic range. We show that the
 Andean species have larger climatic niches than the African species,
 suggesting that niche size is not explaining higher species richness in
 the Andes. Instead, a striking pattern for species with overlapping
 geographic ranges emerged: the Andean species show less climatic niche
 overlap than the African species, indicating more effective niche
 separation among Andean species. We hypothesise that a different pattern
 of resource partitioning, specifically increased niche separation among
 geographically overlapping species in the Andes compared to the eastern
 African mountains, contribute to the species richness difference between
 these tropical alpine biodiversity hotspots.
description: # Data and code from: The overlooked link between different resource
 partitioning strategies and plant species richness in tropical alpine
 ecosystems #### Data We studied six Asterales lineages in the tropical
 alpine ecosystems of South America and East Africa, i.e., Loricaria,
 Senecio, and Oritrophium in South America and Dendrosenecio, Helichrysum,
 and Lobelia in East Africa. We compiled occurrence information from
 herbaria and supplemented it with GBIF data
 ([https://doi.org/10.15468/dd.8cpqns](https://doi.org/10.15468/dd.8cpqns)). The table contains all columns as provided by GBIF (simple format; [https://techdocs.gbif.org/en/data-use/download-formats#simple](https://techdocs.gbif.org/en/data-use/download-formats#simple)), for the occurrence data from herbaria, some column information was not available and is coded as NA (not available). Phylogenetic data for each lineage are based on Compositae1061 loci (Mandel et al., 2014); newly sequenced material is available under Bioproject PRJNA1092049. For Dendrosenecio, Loricaria, and Oritrophium, existing phylogenetic estimates were available, and the respective authors shared them. For the remaining lineages, we reconstructed phylogenetic trees using RAxML-NG that were then made ultrametric using treePL. Each lineage has its own folder that contains the respective data in a computer readable formats. ``` Supplementary_Material__S3_associated_data.zip |- Dendrosenecio/ | |- raxmlng.support.reroot | |- treepl_Dendrosenecio.tre |- Helichrysum/ | |- concatenated50_70.fasta | |- RAxMLpartitions.txt | |- raxmlng.support.reroot | |- treepl_Helichrysum.tre |- Lobelia/ | |- concatenated50_70.fasta | |- RAxMLpartitions.txt | |- raxmlng.support.reroot | |- treepl_Lobelia.tre |- Loricaria/ | |- concatenated50_70.fasta | |- RAxMLpartitions.txt | |- raxmlng.support.reroot | |- treepl_Loricaria.tre |- Oritroppl_Oritrophium.tre |- Senecio/ | |- concatenated50_70.fasta | |- RAxMLpartitions.txt | |- raxmlng.support.reroot | |- treepl_Senecio.tre |- cleaned_occ_v1.0.csv ``` All niche and range analyses conducted for the associated publication are available via R scripts submitted to Zenodo (NicheSizeDifferences-main.zip). Scripts are numbered from zero to seven and reflect order of execution. ``` NicheSizeDifferences-main.zip |- FUN/ | |- 00_all_myfun_combined.R | |- 00_func_red_code.R | |- 00_fun_for_global.R | |- 00_load_packages_kubernetes.R | |- 001_get_started.R | |- 01a_clean_occ.R | |- 01d_clean_occ_ingroup.R | |- 03a_prepare_pcaallenv_occonly.R | |- 03b_plot_pca.R | |- 04a_calc_geo_area.R | |- 04b_make_zscore.R | |- 04c_calc_niche_area.R | |- 04d_calc_SchoenersD.R | |- 04e_pgls_looop.R | |- 04f_combine_data.R | |- 05_permutation_niche.R | |- 05_permutation_range.R | |- 06_gendist_niche.R | |- 07_habitat_heterogeneity_rasterdiv.R |- LICENSE |- README.md ``` * Scripts starting with 00_* contain different functions that are needed. * Script 001_get_started.R needs to be adapted to reflect working directory, path to climatic data and elevation as well as to phylogenetic trees. * Scripts starting with 01* are used to clean occurrence information. * Scripts starting with 03* are used to make a PCAenv. * Scripts starting with 04* should be executed in order to calculate range size, niche size, niche overlap, PGLS analyses, and combine all results into a data-frame. * Script starting with 05* were used to permute niche and range size. * Script 06_gendist_niche.R calculates the genetic distances in relation to niche and range characters. * Script 07_habitat_heterogeneity_rasterdiv.R calculates the different estimates of habitat heterogeneity. Further details on how datasets were generated can be found in the associated article.