DOI: 10.5061/dryad.djh9w0vwp
title: Discordant phylogenetic endemism patterns in a recently diversified Brassicaceae lineage from the Atacama Desert: when choices in phylogenetic and species distribution information matter

description: Aim: Phylogenetic endemism (PE) has become a useful estimator of
 evolutionary history in conservation, given its capacity to estimate
 diversity hotspots as the combination of phylogenetic diversity (PD) and
 range size distributions of co-occurring taxa. However, potential
 limitations could preclude a general assessment of PE, especially in the
 presence of incongruent phylogenetic signals and the use of different
 estimates of species distribution at fine spatial scales. Here, we assess
 the utility of using PE in a recently diversified plant tribe. Location:
 Atacama Desert, Argentina, Chile, and Peru. Taxon: Schizopetalae tribe
 (Brassicaceae). Methods: We assessed PD and PE to determine whether
 incongruent phylogenetic trees derived from nuclear and chloroplast DNA
 and different estimates of species distribution (based on species
 distribution modelling-SDM- and minimum convex polygons-MCP) impact the
 location of PE hotspots. Results: Results show no influence from
 discordant phylogenetic signal between gene trees on PE estimates.
 Instead, the choice of the summary of species’ range (i.e., SDM or MCP)
 has greater influence on the location of PE hotspots. Main conclusions:
 Despite the observed discrepancies, results in PE accumulation are
 congruent enough to support the use of this index in conservation-related
 analyses for the Atacama Desert flora. Nonetheless, further analyses are
 recommended to determine and contextualize the impacts of phylogenetic
 incongruence and species distributional estimates on PE, especially when
 other scenarios involving larger spatial and taxonomic sampling scales
 remain unexplored.
description: Files
 Schizopetalae_Bayes_JBIOG_5_window_size.bps: Biodiverse file
 (tested on Biodiverse 2.0) which contains the results of all spatial
 indices presented in the manuscript, at 5 different neighbor window
 sampler sizes: 10, 20, 30, 40 and 50 km. Indices were obtained from the
 modules "Endemism" and "Phylogenetic Indices", as
 available in Biodiverse.
 Schizopetalae_Bayes_JBIOG_5_GridCell_Size.bps: Biodiverse file
 (tested on Biodiverse 2.0) which contains the results of all spatial
 indices obtained with 3 different grid cell sizes: 25, 50 and 100 km.
 Indices were obtained from the modules "Endemism" and
 "Phylogenetic Indices", as available in Biodiverse.
 Schizopetalae_Bayes_JBIOG_5_Randomizations.bps: Biodiverse file
 (tested on Biodiverse 2.0) which contains the results of randomization on
 all spatial indices obtained. Indices were obtained from the modules
 "Endemism" and "Phylogenetic Indices",  as available
 in Biodiverse. Ratio_plots.xlsx: Excel file with ratios
 obtained from standarized PD and PE values (plotted in Fig. 4). The table
 presents a labele in each column header, which includes the index, the
 dataset and the resolution (e.g., PD_CV_30). Respective ratios are found
 in a respective third column, defined with a “r” letter (e.g., r_PD_30).
 The rest of the matrix includes coordinates for plotting the cell grid
 (Axis_0 and Axis_1) and the final columns present the labeled hotspots for
 each cell. At the end of each column, minimum, maximum and percentile
 values are calculated. All data was generated from Biodiverse 1.0 and it
 can be plotted in any GIS system.