DOI: 10.5061/dryad.cc2fqz68k
title: Data from: Between the Cape Fold Mountains and the deep blue sea: comparative phylogeography of selected codistributed ectotherms reveals asynchronous cladogenesis. Sampling locations and MaxEnt input files

description: We compare the phylogeographic structure of thirteen codistributed
 ectotherms including four reptiles (a snake, a legless skink and two
 tortoise species) and nine invertebrates (six freshwater crabs and three
 velvet worm species) to test the presence of congruent evolutionary
 histories. Phylogenies were estimated and dated using maximum
 likelihood and Bayesian methods with combined mitochondrial and nuclear
 DNA sequence datasets. All taxa demonstrated a marked east/west
 phylogeographic division, separated by the Cape Fold Mountain
 range. Phylogeographic concordance factors were calculated to
 assess the degree of evolutionary congruence among the study species
 and generally supported a shared pattern of diversification along
 the east/west longitudinal axis. Testing simultaneous divergence between
 the eastern and western phylogeographic regions
 indicated pseudo-congruent evolutionary histories among the study
 taxa, with at least three separate divergence events throughout the
 Mio/Plio/Pleistocene epochs. Climatic refugia were identified for
 each species using climatic niche modeling, demonstrating
 taxon-specific responses to climatic fluctuations. Climate and the Cape
 Fold Mountain barrier explained the highest proportion of genetic
 diversity in all taxa, while climate was the most significant individual
 abiotic variable. This study highlights the complex interactions
 between the Cape Fold Mountains and past climatic oscillations during the
 Mio/Plio/Pleistocene. The congruent east/west phylogeographic division
 observed in all taxa lends support to the conclusion that the longitudinal
 climatic gradient within the Greater Cape Floristic Region, mediated in
 part by the barrier to dispersal posed by the Cape Fold Mountains, plays a
 major role in lineage diversification and population differentiation.
description: In order to determine whether the major phylogenetic
 patterns uncovered by this study aligned with congruent climatic refugia
 among the study taxa, a niche modeling approach was used. Maxent 3.4.1 was
 used to identify persistent Pleistocene refugia based on several
 contemporary and paleoclimatic scenarios, namely the current (1950-2000),
 mid-Holocene (6 Ka), last glacial maximum (22 ka) and last interglacial
 (120-140 ka) time periods. All 19 bioclimatic variables were downloaded
 from the WorldClim database and cropped to the geographical extent of
 South Africa using ArcGIS (ESRI, 2012).  Correlated variables (with a
 Pearson’s correlation coefficient &gt;0.7) for each species were
 assessed using the r package CorrPlot in RStudio 2021.09.1 and were
 removed, preferentially retaining variables known to influence the
 distribution of each taxon and the remaining limiting climatic variables
 were used to generate the models. A custom R script was used to specify a
 fixed distance buffer of 50km based on the occurrence records for model
 building in order to correct the models for overprediction, as well as to
 produce minimum convex polygons of the distribution for each taxon.
 ENMeval 2.0 was used to determine the optimum feature class and
 regularisation multiplier for model construction, after which Maxent
 3.4.1was used to generate the SDMs. The models were converted from
 continuous probability surfaces to binary models representing either
 suitable or unsuitable climatic conditions based on a 10% training
 presence cloglog threshold using QGIS 3.24.2. Possible climatic refugia
 were inferred for each taxon by overlaying the binary models over the
 various time periods, thereby identifying areas which remained within the
 habitat requirements of the taxa over time. Finally, the species-specific
 refugia were intersected in order to determine the shared regions of
 climatic stability. The final maps were generated using QGIS
 3.24.2.
description: QGIS