DOI: 10.5061/dryad.fm466
title: Data from: Pleistocene niche stability and lineage diversification in the subtropical spider Araneus omnicolor (Araneidae)

description: The influence of Quaternary climate oscillations on the diversification of
 the South American fauna is being increasingly explored. However, most of
 these studies have focused on taxa that are endemic to tropical
 environments, and relatively few have treated organisms restricted to
 subtropical biomes. Here we used an integrative phylogeographical
 framework to investigate the effects of these climate events on the
 ecological niche and genetic patterns of the subtropical orb-weaver spider
 Araneus omnicolor (Araneidae). We analyzed the mitochondrial (Cytochrome
 Oxidase I, COI) and nuclear (Internal Transcribed Subunit II, ITS2) DNA of
 130 individuals throughout the species’ range, and generated distribution
 models in three different climate scenarios [present, Last Glacial Maximum
 (LGM), and Last Interglacial Maximum (LIG)]. Additionally, we used an
 Approximate Bayesian Computation (ABC) approach to compare possible
 demographic scenarios and select the hypothesis that better explains the
 genetic patterns of A. omnicolor. We obtained high haplotype diversity but
 low nucleotide variation among sequences. The population structure and
 demographic analyses showed discrepancies between markers, suggesting
 male-biased dispersal in the species. The time-calibrated COI phylogenetic
 inference showed a recent diversification of lineages (Middle/Late
 Pleistocene), while the paleoclimate modeling indicated niche stability
 since ~120 Kya. The ABC results agreed with the niche models, supporting a
 panmictic population as the most likely historical scenario for the
 species. These results indicate that A. omnicolor experienced no niche or
 population reductions during the Late Pleistocene, despite the intense
 landscape modifications that occurred in the subtropical region, and that
 other factors beside LGM and LIG climate oscillations might have
 contributed to the demographic history of this species. This pattern may
 be related to the high dispersal ability and wide environmental tolerance
 of A. omnicolor, highlighting the need for more phylogeographical studies
 with invertebrates and other generalist taxa, in order to understand the
 effects of Quaternary climate changes on Neotropical biodiversity.
description: Geographic and haplotype
 information for Araneus omnicolor samples.xlsx file containing
 the voucher, sex, locality, collection date and haplotypes of each A.
 omnicolor individual used in the present study.Peres_et_al_geographic_and_haplotypic_information.xlsxAraneus omnicolor occurrence records.xls file containing the geographical coordinates of the 52 unique occurrence points used in the species distribution modelling.Peres_et_al_occurrence_records.xlsBEAST XML input file of the COI Bayesian Inference analysis.xml input file used for the COI Bayesian Inference analysis in the software BEAST 1.8.Peres_et_al_COI_bayesian_inference.xmlBEAST XML input file of the multilocus EBSP analysis.xml input file used for the multilocus Extended Bayesian Skyline Plot analysis in the software BEAST 1.8.Peres_et_al_EBSP.xmlms Python scrips used for data simulations in the ABC analyses.rar compressed file containing the ms Python scripts used for data simulations in the Approximate Bayesian Computation (ABC) analyses. Simulation 1: data simulation for model comparison within each scenario with flat prior parameters; Simulation 2: data simulation for model comparison within each scenario with restricted prior parameters (restriction based on simulation 1); Simulation 3: data simulation for comparison among scenarios.Peres_et_al_simulations_ms_python_scripts.rar