DOI: 10.5061/dryad.ps12h
title: Data from: Strong spatial structure, Pliocene diversification and cryptic diversity in the Neotropical dry forest spider Sicarius cariri

description: The Brazilian Caatinga is part of the seasonally dry tropical forests, a
 vegetation type disjunctly distributed throughout the Neotropics. It has
 been suggested that during Pleistocene glacial periods, these dry forests
 had a continuous distribution, so that these climatic shifts may have
 acted as important driving forces of the Caatinga biota diversification.
 To address how these events affected the distribution of a dry forest
 species, we chose Sicarius cariri, a spider endemic to the Caatinga, as a
 model. We studied the phylogeography of one mitochondrial and one nuclear
 gene and reconstructed the paleodistribution of the species using
 modelling algorithms. We found two allopatric and deeply divergent clades
 within S. cariri, suggesting that this species as currently recognized
 might consist of more than one independently evolving lineage. Sicarius
 cariri populations are highly structured, with low haplotype sharing among
 localities, high fixation index and isolation by distance. Models of
 paleodistribution, Bayesian reconstructions and coalescent simulations
 suggest that this species experienced a reduction in its population size
 during glacial periods, rather than the expansion expected by previous
 hypotheses on the paleodistribution of dry forest taxa. In addition to
 that, major splits of intraspecific lineages of S. cariri took place in
 the Pliocene. Taken together, these results indicate S. cariri has a
 complex diversification history dating back to the Tertiary, suggesting
 the history of dry forest taxa may be significantly older than previously
 thought.
description: Geographical coordinates
 of presence and absence points for Sicarius caririGeographical coordinates
 of presence and absence points used for modelling the distribution of
 Sicarius cariri (Araneae: Sicariidae). Presence points taken from
 Magalhães et al. (2011, Zootaxa 3599, 101-135). Absence points are 1)
 points where other species of Sicarius occur, but not S. cariri 2)
 localities visited during our fieldwork or localities where extensive
 inventories have been carried out and S. cariri has not been
 detected.Magalhaes_et_al_Sicarius_cariri_absence_presence_occurrence_points.txtBAYESSC-COI-1-SP.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 1, stable populationMagalhaes_et_al_Sicarius_cariri_BAYESSC-COI-1-SP.parBAYESSC-COI-2-GB.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 2, glacial bottleneckMagalhaes_et_al_Sicarius_cariri_BAYESSC-COI-2-GB.parBAYESSC-COI-3-MR.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 3, glacial multiple refugiaMagalhaes_et_al_Sicarius_cariri_BAYESSC-COI-3-MR.parBAYESSC-COI-4-GE.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 4, glacial expansionMagalhaes_et_al_Sicarius_cariri_BAYESSC-COI-4-GE.parBAYESSC-COI-5-WPB.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 5, wet phase bottlenecksMagalhaes_et_al_Sicarius_cariri_BAYESSC-COI-5-WPB.parBAYESSC-H3-1-SP.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 1, stable populationMagalhaes_et_al_Sicarius_cariri_BAYESSC-H3-1-SP.parBAYESSC-H3-2-GB.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 2, glacial bottlenecksMagalhaes_et_al_Sicarius_cariri_BAYESSC-H3-2-GB.parBAYESSC-H3-3-MR.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 3, glacial multiple refugiaMagalhaes_et_al_Sicarius_cariri_BAYESSC-H3-3-MR.parBAYESSC-H3-4-GE.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 4, glacial expansionsMagalhaes_et_al_Sicarius_cariri_BAYESSC-H3-4-GE.parBAYESSC-H3-5-WPB.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 5, wet phases bottleneckMagalhaes_et_al_Sicarius_cariri_BAYESSC-H3-5-WPB.parBeast XML input file for COI gene treeBeast XML input file for estimating the COI gene tree for Sicarius from the Brazilian Caatinga; divergence times are estimated simultaneously with the topology based on a mutation rate estimated for dysderid spidersMagalhaes_et_al_Sicarius_cariri_Beast_input_COI.xmlBeast XML input file for H3 gene treeBeast XML input file for estimating the H3 gene tree for Sicarius from the Brazilian Caatinga; divergence times are estimated simultaneously with the topology based on a mutation rate estimated for dysderid spidersMagalhaes_et_al_Sicarius_cariri_Beast_input_H3.xml*Beast XML input file for species delimitation analysis (hypothesis 1)*Beast XML input file for species delimitation analysis (hypothesis 1). This file includes data from both markers (COI and H3) and individuals sorted into four species (Sicarius cariri, Sicarius tropicus, Sicarius ornatus, Sicarius diadorim)Magalhaes_et_al_Sicarius_cariri_Beast_input_delimitation_hypothesis1.xml*Beast XML input file for species delimitation analysis (hypothesis 2)*Beast XML input file for species delimitation analysis (hypothesis 1). This file includes data from both markers (COI and H3) and individuals sorted into five species (Sicarius cariri clade 1, Sicarius cariri clade 2, Sicarius tropicus, Sicarius ornatus, Sicarius diadorim)Magalhaes_et_al_Sicarius_cariri_Beast_input_delimitation_hypothesis2.xmlBeast XML input file for EBSP analysis of Sicarius cariri clade 1Beast XML input file for the Extended Bayesian Skyline Plot (EBSP) analysis for reconstructing the demographic history of Sicarius cariri clade 1, including data from both markers (COI and H3)Magalhaes_et_al_Sicarius_cariri_Beast_XML_EBSP_Clade1.xmlBeast XML input file for EBSP analysis of Sicarius cariri clade 2Beast XML input file for the Extended Bayesian Skyline Plot (EBSP) analysis for reconstructing the demographic history of Sicarius cariri clade 2, including data from both markers (COI and H3)Magalhaes_et_al_Sicarius_cariri_Beast_XML_EBSP_Clade2.xmlBeast XML input file for COI gene trees - preliminary runs.rar file including 12 Beast XML input files with distinct population/clock models used for defining the best-fit priors for estimating the COI gene tree for Sicarius from the Brazilian CaatingaMagalhaes_et_al_Sicarius_cariri_Beast_XML_preliminary_runs_COI.rarBeast XML input file for H3 gene tree - preliminary runs.rar file including 12 Beast XML input files with distinct population/clock models used for defining the best-fit priors for estimating the H3 gene tree for Sicarius from the Brazilian CaatingaMagalhaes_et_al_Sicarius_cariri_Beast_XML_preliminary_runs_H3.rar.rarCOI gene treeAnnotated COI gene tree for Sicarius from the Brazilian Caatinga, with divergence time estimatesMagalhaes_et_al_Sicarius_cariri_Gene_tree_COI.treeH3 gene treeAnnotated gene tree for H3 for Sicarius from the Brazilian Caatinga, including divergence times estimatesMagalhaes_et_al_Sicarius_cariri_Gene_tree_H3.treeAlignment of COI sequences from Sicarius from the Brazilian Caatinga715 base pairs alignment of COI sequences from Sicarius from the Brazilian CaatingaMagalhaes_et_al_Sicarius_cariri_COI_alignment.fasAlignment of H3 sequences from Sicarius from the Brazilian Caatinga327 base pairs unphased alignment of H3 sequences from Sicarius from the Brazilian CaatingaMagalhaes_et_al_Sicarius_cariri_H3_unphased_alignment.fasGeographic and haplotypic information for Sicarius samples from the Brazilian CaatingaTab-delimited text file with voucher, geographic and haplotypic data for all samples used in this study. Voucher= institution acronym and number for the voucher individual. Pop= population number (check Figure 3 from the manuscript). Code= code used for this study (the same used for the tree/alignment files). Sex= M, male; F, female; J, juvenile. Type= whether the sample was freshly collected or was deposited in 80% ethanol in a museum. Hap-COI and Hap-H3= codes for haplotypes (the same used in table S2 and in the GenBank submission). Locality= name of the locality where the sample was collected, followed by latitude and longitude information.Magalhaes_et_al_Sicarius_cariri_geographic_genotypic_information.txt