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.
Geographical coordinates of presence and absence points for Sicarius cariri
Geographical 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.txt
BAYESSC-COI-1-SP
.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 1, stable population
Magalhaes_et_al_Sicarius_cariri_BAYESSC-COI-1-SP.par
BAYESSC-COI-2-GB
.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 2, glacial bottleneck
Magalhaes_et_al_Sicarius_cariri_BAYESSC-COI-2-GB.par
BAYESSC-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 refugia
Magalhaes_et_al_Sicarius_cariri_BAYESSC-COI-3-MR.par
BAYESSC-COI-4-GE
.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 4, glacial expansion
Magalhaes_et_al_Sicarius_cariri_BAYESSC-COI-4-GE.par
BAYESSC-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 bottlenecks
Magalhaes_et_al_Sicarius_cariri_BAYESSC-COI-5-WPB.par
BAYESSC-H3-1-SP
.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 1, stable population
Magalhaes_et_al_Sicarius_cariri_BAYESSC-H3-1-SP.par
BAYESSC-H3-2-GB
.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 2, glacial bottlenecks
Magalhaes_et_al_Sicarius_cariri_BAYESSC-H3-2-GB.par
BAYESSC-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 refugia
Magalhaes_et_al_Sicarius_cariri_BAYESSC-H3-3-MR.par
BAYESSC-H3-4-GE
.par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 4, glacial expansions
Magalhaes_et_al_Sicarius_cariri_BAYESSC-H3-4-GE.par
BAYESSC-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 bottleneck
Magalhaes_et_al_Sicarius_cariri_BAYESSC-H3-5-WPB.par
Beast XML input file for COI gene tree
Beast 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 spiders
Magalhaes_et_al_Sicarius_cariri_Beast_input_COI.xml
Beast XML input file for H3 gene tree
Beast 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 spiders
Magalhaes_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.xml
Beast XML input file for EBSP analysis of Sicarius cariri clade 1
Beast 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.xml
Beast XML input file for EBSP analysis of Sicarius cariri clade 2
Beast 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.xml
Beast 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 Caatinga
Magalhaes_et_al_Sicarius_cariri_Beast_XML_preliminary_runs_COI.rar
Beast 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 Caatinga
Magalhaes_et_al_Sicarius_cariri_Beast_XML_preliminary_runs_H3.rar.rar
COI gene tree
Annotated COI gene tree for Sicarius from the Brazilian Caatinga, with divergence time estimates
Magalhaes_et_al_Sicarius_cariri_Gene_tree_COI.tree
H3 gene tree
Annotated gene tree for H3 for Sicarius from the Brazilian Caatinga, including divergence times estimates
Magalhaes_et_al_Sicarius_cariri_Gene_tree_H3.tree
Alignment of COI sequences from Sicarius from the Brazilian Caatinga
715 base pairs alignment of COI sequences from Sicarius from the Brazilian Caatinga
Magalhaes_et_al_Sicarius_cariri_COI_alignment.fas
Alignment of H3 sequences from Sicarius from the Brazilian Caatinga
327 base pairs unphased alignment of H3 sequences from Sicarius from the Brazilian Caatinga
Magalhaes_et_al_Sicarius_cariri_H3_unphased_alignment.fas
Geographic and haplotypic information for Sicarius samples from the Brazilian Caatinga
Tab-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