Data from: Strong spatial structure, Pliocene diversification and cryptic diversity in the Neotropical dry forest spider Sicarius cariri

Magalhaes ILF, Oliveira U, Santos FR, Vidigal THDA, Brescovit AD, Santos AJ

Date Published: September 24, 2014

DOI: http://dx.doi.org/10.5061/dryad.ps12h

 

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Title Geographical coordinates of presence and absence points for Sicarius cariri
Downloaded 8 times
Description 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.
Download Magalhaes_et_al_Sicarius_cariri_absence_p...ts.txt (4.427 Kb)
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Title BAYESSC-COI-1-SP
Downloaded 13 times
Description .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 1, stable population
Download Magalhaes_et_al_Sicarius_cariri_BAYESSC-C...SP.par (490 bytes)
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Title BAYESSC-COI-2-GB
Downloaded 6 times
Description .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 2, glacial bottleneck
Download Magalhaes_et_al_Sicarius_cariri_BAYESSC-C...GB.par (721 bytes)
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Title BAYESSC-COI-3-MR
Downloaded 6 times
Description .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 3, glacial multiple refugia
Download Magalhaes_et_al_Sicarius_cariri_BAYESSC-C...MR.par (1.684 Kb)
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Title BAYESSC-COI-4-GE
Downloaded 3 times
Description .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 4, glacial expansion
Download Magalhaes_et_al_Sicarius_cariri_BAYESSC-C...GE.par (714 bytes)
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Title BAYESSC-COI-5-WPB
Downloaded 6 times
Description .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 5, wet phase bottlenecks
Download Magalhaes_et_al_Sicarius_cariri_BAYESSC-C...PB.par (1.614 Kb)
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Title BAYESSC-H3-1-SP
Downloaded 4 times
Description .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 1, stable population
Download Magalhaes_et_al_Sicarius_cariri_BAYESSC-H...SP.par (490 bytes)
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Title BAYESSC-H3-2-GB
Downloaded 6 times
Description .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 2, glacial bottlenecks
Download Magalhaes_et_al_Sicarius_cariri_BAYESSC-H...GB.par (721 bytes)
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Title BAYESSC-H3-3-MR
Downloaded 3 times
Description .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 3, glacial multiple refugia
Download Magalhaes_et_al_Sicarius_cariri_BAYESSC-H...MR.par (1.686 Kb)
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Title BAYESSC-H3-4-GE
Downloaded 1 time
Description .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 4, glacial expansions
Download Magalhaes_et_al_Sicarius_cariri_BAYESSC-H...GE.par (714 bytes)
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Title BAYESSC-H3-5-WPB
Downloaded 5 times
Description .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 5, wet phases bottleneck
Download Magalhaes_et_al_Sicarius_cariri_BAYESSC-H...PB.par (1.614 Kb)
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Title Beast XML input file for COI gene tree
Downloaded 7 times
Description 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
Download Magalhaes_et_al_Sicarius_cariri_Beast_inp...OI.xml (196.0 Kb)
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Title Beast XML input file for H3 gene tree
Downloaded 1 time
Description 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
Download Magalhaes_et_al_Sicarius_cariri_Beast_input_H3.xml (26.74 Kb)
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Title *Beast XML input file for species delimitation analysis (hypothesis 1)
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Description *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)
Download Magalhaes_et_al_Sicarius_cariri_Beast_inp...s1.xml (431.7 Kb)
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Title *Beast XML input file for species delimitation analysis (hypothesis 2)
Downloaded 5 times
Description *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)
Download Magalhaes_et_al_Sicarius_cariri_Beast_inp...s2.xml (432.1 Kb)
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Title Beast XML input file for EBSP analysis of Sicarius cariri clade 1
Downloaded 7 times
Description 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)
Download Magalhaes_et_al_Sicarius_cariri_Beast_XML...e1.xml (296.7 Kb)
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Title Beast XML input file for EBSP analysis of Sicarius cariri clade 2
Downloaded 3 times
Description 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)
Download Magalhaes_et_al_Sicarius_cariri_Beast_XML...e2.xml (97.76 Kb)
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Title Beast XML input file for COI gene trees - preliminary runs
Downloaded 3 times
Description .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
Download Magalhaes_et_al_Sicarius_cariri_Beast_XML...OI.rar (104.2 Kb)
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Title Beast XML input file for H3 gene tree - preliminary runs
Downloaded 34 times
Description .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
Download Magalhaes_et_al_Sicarius_cariri_Beast_XML...ar.rar (39.34 Kb)
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Title COI gene tree
Downloaded 5 times
Description Annotated COI gene tree for Sicarius from the Brazilian Caatinga, with divergence time estimates
Download Magalhaes_et_al_Sicarius_cariri_Gene_tree_COI.tree (245.5 Kb)
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Title H3 gene tree
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Description Annotated gene tree for H3 for Sicarius from the Brazilian Caatinga, including divergence times estimates
Download Magalhaes_et_al_Sicarius_cariri_Gene_tree_H3.tree (41.67 Kb)
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Title Alignment of COI sequences from Sicarius from the Brazilian Caatinga
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Description 715 base pairs alignment of COI sequences from Sicarius from the Brazilian Caatinga
Download Magalhaes_et_al_Sicarius_cariri_COI_alignment.fas (166.4 Kb)
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Title Alignment of H3 sequences from Sicarius from the Brazilian Caatinga
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Description 327 base pairs unphased alignment of H3 sequences from Sicarius from the Brazilian Caatinga
Download Magalhaes_et_al_Sicarius_cariri_H3_unphas...nt.fas (69.94 Kb)
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Title Geographic and haplotypic information for Sicarius samples from the Brazilian Caatinga
Downloaded 7 times
Description 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.
Download Magalhaes_et_al_Sicarius_cariri_geographi...on.txt (23.52 Kb)
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When using this data, please cite the original publication:

Magalhaes ILF, Oliveira U, Santos FR, Vidigal THDA, Brescovit AD, Santos AJ (2014) Strong spatial structure, Pliocene diversification and cryptic diversity in the Neotropical dry forest spider Sicarius cariri. Molecular Ecology 23(21): 5323-5336. http://dx.doi.org/10.1111/mec.12937

Additionally, please cite the Dryad data package:

Magalhaes ILF, Oliveira U, Santos FR, Vidigal THDA, Brescovit AD, Santos AJ (2014) Data from: Strong spatial structure, Pliocene diversification and cryptic diversity in the Neotropical dry forest spider Sicarius cariri. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.ps12h
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