DOI: 10.5281/zenodo.11062112
title: Supplementary figures and data for "Complete phylogeny of Micrathena spiders suggests multiple dispersal events among Neotropical rainforests, islands, and landmasses, and indicates Andean orogeny promotes speciation"

description: Supplementary figures and data for "Complete phylogeny of Micrathena spiders suggests multiple dispersal events among Neotropical rainforests, islands, and landmasses, and indicates Andean orogeny promotes speciation" by Ivan L. F. Magalhaes, Pedro H. Martins, Bárbara T. Faleiro, Teofânia H. D. A. Vidigal, Fabrício R. Santos, Leonardo S. Carvalho, Adalberto J. Santos, submitted to Cladistics. 

Supplementary Figures S1 – S15

Supplementary data S16: Complete specimen data of specimens used as vouchers for morphological scorings in Excel spreadsheet format.Supplementary data S17: Discrete character matrix with morphological scorings in Nexus format.Supplementary data S18: Complete specimen data of specimens used as vouchers for DNA sequencing in Excel spreadsheet format.Supplementary data S19: Alignment of cytochrome oxidase I sequences in Fasta format.Supplementary data S20: Alignment of histone H3 sequences in Fasta format.Supplementary data S21: Alignment of 28S ribosomal sequences in Fasta format.Supplementary data S22: Alignment of internal transcribed spacer sequences in Fasta format.Supplementary data S23: Alignment of 16S ribosomal sequences in Fasta format.Supplementary data S24: Zipped folder containing the inputs for estimating the phylogeny using morphological data in IQ-Tree: matrix in nexus format, partition file, and command file in plain text.Supplementary data S25: Zipped folder containing the inputs for estimating the phylogeny using sequence data aligned with Muscle in IQ-Tree: matrix in nexus format, partition file, and command file in plain text.Supplementary data S26: Zipped folder containing the inputs for estimating the phylogeny using sequence data aligned with MAFFT in IQ-Tree: matrix in nexus format, partition file, and command file in plain text.Supplementary data S27: Zipped folder containing the inputs for estimating the phylogeny using morphological and sequence data aligned with MUSCLE in IQ-Tree: matrix in nexus format, partition file, and command file in plain text.Supplementary data S28: Input Nexus for estimating the phylogeny using morphological data in MrBayes.Supplementary data S29: Input Nexus for estimating the phylogeny using sequence data aligned with Muscle in MrBayes.Supplementary data S30: Input Nexus for estimating the phylogeny using sequence data aligned with MAFFT in MrBayes.Supplementary data S31: Input Nexus for estimating the phylogeny using morphological and sequence data aligned with Muscle in MrBayes.Supplementary data S32: Input XML for estimating the dated phylogeny under Bayesian inference in BEAST.Supplementary data S33: Distribution maps for all Micrathena species included in this study, the database with the original records and their source, and the R script used to generate the maps.Supplementary data S34: Zipped folder containing all the inputs for estimating ancestral ranges and performing biogeographic stochastic mapping in R. This contains (0) the scripts for performing model selection and estimating ancestral states over a distribution of posterior trees, followed by stochastic mapping; (1) the geography and tree files (MMCT, and 100 trees randomly drawn from the posterior distribution);  (2) the dispersal matrix and (3) the files for performing the time-stratified analysis to test the influence of the closure of the Isthmus of Panama on Micrathena dispersal.Supplementary data S35: R script for generating the in-situ-speciation-through-time graphs from the results of biogeographic stochastic maps, as seen in Fig. 5.Supplementary data S36: R script for getting and plotting elevations from individual records of Micrathena.Supplementary data S37: R script for performing the GeoHiSSE estimation of net diversification rates among areas.Supplementary data S38: Zipped folder containing the optimal trees found as a result of analysing inputs S24–S32 (IQ-Tree, MrBayes and BEAST).Supplementary data S39: Zipped folder containing the ancestral range estimation results under competing models in BioGeoBEARS.Supplementary data S40: Excel spreadsheet with parameter values of competing biogeographic models in BioGeoBEARS.Supplementary data S41: Excel spreadsheet with results of biogeographic stochastic mapping over 100 different trees from the posterior distribution; includes all Micrathena species.Supplementary data S42: Excel spreadsheet with results of biogeographic stochastic mapping over 100 different trees from the posterior distribution; includes only Micrathena species which had their DNA sequenced.Supplementary data S43: Excel spreadsheet with the geography matrix, indicating which Micrathena species may be found in each area, and indicating the proportion of species from each area that are missing from the incomplete dataset  (i.e., excluding species with unavailable DNA sequences).Supplementary data S44: Excel spreadsheet with parameter values of competing biogeographic models estimated in GeoHiSSE.