Data for Stiller et al. Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates

Data accompanying "Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates" in BMC Biology.<br>This repository contains data and scripts accompanying the manuscript "Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates" in BMC Biology<br><br>For questions, please contact [e-mail].<br>The following files or gtar compressed collections of files are available:<b><br></b><b>Additional_file_2.tsv</b>Table of sampling data for all included specimens.<br><b>assembly.conf</b> Contains the configuration file used by PHYLUCE to build assemblies.<br><b>1_assemblies.gtar</b> Contains the assemblies for all samples generated by SPADES (directory spades-assemblies/contigs/) and ABYSS (directory abyss-assemblies/) and the chosen best assemblies (directory best/contigs/).<br><b>2_238taxa_concatenation.gtar</b> Contains the concatenated matrices for the 238 taxa dataset and IQTREE log files and intermediate files and the tree file.<br><b>3_238taxa_gene_trees_ASTRAL.gtar</b> Contains the alignments, IQTREE log files gene trees intermediate files and the tree files for the individual gene trees for the 238 taxa dataset. Also contains input and output files from ASTRAL-III analysis.<br><b>4_361taxa_concatenation.gtar</b> Contains the concatenated matrices for the 361 taxa dataset and IQTREE log files and intermediate files and the tree file.<br><b>5_361taxa_gene_trees_ASTRAL.gtar</b> Contains the alignments, IQTREE log files gene trees intermediate files and the tree files for the individual gene trees for the 361 taxa dataset. Also contains input and output files from ASTRAL-III analysis.<br><b>6_beast_analyses.gtar</b> Contains BEAST2 run files for the calibration analyses inclduing xml infiles, log and trees files from the runs.<br><b>7_barcodes_blast.gtar</b><br>Contains COI barcodes from BOLD used to blastn against the assemblies (directory best/contigs/ of 1_assemblies.gtar) to assist in species identification and delimitation. Output files are given in directory blast_hits/ as tab delimited text files, which are in blast's output format 6. Not all samples are represented because not all resulted in blast hits against the COI barcodes.<br><b>8_phylogenetic_diversity_endemism.gtar</b>Contains the presence absence matrix and the tables of calculated phylogenetic diversity and phylogenetic endemism.<br><b>9_BioGeoBEARS_biogeographic_reconstructions.gtar</b>Input files, R scripts, output files and plots for ancestral biogeographic range reconstruction and Bayesian Stochastic Mapping (BSM) of Syngnathiformes.<br><b>10_Diversification_rates.gtar</b>Input files, commands, output files for diversification rate analyses of - ClaDS run in Julia- Episodic Birth Death model run in RevBayes.<br><br>