DOI: 10.6084/m9.figshare.1579291
title: Data & Results from: Rocha et al (2016) Speciation history and species-delimitation within the Seychelles Bronze geckos, Ailuronyx spp.: molecular and morphological evidence. Biological Journal of the Linnean Society, In press

description: DNA sequence data and full input and output files of several inferences from the data as presented in "Speciation history and species-delimitation within the Seychelles Bronze geckos, <i>Ailuronyx</i> spp.: molecular and morphological evidence". <i>Biological Journal of the Linnean Society</i>, <b>2016</b> (In press)<br>Input files used for phylogenetic analyses, networks, summary statistics, species delimitations, etc. Output files for some of the analyses are also given (gene-trees; species-trees; species-delimitation). See main ms and file descriptions bellow.<br><b>FILE TITLE:</b> 1_ail_citb_allseqs.fasta<b>DESCRIPTION:</b> fasta file of all cytochrome-b sequences obtained in this work. Can also be obtained from genbank with acession nrs provided in manuscript (Table S1). Please note that some sequence IDs may be slightly different from the respective on genbank but all are perfectly trackable. Across all sequences "_1" and "_2" terminations denote <i>A. seychellensis </i>individuals; "_3" and "_4" <i>A. tachyscopaeus</i> and "_5" <i>A. trachygaster.</i><br><b>FILE TITLE: </b>1_ail_cytb_haps.nex<b>DESCRIPTION:</b> nexus file containing only the haplotypes from previous (1_ail_citb_allseqs.fasta) alignment<br><b>FILE TITLE: </b>1_ail_cytb.con.tree<b>DESCRIPTION:</b> Bayesian inference (BI) 50% majority-rule consensus tree for cytochrome (cyt b) mitochodrial DNA fragment(haplotypes) as presented in Figure 2 of the manuscript.<br><b>FILE TITLE: </b>11_ail_citb_RAxML_bipartitions.tree<b>DESCRIPTION:</b> ML tree for cytochrome (cyt b) mitochodrial DNA fragment (haplotypes) with bootstraps, as estimated with RaxML (see manuscript).<br><b>FILE TITLE:</b> 2_ail_cmos_original.fasta<b>DESCRIPTION:</b> fasta file with all unphased cmos sequences<br><b>FILE TITLE:</b> 2_ail_cmos_phased.fasta<b>DESCRIPTION:</b> fasta file with cmos sequences phased as described in manuscript (used for network construction)<br><b>FILE TITLE:</b> 3_ail_reln_original_mafft_main2phase.fasta<b>DESCRIPTION:</b> fasta file with 55 unphased RELN sequences<br><b>FILE TITLE:</b> 3_ail_reln_original_mafft_known2phase.fasta<b>DESCRIPTION:</b> fasta file with RELN sequences from 6 individuals (12 sequences) which were heterozygous for indels, thus both strands were read directly (phased) from electropherograms.<br><b>FILE TITLE: </b>3_ail_reln_phased.fasta<b>DESCRIPTION: </b>fasta file with all RELN sequences used in analyses (the 6 individuals for which phase was determined directly ples the 55 for which it was infered).<br><b>FILE TITLE:</b> 4a_inputs_outputs_starbeast_10sp.zip<b>DESCRIPTION:</b> folder with nexus input files used for building starbeast xml of 10 "species" (dummy sequences added for some genes/lineages), xml, log, gene-trees and species-tree distribution output files<br><b>FILE TITLE:</b> 4b_inputs_outputs_starbeast_4_5_sp.zip<b>DESCRIPTION:</b> folder with nexus input files used for building starbeast xml of 4 and 5 "species" (see supplemetary material of main manuscript), xml, logs, gene-trees and species-tree distribution output files.<br><b>FILE TITLE:</b> 5a_BPP_inputs_and_outputs.zip<b>DESCRIPTION:</b> folder with all inputs and main outputs of BPP analyses described in the manuscript<br><b>FILE TITLE:</b> 5b_PTP_inputs_and_outputs.zip<b>DESCRIPTION:</b> folder with inputs and outputs of PTP analyses performed<br><b>FILE TITLE:</b> 6_inputs_outputs_IMa_pairwise.zip<b>DESCRIPTION:</b> inputs and outputs for IMa analyses presented in the manuscript<br><b>FILE TITLE: </b>7_dataset_morphology.cvs<b>DESCRIPTION: </b>csv file with the measurements used in the morphological analysis. snout–vent length (SVL), head width (HW), head height (HH), snout–eye distance (SED), eye–ear distance (EED), eye diameter (ED), relative snout length (RSL = SED/EED), relative head shape (RHS = HW/HH), and relative head length [RHL = (SED + ED + EED)/SVL].<br><br>