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

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>

本数据集包含《塞舌尔青铜壁虎<i>Ailuronyx</i>属物种形成历史与物种界定：分子与形态学证据》一文（刊载于《林奈学会生物学杂志》，2016年，即将刊印）中的DNA序列数据，以及基于该数据开展的多项推断的完整输入输出文件。<br>本数据集提供了用于系统发育分析、网络构建、汇总统计、物种界定等分析的输入文件，同时附带部分分析的输出文件，包括基因树、物种树、物种界定结果。详细信息请参见正文与下文的文件说明。<br><b>文件标题：</b>1_ail_cytb_allseqs.fasta<b>文件说明：</b>本FASTA格式文件包含本研究中获得的全部细胞色素b（cytochrome b, cyt b）序列。这些序列也可通过论文附表S1中列出的GenBank（基因银行）登录号获取。请注意，部分序列ID与GenBank中的对应序列略有差异，但所有序列均可完整溯源。所有序列末尾的“_1”和“_2”代表<i>A. seychellensis</i>个体；“_3”和“_4”代表<i>A. tachyscopaeus</i>，“_5”代表<i>A. trachygaster</i>。<br><b>文件标题：</b>1_ail_cytb_haps.nex<b>文件说明：</b>本NEXUS格式文件仅包含前述1_ail_cytb_allseqs.fasta比对文件中的单倍型序列。<br><b>文件标题：</b>1_ail_cytb.con.tree<b>文件说明：</b>本文件为基于细胞色素b线粒体DNA片段（单倍型）的贝叶斯推断（Bayesian inference, BI）50%多数一致性树，对应论文中图2的结果。<br><b>文件标题：</b>11_ail_cytb_RAxML_bipartitions.tree<b>文件说明：</b>本文件为使用RAxML软件构建的、带有自举支持值的细胞色素b线粒体DNA片段（单倍型）最大似然（Maximum Likelihood, ML）树，具体构建方法详见论文。<br><b>文件标题：</b>2_ail_cmos_original.fasta<b>文件说明：</b>本FASTA格式文件包含全部未定相的cmos基因序列。<br><b>文件标题：</b>2_ail_cmos_phased.fasta<b>文件说明：</b>本FASTA格式文件包含经定相的cmos基因序列，定相方法详见论文，该序列用于网络构建。<br><b>文件标题：</b>3_ail_reln_original_mafft_main2phase.fasta<b>文件说明：</b>本FASTA格式文件包含55条未定相的RELN基因序列。<br><b>文件标题：</b>3_ail_reln_original_mafft_known2phase.fasta<b>文件说明：</b>本FASTA格式文件包含来自6个个体的RELN基因序列（共12条），这些个体存在插入缺失杂合性，因此直接从电泳图谱中读取了两条链的序列并完成定相。<br><b>文件标题：</b>3_ail_reln_phased.fasta<b>文件说明：</b>本FASTA格式文件包含本研究中用于分析的全部RELN基因序列，包括6个直接完成定相的个体序列，加上55条经推断完成定相的个体序列。<br><b>文件标题：</b>4a_inputs_outputs_starbeast_10sp.zip<b>文件说明：</b>该文件夹包含用于构建10个“物种”的STARBEAST XML文件的NEXUS格式输入文件，附带XML文件、日志文件、基因树与物种树分布结果输出文件，部分基因/支系添加了虚拟序列。<br><b>文件标题：</b>4b_inputs_outputs_starbeast_4_5_sp.zip<b>文件说明：</b>该文件夹包含用于构建4个和5个“物种”的STARBEAST XML文件的NEXUS格式输入文件，详见论文补充材料，附带XML文件、日志文件、基因树与物种树分布结果输出文件。<br><b>文件标题：</b>5a_BPP_inputs_and_outputs.zip<b>文件说明：</b>该文件夹包含论文中描述的BPP分析的全部输入文件与主要输出文件。<br><b>文件标题：</b>5b_PTP_inputs_and_outputs.zip<b>文件说明：</b>该文件夹包含已开展的PTP分析的输入文件与输出文件。<br><b>文件标题：</b>6_inputs_outputs_IMa_pairwise.zip<b>文件说明：</b>该文件夹包含论文中呈现的IMa分析的输入文件与输出文件。<br><b>文件标题：</b>7_dataset_morphology.csv<b>文件说明：</b>本CSV格式文件包含形态学分析所用的测量数据，包括吻肛长（snout–vent length, SVL）、头宽（head width, HW）、头高（head height, HH）、吻-眼距（snout–eye distance, SED）、眼-耳距（eye–ear distance, EED）、眼径（eye diameter, ED）、相对吻长（relative snout length, RSL = SED/EED）、相对头形（relative head shape, RHS = HW/HH）以及相对头长（relative head length, RHL = (SED + ED + EED)/SVL）。