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>

本数据集配套发表于《BMC Biology》的论文《海龙科（Syngnathidae）系统基因组学分析揭示全新演化关系、特有多样性起源与多样化速率差异》。
本仓库包含上述论文配套的数据与分析脚本。

如有疑问，请联系邮箱：[e-mail]。

<b>Additional_file_2.tsv</b>：所有纳入标本的采样信息表。
<b>assembly.conf</b>：用于PHYLUCE构建组装集的配置文件。
<b>1_assemblies.gtar</b>：包含所有样本的组装结果，其中SPADES生成的组装结果位于spades-assemblies/contigs/目录，ABYSS生成的组装结果位于abyss-assemblies/目录，筛选出的最优组装结果位于best/contigs/目录。
<b>2_238taxa_concatenation.gtar</b>：包含238个分类群数据集的串联矩阵、IQTREE日志文件、中间文件与系统发育树文件。
<b>3_238taxa_gene_trees_ASTRAL.gtar</b>：包含238个分类群数据集的序列比对文件、IQTREE日志文件、单基因树中间文件与单基因树文件，同时包含ASTRAL-III分析的输入与输出文件。
<b>4_361taxa_concatenation.gtar</b>：包含361个分类群数据集的串联矩阵、IQTREE日志文件、中间文件与系统发育树文件。
<b>5_361taxa_gene_trees_ASTRAL.gtar</b>：包含361个分类群数据集的序列比对文件、IQTREE日志文件、单基因树中间文件与单基因树文件，同时包含ASTRAL-III分析的输入与输出文件。
<b>6_beast_analyses.gtar</b>：包含校准分析所用的BEAST2运行文件，包括分析所需的XML输入文件、运行生成的日志文件与树文件。
<b>7_barcodes_blast.gtar</b>：包含源自BOLD数据库的COI条形码序列，用于与1_assemblies.gtar中的最优组装结果（目录best/contigs/）进行blastn比对，以辅助物种鉴定与物种分界。比对结果以制表符分隔的文本文件形式存储于blast_hits/目录中，格式为BLAST输出格式6。由于部分样本未获得COI条形码比对结果，因此并非所有样本均有对应输出文件。
<b>8_phylogenetic_diversity_endemism.gtar</b>：包含存在/缺失矩阵，以及计算得到的系统发育多样性与系统发育特有性表格。
<b>9_BioGeoBEARS_biogeographic_reconstructions.gtar</b>：包含海龙目（Syngnathiformes）祖先生物地理范围重建的输入文件、R脚本、输出文件与可视化图表，以及贝叶斯随机映射（Bayesian Stochastic Mapping, BSM）分析相关文件。
<b>10_Diversification_rates.gtar</b>：包含多样化速率分析的输入文件、命令脚本与输出文件，具体包括在Julia中运行的ClaDS分析，以及在RevBayes中运行的阶段性出生-死亡模型分析。