Data for article "Phylogeny, biogeography, and rapid diversification of the mining bee family Andrenidae'

This readme.txt file was generated on 2021-SEPT-3 by Silas Bossert<br>GENERAL INFORMATION<br>This readme files describes the supplementary files associated with the research article<br>Phylogeny, biogeography, and rapid diversification of the mining bee family Andrenidae<br>by Silas Bossert, Thomas J. Wood, Sébastien Patiny, Denis Michez, Eduardo A.B. Almeida, Robert L. Minckley, Laurence Packer, John L. Neff, Robert S. Copeland, Jakub Straka, Alain Pauly, Terry Griswold, Seán G. Brady, Bryan N. Danforth, Elizabeth A. Murray<br>For questions and/or concerns please contact the lead author of the paper under silas.bossert [at] wsu.edu<br>This repository consists of 6 files.<br>###1. Supplementary_Material.pdf###<br>This Pdf file is a detailed compilation of methods and results, and is instrumental for understanding the deposited files.<br>###2. Assembly_Files.tar.gz###<br>This compressed archive contains all UCE assembly files used in this study. This includes all assembly files generated in the course of this study, as well those from previously published research as described in the Supplementary Material Pdf.<br>###2. Concatenated_Alignment.tar.gz###<br>This archive contains the concatenated DNA sequence matrix used for phylogenetic estimates.<br>###3. Gene_Trees.tar.gz###<br>This archive contains 1,388 UCE gene trees estimates with IQ-Tree 2.<br>###4. Input_Files_Information.tar.gz###<br>This file contains various input and configuration files used in the above mentioned study. Specifically, it contains the input for the following analyses: (1) Method-of-Moments estimates, (2) BioGeoBEARS analyses, (3) BAMM analyses, (4) MrBayes runs, (5) RevBayes runs, (6) Spruceup run. Lastly, it contains the file specifying the numbers used to code species diversity of Andrenidae.<br>###5. Species_Tree_Files.tar.gz###<br>This file contains all species trees generated in the study in Newick format.

本readme.txt文件由Silas Bossert于2021年9月生成。
# 通用说明
本说明文档用于介绍与研究论文《隧蜂科（Andrenidae）的系统发育、生物地理学与快速多样化》配套的补充文件，论文作者包括：Silas Bossert、Thomas J. Wood、Sébastien Patiny、Denis Michez、Eduardo A.B. Almeida、Robert L. Minckley、Laurence Packer、John L. Neff、Robert S. Copeland、Jakub Straka、Alain Pauly、Terry Griswold、Seán G. Brady、Bryan N. Danforth、Elizabeth A. Murray。
如有疑问或建议，请联系论文第一作者，邮箱地址为[e-mail]。
本仓库共包含6个文件：
###1. Supplementary_Material.pdf###
该PDF文件为研究方法与结果的详细汇编，是理解本仓库所存文件的核心参考资料。
###2. Assembly_Files.tar.gz###
该压缩归档包含本研究中使用的所有超保守元件（Ultra-Conserved Elements, UCE）组装文件，既涵盖本研究过程中生成的组装文件，也包括补充材料PDF中提及的已发表研究的相关组装文件。
###2. Concatenated_Alignment.tar.gz###
该归档包含用于系统发育推断的串联DNA序列矩阵。
###3. Gene_Trees.tar.gz###
该归档包含基于IQ-Tree 2生成的1388条UCE基因树推断结果。
###4. Input_Files_Information.tar.gz###
该文件包含本研究中使用的各类输入与配置文件，具体涵盖以下分析的输入数据：(1) 矩法（Method-of-Moments）估计；(2) BioGeoBEARS分析；(3) BAMM分析；(4) MrBayes运行；(5) RevBayes运行；(6) Spruceup运行。此外，该文件还包含用于编码隧蜂科物种多样性数值的说明文件。
###5. Species_Tree_Files.tar.gz###
该文件包含本研究中生成的所有物种树，格式为Newick格式（纽克格式）。