Molecular evidence for introgressive hybridization in New Zealand masked gulls
收藏资源简介：
Genetic data and codes to reproduce the analyses from the manuscript :<br> <br> Given, A. D., Mills, J. A., Momigliano, P., & Baker, A. J. (2022). Molecular evidence for introgressive hybridization in New Zealand masked gulls. <em>Ibis</em>. https://doi.org/10.1111/ibi.13117 The data and codes are in two zipped folders FSC.zip PopGen.zip The FSC.zip folder contains data and scripts to reproduce the fastsimcoal simulations and to calculate summary statistics from observed and simulated data. It also includes the results from these analyses and an R script to run ABC model selection via random forest. The PopGen.zip folder contains the microsatellite dataset in both <em>genepop</em> (RB-BB.gen)<em> </em>and <em>structure </em>(RB-BB.str) formats , the results from STRUCTURE analyses (folder RB-BB_STRUCT), and an R script (Popgen_analyses.r) to reproduce population genetic analyses (PCA and summary statistics: <em>F</em><sub>ST</sub>, and estimate HWE, <em>H</em><sub>O</sub> and <em>H</em><sub>E</sub>) and plots.
本数据集包含用于复现对应论文分析流程的遗传数据与代码： Given, A. D.、Mills, J. A.、Momigliano, P. 与 Baker, A. J. 于2022年发表于《Ibis》的论文《新西兰蒙面鸥渐渗杂交的分子证据》，DOI: 10.1111/ibi.13117。 数据集与代码存储于两个压缩文件夹：FSC.zip 与 PopGen.zip。 其中FSC.zip文件夹包含用于复现fastsimcoal模拟分析、从观测与模拟数据中计算汇总统计量的代码与数据，同时包含上述分析的结果，以及一段用于通过随机森林实现近似贝叶斯计算（Approximate Bayesian Computation，ABC）模型选择的R脚本。 PopGen.zip文件夹包含两种格式的微卫星数据集：genepop格式（RB-BB.gen）与structure格式（RB-BB.str），STRUCTURE分析结果文件夹RB-BB_STRUCT，以及一段名为Popgen_analyses.r的R脚本，用于复现群体遗传学分析（包括主成分分析（Principal Component Analysis，PCA）、汇总统计量F_ST、哈迪-温伯格平衡（Hardy-Weinberg Equilibrium，HWE）检验、观测杂合度H_O与期望杂合度H_E的估算）及可视化绘图。
