Robledo-Ruiz et al. 2021 Molecular Ecology Resources (Supporting data)

Supporting data for the manuscript: Robledo-Ruiz, D. A., Pavlova, A., Clarke, R. H., Magrath, M. J. L., Quin, B., Harrisson, K. A., Gan, H. M., Low, G. W., & Sunnucks, P. (2021). A novel framework for evaluating in situ breeding management strategies in endangered populations. Molecular Ecology Resources.Feel free to contact me for a copy of the paper. You can find it here: https://doi.org/10.1111/1755-0998.13476. Preliminary version (open access) here: https://www.researchgate.net/publication/353388070_A_novel_framework_for_evaluating_in-situ_breeding_management_strategies_in_endangered_populations Each zipped folder contains the data files and scripts used for the steps in the analysis:0_SNPcalling_rawDArTs.zip - SNP calling from raw DArT reads. Final SNP dataset is called "p1r9_ld_50kb_1kb_removed_missing_0.61_no_sexlinked_HW.recode.vcf"1_Sex_check_DArT_files.zip - Check assigned sex using DArT data2_ParentageAnalysis_COLONY.zip - Parentage Analysis using COLONY2 software3_Kinship_Inbreeding_COANCESTRY.zip - Calculation of kinship and inbreeding using COANCESTRY software4_MSI_PMx.zip - Tranformation of kinship to Mate Suitability Index (MSI) using PMx software5_Kinship_ActualPairs.zip - Identification of kinship for actual pairs 5_MSI_ActualPairs.zip - Identification of MSI for actual pairs6_Kinship_BestPairs.zip - Simulation of the kinship of best pairs6_MSI_BestPairs.zip - Simulation of the MSI of best pairs7_Kinship_RandomPairs.zip - Simulation of the kinship of random pairs7_MSI_RandomPairs.zip - Simulation of the MSI of random pairs8_Kinship_IdealPairs.zip - Simulation of the kinship of ideal pairs8_MSI_IdealPairs.zip - Simulation of the MSI of best ideal9_Kinship_Management1Pairs.zip - Simulation of the kinship of management pairs9_MSI_Management1Pairs.zip - Simulation of the MSI of management pairs10_Kinship_FinalComparison.zip - Statistical analysis comparing kinship10_MSI_FinalComparison.zip - Statistical analysis comparing MSI11_PCA.zip - Principal Coordinates Analysis12_Kinship_Management2Pairs.zip - Simulation of the kinship of management 2 pairs12_MSI_Management2Pairs.zip - Simulation of the MSI of management 2 pairs

本数据集为论文Robledo-Ruiz, D. A.、Pavlova, A.、Clarke, R. H.、Magrath, M. J. L.、Quin, B.、Harrisson, K. A.、Gan, H. M.、Low, G. W. 与Sunnucks, P.于2021年发表于《Molecular Ecology Resources》的《濒危物种种内地繁育管理策略评估的新型框架》的配套支撑数据。如需获取论文原文可联系作者，原文链接为https://doi.org/10.1111/1755-0998.13476；开放获取的预印本可访问：https://www.researchgate.net/publication/353388070_A_novel_framework_for_evaluating_in-situ_breeding_management_strategies_in_endangered_populations。

每个压缩文件夹均包含对应分析步骤所用的数据文件与脚本：
0_SNPcalling_rawDArTs.zip：基于原始DArT（多样性阵列技术，Diversity Arrays Technology）测序读段进行SNP（单核苷酸多态性，Single Nucleotide Polymorphism）调用，最终SNP数据集文件名为"p1r9_ld_50kb_1kb_removed_missing_0.61_no_sexlinked_HW.recode.vcf"
1_Sex_check_DArT_files.zip：利用DArT数据对已分配的个体性别进行校验
2_ParentageAnalysis_COLONY.zip：使用COLONY2软件开展亲权分析
3_Kinship_Inbreeding_COANCESTRY.zip：使用COANCESTRY软件计算亲缘关系系数与近交系数
4_MSI_PMx.zip：使用PMx软件将亲缘关系转换为交配适宜性指数（Mate Suitability Index, MSI）
5_Kinship_ActualPairs.zip：识别真实配对的亲缘关系；5_MSI_ActualPairs.zip：识别真实配对的交配适宜性指数
6_Kinship_BestPairs.zip：模拟最优配对的亲缘关系；6_MSI_BestPairs.zip：模拟最优配对的交配适宜性指数
7_Kinship_RandomPairs.zip：模拟随机配对的亲缘关系；7_MSI_RandomPairs.zip：模拟随机配对的交配适宜性指数
8_Kinship_IdealPairs.zip：模拟理想配对的亲缘关系；8_MSI_IdealPairs.zip：模拟理想配对的交配适宜性指数
9_Kinship_Management1Pairs.zip：模拟管理配对1的亲缘关系；9_MSI_Management1Pairs.zip：模拟管理配对1的交配适宜性指数
10_Kinship_FinalComparison.zip：开展亲缘关系对比的统计分析；10_MSI_FinalComparison.zip：开展交配适宜性指数对比的统计分析
11_PCA.zip：主坐标分析（Principal Coordinates Analysis）
12_Kinship_Management2Pairs.zip：模拟管理配对2的亲缘关系；12_MSI_Management2Pairs.zip：模拟管理配对2的交配适宜性指数