Metapopulation genetic management of the Macquarie perch

This repository contains data and R script script used in the manuscriptA shift to metapopulation genetic management for persistence of a species threatened by fragmentation: the case of an endangered Australian freshwater fish, by Pavlova A, Tonkin Z, Pearce L, Robledo-Ruiz D, Lintermans M, Ingram B, Lyon J, Beitzel M, Broadhurst B, Rourke ML, Sturgiss F, Lake E, Castrejón-Figueroa, Stocks JR, and Sunnucks P. Molecular Ecology MEC-24-1090.R1, accepted pending minor revision.The content of this data repository:MaccaGM_SNPs.R –– R script for analyses of DArT SNP genotypic data and plotting the results of analyses of JeDi pipelineInput files for MaccaGM_SNPs.R:Report_DMacq23-8576_14_moreOrders_SNP_mapping_1.csv –– DArT genotypes in original formatCovariate_MaccaGM_recaller25inds_then_max50per_pop.csv –– covariate file for individualsUnbiased genetic diversity: outputs of JeDi pipeline Estimates of unbiased heterozygosity (piawka_uHe) resulting from JeDi pipeline run for all sites, biallelic sites and tri- and tetra-allelic sites. Analyses were run with 9 different settings (A-H). Estimates of individual unbiased heterozygosity from JeDi pipeline are appended to the individual covariate file with results of analyses of SNP dataset (SNP heterozygosity, PHt, and membership in STRUCTURE clusters (X1of15 to X15of15).ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP10_SETA.csv –– Output of SetA: Piawka run with Settings: no (-B), QUAL30, MinDP10, No doubleton filterind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual30_minDP10_SETB.csv –– Output of SetB: Piawka run with Settings: (-B), QUAL30, MinDP10, No doubleton filterind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual40_minDP10_SETC.csv –– Output of SetC: Piawka run with Settings: (-B), QUAL40, MinDP10, No doubleton filterind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual30_minDP12_setD.csv –– Output of SetD: Piawka run with Settings: (-B), QUAL30, MinDP12, No doubleton filterind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual30_minDP10_doubleton_SETE.csv–– Output of SetE: Piawka run with Settings: (-B), QUAL30, MinDP10, doubleton filterind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual50_minDP15_SETF.csv–– Output of SetF: Piawka run with Settings : (-B), QUAL50, MinDP15, No doubleton filterind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP10_doub_SETG.csv–– Output of SetG: Piawka run with Settings: No (-B), QUAL30, MinDP10, doubleton filterind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP10_doub_sing_SETH.csv–– Output of SetH: Piawka run with Settings: No (-B), QUAL30, MinDP10, doubleton and singleton filterind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP15_doub_sing_SETI.csv–– Output of SetI: Piawka run with Settings: No (-B), QUAL30, MinDP15, doubleton and singleton filterEstimates of population nucleotide diversity (pi): outputs of JeDi pipeline run under three settings:genomic_pi_table_SETA.tsv—pi from JeDi pipeline run under Settings A: no (-B), QUAL30, MinDP10, No doubleton filtergenomic_pi_table SETG.tsv—pi from JeDi pipeline run under Settings G: No (-B), QUAL30, MinDP10, doubleton filtergenomic_pi_table - SETH.tsv—pi from JeDi pipeline run under Settings H: No (-B), QUAL30, MinDP10, doubleton and singleton filterPopulation summaries of the genetic estimates from SNP dataset (Ho- observed heterozygosity, He-expected heterozygosity, private.alleles.dartr.one2rest and PA- number of private alleles per population including and excluding three with sample size

本仓库包含帕夫洛娃（Pavlova A）等作者的手稿配套数据与R脚本（R script）。该手稿题为《面向受生境破碎化威胁物种存续的集合种群遗传管理转型——以一种濒危澳大利亚淡水鱼类为例》（A shift to metapopulation genetic management for persistence of a species threatened by fragmentation: the case of an endangered Australian freshwater fish），作者包括Pavlova A、Tonkin Z、Pearce L、Robledo-Ruiz D、Lintermans M、Ingram B、Lyon J、Beitzel M、Broadhurst B、Rourke ML、Sturgiss F、Lake E、Castrejón-Figueroa、Stocks JR及Sunnucks P，稿件编号为MEC-24-1090.R1，已通过审核并待小修后接收。

本数据仓库包含以下内容：
1. MaccaGM_SNPs.R：用于分析DArT SNP（DArT SNP）基因型数据，并可视化JeDi分析流水线（JeDi pipeline）分析结果的R脚本。
2. MaccaGM_SNPs.R的输入文件：
- Report_DMacq23-8576_14_moreOrders_SNP_mapping_1.csv：原始格式的DArT基因型数据文件
- Covariate_MaccaGM_recaller25inds_then_max50per_pop.csv：个体协变量文件
3. 无偏遗传多样性模块：JeDi分析流水线的输出结果
包含针对所有位点、双等位基因位点以及三、四等位基因位点运行JeDi流水线得到的无偏杂合度（piawka_uHe）估计值。本次分析共设置9组参数组合（编号A至H）。从JeDi流水线获取的个体无偏杂合度估计值已追加至个体协变量文件中，同时附带SNP数据集分析结果：SNP杂合度（SNP heterozygosity）、PHt值以及STRUCTURE聚类（STRUCTURE clusters）成员归属标签（X1of15至X15of15）。
各参数组合的输出文件如下：
- ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP10_SETA.csv：SetA的分析输出，对应参数设置为无-B过滤、QUAL30、最小测序深度MinDP10、未过滤双位点，基于该设置运行Piawka得到的结果
- ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual30_minDP10_SETB.csv：SetB的分析输出，对应参数设置为启用-B过滤、QUAL30、MinDP10、未过滤双位点，基于该设置运行Piawka得到的结果
- ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual40_minDP10_SETC.csv：SetC的分析输出，对应参数设置为启用-B过滤、QUAL40、MinDP10、未过滤双位点，基于该设置运行Piawka得到的结果
- ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual30_minDP12_setD.csv：SetD的分析输出，对应参数设置为启用-B过滤、QUAL30、MinDP12、未过滤双位点，基于该设置运行Piawka得到的结果
- ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual30_minDP10_doubleton_SETE.csv：SetE的分析输出，对应参数设置为启用-B过滤、QUAL30、MinDP10、过滤双位点，基于该设置运行Piawka得到的结果
- ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual50_minDP15_SETF.csv：SetF的分析输出，对应参数设置为启用-B过滤、QUAL50、MinDP15、未过滤双位点，基于该设置运行Piawka得到的结果
- ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP10_doub_SETG.csv：SetG的分析输出，对应参数设置为无-B过滤、QUAL30、MinDP10、过滤双位点，基于该设置运行Piawka得到的结果
- ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP10_doub_sing_SETH.csv：SetH的分析输出，对应参数设置为无-B过滤、QUAL30、MinDP10、同时过滤双位点与单位点，基于该设置运行Piawka得到的结果
- ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP15_doub_sing_SETI.csv：SetI的分析输出，对应参数设置为无-B过滤、QUAL30、MinDP15、同时过滤双位点与单位点，基于该设置运行Piawka得到的结果
4. 群体核苷酸多样性（pi）估计模块：JeDi分析流水线在3组参数设置下的输出结果：
- genomic_pi_table_SETA.tsv：基于设置A（无-B过滤、QUAL30、MinDP10、未过滤双位点）运行JeDi流水线得到的群体核苷酸多样性pi值
- genomic_pi_table_SETG.tsv：基于设置G（无-B过滤、QUAL30、MinDP10、过滤双位点）运行JeDi流水线得到的群体核苷酸多样性pi值
- genomic_pi_table_SETH.tsv：基于设置H（无-B过滤、QUAL30、MinDP10、同时过滤双位点与单位点）运行JeDi流水线得到的群体核苷酸多样性pi值
5. 基于SNP数据集的遗传估计值群体汇总：包含观测杂合度（Ho，observed heterozygosity）、期望杂合度（He，expected heterozygosity）、私有等位基因相关指标，其中private.alleles.dartr.one2rest指按dartr.one2rest规则计算的各群体私有等位基因数，PA指包含与排除3个样本量异常种群后的各群体私有等位基因数量。