Metapopulation genetic management of the Macquarie perch

This repository contains data and R script script used in the manuscript<br><b>A 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. </b><b><i>Molecular Ecology</i></b><b> MEC-24-1090.R1, accepted pending minor revision.</b><br>The content of this data repository:<br><b><i>MaccaGM_SNPs.R</i></b> –– R script for analyses of DArT SNP genotypic data and plotting the results of analyses of JeDi pipeline<br>Input files for MaccaGM_SNPs.R:<br><b><i>Report_DMacq23-8576_14_moreOrders_SNP_mapping_1.csv</i></b> –– DArT genotypes in original format<b><i>Covariate_MaccaGM_recaller25inds_then_max50per_pop.csv</i></b> –– covariate file for individuals<b>Unbiased genetic diversity: </b><b>outputs of </b><b><i>JeDi</i></b><b> pipeline</b><b> </b>Estimates of unbiased heterozygosity (piawka_uHe) resulting from <i>JeDi</i> 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 <i>JeDi </i>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).<b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP10_SETA.csv</i></b> –– Output of SetA: Piawka run with Settings: no (-B), QUAL30, MinDP10, No doubleton filter<b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual30_minDP10_SETB.csv</i></b> –– Output of SetB: Piawka run with Settings: (-B), QUAL30, MinDP10, No doubleton filter<b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual40_minDP10_SETC.csv</i></b> –– Output of SetC: Piawka run with Settings: (-B), QUAL40, MinDP10, No doubleton filter<b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual30_minDP12_setD.csv</i></b> –– Output of SetD: Piawka run with Settings: (-B), QUAL30, MinDP12, No doubleton filter<b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual30_minDP10_doubleton_SETE.csv</i></b>–– Output of SetE: Piawka run with Settings: (-B), QUAL30, MinDP10, doubleton filter<b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual50_minDP15_SETF.csv</i></b>–– Output of SetF: Piawka run with Settings : (-B), QUAL50, MinDP15, No doubleton filter<b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP10_doub_SETG.csv</i></b>–– Output of SetG: Piawka run with Settings: No (-B), QUAL30, MinDP10, doubleton filter<b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP10_doub_sing_SETH.csv</i></b>–– Output of SetH: Piawka run with Settings: No (-B), QUAL30, MinDP10, doubleton and singleton filter<b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP15_doub_sing_SETI.csv</i></b>–– Output of SetI: Piawka run with Settings: No (-B), QUAL30, MinDP15, doubleton and singleton filterEstimates of population nucleotide diversity (pi): outputs of <i>JeDi</i> pipeline run under three settings:<b>genomic_pi_table_SETA.tsv</b>—pi from JeDi pipeline run under Settings A: no (-B), QUAL30, MinDP10, No doubleton filter<b>genomic_pi_table SETG.tsv</b>—pi from JeDi pipeline run under Settings G: No (-B), QUAL30, MinDP10, doubleton filter<b>genomic_pi_table - SETH.tsv</b>—pi from JeDi pipeline run under Settings H: No (-B), QUAL30, MinDP10, doubleton and singleton filterPopulation summaries of the genetic estimates from SNP dataset (<i>Ho</i>- observed heterozygosity, <i>He</i>-expected heterozygosity, <i>private.alleles.dartr.one2rest</i> and <i>PA</i>- number of private alleles per population including and excluding three with sample size &lt;13, <i>Mean_Allelic_Richness</i>- allelic richness, <i>Ne</i>- effective population size estimated by LDNe) and sequencing dataset (<i>pi_SetI</i> and <i>pi_SetH</i>- nucleotide diversity estimated with settings I and H, <i>mean_uHe_SetI</i> and <i>mean_uHe_SetH</i>- mean unbiased heterozygosity estimated with setting I and H, respectively):<b><i>Pop.genetic.div.estimates.csv</i></b>––collated population outputs of the script <b><i>MaccaGM_SNPs.R</i></b> and <i>JeDi</i> pipeline<br><b>Metapop2 files:</b><b>Metapop_res.csv</b> –– results of the Metapop2 analyses to create a new population (Fig. 4 of the manuscript)<b>Metapop2_24sims.zip</b>––input and output files for 24 realistic simulations (Table 3 of the main manuscript).<br><b>SRA_PRJNA1242510_accession_numbers.txt</b>––GenBank SRA accession numbers for DArT sequences<br>Appendices for the manuscript:<b>Pavlova_etal_AppendixA_Genetic_augmentations.xlsx</b>–– Genetic augmentation of Macquarie perch via translocations and stocking conducted from 2010 onwards.<b>Pavlova_et_al_AppendixB_JeDi_pipeline_revised.png</b>–– Schematic representation of revised <i>JeDi</i> pipeline for estimating unbiased individual heterozygosity and population nucleotide diversity from reduced-representation sequencing data, in presence of reference genome.<b>Pavlova_et_al_MEC_Supplemental_Information_revised.docx</b>––Supplementary Information for the revised version of the main manuscript: <i>S1.</i> Additional tables and figures, <i>S2.</i> Details and optimization of the <i>JeDi </i>pipeline.<br>We acknowledge the First Nations throughout Australia, recognise their continuing connection to land, waters and culture, and pay our respects to their Elders past, present and emerging. This research was conducted on Ngarigo, Ngambri and Ngunnawal, Taungurung, Wirajuri and Wurundjeri Woi-wurrung Countries.<br>

本仓库包含用于以下手稿的数据及R脚本：<br><b>《转向集合种群遗传管理（metapopulation genetic management）以促进受生境破碎化（fragmentation）威胁物种的存续——以澳大利亚濒危淡水鱼类为例》，作者：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。</b><b><i>分子生态学（Molecular Ecology）</i></b><b>，稿件编号MEC-24-1090.R1，已接收待 minor revision。</b><br>本数据仓库内容如下：<br><b><i>MaccaGM_SNPs.R</i></b>——用于分析DArT SNP基因型数据及绘制JeDi流程（JeDi pipeline）分析结果的R脚本<br>MaccaGM_SNPs.R的输入文件：<br><b><i>Report_DMacq23-8576_14_moreOrders_SNP_mapping_1.csv</i></b>——原始格式的DArT基因型文件<br><b><i>Covariate_MaccaGM_recaller25inds_then_max50per_pop.csv</i></b>——个体协变量文件<br><b>无偏遗传多样性（Unbiased genetic diversity）：</b><b>JeDi流程（JeDi pipeline）的输出</b> 基于JeDi流程对所有位点、双等位基因位点及三/四等位基因位点的分析结果，得到无偏杂合度（unbiased heterozygosity，piawka_uHe）的估计值。分析采用9种不同设置（A-I）。JeDi流程得到的个体无偏杂合度估计值被附加至个体协变量文件中，同时包含SNP数据集的分析结果（SNP杂合度、PHt及STRUCTURE聚类成员身份（STRUCTURE clusters，X1of15至X15of15））。<br><b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP10_SETA.csv</i></b>——SetA的输出：Piawka运行设置为无(-B)、QUAL30、MinDP10、无doubleton过滤<br><b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual30_minDP10_SETB.csv</i></b>——SetB的输出：Piawka运行设置为(-B)、QUAL30、MinDP10、无doubleton过滤<br><b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual40_minDP10_SETC.csv</i></b>——SetC的输出：Piawka运行设置为(-B)、QUAL40、MinDP10、无doubleton过滤<br><b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual30_minDP12_setD.csv</i></b>——SetD的输出：Piawka运行设置为(-B)、QUAL30、MinDP12、无doubleton过滤<br><b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual30_minDP10_doubleton_SETE.csv</i></b>——SetE的输出：Piawka运行设置为(-B)、QUAL30、MinDP10、doubleton过滤<br><b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.B_qual50_minDP15_SETF.csv</i></b>——SetF的输出：Piawka运行设置为(-B)、QUAL50、MinDP15、无doubleton过滤<br><b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP10_doub_SETG.csv</i></b>——SetG的输出：Piawka运行设置为无(-B)、QUAL30、MinDP10、doubleton过滤<br><b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP10_doub_sing_SETH.csv</i></b>——SetH的输出：Piawka运行设置为无(-B)、QUAL30、MinDP10、doubleton及singleton过滤<br><b><i>ind.gen.div_nonaPHt_noNAuHe.with.PHt.residuals.noB_qual30_minDP15_doub_sing_SETI.csv</i></b>——SetI的输出：Piawka运行设置为无(-B)、QUAL30、MinDP15、doubleton及singleton过滤<br>种群核苷酸多样性（nucleotide diversity，pi）的估计：JeDi流程在三种设置下的输出：<br><b>genomic_pi_table_SETA.tsv</b>——JeDi流程在设置A（无(-B)、QUAL30、MinDP10、无doubleton过滤）下运行得到的pi值<br><b>genomic_pi_table SETG.tsv</b>——JeDi流程在设置G（无(-B)、QUAL30、MinDP10、doubleton过滤）下运行得到的pi值<br><b>genomic_pi_table - SETH.tsv</b>——JeDi流程在设置H（无(-B)、QUAL30、MinDP10、doubleton及singleton过滤）下运行得到的pi值<br>SNP数据集及测序数据集遗传估计的种群汇总（SNP数据集：<i>Ho</i>—观测杂合度（observed heterozygosity）、<i>He</i>—期望杂合度（expected heterozygosity）、<i>private.alleles.dartr.one2rest</i>及<i>PA</i>—包含/排除样本量<13的三个种群后的每种群私有等位基因数、<i>Mean_Allelic_Richness</i>—等位基因丰富度（allelic richness）、<i>Ne</i>—通过LDNe估计的有效种群大小（effective population size）；测序数据集：<i>pi_SetI</i>及<i>pi_SetH</i>—设置I和H下估计的核苷酸多样性、<i>mean_uHe_SetI</i>及<i>mean_uHe_SetH</i>—分别在设置I和H下估计的平均无偏杂合度）：<br><b><i>Pop.genetic.div.estimates.csv</i></b>——脚本<b><i>MaccaGM_SNPs.R</i></b>及JeDi流程的种群输出汇总文件<br><b>Metapop2文件：</b><br><b>Metapop_res.csv</b>——创建新种群的Metapop2分析结果（手稿图4）<br><b>Metapop2_24sims.zip</b>——24次真实模拟的输入及输出文件（主手稿表3）<br><b>SRA_PRJNA1242510_accession_numbers.txt</b>——DArT序列的GenBank SRA登录号<br>手稿附录：<br><b>Pavlova_etal_AppendixA_Genetic_augmentations.xlsx</b>——2010年以来通过 translocation 和 stocking 进行的麦夸里鲈遗传增强（genetic augmentation）<br><b>Pavlova_et_al_AppendixB_JeDi_pipeline_revised.png</b>——修订后的JeDi流程示意图，用于在有参考基因组的情况下，从简化基因组测序数据中估计个体无偏杂合度及种群核苷酸多样性<br><b>Pavlova_et_al_MEC_Supplemental_Information_revised.docx</b>——主手稿修订版的补充信息：<i>S1.</i> 附加表格及图表；<i>S2.</i> JeDi流程的细节及优化<br>我们感谢澳大利亚各地的原住民部落（First Nations），认可他们与土地、水域及文化的持续联系，并向其过往、当下及未来的长者致以敬意。本研究在Ngarigo、Ngambri与Ngunnawal、Taungurung、Wirajuri及Wurundjeri Woi-wurrung领地开展。