Metapopulation genetic management of the Macquarie perch

<p dir="ltr">This repository contains data and R script script used in the manuscript</p><p><br></p><p dir="ltr"><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></p><p><br></p><p dir="ltr">The content of this data repository:</p><p><br></p><p dir="ltr"><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</p><p><br></p><p dir="ltr">Input files for MaccaGM_SNPs.R:</p><p><br></p><p dir="ltr"><b><i>Report_DMacq23-8576_14_moreOrders_SNP_mapping_1.csv</i></b> –– DArT genotypes in original format</p><p dir="ltr"><b><i>Covariate_MaccaGM_recaller25inds_then_max50per_pop.csv</i></b> –– covariate file for individuals</p><p dir="ltr"><b>Unbiased genetic diversity: </b><b>outputs of </b><a href="https://github.com/drobledoruiz/JeDi" rel="noreferrer" target="_blank"><b><i><u>JeDi</u></i></b><b><u> pipeline</u></b></a><b> </b></p><p dir="ltr">Estimates of unbiased heterozygosity (piawka_uHe) resulting from <a href="https://github.com/drobledoruiz/JeDi" rel="noreferrer" target="_blank"><i><u>JeDi</u></i><u> pipeline</u></a> 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).</p><p dir="ltr"><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</p><p dir="ltr"><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</p><p dir="ltr"><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</p><p dir="ltr"><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</p><p dir="ltr"><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</p><p dir="ltr"><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</p><p dir="ltr"><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</p><p dir="ltr"><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</p><p dir="ltr"><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 filter</p><p dir="ltr">Estimates of population nucleotide diversity (pi): outputs of <a href="https://github.com/drobledoruiz/JeDi" rel="noreferrer" target="_blank"><i><u>JeDi</u></i><u> pipeline</u></a> run under three settings:</p><p dir="ltr"><b>genomic_pi_table_SETA.tsv</b>—pi from JeDi pipeline run under Settings A: no (-B), QUAL30, MinDP10, No doubleton filter</p><p dir="ltr"><b>genomic_pi_table SETG.tsv</b>—pi from JeDi pipeline run under Settings G: No (-B), QUAL30, MinDP10, doubleton filter</p><p dir="ltr"><b>genomic_pi_table - SETH.tsv</b>—pi from JeDi pipeline run under Settings H: No (-B), QUAL30, MinDP10, doubleton and singleton filter</p><p dir="ltr">Population 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 <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):</p><p dir="ltr"><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</p><p dir="ltr"><br></p><p dir="ltr"><b>Metapop2 files:</b></p><p dir="ltr"><b>Metapop_res.csv</b> –– results of the Metapop2 analyses to create a new population (Fig. 4 of the manuscript)</p><p dir="ltr"><b>Metapop2_24sims.zip</b>––input and output files for 24 realistic simulations (Table 3 of the main manuscript).</p><p dir="ltr"><br></p><p dir="ltr"><b>SRA_PRJNA1242510_accession_numbers.txt</b>––GenBank SRA accession numbers for DArT sequences</p><p dir="ltr"><br></p><p dir="ltr">Appendices for the manuscript:</p><p dir="ltr"><b>Pavlova_etal_AppendixA_Genetic_augmentations.xlsx</b>–– Genetic augmentation of Macquarie perch via translocations and stocking conducted from 2010 onwards.</p><p dir="ltr"><b>Pavlova_et_al_AppendixB_JeDi_pipeline_revised.png</b>–– Schematic representation of revised <a href="https://github.com/drobledoruiz/JeDi" rel="noreferrer" target="_blank"><i>JeDi</i> pipeline</a> for estimating unbiased individual heterozygosity and population nucleotide diversity from reduced-representation sequencing data, in presence of reference genome.</p><p dir="ltr"><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.</p><p dir="ltr"><br></p><p dir="ltr">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.</p><p dir="ltr"><br></p>