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

Supporting data for the manuscript:<br> Robledo-Ruiz, D. A., Pavlova, A., Clarke, R. H., Magrath, M. J. L., Quin, B., Harrisson, K. A., Gan, H. M., Low, G. W., &amp; Sunnucks, P. (2021). <b>A novel framework for evaluating <i>in situ </i>breeding management strategies in endangered populations</b>. <i>Molecular Ecology Resources</i>.<br>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 <br><br>Each zipped folder contains the data files and scripts used for the steps in the analysis:<br><br>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"<br>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<br><b></b>