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 data

2_ParentageAnalysis_COLONY.zip - Parentage Analysis using COLONY2 software

3_Kinship_Inbreeding_COANCESTRY.zip - Calculation of kinship and inbreeding using COANCESTRY software

4_MSI_PMx.zip - Tranformation of kinship to Mate Suitability Index (MSI) using PMx software

5_Kinship_ActualPairs.zip - Identification of kinship for actual pairs

5_MSI_ActualPairs.zip - Identification of MSI for actual pairs

6_Kinship_BestPairs.zip - Simulation of the kinship of best pairs

6_MSI_BestPairs.zip - Simulation of the MSI of best pairs

7_MSI_RandomPairs.zip - Simulation of the MSI of random pairs

8_MSI_IdealPairs.zip - Simulation of the MSI of best ideal

9_MSI_Management1Pairs.zip - Simulation of the MSI of management pairs

10_Kinship_FinalComparison.zip - Statistical analysis comparing kinship

10_MSI_FinalComparison.zip - Statistical analysis comparing MSI

11_PCA.zip - Principal Coordinates Analysis

12_MSI_Management2Pairs.zip - Simulation of the MSI of management 2 pairs