Data

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

Monash University
Alexandra Pavlova (Aggregated by) Diana Robledo Ruiz (Aggregated by) Paul Sunnucks (Aggregated by)
Viewed: [[ro.stat.viewed]] Cited: [[ro.stat.cited]] Accessed: [[ro.stat.accessed]]
ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.26180/13193465&rft.title=Robledo-Ruiz et al. 2021 Molecular Ecology Resources (Supporting data)&rft.identifier=https://doi.org/10.26180/13193465&rft.publisher=Monash University&rft.description=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.vcf1_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&rft.creator=Alexandra Pavlova&rft.creator=Diana Robledo Ruiz&rft.creator=Paul Sunnucks&rft.date=2022&rft_rights=CC-BY-4.0&rft_subject=genetic management&rft_subject=inbreeding&rft_subject=inbreeding avoidance&rft_subject=kinship&rft_subject=Mate Suitability Index&rft_subject=PMx&rft_subject=helmeted honeyeater&rft_subject=RDSI&rft_subject=ARDC Data Retention Project&rft_subject=Population, Ecological and Evolutionary Genetics&rft.type=dataset&rft.language=English Access the data
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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_Kinship_RandomPairs.zip - Simulation of the kinship of random pairs
7_MSI_RandomPairs.zip - Simulation of the MSI of random pairs
8_Kinship_IdealPairs.zip - Simulation of the kinship of ideal pairs
8_MSI_IdealPairs.zip - Simulation of the MSI of best ideal
9_Kinship_Management1Pairs.zip - Simulation of the kinship of management pairs
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_Kinship_Management2Pairs.zip - Simulation of the kinship of management 2 pairs
12_MSI_Management2Pairs.zip - Simulation of the MSI of management 2 pairs

Issued: 2021-05-27

Created: 2021-10-15

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Subjects
ARDC Data Retention Project | Mate Suitability Index | PMx | Population, Ecological and Evolutionary Genetics | RDSI | genetic management | helmeted honeyeater | inbreeding | inbreeding avoidance | kinship |

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Identifiers
ACN 633 798 857