Data from: Estimating relatedness and inbreeding using molecular markers and pedigrees: the effect of demographic history

 

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Title file 1 - x0 data for MasterBayes
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Description Microsatellite genotypes observed in the experimental control population formatted for the MasterBayes package in R. This file must be in the working directory of R for many of the simulations below to run. Markers are named using internal lab id numbers, see accompanying file for how these relate to locus names.
Download file 1 - x0 data for MasterBayes.txt (24.93 Kb)
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Title file 2 - x1 data for MasterBayes
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Download file 2 - x1 data for MasterBayes.txt (24.13 Kb)
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Title file 3 - x5 data for MasterBayes
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Download file 3 - x5 data for MasterBayes.txt (25.38 Kb)
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Title file 4 - x0 data for MasterBayes null alleles removed
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Description Microsatellite genotypes observed in the experimental control population formatted for the MasterBayes package in R with loci indicated by MICRO-CHECKER as containing null alleles removed. Markers are named using internal lab id numbers, see accompanying file (Microsatellite list) for how these relate to locus names.
Download file 4 - x0 data for MasterBayes null all...ed.txt (18.17 Kb)
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Title file 5 - x1 data for MasterBayes null alleles removed
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Description Microsatellite genotypes observed in the experimental N = 10 x 1 population formatted for the MasterBayes package in R with loci indicated by MICRO-CHECKER as containing null alleles removed. Markers are named using internal lab id numbers, see accompanying file (Microsatellite list) for how these relate to locus names.
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Download file 5 - x1 data for MasterBayes null all...ed.txt (15.30 Kb)
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Title file 6 - x5 data for MasterBayes null alleles reomoved
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Description Microsatellite genotypes observed in the experimental N = 10 x 5 population formatted for the MasterBayes package in R with loci indicated by MICRO-CHECKER as containing null alleles removed. Markers are named using internal lab id numbers, see accompanying file (Microsatellite list) for how these relate to locus names.
Download file 6 - x5 data for MasterBayes null all...ed.txt (18.28 Kb)
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Title file 7 - Microsatellite list
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Description List of internal lab id numbers used to label loci in accompanying files along with locus names and genetic locations.
Download file 7 - Microsatellite list.xlsx (56.36 Kb)
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Title file 8 - R code for simulations based on allele frequencies in experimental populations
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Description This code runs simulations based on observed allele frequencies in experimental populations. This method does not take linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates. Instructions on the first line detail how to change the input for the desired population. This code links to the following files, which must be in the working directory: files 1 - 3, and file 23 - 25.
Download file 8 - R code for simulations based on al...ns.R (6.758 Kb)
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Title file 9 - R code for simulations based on allele frequencies in experimental populations (linkage taken into account)
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Download file 9 - R code for simulations based on al...t).R (8.492 Kb)
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Title file 10 - R code for simulated bottleneck in the N=10 x1 population
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Description This code runs a simulation of the bottleneck and subsequent pedigree used for the N=10 x1 population. Once the bottleneck is simulated, only the allele frequencies are used to generate the subsequent pedigree so variance in individual IBD generated during the bottleneck is not retained. This method takes linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates as well as number of alleles per locus. This code links to the following files, which must be in the working directory: files 16 – 17 and files 23 – 27.
Download file 10 - R code for simulated bottleneck in the N (13.39 Kb)
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Title file 11 - R code for simulated bottleneck in the N=10 x5 population
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Description This code runs a simulation of the bottleneck and subsequent pedigree used for the N=10 x5 population. Once the bottleneck is simulated, only the allele frequencies are used to generate the subsequent pedigree so variance in individual IBD generated during the bottleneck is not retained. This method takes linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates as well as number of alleles per locus. This code links to the following files, which must be in the working directory: files 16 – 17, files 23 – 26 and file 28.
Download file 11 - R code for simulated bottleneck in the N (14.40 Kb)
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Title file 12 - R code for simulated bottleneck in the N=10 x1 population with variance in individual IBD retained
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Description This code runs a simulation of the bottleneck and subsequent pedigree used for the N=10 x1 population. Variance in individual IBD generated during the bottleneck retained through the pedigree. This method takes linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates as well as number of alleles per locus. This code links to the following files, which must be in the working directory: files 16 – 17 and files 24 – 27.
Download file 12 - R code for simulated bottleneck in the N (10.27 Kb)
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Title file 13 - R code for simulated bottleneck in the N=10 x5 population with variance in individual IBD retained
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Description This code runs a simulation of the bottleneck and subsequent pedigree used for the N=10 x5 population. Variance in individual IBD generated during the bottleneck retained through the pedigree. This method takes linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates as well as number of alleles per locus. This code links to the following files, which must be in the working directory: files 16 – 17, files 24 – 26 and file 28.
Download file 13 - R code for simulated bottleneck in the N (11.12 Kb)
Download README (6.235 Kb)
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Title file 14 - R code for simulations with null alleles introduced to all loci with frequency = 0.05
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Description This code runs simulations based on observed allele frequencies in the control population but with null alleles artificially introduced to all loci at a frequency of 0.05. This method does not take linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates. This code links to the following files, which must be in the working directory: files 22 – 25.
Download file 14 - R code for simulations with null...ency (6.235 Kb)
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Title file 15 - R code for simulations with null alleles introduced to three loci or three loci removed
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Description This code runs simulations based on observed allele frequencies in the control population but with null alleles artificially introduced to three randomly selected loci at a frequency of 0.05 or these same three loci removed from the data set. This method does not take linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates. This code links to the following files, which must be in the working directory: file 1 and files 22 – 25.
Download file 15 - R code for simulations with null ...ed.R (12.16 Kb)
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Title file 16 - x0 data for MasterBayes cr2 only
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Description Microsatellite genotypes for markers residing on chromosome two observed in the experimental control population formatted for the MasterBayes package in R. This file must be in the working directory of R for many of the simulations above to run.
Download file 16 - x0 data for MasterBayes cr2 only.txt (16.16 Kb)
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Title file 17 - x0 data for MasterBayes cr3 only
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Description Microsatellite genotypes for markers residing on chromosome three observed in the experimental control population formatted for the MasterBayes package in R. This file must be in the working directory of R for many of the simulations above to run.
Download file 17 - x0 data for MasterBayes cr3 only.txt (10.85 Kb)
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Title file 18 - x1 data for MasterBayes cr2 only
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Description Microsatellite genotypes for markers residing on chromosome two observed in the experimental N = 10 x 1 population formatted for the MasterBayes package in R. This file must be in the working directory of R for many of the simulations above to run.
Download file 18 - x1 data for MasterBayes cr2 only.txt (15.48 Kb)
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Title file 19 - x1 data for MasterBayes cr3 only
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Description Microsatellite genotypes for markers residing on chromosome three observed in the experimental N = 10 x 1 population formatted for the MasterBayes package in R. This file must be in the working directory of R for many of the simulations above to run.
Download file 19 - x1 data for MasterBayes cr3 only.txt (10.44 Kb)
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Title file 20 - x5 data for MasterBayes cr2 only
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Description Microsatellite genotypes for markers residing on chromosome two observed in the experimental N = 10 x 5 population formatted for the MasterBayes package in R. This file must be in the working directory of R for many of the simulations above to run.
Download file 20 - x5 data for MasterBayes cr2 only.txt (16.45 Kb)
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Title file 21 - x5 data for MasterBayes cr3 only
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Description Microsatellite genotypes for markers residing on chromosome three observed in the experimental N = 10 x 5 population formatted for the MasterBayes package in R. This file must be in the working directory of R for many of the simulations above to run.
Download file 21 - x5 data for MasterBayes cr3 only.txt (11.11 Kb)
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Title file 22 - x0 data for MasterBayes 5percent nulls
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Description Microsatellite genotypes observed in the experimental control population formatted for the MasterBayes package in R with null alleles artificially encoded at a frequency of 0.05. This file must be in the working directory of R for many of the simulations above to run.
Download file 22 - x0 data for MasterBayes 5percen...ls.txt (25.66 Kb)
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Title file 23 - pedigree
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Description Pedigree, formatted for the pedantics package in R, which is the same as that which was used to generate individuals of varying inbreeding and relatedness in our experimental populations. This file must be in the working directory of R for many of the simulations above to run.
Download file 23 - pedigree.txt (4.956 Kb)
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Title file 24 - pedigree relatedness
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Description List of pairwise coefficient of relatedness between possible combination of final generation individuals in the pedigree. This file must be in the working directory of R for many of the simulations above to run.
Download file 24 - pedigree relatedness.txt (162.5 Kb)
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Title file 25 - expected_f
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Description List of inbreeding coefficients for each final generation individual in the pedigree.
Download file 25 - expected_f.txt (726 bytes)
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Title file 26 - pedigree for founder simulation
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Description Pedigree used in simulation of bottlenecks.
Download file 26 - pedigree for founder simulation.txt (3.701 Kb)
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Title file 27 - bottleneck pedigree for x1 founder simulation
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Description Pedigree needed as part of simulate the n = 10 x 1 bottleneck while maintaining variance in individual IBD.
Download file 27 - bottleneck pedigree for x1 foun...on.txt (131 bytes)
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Title file 28 - bottleneck pedigree for x5 founder simulation
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Description Pedigree needed as part of simulate the n = 10 x 5 bottleneck while maintaining variance in individual IBD.
Download file 28 - bottleneck pedigree for x5 foun...on.txt (713 bytes)
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Title list of file names and descriptions
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Download list of file names and descriptions.txt (10.30 Kb)
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When using this data, please cite the original publication:

Robinson SP, Simmons LW, Kennington WJ (2013) Estimating relatedness and inbreeding using molecular markers and pedigrees: the effect of demographic history. Molecular Ecology 22(23): 5779–5792. http://dx.doi.org/10.1111/mec.12529

Additionally, please cite the Dryad data package:

Robinson SP, Simmons LW, Kennington WJ (2013) Data from: Estimating relatedness and inbreeding using molecular markers and pedigrees: the effect of demographic history. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.060b1
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