Data from: Using genomic tools to maintain diversity and fitness in conservation programmes

de Cara MAR, Villanueva B, Toro MA, Fernández J

Date Published: October 14, 2013

DOI: http://dx.doi.org/10.5061/dryad.8654d

 

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Title Codes and data for "Using genomic tools to maintain diversity and fitness in conservation programmes"
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Description Files included in file DryaData.tar.gz : BigPopMSD.f90, genotiposCGD.dat, OCgen_ranmat.f90, OCroh_ranmat.f90, DistFreqsSeg_overReps.f90, genotiposMukai.dat, OCmol_ranmat.f90. Genotype data: genotiposCGD.dat and genotiposMukai.dat are obtained after 10000 generations of mutation-selection-drift with BigPopMSD.f90 for the CGD and the Mukai scenarios, respectively. Population size is kept constant at 1000 diploid individuals (500 females and 500 males), and the genome is assumed to have 20 chromosomes of 1 Morgan each. Every chromosome includes 2000 neutral loci, 1000 selected loci and 1000 marker loci, all of them biallelic. For the CGD scenario, the parameters used are lambda is 0.03, beta is 2.3, mean s is 0.264, and mean h is 0.2. For the Mukai scenario, the parameters used are lambda equals 0.5, beta 1, mean s is 0.05, and mean h equals 0.3. BigPopMSD.f90 generates the base population. OCgen_ranmat.f90 performs 10 generations of optimal contributions for population management with random matings between the individuals who contribute. Contributions are calculated to optimise genealogical coancestry, which is calculated assuming the founder individuals are unrelated. The number of replicates is 100, but can be varied, as well as the population size during management. OCmol_ranmat.f90 performs 10 generations of optimal contributions for population management with random matings between the individuals who contribute. Contributions are calculated to optimise molecular coancestry, calculated as identity by state (see Toro et al 2002, Conservation Genetics). The number of replicates is 100, but can be varied, as well as the population size during management. OCroh_ranmat.f90 performs 10 generations of optimal contributions for population management with random matings between the individuals who contribute. Contributions are calculated to optimise IBD-based coancestry, calculated as the proportion of the genome that is identical by descent between individuals. It is calculated by looking only at marker loci, and it requires a minimum length of a segment for it to be considered identical by descent. The number of replicates is 100, but can be varied, as well as the population size during management. DistFreqsSeg_overReps.f90 analyses replicates from the base population to calculate the average number of markers segregating and the average number of runs of homozygosity in the base population. Note that the codes sometimes assume reading from a file not in the same directory. OC...f90 all read from file ../genotipos_1.dat but that can be easily changed to whichever genotypes you want to read. Should you have any issues, contact angeles.decara AT gmail
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When using this data, please cite the original publication:

de Cara MAR, Villanueva B, Toro MA, Fernández J (2013) Using genomic tools to maintain diversity and fitness in conservation programmes. Molecular Ecology 22(24): 6091–6099. http://dx.doi.org/10.1111/mec.12560

Additionally, please cite the Dryad data package:

de Cara MAR, Villanueva B, Toro MA, Fernández J (2013) Data from: Using genomic tools to maintain diversity and fitness in conservation programmes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8654d
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