Data from: Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear.

Skrbinšek T, Jelenčič M, Waits LP, Potočnik H, Trontelj P

Date Published: July 6, 2012

DOI: http://dx.doi.org/10.5061/dryad.qt3j5

 

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Title Brown bear genotypes from Slovenia (Northern Dinaric Mountains) - tab delimited txt
Downloaded 67 times
Description The dataset contains genotypes of 513 brown bears genotyped on 20 microsatellite loci. They were obtained by genotyping tissue samples of legally killed bears between 2003 and 2008. The genotypes are mostly complete, there are missing data on a single locus in two samples (denoted "NA"). | Columns in the table: | sample - laboratory name of the sample | sex - sex of the animal (recorded by the field crew and rechecked by genotyping the SRY marker) | Genotypes: alleles at each locus are recorded in two columns, e.g. Cxx20_1, Cxx20_2. Missing data are recorded as "NA". | Note: this dataset mostly corresponds to the dataset used in the manuscript: Skrbinšek T, Jelenčič M, Waits L, Kos I, Jerina K, Trontelj P (2012). Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches. Molecular Ecology 21(4): 862-875. Data: doi:10.5061/dryad.22rm1728. This present dataset doesn't have age data for the animals, but includes genotypes of three additional individuals for which we had no age data available.
Download Slovenia_Bear_Genotypes.txt (82.70 Kb)
Download README.txt (3.973 Kb)
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Title Brown bear genotypes from Slovenia (Northern Dinaric Mountains) - MS Excel
Downloaded 90 times
Description The dataset contains genotypes of 513 brown bears genotyped on 20 microsatellite loci. They were obtained by genotyping tissue samples of legally killed bears between 2003 and 2008. The genotypes are mostly complete, there are missing data on a single locus in two samples (denoted "NA"). | Columns in the table: | sample - laboratory name of the sample | sex - sex of the animal (recorded by the field crew and rechecked by genotyping the SRY marker) | Genotypes: alleles at each locus are recorded in two columns, e.g. Cxx20_1, Cxx20_2. Missing data are recorded as "NA". | Note: this dataset mostly corresponds to the dataset used in the manuscript: Skrbinšek T, Jelenčič M, Waits L, Kos I, Jerina K, Trontelj P (2012). Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches. Molecular Ecology 21(4): 862-875. Data: doi:10.5061/dryad.22rm1728. This present dataset doesn't have age data for the animals, but includes genotypes of three additional individuals for which we had no age data available.
Download Slovenia_Bear_Genotypes.xlsx (113.0 Kb)
Download README.txt (3.927 Kb)
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Title R package "resamplediversity" containing genotypes of brown bears from Dinaric Mountains and all functions required to use the reference population approach.
Downloaded 81 times
Description This is an R package containing all data and functions for running analyses presented in the manuscript. You will need R (www.r-project.org). You will need to install adegenet package (command: install.packages("adegenet")), and then this downloaded file (command: install.packages(file.choose(),repos=NULL)). Select resamplediversity_1.0.zip when the "File" dialog pops up. When the package is installed, invoke it from within R with library(resamplediversity). There is a user-friendly vignette: vignette("resamplediversity").
Download resamplediversity_1.0.zip (318.3 Kb)
Download README.txt (3.973 Kb)
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Title Vignette for "resamplediversity" package.
Downloaded 86 times
Description User friendly, hands-on, example based tutorial to the data and functions provided in resamplediversity package. Includes a walk-through through the analyses presented in the manuscript.
Download resamplediversity-vignette.pdf (292.0 Kb)
Download README.txt (3.927 Kb)
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When using this data, please cite the original publication:

Skrbinšek T, Jelenčič M, Waits LP, Potočnik H, Trontelj P (2012) Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear. Heredity 109: 299-305. http://dx.doi.org/10.1038/hdy.2012.42

Additionally, please cite the Dryad data package:

Skrbinšek T, Jelenčič M, Waits LP, Potočnik H, Trontelj P (2012) Data from: Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.qt3j5
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