Data from: The impacts of inbreeding, drift, and selection on genetic diversity in captive breeding populations

Willoughby JR, Fernandez NB, Lamb MC, Ivy JA, Lacy RC, DeWoody JA

Date Published: November 26, 2014

DOI: http://dx.doi.org/10.5061/dryad.8q153

 

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Title pedigree data for 6 captive populations
Downloaded 23 times
Description Tab delimited file containing pedigree information for 6 populations, bred at the Brookfield Zoo in Chicago, Illinois. Populations are listed under 'Treatment' and 'WildCaught' individuals were progenitors of all populations. Other columns include: ID-unique ID numbers; SEX-m=male, f=female; F-inbreeding coefficient; GEN-generation; DAM-dam of individual; SIRE-sire of individual; GNAW-time spent gnawing; FLIP-time spent flipping.
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Title microsatellite genotypes for 6 captive populations
Downloaded 15 times
Description Tab delimited file containing microsatellite genotypes for 11 loci. Column labels include: SampleID-unique sample ID, Pop-label for each of 6 populations plus original 20 founders for all populations, Gen-generation the samples were taken from, followed by 22 locus specific columns. Each locus is given in two columns (labeled A and B) to display both alleles for each individual.
Download msattgenotypes.txt (28.66 Kb)
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Title dloop sequences from captive population
Downloaded 10 times
Description FASTA file containing 9 haplotypes identified.
Download dloopPleucopusFINAl.TXT (4.246 Kb)
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Title simulations
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Description Code, inputfiles, and output files from simulation of mean kinship, random mating, and selecting for docility in captive populations. Code (simulations.R) was written for R, and has a number of package dependencies listed at the top. Also required to run the code are the input cdv files: Weanded.csv lists number of individuals weaned in each population, founders.csv contains microsatellite genotypes for the populations founders, and mtDNA.csv contains the dloop haplotypes for each founder. Docility.txt, MeanKinship.txt, MKplus.txt, and RandomMating.txt are all output files from running the simulation code.
Download simulations.zip (227.6 Kb)
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When using this data, please cite the original publication:

Willoughby JR, Fernandez NB, Lamb MC, Ivy JA, Lacy RC, DeWoody JA (2015) The impacts of inbreeding, drift, and selection on genetic diversity in captive breeding populations. Molecular Ecology 5(1): 98-110. http://dx.doi.org/10.1111/mec.13020

Additionally, please cite the Dryad data package:

Willoughby JR, Fernandez NB, Lamb MC, Ivy JA, Lacy RC, DeWoody JA (2014) Data from: The impacts of inbreeding, drift, and selection on genetic diversity in captive breeding populations. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8q153
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