DOI: 10.5061/dryad.8q153
title: Data from: The impacts of inbreeding, drift, and selection on genetic diversity in captive breeding populations

description: The goal of captive breeding programs is often to maintain genetic
 diversity until reintroductions can occur. However, due in part to changes
 that occur in captive populations, approximately one-third of
 reintroductions fail. We evaluated genetic changes in captive populations
 using microsatellites and mtDNA. We analyzed six populations of
 white-footed mice that were propagated for 20 generations using two
 replicates of three protocols: random mating (RAN), minimizing mean
 kinship (MK), and selection for docility (DOC). We found that MK resulted
 in the slowest loss of microsatellite genetic diversity compared to RAN
 and DOC. However, the loss of mtDNA haplotypes was not consistent among
 replicate lines. We compared our empirical data to simulated data and
 found no evidence of selection in the MK lines although some evidence of
 selection in the RAN lines was present. Our results suggest that although
 the effects of drift may not be fully mitigated, MK reduces the loss of
 alleles due to inbreeding more effectively than random mating or docility
 selection. Therefore, MK should be preferred for captive breeding.
 Furthermore, our simulations show that incorporating microsatellite data
 into the MK framework reduced the magnitude of drift, which may have
 applications in long-term or extremely genetically depauperate captive
 populations.
description: pedigree data for 6
 captive populationsTab 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.pedigree.txtmicrosatellite genotypes for 6 captive populationsTab 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.msattgenotypes.txtdloop sequences from captive populationFASTA file containing 9 haplotypes identified.dloopPleucopusFINAl.TXTsimulationsCode, 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.