DOI: 10.5061/dryad.22g66
title: Data from: A comparison of pedigree- and genetic-based measures for identifying inbreeding depression in the critically endangered Attwater’s Prairie-chicken

description: The primary goal of captive breeding programs for endangered species is to
 prevent extinction, a component of which includes the preservation of
 genetic diversity and avoidance of inbreeding. This is typically
 accomplished by minimizing mean kinship in the population, thereby
 maintaining equal representation of the genetic founders used to initiate
 the captive population. If errors in the pedigree do exist, such an
 approach becomes less effective for minimizing inbreeding depression. In
 this study both pedigree- and DNA-based methods were used to assess
 whether inbreeding depression existed in the captive population of the
 critically endangered Attwater's Prairie-chicken (Tympanuchus cupido
 attwateri), a subspecies of prairie grouse that has experienced a
 significant decline in abundance and concurrent reduction of neutral
 genetic diversity. When examining the captive population for signs of
 inbreeding, variation in pedigree-based inbreeding coefficients
 (f_pedigree) was less than that obtained from DNA-based methods (f_DNA).
 Mortality of chicks and adults in captivity were also positively
 correlated with parental relatedness (r_DNA) and f_DNA, respectively,
 while no correlation was observed with pedigree-based measures when
 controlling for additional variables such as age, breeding facility,
 gender, and captive/release status. Further, individual homozygosity by
 loci (HL) and parental r_DNA values were positively correlated with adult
 mortality in captivity and the occurrence of a lethal congenital defect in
 chicks, respectively, suggesting that inbreeding may be a contributing
 factor increasing the frequency of this condition among Attwater's
 Prairie-chickens. This study highlights the importance of using DNA-based
 methods to better inform management decisions when pedigrees are
 incomplete or errors may exist due to uncertainty in pairings.
description: Microsatellite genotypes
 for temporal Attwater Prairie-chicken populationsGenotypes for 5
 microsatellite loci used to compare genetic diversity levels among
 historic (1887-1948), pre-captive (1990-94) and captive (2006)
 Attwater's Prairie-chicken populations.APC_hist_and_contemp_5loci_genotypes.xlsxmtDNA control region sequence alignment for temporal Attwater's Prairie-chicken populationsMitochondrial control region domain I partial sequence alignment used to compare diversity levels among historic (1987-1948), pre-captive (1990-1994) and captive (2006) Attwater's Prairie-chicken populations.Attwater_mtDNA_control_region_seq_alignment.nexMicrosatellite genotypes for the captive 2006 Attwater's Prairie-chicken populationMicrosatellite genotypes (8 loci) from the captive Attwater's Prairie-chicken population used in the mixed model analyses. All living individuals in captivity as of March 2006 were sampled.APC_adult_2006_8loci_genotypes.xlsxSPSS input file for adult Attwater's Prairie-chicken Cox proportional hazards model analysesSPSS input file used to conduct Cox proportional harzards model analyses to explore the effects of several potential explanatory variables simultaneously on juvenile (&gt;8 months) and adult Attwater’s Prairie-chicken survival in captivity.APC_adult_survival_Final.savSPSS input file for chick Attwater's Prairie-chicken Cox proportional harzards model analysesSPSS input file used to conduct Cox proportional harzards model analyses to explore the effects of several potential explanatory variables simultaneously on Attwater’s Prairie-chicken chick survival in captivity to 14 and 50 days post-hatch.APC_chick_survival_Final.sav