A comparison of pedigree- and DNA-based measures for identifying inbreeding depression in the critically endangered Attwater's Prairie-chicken

• Published in: Molecular ecology Vol. 22; no. 21; pp. 5313 - 5328
• Main Authors: Hammerly, Susan C., Morrow, Michael E., Johnson, Jeff A.
• Format: Journal Article
• Language: English
• Published: Oxford Blackwell Publishing Ltd 01-11-2013; Blackwell
• Subjects: Animal and plant ecology; Animal, plant and microbial ecology; Animals; Biological and medical sciences; Biological evolution; Conservation of Natural Resources; Deoxyribonucleic acid; DNA; Endangered & extinct species; Endangered Species; ex situ population management; fitness; Fundamental and applied biological sciences. Psychology; Galliformes - genetics; genetic diversity; Genetic Fitness; Genetic Variation; Genetics of eukaryotes. Biological and molecular evolution; Genotype; heterozygosity; Heterozygote; Inbreeding; Microsatellite Repeats; Models, Genetic; Pedigree; Population genetics, reproduction patterns; Poultry; prairie grouse; Proportional Hazards Models; Sequence Analysis, DNA - methods; Synecology; Terrestrial ecosystems; Tympanuchus cupido attwateri; Grassland; prairie grouse; Inbreeding depression; Population management; Endangered species; ex situ population management; Genetic diversity; Heterozygosity; Vertebrata; DNA; Inbreeding; Chicken; Aves; Fitness; genetic diversity; heterozygosity; inbreeding; fitness
• ISSN: 0962-1083; 1365-294X
• DOI: 10.1111/mec.12482

The primary goal of captive breeding programmes 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 in neutral genetic diversity. When examining the captive population for signs of inbreeding, variation in pedigree‐based inbreeding coefficients (fpedigree) was less than that obtained from DNA‐based methods (fDNA). Mortality of chicks and adults in captivity were also positively correlated with parental relatedness (rDNA) and fDNA, 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 rDNA 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.