title: Estimating Inbreeding Rates in Natural Populations: Addressing the Problem of Incomplete Pedigrees.
abstract: Understanding and estimating inbreeding is essential for managing threatened and endangered wildlife populations. However, determination of inbreeding rates in natural populations is confounded by incomplete parentage information. We present an approach for quantifying inbreeding rates for populations with incomplete parentage information. The approach exploits knowledge of pedigree configurations that lead to inbreeding coefficients of F = 0.25 and F = 0.125, allowing for quantification of Pr(I|k): the probability of observing pedigree I given the fraction of known parents (k). We developed analytical expressions under simplifying assumptions that define properties and behavior of inbreeding rate estimators for varying values of k. We demonstrated that inbreeding is overestimated if Pr(I|k) is not taken into consideration and that bias is primarily influenced by k. By contrast, our new estimator, incorporating Pr(I|k), is unbiased over a wide range of values of k that may be observed in empirical studies. Stochastic computer simulations that allowed complex inter- and intragenerational inbreeding produced similar results. We illustrate the effects that accounting for Pr(I|k) can have in empirical data by revisiting published analyses of Arabian oryx (Oryx leucoryx) and Red deer (Cervus elaphus). Our results demonstrate that incomplete pedigrees are not barriers for quantifying inbreeding in wild populations. Application of our approach will permit a better understanding of the role that inbreeding plays in the dynamics of populations of threatened and endangered species and may help refine our understanding of inbreeding avoidance mechanisms in the wild.
authors.affiliation: US Geological Survey Forest and Rangeland Ecosystem Science Center, 3200 SW Jefferson Way, Corvallis, OR 97331; Smithsonian National Zoological Park, Conservation Biology Institute, Front Royal, VA; and USDA Forest Service Pacific Northwest Research Station, Seattle, WA.
authors.forename: Mark P
authors.initials: MP
authors.lastname: Miller
authors.affiliation: US Geological Survey Forest and Rangeland Ecosystem Science Center, 3200 SW Jefferson Way, Corvallis, OR 97331; Smithsonian National Zoological Park, Conservation Biology Institute, Front Royal, VA; and USDA Forest Service Pacific Northwest Research Station, Seattle, WA.
authors.forename: Susan M
authors.initials: SM
authors.lastname: Haig
authors.affiliation: US Geological Survey Forest and Rangeland Ecosystem Science Center, 3200 SW Jefferson Way, Corvallis, OR 97331; Smithsonian National Zoological Park, Conservation Biology Institute, Front Royal, VA; and USDA Forest Service Pacific Northwest Research Station, Seattle, WA.
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Ballou
authors.affiliation: US Geological Survey Forest and Rangeland Ecosystem Science Center, 3200 SW Jefferson Way, Corvallis, OR 97331; Smithsonian National Zoological Park, Conservation Biology Institute, Front Royal, VA; and USDA Forest Service Pacific Northwest Research Station, Seattle, WA.
authors.forename: E Ashley
authors.initials: EA
authors.lastname: Steel
mesh_terms: D000818:Animals; D003198:Computer Simulation; D003670:Deer / Q000235:genetics*; D056727:Endangered Species; D005828:Genetics, Population / Q000379:methods*; D007178:Inbreeding; D008957:Models, Genetic; D010375:Pedigree
keywords: coefficient; inbreeding conservation; management; mating between related individuals; natural populations; pedigree