Genetic structure analysis of a highly inbred captive population of the African antelope Addax nasomaculatus. Conservation and management implications

Abstract

The African antelope Addax nasomaculatus is a rare mammal at high risk of extinction, with no more than 300 individuals in the wild and 1,700 captive animals distributed in zoos around the world. In this work, we combine genetic data and genealogical information to assess the structure and genetic diversity of a captive population located at Parque Lecocq Zoo (N=27), originated from only two founders. We amplified 39 microsatellites previously described in other Artiodactyls but new to this species. Seventeen markers were polymorphic, with 2-4 alleles per locus (mean=2.71). Mean expected heterozygosity (He) per locus was between 0.050 (marker ETH3) and 0.650 (marker D5S2), with a global He of 0.43. The mean inbreeding coefficient of the population computed from pedigree records of all registered individuals (N=53) was 0.222. The mean coancestry of the population was 0.298 and F(IS) index was -0.108. These results reflect the importance of an adequate breeding management on a severely bottlenecked captive population, which would benefit by the incorporation of unrelated individuals. Thanks to the successful amplification of a large number of microsatellites commonly used in domestic bovids, this study will provide useful information for the management of this population and serve as future reference for similar studies in other captive populations of this species.

Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse

“…Moreover, they are more or less sensitive to the level of pedigree knowledge and to some parameters related to breeding conditions, such as the existence of population subdivisions or departure of the random mating hypothesis, which may lead to biased N e estimates. Depending on the context and the authors, one or several of these methods have been applied to domestic breeds [10-14] and captive animal populations [15,16]. More specifically, the fact that in a number of breeds, no pedigree information is available, the simplest approximation of N e (computed on the basis of number of breeding males and females) has been used to classify the endangerment level of breeds by the European Association for Animal Production (EAAP), and the Food and Agriculture Organisation (FAO).…”

Genetic structure of captive and free-ranging okapi (Okapia johnstoni) with implications for management

“…Many other captive populations have also been shown to demonstrate considerable genetic structure (e.g. Guan et al 2009;Henry et al 2009;Armstrong et al 2011;Witzenberger and Hochkirch 2013), but the management implications of this are not always clear. Captive management generally aims to maintain genetic variation both within and among sub-populations, however the appropriate proportions of each are difficult to determine (Wang 2004).…”

“…It may also indicate an accumulation of genetic load due to relaxed selection, which may ultimately result in inbreeding depression (Boakes et al 2006). Studies have shown that genetic structure can be introduced rapidly in captive populations due to founder effect (Hu et al 2007;Armstrong et al 2011;Witzenberger and Hochkirch 2013), although relatively few use a dataset as comprehensive as the present study, with representative samples from the wild, founders and captives (McGreevy et al 2009;Shen et al 2009;Gonçalves da Silva et al 2010).…”

A Suite of Microsatellite Markers Optimized for Amplification of DNA From Addax (Addax nasomaculatus) Blood Preserved on FTA Cards

“…We tested amplification for 66 microsatellite markers previously described in other ungulate species, including 14 known to be polymorphic in addax [Armstrong et al, ]. PCR was performed in 10 µL reactions containing the washed punch, 0.2 mM each dNTP, 5 pmol forward and reverse primers, 1.5 mM MgCl 2 , and 1 Unit Taq DNA polymerase in 1× PCR buffer.…”