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

Pedigree analysis in the mhorr gazelle (Nanger dama mhorr): Genetic variability evolution of the captive population

Breeding programs have an essential role in the recovery of threatened populations through optimal genetic management and mating strategies. The dama gazelle (Nanger dama) is a North African ungulate listed as critically endangered. The mhorr subspecies is extinct in the wild and currently survives thanks to the creation in 1971 of an ex situ breeding program. The aim of the present study was to assess the evolution of genetic variability in this mhorr gazelle captive population, as well as the mating strategy used in two reference populations studied (Almeria and Europe). The entire pedigree, with 2739 animals, was analyzed to measure demographic characters, pedigree completeness level, probability of gene origin, level of relatedness and genetic structure of the population. The population size has been progressively increasing, with up to 264 individuals alive in Europe at the time of the study. The average number of equivalent complete generations was 5.55. The effective number of founders and ancestors was both 3, and the founder genome equivalent was 1.99. The genetic contributions of the four main ancestors were unbalanced. The average values of inbreeding and average relatedness for the whole pedigree were, respectively, 28.34% and 50.14%. The effective population size was 8.7 by individual increase in inbreeding and 9.8 by individual increase in coancestry. F-statistics evidenced a very small level of population subdivision (F ST = 0.033370). The mating strategy used, based on the minimum coancestry of the individuals, has minimized the losses of genetic variability and helped to balance the genetic contributions between ancestors. The strategy also avoided large subdivisions within the population and the appearance of new bottlenecks. This study shows how pedigree analysis can both be used to determine the genetic variability of the population and to assess the influence of the mating strategy used in the breeding program on such variability.

Genetic diversity in global populations of the critically endangered addax (Addax nasomaculatus) and its implications for conservation

Threatened species are frequently patchily distributed across small wild populations, ex situ populations managed with varying levels of intensity and reintroduced populations. Best practice advocates for integrated management across in situ and ex situ populations. Wild addax (Addax nasomaculatus) now number fewer than 100 individuals, yet 1000 of addax remain in ex situ populations, which can provide addax for reintroductions, as has been the case in Tunisia since the mid-1980s. However, integrated management requires genetic data to ascertain the relationships between wild and ex situ populations that have incomplete knowledge of founder origins, management histories, and pedigrees. We undertook a global assessment of genetic diversity across wild, ex situ and reintroduced populations in Tunisia to assist conservation planning for this Critically Endangered species. We show that the remnant wild populations retain more mitochondrial haplotypes that are more diverse than the entirety of the ex situ populations across Europe, North America and the United Arab Emirates, and the reintroduced Tunisian population. Additionally, 1704 SNPs revealed that whilst population structure within the ex situ population is minimal, each population carries unique diversity. Finally, we show that careful selection of founders and subsequent genetic management is vital to ensure genetic diversity is provided to, and minimize drift and inbreeding within reintroductions. Our results highlight a vital need to conserve the last remaining wild addax population, and we provide a genetic foundation for determining integrated conservation strategies to prevent extinction and optimize future reintroductions.

Rescued back from extinction in the wild: past, present and future of the genetics of the Arabian oryx in Oman

The Arabian oryx was the first species to be rescued from extinction in the wild by the concerted efforts of captive programmes in zoos and private collections around the world. Reintroduction efforts have used two main sources: the 'World Herd', established at the Phoenix Zoo, and private collections in Saudi Arabia. The breeding programme at the Al-Wusta Wildlife Reserve (WWR) in Oman has played a central role in the rescue of the oryx. Individuals from the 'World Herd' and the United Arab Emirates have been the main source for the WWR programme. However, no breeding strategies accounting for genetic diversity have been implemented. To address this, we investigated the diversity of the WWR population and historical samples using mitochondrial DNA (mtDNA) and single nucleotide polymorphisms (SNPs). We found individuals at WWR contain 58% of the total mtDNA diversity observed globally. Inference of ancestry and spatial patterns of SNP variation shows the presence of three ancestral sources and three different groups of individuals. Similar levels of diversity and low inbreeding were observed between groups. We identified individuals and groups that could most effectively contribute to maximizing genetic diversity. Our results will be valuable to guide breeding and reintroduction programmes at WWR.

Genetic diversity in natural range remnants of the critically endangered hirola antelope

The hirola antelope (Beatragus hunteri) is considered to be the most endangered antelope in the world. In the ex situ translocated population at Tsavo East National Park, calf mortality and the critically low population numbers might suggest low genetic diversity and inbreeding depression. Consequently, a genetic study of the wild population is pivotal to gain an understanding of diversity and differentiation within its range before designing future translocation plans to increase the genetic diversity of the ex situ population. For that purpose, we assessed 55 individuals collected across five localities in eastern Kenya, covering its entire natural range. We used the complete mitochondrial DNA control region and microsatellite genotyping to estimate genetic diversity and differentiation across its range. Nuclear genetic diversity was moderate in comparison to other endangered African antelopes, with no signals of inbreeding. However, the mitochondrial data showed low nucleotide diversity, few haplotypes and low haplotypic differentiation. Overall, the inferred low degree of genetic differentiation and population structure suggests a single population of hirola across the natural range. An overall stable population size was inferred over the recent history of the species, although signals of a recent genetic bottleneck were found. Our results show hope for ongoing conservation management programmes and that there is a future for the hirola in Kenya.

Characterization of the genetic diversity of a population of Odocoileus virginianus veraecrucis in captivity using microsatellite markers

The genetic diversity and effective population size (Ne) of a population of Odocoileus virginianus veraecrucis in captivity were characterized in the Wildlife Management Unit “El Pochote”, located in Ixtaczoquitlán, Veracruz, Mexico. Blood tissue was collected from 20 individuals of the reproductive nucleus, its genomic DNA was extracted, and genetic diversity was characterized by six microsatellites amplified by PCR and visualized in polyacrylamide gels. With four polymorphic microsatellites, 66.7% of the population’s genetic variation was explained, which was characterized by an allelic diversity that fluctuated between 9 and 28 alleles (18 average alleles), suggesting a mean allelic diversity (Shannon index = 2.6 ± 0.25), but only 12 ± 2.9 effective alleles would be fixed in the next generation. The heterozygosity observed (Ho= 0.81) exceeded that expected (He= 0.79) and these were significantly different (P> 0.05), as a result of a low genetic structure in the population (fixation index F = -0.112 ± 0.03), due to the genetic heterogeneity that each sample contributed, since the specimens came from different geographical regions. The Ne was 625 individuals and a 1:25 male:female ratio, with which 100% of the genetic diversity observed can be maintained for 100 years. The information obtained in the study can help in the design of a reproductive management program to maintain the present genetic diversity, without risk of losses due to genetic drift and inbreeding.

A high-density BAC physical map covering the entire MHC region of addax antelope genome

BACKGROUND

The mammalian major histocompatibility complex (MHC) harbours clusters of genes associated with the immunological defence of animals against infectious pathogens. At present, no complete MHC physical map is available for any of the wild ruminant species in the world.

RESULTS

The high-density physical map is composed of two contigs of 47 overlapping bacterial artificial chromosome (BAC) clones, with an average of 115 Kb for each BAC, covering the entire addax MHC genome. The first contig has 40 overlapping BAC clones covering an approximately 2.9 Mb region of MHC class I, class III, and class IIa, and the second contig has 7 BAC clones covering an approximately 500 Kb genomic region that harbours MHC class IIb. The relative position of each BAC corresponding to the MHC sequence was determined by comparative mapping using PCR screening of the BAC library of 192,000 clones, and the order of BACs was determined by DNA fingerprinting. The overlaps of neighboring BACs were cross-verified by both BAC-end sequencing and co-amplification of identical PCR fragments within the overlapped region, with their identities further confirmed by DNA sequencing.

CONCLUSIONS

We report here the successful construction of a high-quality physical map for the addax MHC region using BACs and comparative mapping. The addax MHC physical map we constructed showed one gap of approximately 18 Mb formed by an ancient autosomal inversion that divided the MHC class II into IIa and IIb. The autosomal inversion provides compelling evidence that the MHC organizations in all of the ruminant species are relatively conserved.

Genomic resources and genetic diversity of captive lesser kudu (Tragelaphus imberbis)

The lesser kudu (Tragelaphus imberbis) is a spiral-horned antelope native to northeastern Africa. Individuals kept in zoological gardens are suspected to be highly inbred due to few founder individuals and a small breeding stock. A morphological study suggested two distinct subspecies of the lesser kudu. However, subspecies designation and population structure in zoological gardens has not been analyzed using molecular markers. We analyzed one mitochondrial marker and two nuclear intron loci (total: 2,239 nucleotides) in 52 lesser kudu individuals. Of these, 48 individuals were bred in captivity and sampled from seven different zoos. The four remaining individuals were recently captured in Somalia and are currently held in the Maktoum zoo. Maternally inherited mitochondrial sequences indicate substantial amounts of genetic variation in the zoo populations, while the biparentally inherited intron sequences are, as expected, less variable. The analyzed individuals show 10 mitochondrial haplotypes with a maximal distance of 10 mutational steps. No prominent subspecies structure is detectable in this study. For further studies of the lesser kudu population genetics, we present microsatellite markers from a low-coverage genome survey using 454 sequencing technology.

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

Background

Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate.

Results

Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species.

Conclusions

When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied.