Impact of selection and breeding on the genetic diversity in Douglas-fir

Genetic changes following domestication of Douglas-fir were studied using isozyme data derived from two generations of seed orchards and their 49 wild progenitor populations. In addition, the breeding, production, and infusion populations used in the seed orchards were compared to their wild counterparts. Several parameters of gene diversity were measured (number of alleles per locus N _a, per cent of polymorphic loci PLP, and expected heterozygosity H, and population divergence D). These measures were similar or higher in the domesticated populations compared to their natural progenitors, indicating that early selection and breeding of a highly polymorphic species does not significantly reduce genetic variation. The two generations of seed orchards also did not differ, indicating that genetic variation may remain stable over future generations of forest plantations. Interestingly, compared to the natural populations, heterozygosity was higher in the seed orchards, probably due to pooling of widely distributed natural populations; however, rare localized or private alleles seemed to be less frequent in the domesticated populations. Differentiation values were not significant between the first generation orchards and the natural populations, but significant differences were observed between the second generation orchards and the wild progenitor populations, probably due to the interbreeding that forms the advanced generation seed orchards.     

Genetic assessment of the Iberian wolf Canis lupus signatus captive breeding program

The main goal of ex situ conservation programs is to improve the chances of long term survival of natural populations by founding and managing captive colonies that can serve as a source of individuals for future reintroductions or to reinforce existing populations. The degree in which a captive breeding program has captured the genetic diversity existing in the source wild population has seldom been evaluated. In this study we evaluate the genetic diversity in wild and captive populations of the Iberian wolf, Canis lupus signatus, in order to assess how much genetic diversity is being preserved in the ongoing ex situ conservation program for this subspecies. A sample of domestic dogs was also included in the analysis for comparison. Seventy-four wolves and 135 dogs were genotyped at 13 unlinked microsatellite loci. The results show that genetic diversity in Iberian wolves is comparable in magnitude to that of other wild populations of gray wolf. Both the wild and the captive Iberian wolf populations have a similarly high genetic diversity indicating that no substantial loss of diversity has occurred in the captive-breeding program. The effective number of founders of the program was estimated as ∼ ∼16, suggesting that all founders in the studbook pedigree were genetically independent. Our results emphasize also the genetic divergence between wolves and domestic dogs and indicate that our set of 13 microsatellite loci provide a powerful diagnostic test to distinguish wolves, dogs and their hybrids.     

Population structure and genetic diversity distribution in wild and cultivated populations of the traditional Chinese medicinal plant Magnolia officinalis subsp. biloba (Magnoliaceae)

Magnolia officinalis subsp. biloba, a traditional Chinese medicinal plant, experienced severe declines in the number of populations and the number of individuals in the late 20th century due to the widespread harvest of the subspecies. A large-scale cultivation program was initiated and cultivated populations rapidly recovered the loss in individual plant numbers, but wild populations remained small as a consequence of cutting. In this study, the levels of genetic variation and genetic structure of seven wild populations and five domestic populations of M. officinalis subsp. biloba were estimated employing an AFLP methodology. The plant exhibited a relatively high level of intra-population genetic diversity (h = 0.208 and H _j = 0.268). The cultivated populations maintained approximately 95% of the variation exhibited in wild populations, indicating a slight genetic bottleneck in the cultivated populations. The analysis of genetic differentiation revealed that most of the AFLP diversity resided within populations both for the wild group (78.22%) and the cultivated group (85.92%). Genetic differentiation among populations in the wild group was significant (F _ST = 0.1092, P < 0.005), suggesting wild population level genetic structure. Principal coordinates analysis (PCO) did not discern among wild and cultivated populations, indicating that alleles from the wild population were maintained in the cultivated gene pool. Results from the present study provide important baseline data for effectively conserving the genetic resources of this medicinal subspecies.     

Conservation implications of prey responses to wild dogs Lycaon pictus during the denning season on wildlife ranches

The spread of game ranching in southern Africa provides opportunities for the reestablishment of populations of endangered wild dogs extirpated by livestock ranchers. However, this potential has not been realized, partly because of negative rancher perceptions. Some ranchers believe that wild dogs impart costs by killing wildlife that could be utilized consumptively. Others complain that wild dogs make ungulates 'skittish' and cause local reductions in prey densities while denning. We compared the skittishness and density of prey species inside and outside the denning home ranges of nine wild dog packs in Zimbabwe. Wild dogs had no impact on prey skittishness, but prey species did occur at lower densities inside denning home ranges. In some scenarios, and particularly on fenced game ranches, wild dogs could cause prey population declines during denning. On small game ranches, the use of fences as a tool by wild dogs during hunting can increase the proportion of large prey species in their diet by up to 11 times, and thus increase the minimum area required to support that diet. In addition, game fencing is typically permeable to wild dogs but not their prey, preventing the recovery of prey populations through the natural influx of prey animals into the denning area following departure of the dogs. Wild dogs could thus impose significant financial costs to game ranchers hosting denning packs. Our findings emphasize the importance of promoting the formation of conservancies, where neighbouring landowners remove boundary fences to create larger contiguous wildlife areas.     

Population structure of the olive flounder (Paralichthys olivaceus) in Korea inferred from microsatellite marker analysis

The population structure of olive flounder Paralichthys olivaceus was estimated using nine polymorphic microsatellite (MS) loci in 459 individuals collected from eight populations, including five wild and three hatchery populations in Korea. Genetic variation in hatchery (mean number of alleles per locus, A = 10·2–12·1; allelic richness, A_R = 9·3–10·1; observed heterozygosity, H_O = 0·766–0·805) and wild (mean number of alleles per locus, A = 11·8–19·6; allelic richness, A_R = 10·9–16·1; observed heterozygosity, H_O = 0·820–0·888) samples did not differ significantly, suggesting a sufficient level of genetic variation in these well‐managed hatchery populations, which have not lost a substantial amount of genetic diversity. Neighbour‐joining tree and principal component analyses showed that genetic separation between eastern and pooled western and southern wild populations in Korea was probably influenced by restricted gene flow between regional populations due to the barrier effects of sea currents. The pooled western and southern populations are genetically close, perhaps because larval dispersal may depend on warm currents. One wild population (sample from Wando) was genetically divergent from the main distribution, but it was genetically close to hatchery populations, indicating that the genetic composition of the studied populations may be affected by hydrographic conditions and the release of fish stocks. The estimated genetic population structure and potential applications of MS markers may aid in the proper management of P. olivaceus populations.     

Assessment of genetic structure of Greek brown hare (Lepus europaeus) populations based on variation in random amplified polymorphic DNA (RAPD)

The RAPD method was used to assess the genetic differentiation of brown hare (Lepus europaeus) populations from Central Greece. Greek wild populations were compared with samples from Austria, Poland, Germany, France, and Bulgaria, as well as with reared/released hares to investigate the impact of the releases on the native populations' genetic structure. The absence of diagnostic bands distinguishing between L. europaeus populations confirmed the high level of gene flow between brown hare populations over long geographic distances reported by other authors. Phylogenetic trees, derived from genetic distances estimated by RAPD band frequencies, suggested one major partitioning event of nuclear DNA lineages found in the samples. The reared individuals clustered with the Austrian, Polish, German, and French populations, whereas the Greek populations clustered apart with the Bulgarian population. Within Greece the distribution of the six wild populations did not follow any geographical trend, since their genetic divergence did not seem to correlate to geographic distances. However, RAPD profiles of some reared and wild specimens were different from the common RAPD pattern observed in the vast majority of sampled hares, probably reflecting an admixture of genetically differentiated individuals. The RAPD analysis indicates that releases might have begun to affect Greek population structure and reinforces the view that appropriate management is needed, adjusted to the local populations' biology and ecology.     

Genetic composition of the Jadro softmouth trout following translocation into a new habitat

Genetic founder effects of a historical translocation (1965; app. 12 generations ago) of endangered softmouth trout from the only remaining indigenous population to an adjacent uninhabited river were investigated. A comparison of 15 microsatellites from contemporary samples in both the source and re-established populations indicated a very low level of genetic diversity within the two populations. Furthermore, considerable differences in estimates of variability and effective population sizes were detected between populations, but no recent bottlenecks were evident. Our data suggest that the re-established population has lost variation due to genetic drift associated with founder effects following the translocation. Accordingly, in relation to management, we suggest that the re-established population could serve as a secondary source of individuals to buffer possible extinction due to demographic events. Finally, conservation initiatives to enhance the census population size and increase levels of variability in the re-established population are proposed. Electronic Supplementary Material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Genetic wealth,population health: Major histocompatibility complex variation in captive and wild ring‐tailed lemurs (Lemur catta)

Across species, diversity at the major histocompatibility complex (MHC) is critical to individual disease resistance and, hence, to population health; however, MHC diversity can be reduced in small, fragmented, or isolated populations. Given the need for comparative studies of functional genetic diversity, we investigated whether MHC diversity differs between populations which are open, that is experiencing gene flow, versus populations which are closed, that is isolated from other populations. Using the endangered ring‐tailed lemur (Lemur catta) as a model, we compared two populations under long‐term study: a relatively “open,” wild population (n = 180) derived from Bezà Mahafaly Special Reserve, Madagascar (2003–2013) and a “closed,” captive population (n = 121) derived from the Duke Lemur Center (DLC, 1980–2013) and from the Indianapolis and Cincinnati Zoos (2012). For all animals, we assessed MHC‐DRB diversity and, across populations, we compared the number of unique MHC‐DRB alleles and their distributions. Wild individuals possessed more MHC‐DRB alleles than did captive individuals, and overall, the wild population had more unique MHC‐DRB alleles that were more evenly distributed than did the captive population. Despite management efforts to maintain or increase genetic diversity in the DLC population, MHC diversity remained static from 1980 to 2010. Since 2010, however, captive‐breeding efforts resulted in the MHC diversity of offspring increasing to a level commensurate with that found in wild individuals. Therefore, loss of genetic diversity in lemurs, owing to small founder populations or reduced gene flow, can be mitigated by managed breeding efforts. Quantifying MHC diversity within individuals and between populations is the necessary first step to identifying potential improvements to captive management and conservation plans.     

Genetic variability and population differentiation in captive baird's Tapirs (Tapirus bairdii)

The objectives of this study were to assess the level of genetic variability and population differentiation within captive populations of an endangered large mammal, Baird's tapir (Tapirus bairdii). We genotyped 37 captive animals from North American (NA) and Central American (CA) zoos and conservation ranches using six polymorphic microsatellite loci. Standard indices of genetic variability (allelic richness and diversity, and heterozygosity) were estimated and compared between captive populations, and between captive and wild population samples. In addition, we evaluated levels of population differentiation using Weir and Cockerham's version of Wright's F-statistics. The results indicate that the NA and CA captive populations of Baird's tapirs have retained levels of genetic variability similar to that measured in a wild population. However, inbreeding coefficients estimated from the molecular data indicate that the CA captive population is at increased risk of losing genetic variability due to inbreeding. Despite this, estimated levels of population differentiation indicate limited divergence of the CA captive population from the wild population. Careful management appears to have kept inbreeding coefficients low in the NA captive population; however, population differentiation levels indicate that the NA population has experienced increased divergence from wild populations due to a founder effect and isolation. Based on these results, we conclude that intermittent exchanges of Baird's tapirs between the NA and CA captive populations will benefit both populations by increasing genetic variability and effective population size, while reducing inbreeding and divergence from wild populations. Zoo Biol 23:521–531, 2004. © 2004 Wiley-Liss, Inc.     

Survival of the endangered butterfly Lycaena helle in a fragmented environment: Genetic analyses over 15 years

Temporal changes in allele frequencies are often assumed in studies addressing the history of populations affected by different anthropogenic and natural impacts at different time scales. Yet, few studies directly compare the genetic composition of populations over time spans of more than 10 years. Therefore, to test the genetic effects of 15 years of population isolation in the butterfly Lycaena helle, we analysed 472 individuals from 27 samples, of which nine were collected in 1991 and 18 in 2006. Sampling was performed in five mountain regions (Pyrenees, Massif Central, Jura, Vosges and Ardennes). Genetic analyses were performed using five polymorphic microsatellites. Old and new samples of identical or neighbouring populations revealed similar genetic differentiations among these five mountain regions. A comparatively strong genetic differentiation among populations combined with a high amount of private alleles for each mountain area was detected, but mountain‐specific alleles were in most cases identical in 1991 and 2006. Nevertheless, the obtained data also indicate moderate changes between 1991 and 2006 in the species’ genetic structure – genetic differentiation among local populations increased marginally and allele frequencies showed corresponding modifications. A significant decline in genetic diversity was not detectable, and nine private alleles exclusive to a single mountain region were only detected in samples from the year 1991, whereas eleven were only observed in the individuals collected in 2006. These observations might indicate the results of genetic drift within isolated populations.     

Genetic diversity and spatial genetic structure of African wild dogs (<Emphasis Type="Italic">Lycaon pictus</Emphasis>) in the Greater Limpopo transfrontier conservation area

The Greater Limpopo Transfrontier Conservation Area (GLTFCA) is one of the last refuges for the endangered African wild dog and hosts roughly one-tenth of the global population. Wild dogs in this area are currently threatened by human encroachment, habitat fragmentation and scarcity of suitable connecting habitat between protected areas. We derived genetic data from mitochondrial and nuclear markers to test the following hypotheses: (i) demographic declines in wild dogs have caused a loss of genetic variation, and (ii) Zimbabwean and South African populations in the GLTFCA have diverged due to the effects of isolation and genetic drift. Genetic patterns among five populations, taken with comparisons to known information, illustrate that allelic richness and heterozygosity have been lost over time, presumably due to effects of inbreeding and genetic drift. Genetic structuring has occurred due to low dispersal rates, which was most apparent between Kruger National Park and the Zimbabwean Lowveld. Immediate strategies to improve gene flow should focus on increasing the quality of habitat corridors between reserves in the GLTFCA and securing higher wild dog survival rates in unprotected areas, with human-mediated translocation only undertaken as a last resort.     

Impacts of acidification on brown trout Salmo trutta populations and the contribution of stocking to population recovery and genetic diversity

Anthropogenic acidification in SW-Scotland, from the early 19th Century onwards, led to the extinction of several loch (lake) brown trout (Salmo trutta) populations and substantial reductions in numbers in many others. Higher altitude populations with no stocking influence, which are isolated above natural and artificial barriers and subjected to the greatest effect of acidification, exhibited the least intrapopulation genetic diversity (34% of the allelic richness of the populations accessible to anadromous S. trutta). These, however, were characterised by the greatest interpopulation divergence (highest pairwise D_EST 0.61 and F_ST 0.53 in contemporary samples) based on 16 microsatellite loci and are among the most differentiated S. trutta populations in NW-Europe. Five lochs above impassable waterfalls, where S. trutta were thought to be extinct, are documented as having been stocked in the late 1980s or 1990s. All five lochs now support self-sustaining S. trutta populations; three as a direct result of restoration stocking and two adjoining lochs largely arising from a small remnant wild population in one, but with some stocking input. The genetically unique Loch Grannoch S. trutta, which has been shown to have a heritable increased tolerance to acid conditions, was successfully used as a donor stock to restore populations in two acidic lochs. Loch Fleet S. trutta, which were re-established from four separate donor sources in the late 1980s, showed differential contribution from these ancestors and a higher genetic diversity than all 17 natural loch populations examined in the area. Genetically distinct inlet and outlet spawning S. trutta populations were found in this loch. Three genetically distinct sympatric populations of S. trutta were identified in Loch Grannoch, most likely representing recruitment from the three main spawning rivers. A distinct genetic signature of Loch Leven S. trutta, the progenitor of many Scottish farm strains, facilitated detection of stocking with these strains. One artificially created loch was shown to have a population genetically very similar to Loch Leven S. trutta. In spite of recorded historical supplemental stocking with Loch Leven derived farm strains, much of the indigenous S. trutta genetic diversity in the area remains intact, aside from the effects of acidification induced bottlenecks. Overall genetic diversity and extant populations have been increased by allochthonous stocking.     

Subspecific identity and a comparison of genetic diversity between wild and ex situ wildebeest

The original North American ex situ wildebeest population was believed to originate from the white-bearded wildebeest (Connochaetes taurinus albojubatus), which is both morphologically distinct and geographically separated from the brindled wildebeest (C. t. taurinus). However, after an import of wildebeest into North America in 2001, managers have suspected that white-bearded and brindled wildebeest were mixed in herds at multiple institutions. We sequenced the mitochondrial control region (d-loop) from a portion of the managed North American population and compared our sequences with previously published sequences from wild individuals to determine the subspecific identity and genetic diversity of our ex situ population. We were able to confidently identify C. t. albojubatus as the subspecies identity of the sampled portion of our population. Within our population, haplotype and nucleotide diversity were low (0.169 and 0.001, respectively) with a single common haplotype (H1) containing 41 of the 45 individuals sequenced, while two rare haplotypes (H2 and H3) were derived from three individuals and a single individual, respectively. Nucleotide and haplotype diversity were greater overall in the wild populations compared with our managed population. However, C. t. albojubatus was found to exhibit lower nucleotide diversity in both wild and ex situ populations when compared to other wild subspecies. Though the overall goal of the North American wildebeest population is for public education and not reintroduction, maintaining genetic diversity is vital for the long-term viability of this managed population, which may benefit from periodic supplementation of wild animals.     

Mitochondrial DNA sequence variability in red-legged partridge, <Emphasis Type="Italic">Alectoris rufa</Emphasis>, Spanish populations and the origins of genetic contamination from <Emphasis Type="Italic">A. chukar</Emphasis>

The analysis of 135 mitochondrial D-loop sequences of the Iberian autochthonous red-legged partridge (Alectoris rufa) from wild population hunting bags from various locations and fowl runs in Spain yielded 37 different haplotypes. Among these, three haplotypes correspond to chukar partridges (Alectoris chukar), indicating genetic introgression from birds illegally introduced for restocking: three individuals carrying such haplotypes where found in natural populations, one appeared among those sampled on a mass reproduction farm and the remaining 10 in another fowl-run. The geographical origin of the contaminating chukar haplotypes could be assigned to the most easterly area of the chukar partridge geographical distribution in China. Molecular diversity parameters in the A. rufa samples indicate a considerable amount of genetic variation. Φ_ST showed significant differences among populations that are not explained by geographical distance alone. Particularly, one northern population (Palencia) shows a certain degree of genetic differentiation that could reflect a previously suggested subspecies division. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Comparisons of population density and genetic diversity in artificial and wild populations of an arborescent coral,Acropora yongei: implications for the efficacy of “artificial spawning hotspots”

We are developing techniques to restore coral populations by enhancing larval supply using “artificial spawning hotspots” that aggregate conspecific adult corals. However, no data were available regarding how natural larval supply from wild coral populations is influenced by fertilization rate and how this is in turn affected by local population density and genetic diversity. Therefore, we assessed population density and genetic diversity of a wild, arborescent coral, Acropora yongei, and compared these parameters with those of an artificially established A. yongei population in the field. The population density of wild arborescent corals was only 0.27% of that in the artificial population, even in a high‐coverage area. Genetic diversity was also low in the wild population compared with the artificial population, and approximately 10% of all wild colonies were clones. Based on these results, the larval supply in the artificial population was estimated to be at least 1,400 times higher than that in wild A. yongei populations for the same area of adult population.     

Inbreeding avoidance influences the viability of reintroduced populations of African wild dogs (Lycaon pictus)

The conservation of many fragmented and small populations of endangered African wild dogs (Lycaon pictus) relies on understanding the natural processes affecting genetic diversity, demographics, and future viability. We used extensive behavioural, life-history, and genetic data from reintroduced African wild dogs in South Africa to (1) test for inbreeding avoidance via mate selection and (2) model the potential consequences of avoidance on population persistence. Results suggested that wild dogs avoided mating with kin. Inbreeding was rare in natal packs, after reproductive vacancies, and between sibling cohorts (observed on 0.8%, 12.5%, and 3.8% of occasions, respectively). Only one of the six (16.7%) breeding pairs confirmed as third-order (or closer) kin consisted of animals that were familiar with each other, while no other paired individuals had any prior association. Computer-simulated populations allowed to experience inbreeding had only a 1.6% probability of extinction within 100 years, whereas all populations avoiding incestuous matings became extinct due to the absence of unrelated mates. Populations that avoided mating with first-order relatives became extinct after 63 years compared with persistence of 37 and 19 years for those also prevented from second-order and third-order matings, respectively. Although stronger inbreeding avoidance maintains significantly more genetic variation, our results demonstrate the potentially severe demographic impacts of reduced numbers of suitable mates on the future viability of small, isolated wild dog populations. The rapid rate of population decline suggests that extinction may occur before inbreeding depression is observed.     

南方红豆杉迁地保护小种群适应性进化机制研究

为了解南方红豆杉迁地保护种群的适应性进化机制,以南京中山植物园内南方红豆杉迁地保护栽培种群和扩散的衍生种群为材料,以引种初始地江西野生种群为对照,对南方红豆杉群落的结构、遗传多样性及遗传结构进行分析和研究。结果表明,南方红豆杉野生种群和迁地保护种群均维持着较高水平的遗传多样性,其中野生种群遗传多样性稍高于迁地保护小种群,但迁地保护种群中南方红豆杉个体密度大于野生种群。同时,种群内的遗传变异所占比例大于种群间的。整体来看,南方红豆杉迁地保护种群还处于演替早期,存在不明显的奠基者效应,有进一步演替发展的可能。     

Assessing re-introductions of the African Wild dog (Lycaon pictus) in the Limpopo Valley Conservancy, South Africa, using the stochastic simulation program VORTEX

The African wild dog (Lycaon pictus) is one of Africa's most endangered species and therefore classified as endangered by IUCN. Earlier distributions included most of Africa but currently the African wild dog only has populations larger than 300 individuals in three countries (Botswana, Tanzania and South Africa). In 1998, a plan was launched in South Africa to manage sub-populations of the African wild dog in several small, geographically isolated, conservation areas. This management program involved the reintroduction of wild dogs into suitable conservation areas and periodic translocations among them. We used the stochastic population simulation model VORTEX to evaluate the Limpopo Valley Conservancy in the north of South Africa, as a possible reintroduction site for African wild dogs. The simulations showed that the size of the initial population released only had a small effect on the population dynamics. However, when individuals were supplemented and harvested over a longer period the probability of persistence increased. Number of females breeding, male mortality, and carrying capacity were key factors in the population dynamics, but according to VORTEX the severity of natural catastrophes had the greatest influence on the extinction risk and inbreeding. We suggest that the reintroduction program may be successful, if areas are properly secured, the dogs are held in a boma before release, wild animals or at least a mix of wild and captive animals are used for the release and the animals are vaccinated against rabies. It is, however, essential to continue monitoring followed by modelling efforts to re-evaluate the success of the reintroduction program.     

Loss of genetic diversity in an outbreeding species: small population effects in the African wild dog <Emphasis Type="Italic">(Lycaon pictus</Emphasis>)

Genetic studies on the endangered African wild dog (Lycaon pictus) have primarily focused on the few remaining large and viable populations. However, investigations on the many isolated small African wild dog populations might also be informative for species management because the majority of extant populations are small and may contain genetic variability that is important for population persistence and for species conservation. Small populations are at higher risk of extinction from stochastic and deterministic demographic processes than larger populations and this is often of more immediate conservation concern than loss of genetic diversity, particularly for species that exhibit out-breeding behaviour such as long distance dispersal which may maintain gene flow. However, the genetic advantages of out-breeding behaviour may be reduced if dispersal is compromised beyond reserve borders (edge effects), further weakening the integrity of small populations. Mitochondrial DNA and 11 microsatellite genetic markers were used to investigate population genetic structure in a small population of out-breeding African wild dogs in Zambia, which occupies an historical dispersal corridor for the species. Results indicated the Zambian population suffered from low allelic richness, and there was significant evidence of a recent population bottleneck. Concurrent ecological data suggests these results were due to habitat fragmentation and restricted dispersal which compromised natural out-breeding mechanisms. This study recommends conservation priorities and management units for the African wild dog that focus on conserving remaining levels of genetic diversity, which may also be applicable for a range of out-breeding species.     

Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus)

Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the major histocompatibility complex (MHC), are increasingly being incorporated into genetic studies. In this study, we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA‐DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (N_e < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structuring of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations, we found that the spatial and temporal structure of microsatellite diversity and MHC diversity were correlated and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift.