Six new polymorphic microsatellite loci isolated and characterized from the African savannah elephant genome

The African savannah elephant (Loxodonta africana) is a ‘keystone’ species that plays a vital role in regulating the dynamics of both plant and animal communities and yet it is endangered and its numbers have been reduced to approximately 500 000 across their entire continental range. Molecular genetic markers are important tools for providing genetic information useful in formulating effective management and conservation strategies for the surviving elephant populations. We describe the isolation and characterization of six new polymorphic microsatellite markers in the African savannah elephant and demonstrate that these loci can be PCR (polymerase chain reaction)‐multiplexed, a desirable attribute that saves costs in large‐scale microsatellite screening.     

Genetic relatedness and disrupted social structure in a poached population of African elephants

We use genetic measures of relatedness and observations of female bonding to examine the demographic signature of historically heavy poaching of a population of free-ranging African elephants. We collected dung samples to obtain DNA and observed behaviour from 102 elephant families over a 25-month period in 2003–2005 in Mikumi National Park, Tanzania. Poaching reduced the population by 75% in the decade prior to the 1989 ivory trade ban; park records indicate that poaching dropped significantly in Mikumi following the ban. Using 10 microsatellite loci, DNA was genotyped in 203 elephants and pair-wise relatedness was calculated among adult females within and between groups. The Mikumi population is characterized by small group size, considerable variation in group relatedness, females with no first-order adult relatives and females that form only weak social bonds. We used gene-drop analysis and a model of a genetically intact pedigree to compare our observed Mikumi group relatedness to a simulated genetically intact unpoached expectation. The majority of groups in Mikumi contain 2 to 3 adults; of these, 45% were classified as genetically disrupted. Bonding, quantified with a pair-wise association index, was significantly correlated with relatedness; however only half of the females formed strong bonds with other females, and relatedness was substantially lower for a given bond strength as compared to an unpoached population. Female African elephants without kin demonstrated considerable behavioural plasticity in this disturbed environment, grouping with other females lacking kin, with established groups, or remaining alone, unable to form any stable adult female-bonds. We interpret these findings as the remaining effect of poaching disturbance in Mikumi, despite a drop in the level of poaching since the commercial trade in ivory was banned 15 years ago.     

The influence of increasing population size and vegetation productivity on elephant distribution in the Kruger National Park

Decisions to reduce the impacts of large herbivores on biodiversity in protected areas are often based on controlling their numbers. However, numbers per se may not be the foremost consideration when managing impacts. This is because density‐related changes in distribution can also affect habitat utilization and hence, impact. In this study we tested whether changes in the distribution of African elephants are associated with increasing population size. We used spatially explicit count data collected during the dry seasons from 1998 to 2004 in South Africa's Kruger National Park. We did this at five spatial scales and in landscapes defined by vegetation, geology, climate and soils. We then investigated whether observed distributions and grid‐cell‐specific densities were associated with the remotely sensed Normalized Difference Vegetation Index (NDVI) as a measure of productivity and therefore food resource availability at the landscape scale. Consistent with density mediated changes, we found that elephant grid‐cell occupancy increased with population size, while grid‐cell‐specific density became less variable. In addition, the combined distribution of bull groups and breeding herds became less clumped with increasing population size. We further found that within landscapes elephants were present on grid‐cells with higher NDVI values, but that the influence of NDVI during the dry season on densities among landscapes may be weak. These results suggest that NDVI was more indicative of structural habitat choices such as woody vegetation than food availability per se. Our study highlights the need to consider factors other than population size alone when formulating management decisions to reduce large herbivore impacts on biodiversity in protected areas.     

The vomeronasal organ and associated structures of the fetal African elephant, Loxodonta africana (Proboscidea, Elephantidae)

The vomeronasal organ (VNO) is a chemosensory structure of the nasal septum found in most tetrapods. Although potential behavioural correlates of VNO function have been shown in two of the three elephant species, its morphology in Loxodonta africana has not been studied. The development of the VNO and its associated structures in the African elephant are described in detail using serially sectioned material from fetal stages. The results show that many components of the VNO complex (e.g. neuroepithelium, receptor‐free epithelium, vomeronasal nerve, paravomeronasal ganglia, blood vessels, vomeronasal cartilage) are well developed even in a 154‐day‐old fetus, in which the VNO opens directly into the oral cavity with only a minute duct present. However, the vomeronasal glands and their ducts associated with the VNO were developed only in the 210‐day‐old fetus. Notably, in this fetus, the vomeronasal–nasopalatine duct system had acquired a pathway similar to that described in the adult Asian elephant; the VNOs open into the oral cavity via the large palatal parts of the nasopalatine ducts, which are lined by a stratified squamous epithelium. The paired palatal ducts initially coursed anteriorly at an angle of 45° from the oral recess and/or the oral cavity mucosa, and merged into the vomeronasal duct. This study confirms the unique characteristics of the elephant VNO, such as its large size, the folded epithelium of the VNO tube, and the dorsomedial position of the neuroepithelium. The palatal position and exclusive communication of the VNO with the oral cavity, as well as the partial reduction of the nasopalatine duct, might be related to the unique elephantid craniofacial morphogenesis, especially the enormous growth of the tusk region, and can be seen as autapomorphies.     

Heard but not seen: an acoustic survey of the African forest elephant population at Kakum Conservation Area, Ghana

This study, designed to survey forest elephants ( Loxodonta africana cyclotis ) at Kakum Conservation Area, Ghana, is the first to apply acoustic methods to elephant abundance estimation and to compare results with independent survey estimates. Nine acoustic sensors gathered sound continuously for 38 days. Low-frequency calling rates have been established as useful elephant abundance indices at a Namibian watering hole and a central African forest clearing. In this study, we estimated elephant population size by applying an abundance index model and detection function developed in central Africa to data from simultaneous sampling periods on Kakum sensors. The sensor array recorded an average of 1.81 calls per 20-min sampling period from an effective detection area averaging 10.27 km². The resulting estimate of 294 elephants (95% CI: 259–329) falls within confidence bounds of recent dung-based surveys. An extended acoustic model, estimating the frequency with which elephants are silent when present, yields an estimate of 350 elephants (95% CI: 315–384). Acoustic survey confidence intervals are at least half as wide as those from dung-based surveys. This study demonstrates that acoustic surveying is a valuable tool for estimating elephant abundance, as well as for detecting other vocal species and anthropogenic noises that may be associated with poaching.     

Reproductive evaluation of elephants culled in Kruger National Park, South Africa between 1975 and 1995

To reduce elephant densities and preserve biological diversity, 14,629 elephants were culled from Kruger National Park, South Africa (1967–1999). Data were catalogued between 1975 and 1996 on 2737 male and female elephants, including pregnancy and lactational status for 1620 females (≥5 years of age) and, uterine and/or ovarian characteristics for 1279. This study used these data to investigate the effects of age and precipitation on reproduction. The youngest age of conception was 8 years (n = 6) and by 12 years of age all females were sexually mature. From the age of 14 years, the percentage of reproductively active females (pregnant and/or lactating) was >90%; however, this percentage declined when females reached 50 years of age. Overall, one-tenth of females were nonreproductive (not pregnant or lactating) at any given time, mostly in the youngest (<15 years) and oldest (>50 years) age classes. Eighteen (3.3%) of the nonpregnant females had reproductive tract pathologies, including endometrial, uterine or ovarian cysts. There was a seasonal distribution of mating activity that correlated with the rainy season. As has been demonstrated in other populations of free-ranging African elephants, most of the females in Kruger National Park were reproductively active; however, age and climate affected reproductive activity.     

Heterogeneity in African savanna elephant distributions and their impacts on trees in Kruger National Park,South Africa

1. Though elephants are a major cause of savanna tree mortality and threaten vulnerable tree species, managing their impact remains difficult, in part because relatively little is known about how elephant impacts are distributed throughout space.
2. This is exacerbated by uncertainty about what determines the distribution of elephants themselves, as well as whether the distribution of elephants is even informative for understanding the distribution of their impacts.
3. To better understand the factors that underlie elephant impacts, we modeled elephant distributions and their damage to trees with respect to soil properties, water availability, and vegetation in Kruger National Park, South Africa, using structural equation modeling.
4. We found that bull elephants and mixed herds differed markedly in their distributions, with bull elephants concentrating in sparsely treed basaltic sites close to artificial waterholes and mixed herds aggregating around permanent rivers, particularly in areas with little grass.
5. Surprisingly, we also found that the distribution of elephant impacts, while highly heterogeneous, was largely unrelated to the distribution of elephants themselves, with damage concentrated instead in densely treed areas and particularly on basaltic soils.
6. Results underscore the importance of surface water for elephants but suggest that elephant water dependence operates together with other landscape factors, particularly vegetation community composition and historical management interventions, to influence elephant distributions.

     

Current population estimate and distribution of the African buffalo in Chebera Churchura National Park,Ethiopia

An investigation into the population status and distribution of the African buffalo (Syncerus caffer Sparrman, 1779) in Chebera Churchura National Park, Ethiopia, was carried out during the wet and dry seasons of 2012–2015. This study tested the hypothesis that buffalo would demonstrate seasonal habitat preferences and changes in population density. Sample counts were carried out in an area of 1215 km². The estimated buffalo population was 5193 individuals, with the population density of 4.3/km². The population showed an increase from 2617 to 5194 individuals during 2006–2015. Males comprised 42.6%, while females 46.7% of the population. Age structure was dominated by adults, which constituted 52.5% of the total population. Subadults comprised 24.3% and young 12.4% of the population. Larger herds of up to 30 individuals were observed during the wet season, and smaller herds of a minimum of four individuals were seen during the dry season. The mean herd sizes during the wet and dry seasons were 29.59 and 16.95, respectively. They were observed more in the riverine vegetation types during the dry season. Of the total, 57.6% utilized riverine habitat during the dry season, whereas 39.8% used this habitat during the wet season. Relative abundance of food sources, green vegetation cover and availability of water were the major factors governing their distribution in the present study area.     

Demography, life history, and social structure in Propithecus diadema edwardsi from 1986-2000 in Ranomafana National Park, Madagascar

Prosimian lemurs differ fundamentally from anthropoid primates in many traits related to social structure. By exploring the demography of Milne-Edwards' sifakas (Propithecus diadema edwardsi), and comparing it to other well-studied primates, we explore the effect of demographic and life-history factors on social structure. Specifically, we compare lemur survivorship and fertility patterns to two published composite models: one created for New World and another created for Old World monkeys. Using longitudinal data collected on individual Propithecus diadema edwardsi from four study groups from 1986-2000 in Ranomafana National Park, Madagascar, we quantify 1) group composition, 2) birth seasonality, 3) interbirth interval, 4) life-table values, and 5) population growth estimates. The mortality, survivorship, and life-expectancy schedules indicate high infant and juvenile mortality. Fertility remains high until death. The intrinsic rate of increase and net reproductive rate indicate a shrinking population. We suggest that high mortality rather than low fertility causes the observed population decline. While sifaka survivorship closely resembles New World patterns, fertility resembles Old World patterns, i.e., like New World monkeys, few sifakas survive to reproductive age, and those that do, reproduce at a slow rate resembling the Old World pattern. This necessarily impacts social structure. An adult sifaka at the end of her lifespan will have one only daughter who survives to reproductive age, compared to 3.4 for New World or 2.7 for Old World monkeys. Demography limits the formation of large kin-based groups for sifakas, and survivorship and fertility patterns do not easily permit sifakas to form large same-sex family groups.     

Disease risk and inter‐institutional transfer of specimens in cooperative breeding programs: Herpes and the elephant species survival plans

Managers of cooperative breeding programs and re‐introduction projects are increasingly concerned with the risk of disease transmission when specimens are transferred among facilities or between facilities and the natural environment. We used data maintained in North American studbooks to estimate the potential risks of disease transmission by direct and indirect contact of specimens in the American Zoo and Aquarium Association’s Elephant Species Survival Plan. Histological evidence for a novel herpesvirus disease transmitted between and within elephant species housed in North American facilities prompted an examination of the scope of possible transmission routes within the captive population. We found that, compared with other species managed through Species Survival Plans, elephants experience relatively few transfers between zoos. Nevertheless, the number of direct contacts with other elephants born during the study period of 1983–1996 (excluding stillbirths) was much higher than we had anticipated (μ = 25 ± 27; N = 59) and the number of potential indirect contacts was surprisingly large (μ = 143 ± 92; N = 59). Although these high rates of potential contacts complicate exact identification of infection pathways for herpesvirus, we were able to propose potential routes of transmission for the histologically identified cases. Furthermore, the extraction of data from studbooks allowed us to readily identify other specimens that did not succumb to the disease despite similar exposure. Moreover, we were able to identify other possible cases to recommend for histological examination. Herein we reveal the possibilities of multiple disease transmission pathways and demonstrate how complex the patterns of transmission can be, confounded by the unknown latency of this novel herpesvirus. This emphasizes the need for zoo veterinarians and cooperative breeding programs to consider the full potential for disease transmission associated with each and every inter‐zoo transfer of specimens. Zoo Biol 20:89–101, 2001. © 2001 Wiley‐Liss, Inc.     

Trends in populations of elephant and other large herbivores in Gonarezhou National Park,Zimbabwe, as revealed by sample aerial surveys

For 30 years, regular aerial surveys in Zimbabwean protected areas were funded, designed and executed primarily to estimate elephant numbers. Other large herbivores were recorded, even though some species were not easily seen from the air in savannah woodlands. Population estimates for species other than elephant provided indices of abundance that could be used to determine temporal trends in population size. This study tests for significant trends in the abundance of large herbivores in Gonarezhou National Park, assuming that data from aerial sample surveys designed for elephant also provide accurate estimates of real trends in the populations of other herbivores. For each species, the exponential rate of population change was calculated using weighted regression, with the variance of this rate based on the sampling variances of the population estimates. Significant population trends were detected for eight species. Before the 1992 drought, elephant number was held approximately constant by frequent culls, but afterwards, it increased at a mean annual rate of 6.2% (confidence limits 4.0% and 8.6%). Elephants in cow herds increased at 7.3%, significantly faster than elephants in bull herds (?0.5%). Buffalo, eland, kudu, nyala, waterbuck, wildebeest and zebra all increased in number, after population declines during the drought.     

Minimum population size,genetic diversity,and social structure of the Asian elephant in Cat Tien National Park and its adjoining areas,Vietnam, based on molecular genetic analyses

Vietnam’s elephant population that has suffered severe declines during the past three decades is now believed to number 60–80 individuals in the wild. Cat Tien National Park is thought to be one of the key areas for the recovery of Vietnam’s elephants. We carried out a molecular genetic study of elephants in Cat Tien National Park and its adjoining areas with the objectives of estimating minimum population size, assessing genetic diversity, and obtaining insights into social organization. We obtained a minimum population size of 11 elephants based on a combination of unique nuclear microsatellite genotypes and mitochondrial haplotypes. While mitochondrial diversity based on a 600-base pair segment was high in this small sample of individuals, the six microsatellite loci examined showed low diversity and the signature of a recent population bottleneck. Along with nuclear genetic depauperation of Cat Tien’s elephants, we also report disruption of normal social organization, with different matrilines having coalesced into a single social group because of anthropogenic disturbance. The results emphasize the critical condition of this elephant population and the need for urgent conservation measures if this population is to be saved.     

A comparison of methods used to count the elephant population of the Addo Elephant National Park, South Africa

Evaluation of alternative techniques used to estimate elephant population sizes is important in order to assess the accuracy of the results obtained, upon which management decisions may be based. Data from annual helicopter surveys carried out in the Addo Elephant National Park (1978–97) are compared with registration counts obtained from intensive ground surveys in which all elephants within the park are individually known. On average, total population size estimated in aerial surveys is 8.0% lower than registration counts (n₁₉₉₇ = 251), aerial calf (< 1 year) counts are 48.8% lower than registration counts, and aerial carcass counts are 50% below the total number of deaths documented in ground surveys. Registration counts provide more accurate demographic data than aerial surveys, the results of which are shown to vary widely and unpredictably, thus compromising their value. Where population estimates rely exclusively on aerial surveys, replicate counts are recommended in order to generate confidence intervals.