Fine-scale population genetic structure in a fission-fusion society

Nonrandom patterns of mating and dispersal create fine-scale genetic structure in natural populations — especially of social mammals — with important evolutionary and conservation genetic consequences. Such structure is well-characterized for typical mammalian societies; that is, societies where social group composition is stable, dispersal is male-biased, and males form permanent breeding associations in just one or a few social groups over the course of their lives. However, genetic structure is not well understood for social mammals that differ from this pattern, including elephants. In elephant societies, social groups fission and fuse, and males never form permanent breeding associations with female groups. Here, we combine 33 years of behavioural observations with genetic information for 545 African elephants ( Loxodonta africana ), to investigate how mating and dispersal behaviours structure genetic variation between social groups and across age classes. We found that, like most social mammals, female matrilocality in elephants creates co-ancestry within core social groups and significant genetic differentiation between groups (Φ_ST = 0.058). However, unlike typical social mammals, male elephants do not bias reproduction towards a limited subset of social groups, and instead breed randomly across the population. As a result, reproductively dominant males mediate gene flow between core groups, which creates cohorts of similar-aged paternal relatives across the population. Because poaching tends to eliminate the oldest elephants from populations, illegal hunting and poaching are likely to erode fine-scale genetic structure. We discuss our results and their evolutionary and conservation genetic implications in the context of other social mammals.     

Single‐nucleotide polymorphism discovery and panel characterization in the African forest elephant

The continuing decline in forest elephant (Loxodonta cyclotis) numbers due to poaching and habitat reduction is driving the search for new tools to inform management and conservation. For dense rainforest species, basic ecological data on populations and threats can be challenging and expensive to collect, impeding conservation action in the field. As such, genetic monitoring is being increasingly implemented to complement or replace more burdensome field techniques. Single‐nucleotide polymorphisms (SNPs) are particularly cost‐effective and informative markers that can be used for a range of practical applications, including population census, assessment of human impact on social and genetic structure, and investigation of the illegal wildlife trade. SNP resources for elephants are scarce, but next‐generation sequencing provides the opportunity for rapid, inexpensive generation of SNP markers in nonmodel species. Here, we sourced forest elephant DNA from 23 samples collected from 10 locations within Gabon, Central Africa, and applied double‐digest restriction‐site‐associated DNA (ddRAD) sequencing to discover 31,851 tags containing SNPs that were reduced to a set of 1,365 high‐quality candidate SNP markers. A subset of 115 candidate SNPs was then selected for assay design and validation using 56 additional samples. Genotyping resulted in a high conversion rate (93%) and a low per allele error rate (0.07%). This study provides the first panel of 107 validated SNP markers for forest elephants. This resource presents great potential for new genetic tools to produce reliable data and underpin a step‐change in conservation policies for this elusive species.     

Origin and phylogeography of African savannah elephants (<Emphasis Type="Italic">Loxodonta africana</Emphasis>) in Kruger and nearby parks in southern Africa

African savannah elephants (Loxodonta africana) occur in fragmented and isolated populations across southern Africa. Transfrontier conservation efforts aim at preventing the negative effects of population fragmentation by maintaining and restoring linkages between protected areas. We sought to identify genetic linkages by comparing the elephants in Kruger National Park (South Africa) to populations in nearby countries (Botswana, Mozambique, Zambia and Zimbabwe). We used a 446 base pair mitochondrial DNA (mtDNA) control region fragment (141 individuals) and 9 nuclear DNA (nDNA) microsatellite markers (69 individuals) to investigate phylogenetic relationships and gene flow among elephant populations. The mtDNA and nDNA phylogeographic patterns were incongruent, with mtDNA patterns likely reflecting the effects of ancient female migrations, with patterns persisting due to female philopatry, and nDNA patterns likely reflecting male-mediated dispersal. Kruger elephant heterozygosity and differentiation were examined, and were not consistent with genetic isolation, a depleted gene pool or a strong founder effect. Mitochondrial DNA geographic patterns suggested that the Kruger population was founded by elephants from areas both north and south of Kruger, or has been augmented through migration from more than one geographic source. We discuss our findings in light of the need for conservation initiatives that aim at maintaining or restoring connectivity among populations. Such initiatives may provide a sustainable, self-regulating management approach for elephants in southern Africa while maintaining genetic diversity within and gene flow between Kruger and nearby regions.     

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.     

Landscape-scale habitat response of African elephants shows strong selection for foraging opportunities in a human dominated ecosystem

Balancing trade-offs between foraging and risk factors is a fundamental behavior that structures the spatial distribution of species. For African elephants Loxodonta africana, human pressures from poaching and conflict are primary drivers of species decline, but little is known about how elephants structure their spatial behavior in the face of human occupancy and predation. We seek to understand how elephants balance trade-offs between resource access, human presence and human predatory risk factors (poaching and conflict killing) in an unfenced, dynamic ecosystem where elephants persist primarily outside protected areas in community rangelands. We used tracking data from 101 elephants collected between 2001 and 2016. We investigated elephant behavior in response to landcover, topography, productivity, water, human features and human predation risk using third-order resource selection functions. We extended this analysis by employing a mixed-effects multinomial regression to identify temporal shifts in habitat use, and evaluated temporal shifts in movement patterns by estimating mean squared displacement across different productivity periods. Across periods, elephants displayed strong selection for productive areas and areas near water. Temporal shifts in habitat use showed that, during the dry period, elephants were clustered around permanent water sources where humans also congregated. At the onset of the wet period, a shift occurred where elephants moved away from permanent water and from permanent settlements towards seasonal water sources and seasonal settlements. Our findings indicate that foraging and water access are important limiting factors affecting elephants that potentially restrain their spatial responses to humans at the scale of our analysis. Given that pastoralists and elephants rely on the same resources, increasing human and livestock populations enhance pressure on shared resources and space in Africa's drylands. The long-term conservation of elephants will require approaches that reduce poaching as well as landscape level planning to prevent negative impacts from increasing competition for preferred resources.     

Genomic inferences from Afrotheria and the evolution of elephants

Recent genetic studies have established that African forest and savanna elephants are distinct species with dissociated cytonuclear genomic patterns, and have identified Asian elephants from Borneo and Sumatra as conservation priorities. Representative of Afrotheria, a superordinal clade encompassing six eutherian orders, the African savanna elephant was among the first mammals chosen for whole-genome sequencing to provide a comparative understanding of the human genome. Elephants have large and complex brains and display advanced levels of social structure, communication, learning and intelligence. The elephant genome sequence might prove useful for comparative genomic studies of these advanced traits, which have appeared independently in only three mammalian orders: primates, cetaceans and proboscideans.     

A population survey of forest elephants (Loxodonta africana cyclotis) in northern Congo

From February to April of 1989 transects were run in four forested areas of northern Congo (Brazzaville) to census elephant populations using dung counts. A total of 401.0 km of line transects was completed during the survey. An overall extrapolated density of 0.7 elephants/km² was obtained with a variation from 0.3 to 0.9 elephants/km². This study shows for the first time that elephants occur in high densities in a number of sites in northern Congo. When elephant dung density is plotted against distance from the nearest village for each transect a significant positive linear correlation results. Based on this correlation we hypothesize that the population of elephants in much of northern Congo is high. Local reports and our own observations indicate that elephant poaching is heavy in northern Congo and that the CITES ban on trade in African elephant ivory has had a limited effect on the level of poaching.     

The evolution and phylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers

Recent genetic results support the recognition of two African elephant species: Loxodonta africana, the savannah elephant, and Loxodonta cyclotis, the forest elephant. The study, however, did not include the populations of West Africa, where the taxonomic affinities of elephants have been much debated. We examined mitochondrial cytochrome b control region sequences and four microsatellite loci to investigate the genetic differences between the forest and savannah elephants of West and Central Africa. We then combined our data with published control region sequences from across Africa to examine patterns at the continental level. Our analysis reveals several deeply divergent lineages that do not correspond with the currently recognized taxonomy: (i) the forest elephants of Central Africa; the forest and savannah elephants of West Africa; and (iii) the savannah elephants of eastern, southern and Central Africa. We propose that the complex phylogeographic patterns we detect in African elephants result from repeated continental-scale climatic changes over their five-to-six million year evolutionary history. Until there is consensus on the taxonomy, we suggest that the genetic and ecological distinctness of these lineages should be an important factor in conservation management planning.     

Characterization of tetranucleotide microsatellite loci in the African Savannah Elephant (Loxodonta africana africana)

Most African elephant (Loxodonta africana africana) populations are isolated and thus threatened by a loss of genetic diversity. As a consequence, genetic analysis of African elephant populations will play an increasing role in their conservation, and microsatellite loci will be an important tool in these analyses. Previously published sets of polymorphic microsatellites developed for African elephants are all dinucleotide repeats, which are prone to typing error. Here, we characterize 11 tetranucleotide microsatellite loci in the African elephant. All loci were polymorphic in 32 faecal samples and two tissue samples from 33 individual African savannah elephants.     

Forest elephant crisis in the Congo Basin

Debate over repealing the ivory trade ban dominates conferences of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Resolving this controversy requires accurate estimates of elephant population trends and rates of illegal killing. Most African savannah elephant populations are well known; however, the status of forest elephants, perhaps a distinct species, in the vast Congo Basin is unclear. We assessed population status and incidence of poaching from line-transect and reconnaissance surveys conducted on foot in sites throughout the Congo Basin. Results indicate that the abundance and range of forest elephants are threatened from poaching that is most intense close to roads. The probability of elephant presence increased with distance to roads, whereas that of human signs declined. At all distances from roads, the probability of elephant occurrence was always higher inside, compared to outside, protected areas, whereas that of humans was always lower. Inside protected areas, forest elephant density was correlated with the size of remote forest core, but not with size of protected area. Forest elephants must be prioritised in elephant management planning at the continental scale.     

Elephants of south‐east Angola in war and peace: their decline,re‐colonization and recent status

Angola’s intermittent 27‐year civil war displaced over four million people and decimated wildlife populations. During the 1980s, African elephants (Loxodonta africana Blumenbach) in Angola drew international alarm with reports of 100,000 elephants killed. Luiana Partial Reserve (PR), a conservation area in south‐east Angola, was the military operations centre for UNITA (National Union for the Total Independence of Angola), which used elephant ivory to pay for arms and meat. However, the full impact of the civil war on elephants is uncertain because there are no reliable estimates of Angolan elephant populations. Following the end of the civil war in 2002, our three aerial surveys of Luiana PR indicated that elephant numbers are increasing rapidly, from 366 in January 2004 to 1827 in November 2005, and expanding their range in the Reserve. Concurrently, elephants tagged with satellite collars in northern Botswana and the Caprivi Strip, Namibia, moved into Luiana PR. To facilitate re‐colonization and conservation of elephants and other wildlife in Luiana PR, we recommend: (i) realignment of the veterinary fence on the Botswana–Namibia border; (ii) development of effective land use management and anti‐poaching programmes; (iii) clearing of landmines; (iv) designation of the Reserve a national park; and (v) development of ecotourism and community conservation programmes.     

Using Poaching Levels and Elephant Distribution to Assess the Conservation Efficacy of Private,Communal and Government Land in Northern Kenya

Efforts to curb elephant poaching have focused on reducing demand, confiscating ivory and boosting security patrols in elephant range. Where land is under multiple uses and ownership, determining the local poaching dynamics is important for identifying successful conservation models. Using 2,403 verified elephant, Loxodonta africana, mortality records collected from 2002 to 2012 and the results of aerial total counts of elephants conducted in 2002, 2008 and 2012 for the Laikipia-Samburu ecosystem of northern Kenya, we sought to determine the influence of land ownership and use on diurnal elephant distribution and on poaching levels. We show that the annual proportions of illegally killed (i.e., poached) elephants increased over the 11 years of the study, peaking at 70% of all recorded deaths in 2012. The type of land use was more strongly related to levels of poaching than was the type of ownership. Private ranches, comprising only 13% of land area, hosted almost half of the elephant population and had significantly lower levels of poaching than other land use types except for the officially designated national reserves (covering only 1.6% of elephant range in the ecosystem). Communal grazing lands hosted significantly fewer elephants than expected, but community areas set aside for wildlife demonstrated significantly higher numbers of elephants and lower illegal killing levels relative to non-designated community lands. While private lands had lower illegal killing levels than community conservancies, the success of the latter relative to other community-held lands shows the importance of this model of land use for conservation. This work highlights the relationship between illegal killing and various land ownership and use models, which can help focus anti-poaching activities.     

Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants

Conservation strategies for African elephants would be advanced by resolution of conflicting claims that they comprise one, two, three or four taxonomic groups, and by development of genetic markers that establish more incisively the provenance of confiscated ivory. We addressed these related issues by genotyping 555 elephants from across Africa with microsatellite markers, developing a method to identify those loci most effective at geographic assignment of elephants (or their ivory), and conducting novel analyses of continent-wide datasets of mitochondrial DNA. Results showed that nuclear genetic diversity was partitioned into two clusters, corresponding to African forest elephants (99.5% Cluster-1) and African savanna elephants (99.4% Cluster-2). Hybrid individuals were rare. In a comparison of basal forest "F" and savanna "S" mtDNA clade distributions to nuclear DNA partitions, forest elephant nuclear genotypes occurred only in populations in which S clade mtDNA was absent, suggesting that nuclear partitioning corresponds to the presence or absence of S clade mtDNA. We reanalyzed African elephant mtDNA sequences from 81 locales spanning the continent and discovered that S clade mtDNA was completely absent among elephants at all 30 sampled tropical forest locales. The distribution of savanna nuclear DNA and S clade mtDNA corresponded closely to range boundaries traditionally ascribed to the savanna elephant species based on habitat and morphology. Further, a reanalysis of nuclear genetic assignment results suggested that West African elephants do not comprise a distinct third species. Finally, we show that some DNA markers will be more useful than others for determining the geographic origins of illegal ivory. These findings resolve the apparent incongruence between mtDNA and nuclear genetic patterns that has confounded the taxonomy of African elephants, affirm the limitations of using mtDNA patterns to infer elephant systematics or population structure, and strongly support the existence of two elephant species in Africa.     

Effects of poaching on bull mating success in a free ranging African elephant (Loxodonta africana) population in Tarangire National Park, Tanzania

Poaching and habitat encroachment for human settlement are the two major factors that caused contraction of elephant populations in Africa. While the effects of poaching on many aspects of elephant social systems have been studied, the impacts on mating patterns are not yet understood and such information is still lacking in most African countries. In this study, we used elephant specific-microsatellite DNA to generate genotypes from 86 elephant samples (84 fresh faeces and two tissue samples) from Tarangire National Park (TNP), Tanzania to assess the mating success of individual males. We also tested whether the oldest bulls are more likely to sire most of the offspring in a severely poached population. Genetic paternity analysis was compared to behavioural observations of matings collected over a 3-year period (1998–2001) to determine the success of bull mating strategy. The genotypes of 26 infants, their known mothers and 10 out of 43 potential breeding bulls in TNP were used to assign 31% of the offspring at 80% confidence level to their potential fathers with simulation assuming that 23% (10/43) of the breeding males were sampled. Mating success of individual bull based on both behavioural and genetic data showed that the oldest remaining bulls performed most of the matings and fathered the majority of infants. We speculate that the lifetime fitness of bulls that have survived poaching may be elevated because their period of dominance increases.     

Estimating population sizes for elusive animals: the forest elephants of Kakum National Park,Ghana

African forest elephants are difficult to observe in the dense vegetation, and previous studies have relied upon indirect methods to estimate population sizes. Using multilocus genotyping of noninvasively collected samples, we performed a genetic survey of the forest elephant population at Kakum National Park, Ghana. We estimated population size, sex ratio and genetic variability from our data, then combined this information with field observations to divide the population into age groups. Our population size estimate was very close to that obtained using dung counts, the most commonly used indirect method of estimating the population sizes of forest elephant populations. As their habitat is fragmented by expanding human populations, management will be increasingly important to the persistence of forest elephant populations. The data that can be obtained from noninvasively collected samples will help managers plan for the conservation of this keystone species.     

Demography of a population with a long history of poaching and the utility of the individual identification technique as a tool for monitoring intermittently studied elephant populations

In many elephant populations in Africa, adverse effects of poaching including altered age and sex structure and long calving intervals continue to negatively impact the rate of recovery. The study reported here characterized the demographic status of the elephant population in Meru National Park, Kenya, so as to determine the size, age and sex structure, and calving interval of the population and to compare its demographic parameters against those from the relatively stable elephant population at Amboseli. Additionally, a demographic study conducted 7 years earlier enabled us to determine the demographic performance of the population and to explicitly test the utility of the individual identification technique in monitoring intermittently studied populations. We found 392 elephants in the park. The proportion of older individuals was lower, and the calving interval was longer than estimates from Amboseli. We recognized 16% of elephants indexed in the previous study. Our results suggest that the individual identification technique may be useful in monitoring demographic changes including poaching in intermittently studied elephant populations. Overall, our results suggest that although the Meru elephant population showed signs of recovery, poaching continues to imperil its recovery.     

Genetic diversity, social structure, and conservation value of the elephants of the Nakai Plateau, Lao PDR, based on non-invasive sampling

The Lao People??s Democratic Republic (PDR) may have the largest Asian elephant population in Indochina. However, elephants on Lao PDR??s Nakai Plateau are potentially threatened by the construction of a hydropower dam that will flood important habitat. We conducted a non-invasive genetic study of elephants in this region to provide baseline data on genetic diversity and social structure prior to dam construction. For the 102 elephants we detected, values of observed heterozygosity (0.711) and allelic diversity (8.0 alleles/locus) at microsatellite loci were higher than those found in elephant populations in India and Vietnam, while mitochondrial diversity (haplotype diversity 0.741; nucleotide diversity 0.011) was similar to that reported for the Lao/Vietnam region. Six mitochondrial haplotypes were detected, representing both major clades previously reported in this species. Relatedness estimates between females and young detected near each other are consistent with familial relationships, and relatedness estimates between adult males and females suggest male locational dispersal. Since family group structure appears to be intact in the Nakai region, these elephants will likely move as relatively large family groups in response to habitat disturbance. These results have positive implications for the viability of the elephant population in this region, demonstrate its conservation significance, and will be valuable for predicting and monitoring the effects of the hydropower dam over time.     

Honest signalling through chemicals by elephants with applications for care and conservation

Chemical signals are difficult to fake because they are often directly associated with phenotype and physiological condition, and hence likely to be honest signals for intraspecific communication. Chemical signals may be modified after release by the sender or by the environment. The proximate and ultimate signal meanings are dependent not only on the condition of the sender, but also on the physiological status of the receiver. Understanding the relationships and linkage among signal modality, signal function and receiver response is an essential first step before using natural signals for animal care and conservation. Our studies on chemical communication in Asian and African elephants combine observational and experimental work in captive and wild settings to further this understanding. Recent discoveries of pheromones in Asian elephants and the biochemistry of these compounds provide strong evidence that such chemical signals are honest indicators of reproductive status. Chemically identifying the signals and verifying their functional context with statistically robust behavioural studies are essential aspects for understanding the communication system. Additionally, the investigative process of discovering, identifying and verifying the function of chemical signals among captive elephants offers safe and stimulating enrichments. The knowledge garnered from such studies has potential conservation benefits for managing wild elephant populations. A firm foundation of scientific information is required for successful behavioural investigations and applied conservation and enrichment components.     

Using genetic analysis to estimate population size,sex ratio,and social organization in an Asian elephant population in conflict with humans in Alur,southern India

With growing human and, possibly, elephant populations and a drastic increase in anthropogenic activities, human–elephant conflict in Asia has been on the rise. The Alur area in Karnataka state, southern India, is one such case in point, which has witnessed increasing levels of human–elephant conflict over the last two decades. The tiny, moderately protected habitat available for elephants in this human-dominated landscape does not appear to be able to support elephants over the long term. Options to deal with the escalating conflict include translocation of elephants, bringing elephants into captivity, and culling. We carried out a molecular genetic study of elephants in the Alur area to estimate the minimum number of elephants using the area, the sex ratio, genetic relatedness between individuals, and genetic structure with regard to the larger population in the landscape, so that informed management decisions could be made. Fresh dung samples were collected from the field and genotyped using 12 microsatellite loci. We found 29 unique individuals in the population, comprising 17 females and 12 males of different age classes. Relatedness between females suggested independent colonisations by discrete, small groups rather than by one cohesive clan of related females. This obviates the need for a single solution for dealing with all the females in the area in order to maintain social integrity, and has implications in terms how these elephants can be dealt with. We demonstrate how social organization inferred through molecular data from non-invasive sampling can inform management decisions.     

Patterns of molecular genetic variation among African elephant populations

The highly threatened African elephants have recently been subdivided into two species, Loxodonta africana (savannah or bush elephant) and L. cyclotis (forest elephant) based on morphological and molecular studies. A molecular genetic assessment of 16 microsatellite loci across 20 populations (189 individuals) affirms species level genetic differentiation and provides robust genotypic assessment of species affiliation. Savannah elephant populations show modest levels of phylogeographic subdivision based on composite microsatellite genotype, an indication of recent population isolation and restricted gene flow between locales. The savannah elephants show significantly lower genetic diversity than forest elephants, probably reflecting a founder effect in the recent history of the savannah species.