Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants

To elucidate the history of living and extinct elephantids, we generated 39,763 bp of aligned nuclear DNA sequence across 375 loci for African savanna elephant, African forest elephant, Asian elephant, the extinct American mastodon, and the woolly mammoth. Our data establish that the Asian elephant is the closest living relative of the extinct mammoth in the nuclear genome, extending previous findings from mitochondrial DNA analyses. We also find that savanna and forest elephants, which some have argued are the same species, are as or more divergent in the nuclear genome as mammoths and Asian elephants, which are considered to be distinct genera, thus resolving a long-standing debate about the appropriate taxonomic classification of the African elephants. Finally, we document a much larger effective population size in forest elephants compared with the other elephantid taxa, likely reflecting species differences in ancient geographic structure and range and differences in life history traits such as variance in male reproductive success.     

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.     

Seed dispersal kernel of the largest surviving megaherbivore—the African savanna elephant

Owing to the late Pleistocene extinctions, the megafauna of Europe, Australia and the Americas disappeared, and with them the dispersal service they offered megafaunal fruit. The African savanna elephant, the largest remaining megaherbivore, offers valuable insights into the seed dispersal services provided by extinct megafauna in prehistoric times. Elephant seed dispersal studies have for the most part concentrated on African and Asian forest elephants. African savanna elephants are morphologically distinct from their forest counterparts. Like the forest elephants they consume large quantities of fruit from a large number of tree species. Despite this little is known of the savanna trees that rely on elephants for their dispersal or the spatial scale at which these seeds are dispersed. We combined information from feeding trials conducted on four park elephants with field telemetry data from 38 collared elephants collected over an 8‐year period in APNR/Kruger National Park to assess the seed dispersal service provided by savanna elephants. This study provides the first detailed account of the spatial scale at which African savanna elephants disperse seeds. Our mechanistic model predicts that 50 percent of seeds are carried over 2.5 km, and distances up to 65 km are achievable in maximum gut passage time. These findings suggest the savanna elephant as the longest distance terrestrial vertebrate disperser yet investigated. Maintaining their ecological role as a seed disperser may prove a significant factor in the conservation of large‐fruited tree diversity within the savannas. These results suggest that extinct megafauna offered a functionally unique dispersal service to megafaunal fruit.     

Elephant Genomes Reveal Accelerated Evolution in Mechanisms Underlying Disease Defenses

Disease susceptibility and resistance are important factors for the conservation of endangered species, including elephants. We analyzed pathology data from 26 zoos and report that Asian elephants have increased neoplasia and malignancy prevalence compared with African bush elephants. This is consistent with observed higher susceptibility to tuberculosis and elephant endotheliotropic herpesvirus (EEHV) in Asian elephants. To investigate genetic mechanisms underlying disease resistance, including differential responses between species, among other elephant traits, we sequenced multiple elephant genomes. We report a draft assembly for an Asian elephant, and defined 862 and 1,017 conserved potential regulatory elements in Asian and African bush elephants, respectively. In the genomes of both elephant species, conserved elements were significantly enriched with genes differentially expressed between the species. In Asian elephants, these putative regulatory regions were involved in immunity pathways including tumor-necrosis factor, which plays an important role in EEHV response. Genomic sequences of African bush, forest, and Asian elephant genomes revealed extensive sequence conservation at TP53 retrogene loci across three species, which may be related to TP53 functionality in elephant cancer resistance. Positive selection scans revealed outlier genes related to additional elephant traits. Our study suggests that gene regulation plays an important role in the differential inflammatory response of Asian and African elephants, leading to increased infectious disease and cancer susceptibility in Asian elephants. These genomic discoveries can inform future functional and translational studies aimed at identifying effective treatment approaches for ill elephants, which may improve conservation.     

Species‐specific germination responses to fire‐associated heat of elephant‐dispersed seeds in Nimule National Park,South Sudan

Fire‐related heat and endozoochory by elephants have independently been found to be important for savanna plant seed germination, yet there is little information on how heat affects germination of elephant‐dispersed seeds. We measured the germination behavior (time to germination and proportion of seeds germinating) of 11 species of seeds extracted from African savanna elephant dung and subjected them to various intensities of heat as a proxy for fire exposure. The effects of heat were inconsistent and varied significantly by species, with some species having increased time to germination in response to heat and others having reduced time to germination. More studies are needed to expand the number of seed species examined and tease apart the interaction between elephant‐mediated endozoochory and fire.     

Forest elephant mitochondrial genomes reveal that elephantid diversification in Africa tracked climate transitions

Among elephants, the phylogeographic patterns of mitochondrial (mt) and nuclear markers are often incongruent. One hypothesis attributes this to sex differences in dispersal and in the variance of reproductive success. We tested this hypothesis by examining the coalescent dates of genetic markers within elephantid lineages, predicting that lower dispersal and lower variance in reproductive success among females would have increased mtDNA relative to nuclear coalescent dates. We sequenced the mitochondrial genomes of two forest elephants, aligning them to mitogenomes of African savanna and Asian elephants, and of woolly mammoths, including the most divergent mitogenomes within each lineage. Using fossil calibrations, the divergence between African elephant F and S clade mitochondrial genomes (originating in forest and savanna elephant lineages, respectively) was estimated as 5.5 Ma. We estimated that the (African) ancestor of the mammoth and Asian elephant lineages diverged 6.0 Ma, indicating that four elephantid lineages had differentiated in Africa by the Miocene–Pliocene transition, concurrent with drier climates. The coalescent date for forest elephant mtDNAs was c. 2.4 Ma, suggesting that the decrease in tropical forest cover during the Pleistocene isolated distinct African forest elephant lineages. For all elephantid lineages, the ratio of mtDNA to nuclear coalescent dates was much greater than 0.25. This is consistent with the expectation that sex differences in dispersal and in variance of reproductive success would have increased the effective population size of mtDNA relative to nuclear markers in elephantids, contributing to the persistence of incongruent mtDNA phylogeographic patterns.     

Enriching the captive elephant population genetic pool through artificial insemination with frozen-thawed semen collected in the wild

The first successful AI in an elephant was reported in 1998, using fresh semen. Since then almost 40 calves have been produced through AI in both Asian and African elephants worldwide. Following these successes, with the objective of enriching the captive population with genetic material from the wild, we evaluated the possibility of using frozen-thawed semen collected from wild bulls for AI in captivity. Semen, collected from a 36-yr-old wild African savanna elephant (Loxodonta africana) in South Africa was frozen using the directional freezing technique. This frozen-thawed semen was used for four inseminations over two consecutive days, two before and two after ovulation, in a 26-yr-old female African savanna elephant in Austria. Insemination dose of 1200 × 10⁶ cells per AI with 61% motility resulted in pregnancy, which was confirmed through ultrasound examination 75, 110 and 141 days after the AI procedure. This represents the first successful AI using wild bull frozen-thawed semen in elephants. The incorporation of AI with frozen-thawed semen into the assisted reproduction toolbox opens the way to preserve and transport semen between distant individuals in captivity or, as was done in this study, between wild and captive populations, without the need to transport stressed or potentially disease-carrying animals or to remove animals from the wild. In addition, cryopreserved spermatozoa, in combination with AI, are useful methods to extend the reproductive lifespan of individuals beyond their biological lifespan and an important tool for genetic diversity management and phenotype selection in these endangered mammals.     

A TECHNIQUE TO ‘TAG’ SPECIFIC VOCALIZATIONS IN TAPE-RECORDINGS OF COMPLEX VOCAL INTERACTIONS

ABSTRACT

It has been suggested that African savanna elephants Loxodonta africana produce 31 different call types (Langbauer 2000). Various researchers have described these calls by associating them with specific behavioural contexts. More recently Leong et al. (2003) have attempted to classify elephant call types based on their physical properties. They classified 8 acoustically distinct call types from a population of captive elephants. This study focuses on one of these call types, the rumble, in a wild population of elephants in Kruger National Park, South Africa. A single family group of elephants was followed to record group behaviours and vocalizations from January through August 2001. By measuring the physical properties of 663 rumbles and subjecting these to cluster analysis, we present evidence that shows that rumbles can be categorized by their physical properties and that the resulting rumble types are associated with specific group behaviours. We characterize three types of rumbles that differ significantly by ten acoustic parameters. Two rumble types were associated with the elephant group feeding and resting, while the third was associated with socializing and agitation.     

New evidence for hybrid zones of forest and savanna elephants in Central and West Africa

The African elephant consists of forest and savanna subspecies. Both subspecies are highly endangered due to severe poaching and habitat loss, and knowledge of their population structure is vital to their conservation. Previous studies have demonstrated marked genetic and morphological differences between forest and savanna elephants, and despite extensive sampling, genetic evidence of hybridization between them has been restricted largely to a few hybrids in the Garamba region of northeastern Democratic Republic of Congo (DRC). Here, we present new genetic data on hybridization from previously unsampled areas of Africa. Novel statistical methods applied to these data identify 46 hybrid samples – many more than have been previously identified – only two of which are from the Garamba region. The remaining 44 are from three other geographically distinct locations: a major hybrid zone along the border of the DRC and Uganda, a second potential hybrid zone in Central African Republic and a smaller fraction of hybrids in the Pendjari–Arli complex of West Africa. Most of the hybrids show evidence of interbreeding over more than one generation, demonstrating that hybrids are fertile. Mitochondrial and Y chromosome data demonstrate that the hybridization is bidirectional, involving males and females from both subspecies. We hypothesize that the hybrid zones may have been facilitated by poaching and habitat modification. The localized geography and rarity of hybrid zones, their possible facilitation from human pressures, and the high divergence and genetic distinctness of forest and savanna elephants throughout their ranges, are consistent with calls for separate species classification.     

Molecular and morphological evidence on the phylogeny of the Elephantidae

The African and Asian elephants and the mammoth diverged ca. 4-6 million years ago and their phylogenetic relationship has been controversial. Morphological studies have suggested a mammoth Asian elephant relationship, while molecular studies have produced conflicting results. We obtained cytochrome b sequences of up to 545 base pairs from five mammoths, 14 Asian and eight African elephants. A high degree of polymorphism is detected within species. With a dugong sequence used as the outgroup, parsimony and maximum-likelihood analyses support a mammoth African elephant clade. As the dugong is a very distant outgroup, we employ likelihood analysis to root the tree with a molecular clock, and use bootstrap and Bayesian analyses to quantify the relative support for different topologies. The analyses support the mammoth African elephant relationship, although other trees cannot be rejected. Ancestral polymorphisms may have resulted in gene trees differing from the species phylogeny Examination of morphological data, especially from primitive fossil members, indicates that some supposed synapomorphies between the mammoth and Asian elephant are variable, others convergent or autapomorphous. A mammoth African elephant relationship is not excluded. Our results highlight the need, in both morphological and molecular phylogenetics, for multiple markers and close attention to within-taxon variation and outgroup selection.     

Elephant distribution around a volcanic shield dominated by a mosaic of forest and savanna (Marsabit, Kenya)

We investigated the factors that influenced the distribution of the African elephant around a volcanic shield dominated by a mosaic of forest and savanna in northern Kenya. Data on elephant distribution were acquired from four female and five bull elephants, collared with satellite-linked geographical positioning system collars. Based on the eigenvalues (variances) of the correlation matrix, the six factors that contributed significantly to high total variances were distance from drinking water (24%), elevation (15%), shrubland (10%), forest (9%), distance from settlements (8%) and distance from minor roads (7%), contributing to 73% in the observed variation of the elephant distribution. The elephants were found at high forested elevations during the dry season but they moved to the lowlands characterized by shrubland during the wet season. Elevation acts as a proxy for the vegetation structure. The presence of elephants near permanent water points (13%) and seasonal rivers (11%) during the dry and wet seasons, respectively, demonstrates that water is the most important determinant of their distribution throughout the year. We conclude that the distribution of elephants in Marsabit Protected Area and its adjacent areas is influenced mainly by drinking water and vegetation structure.     

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.     

Observations on the length of the intestinal tract of African <Emphasis Type="Italic">Loxodonta africana</Emphasis> (Blumenbach 1797) and Asian elephants <Emphasis Type="Italic">Elephas maximus</Emphasis> (Linné 1735)

The digestive tract of elephants is surprisingly short compared to other herbivorous mammals. However, measurements relating the length of the intestine to the body mass of the respective individual are rare. In this study, we report such data for an African elephant and an Asian elephant. Our data support the hypothesis that Asian elephants have a longer intestinal tract than their African counterparts. These findings are in accord with the observation of longer retention times and higher digestion coefficients in Asian as compared to African elephants. This difference between the species could be the reflection of slightly different ecological niches, with Asian elephants adapted to a natural diet with a higher proportion of grass.     

Epigenetic clock and methylation studies in elephants

Age‐associated DNA‐methylation profiles have been used successfully to develop highly accurate biomarkers of age ("epigenetic clocks") in humans, mice, dogs, and other species. Here we present epigenetic clocks for African and Asian elephants. These clocks were developed using novel DNA methylation profiles of 140 elephant blood samples of known age, at loci that are highly conserved between mammalian species, using a custom Infinium array (HorvathMammalMethylChip40). We present epigenetic clocks for Asian elephants (Elephas maximus), African elephants (Loxodonta africana), and both elephant species combined. Two additional human‐elephant clocks were constructed by combining human and elephant samples. Epigenome‐wide association studies identified elephant age‐related CpGs and their proximal genes. The products of these genes play important roles in cellular differentiation, organismal development, metabolism, and circadian rhythms. Intracellular events observed to change with age included the methylation of bivalent chromatin domains, and targets of polycomb repressive complexes. These readily available epigenetic clocks can be used for elephant conservation efforts where accurate estimates of age are needed to predict demographic trends.     

象科动物对当地森林生态系统的影响

现存的象科动物(Elephantidae)分为非洲草原象(Loxodonta africana)、非洲森林象(Loxodonta cyclotis)和亚洲象(Elephas maximus)3 种,作为森林生态系统的关键物种,它们对当地森林生态系统的影响非常复杂,在一定环境条件下,既可能是积极的作用,也可能是消极的作用。积极的作用包括:帮助植物传播种子;促进种子萌发;创造断层,维持群落多样性;为其他动物增加食物资源;为其他动物创造栖息地。消极的作用包括:使一些物种的种群数量减小;使森林变成灌木丛和草原等。而由于活动受限导致的种群密度过高是象科动物对森林生态系统产生消极作用的主要原因。当前象科动物的3 个物种均面临种群数量锐减和生存空间不断缩小的危机,为此迫切需要针对其对生物多样性和生态平衡的影响开展深入和全面的研究,并且应根据实际情况因地制宜地制定管理措施。     

The mastodon mitochondrial genome: a mammoth accomplishment

The mitochondrial genome of an American mastodon was recently sequenced and used to root a phylogenetic analysis that included full mitochondrial genome sequences from woolly mammoths and the two living elephant genera. The study definitively established that mammoth and Asian elephant mitochondrial DNA lineages are more closely related than either is to African elephants. However, it also suggests that a complex evolutionary picture could ultimately emerge and points to similarities between the early evolution of the Elephantidae and that of the gorilla-human-chimpanzee clade.     

Elephants caught in the middle: impacts of war, fences and people on elephant distribution and abundance in the Caprivi Strip, Namibia

We conducted wet [26 March–4 April 2003 (Apr03)] and dry [1–8 November 2005 (Nov05)] season aerial surveys of African elephants ( Loxodonta africana Blumenbach) in the Caprivi Strip, Namibia to provide an updated status report on elephant numbers and distribution and assist with a historical analysis of elephant distribution and abundance in the Caprivi Strip. During the wet season when water was available in seasonal pans, elephants were widely distributed throughout the survey area. In contrast, during the dry season, a majority of elephant herds occurred within 30 km of the perennial Kwando, Linyanti and Okavango rivers and few herds occurred within the West Caprivi Game Reserve where water in the seasonal pans was limited. We estimated 5318 elephants for the 7731-km² survey area (0.71 elephants km⁻²) for the Apr03 wet season survey and 6474 elephants for the 8597-km² survey area (0.75 elephants km⁻²) for the Nov05 dry season survey. Based on our aerial surveys and reports of elephant numbers and distribution from historical aerial surveys and telemetry studies, civil war, veterinary fences and human activities appear to have effected changes in African elephant abundance, distribution and movements in the Caprivi Strip, Namibia since 1988 when the first comprehensive aerial surveys were conducted.     

Is there a future for elephants in West Africa?

The elephants of West Africa have experienced a long history of human disturbance. Before 1800 they were much affected by the precolonial empires of the savanna and Sahelian zones, the trans-Saharan trade routes, and the coastal trade established by the Europeans. During the 19th century, the increasing demand for ivory from Europe and North America, the European penetration of the region, and the evolution of breech-loading rifles devastated the remaining elephants. The elephant population of West Africa collapsed before the outbreak of World War I because of intense hunting for ivory. This collapse pre-empted the decline that would have occurred anyway due to the rapid growth of the human population and consequent loss of habitat. Elephants now find themselves in about 70 small isolated populations that cover only 5% of the region. These fragments are very vulnerable – whether in the arid lands or the humid forests – to poaching and general human disturbance. There are few data on numbers; most of the population estimates are guesses. Two-thirds of the populations are thought to consist of fewer than 200 animals and therefore have a low probability of surviving the next century. As more habitat is lost to human activities, West African elephants will soon remain only in protected areas. But many parks and reserves are managed poorly and cannot offer effective protection; they do not guarantee a future for elephants. In addition, their crop-raiding habit makes elephants unpopular in rural communities surrounding protected areas. Human populations are expected to continue growing and resources for conservation are scarce. The future of West African elephants lies in a small network of well-protected areas.     

The historical development of zoo elephant survivorship

In the discussion about zoo elephant husbandry, the report of Clubb et al. (2008, Science 322: 1649) that zoo elephants had a “compromised survivorship” compared to certain non-zoo populations is a grave argument, and was possibly one of the triggers of a large variety of investigations into zoo elephant welfare, and changes in zoo elephant management. A side observation of that report was that whereas survivorship in African elephants (Loxodonta africana) improved since 1960, this was not the case in Asian elephants (Elephas maximus). We used historical data (based on the Species360 database) to revisit this aspect, including recent developments since 2008. Assessing the North American and European populations from 1910 until today, there were significant improvements of adult (≥10 years) survivorship in both species. For the period from 1960 until today, survivorship improvement was significant for African elephants and close to a significant improvement in Asian elephants; Asian elephants generally had a higher survivorship than Africans. Juvenile (<10 years) survivorship did not change significantly since 1960 and was higher in African elephants, most likely due to the effect of elephant herpes virus on Asian elephants. Current zoo elephant survivorship is higher than some, and lower than some other non-zoo populations. We discuss that in our view, the shape of the survivorship curve, and its change over time, are more relevant than comparisons with specific populations. Zoo elephant survivorship should be monitored continuously, and the expectation of a continuous trend towards improvement should be met.