Generation and Characterization of Antibodies against Asian Elephant (Elephas maximus) IgG,IgM, and IgA

Asian elephant (Elephas maximus) immunity is poorly characterized and understood. This gap in knowledge is particularly concerning as Asian elephants are an endangered species threatened by a newly discovered herpesvirus known as elephant endotheliotropic herpesvirus (EEHV), which is the leading cause of death for captive Asian elephants born after 1980 in North America. While reliable diagnostic assays have been developed to detect EEHV DNA, serological assays to evaluate elephant anti-EEHV antibody responses are lacking and will be needed for surveillance and epidemiological studies and also for evaluating potential treatments or vaccines against lethal EEHV infection. Previous studies have shown that Asian elephants produce IgG in serum, but they failed to detect IgM and IgA, further hampering development of informative serological assays for this species. To begin to address this issue, we determined the constant region genomic sequence of Asian elephant IgM and obtained some limited protein sequence information for putative serum IgA. The information was used to generate or identify specific commercial antisera reactive against IgM and IgA isotypes. In addition, we generated a monoclonal antibody against Asian elephant IgG. These three reagents were used to demonstrate that all three immunoglobulin isotypes are found in Asian elephant serum and milk and to detect antibody responses following tetanus toxoid booster vaccination or antibodies against a putative EEHV structural protein. The results indicate that these new reagents will be useful for developing sensitive and specific assays to detect and characterize elephant antibody responses for any pathogen or vaccine, including EEHV.     

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。     

Trunkloads of Viruses

Elephant populations are under intense pressure internationally from habitat destruction and poaching for ivory and meat. They also face pressure from infectious agents, including elephant endotheliotropic herpesvirus 1 (EEHV1), which kills ∼20% of Asian elephants (Elephas maximus) born in zoos and causes disease in the wild. EEHV1 is one of at least six distinct EEHV in a phylogenetic lineage that appears to represent an ancient but newly recognized subfamily (the Deltaherpesvirinae) in the family Herpesviridae.     

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.     

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.     

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.     

A Comparison of Social Organization in Asian Elephants and African Savannah Elephants

Asian and African elephant species have diverged by ca. 6 million years, but as large, generalist herbivores they occupy similar niches in their respective environments. Although the multilevel, hierarchical nature of African savannah elephant societies is well established, it has been unclear whether Asian elephants behave similarly. Here we quantitatively compare the structure of both species’ societies using association data collected using the same protocol over similar time periods. Sociality in both species demonstrates well-defined structure, but in contrast to the African elephants of Samburu the Uda Walawe Asian elephants are found in smaller groups, do not maintain coherent core groups, demonstrate markedly less social connectivity at the population level, and are socially less influenced by seasonal differences in ecological conditions. The Uda Walawe Asian elephants, however, do maintain a complex, well-networked society consisting of ≥2 differentiated types of associates we term ephemeral and long-term affiliates. These findings imply we must broaden our recognition of multilevel social organization to encompass societies that fall along a gradient of nestedness, and not merely those that exhibit hierarchical nesting. This in turn suggests that multilevel structures may be more diverse and widespread than generally thought, and that phylogenetic comparisons within species-rich clades, such as that of primates, using the methods presented can provide fresh insights into their socioecological basis.     

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.     

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.     

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.     

Endocrine Correlates of Musth in Free-Ranging Asian Elephants (Elephas maximus) Determined by Non-Invasive Faecal Steroid Hormone Metabolite Measurements

The occurrence of musth, a period of elevated levels of androgens and heightened sexual activity, has been well documented for the male Asian elephant (Elephas maximus). However, the relationship between androgen-dependent musth and adrenocortical function in this species is unclear. The current study is the first assessment of testicular and adrenocortical function in free-ranging male Asian elephants by measuring levels of testosterone (androgen) and cortisol (glucocorticoid – a physiological indicator of stress) metabolites in faeces. During musth, males expectedly showed significant elevation in faecal testosterone metabolite levels. Interestingly, glucocorticoid metabolite concentrations remained unchanged between musth and non-musth periods. This observation is contrary to that observed with wild and captive African elephant bulls and captive Asian bull elephants. Our results show that musth may not necessarily represent a stressful condition in free-ranging male Asian elephants.     

Ovarian function in the elephant: luteinizing hormone and progesterone cycles in African and Asian elephants

Serum samples were collected weekly for 3 yr from two female African elephants, for 18 mo from two other female African elephants, and for 2 yr from two female Asian elephants. Animals were not sedated at the time of blood collection. Ovarian cycles, characterized by changes in progesterone and immunoreactive luteinizing hormone (ILH) concentrations, averaged 15.9 +/- 0.6 wk (N = 25) for African females and 14.7 +/- 0.5 wk for Asian females (N = 10). The length of the active luteal phase averaged 10.0 +/- 0.3 wk for African elephants (range 8-14 wk) and 10.6 +/- 0.6 wk for Asian females (range 9-13 wk). Interluteal phases were 5.9 +/- 0.6 wk for African females and 4.2 +/- 0.5 wk for Asian females. One African female (Maliaca) had two extended interluteal phases, both occurring between the months of February and May. Excluding these two periods, there were no differences in the length of the ovarian cycle or the length of the luteal phase between species of elephant. Serum progesterone in both species ranged from less than 50 pg/ml to 933 pg/ml. Average progesterone concentrations during the luteal phase were significantly lower in African elephants compared with Asian elephants (328 +/- 13, N = 30 cycles vs. 456 +/- 23, N = 14 cycles; p less than 0.001). ILH ranged from nondetectable to 11.6 ng/ml. These data suggest that the length of the ovarian cycle in the African elephant is about 16 wk and confirm that the length of the ovarian cycle in the Asian elephant is about 15 wk.     

Conservation status of Asian elephants: the influence of habitat and governance

Understanding the drivers of Asian elephant (Elephas maximus) abundance and distribution is critical for effective elephant conservation, yet no such analysis exists despite decades of assessments and planning. We explored the influence of habitat- and governance-related drivers on elephant abundance across the 13 Asian elephant range countries. We tested competing statistical models by integrating a binary index of elephant abundance (IEA) derived from expert knowledge with different predictor variables including habitat, human population, socioeconomics, and governance data. We employed logistic regression and model-averaging techniques based on Akaike’s Information Criterion to identify the best-performing subset among our 12 candidate models and used the model-averaged results to predict IEA in other areas in Asia where elephant population status is currently unknown. Forest area was our strongest single predictor variable. The best performing model, however, featured a combination of habitat and governance variables including forest area, level of corruption, proportional mix of forest and agriculture, and total agricultural area. Our predictive model identified five areas with medium–high to high probability to have populations with >150 elephants, which we believe should be surveyed to assess their status. Asian elephants persist in areas that are dominated by forest but also seem to benefit from a mix of agricultural activities. A relatively low level of corruption is also important and we conclude that effective governance is essential for maintaining Asian elephant populations. Asian elephant populations cannot be maintained solely in protected areas but need well-managed, mixed-use landscapes where people and elephants coexist.     

Sexual Dimorphism and Inter-Generic Variation in Proboscidean Tusks: Multivariate Assessment of American Mastodons (Mammut americanum) and Extant African Elephants

Characteristics of social structure, mating strategies, and parental investment can be inferred for mammalian species based on degree of sexual dimorphism, especially when males are substantially larger than females. American mastodons (Mammut americanum) and extant African elephants (Loxodonta africana, Loxodonta cyclotis) both exhibit marked dimorphism in tusk size. To evaluate the hypothesis that this dimorphism might be indicative of similar, and possibly conserved, behavioral patterns in each lineage, we undertook a detailed evaluation of the pattern of tusk growth in these two genera. Separate discriminant function analyses (DFA) of 21 adult mastodon tusks of inferred sex and 48 adult elephant tusks of known sex show that patterns of ontogenetic change in tusk circumference, regardless of genus, effectively discriminate between sexes. Canonical variates analysis (CVA) of tusks from male and female mastodons and male and female elephants shows that male tusks in both genera are larger than female tusks across all measurements, especially for maximum tusk circumference and pulp cavity depth. CVA’s emphasis of inter-group differences in tusk morphology also shows that mastodon tusks are more robust than elephant tusks. Overall, this study illustrates that there is a characteristic male and a characteristic female tusk form shared by elephants and mastodons. This shows that elephants and mastodons display a shared syndrome of traits beyond sex-linked differences in tusk size, supporting the hypothesis that mastodons exhibited behaviors similar to those we observe today in African elephants.     

DNA analysis indicates that Asian elephants are native to Borneo and are therefore a high priority for conservation

The origin of Borneo's elephants is controversial. Two competing hypotheses argue that they are either indigenous, tracing back to the Pleistocene, or were introduced, descending from elephants imported in the 16th-18th centuries. Taxonomically, they have either been classified as a unique subspecies or placed under the Indian or Sumatran subspecies. If shown to be a unique indigenous population, this would extend the natural species range of the Asian elephant by 1300 km, and therefore Borneo elephants would have much greater conservation importance than if they were a feral population. We compared DNA of Borneo elephants to that of elephants from across the range of the Asian elephant, using a fragment of mitochondrial DNA, including part of the hypervariable d-loop, and five autosomal microsatellite loci. We find that Borneo's elephants are genetically distinct, with molecular divergence indicative of a Pleistocene colonisation of Borneo and subsequent isolation. We reject the hypothesis that Borneo's elephants were introduced. The genetic divergence of Borneo elephants warrants their recognition as a separate evolutionary significant unit. Thus, interbreeding Borneo elephants with those from other populations would be contraindicated in ex situ conservation, and their genetic distinctiveness makes them one of the highest priority populations for Asian elephant conservation.     

Problem-Elephant Translocation: Translocating the Problem and the Elephant?

Human-elephant conflict (HEC) threatens the survival of endangered Asian elephants (Elephas maximus). Translocating “problem-elephants” is an important HEC mitigation and elephant conservation strategy across elephant range, with hundreds translocated annually. In the first comprehensive assessment of elephant translocation, we monitored 16 translocations in Sri Lanka with GPS collars. All translocated elephants were released into national parks. Two were killed within the parks where they were released, while all the others left those parks. Translocated elephants showed variable responses: “homers” returned to the capture site, “wanderers” ranged widely, and “settlers” established home ranges in new areas soon after release. Translocation caused wider propagation and intensification of HEC, and increased elephant mortality. We conclude that translocation defeats both HEC mitigation and elephant conservation goals.     

Complete Genome Sequences of Elephant Endotheliotropic Herpesviruses 1A and 1B Determined Directly from Fatal Cases

A highly lethal hemorrhagic disease associated with infection by elephant endotheliotropic herpesvirus (EEHV) poses a severe threat to Asian elephant husbandry. We have used high-throughput methods to sequence the genomes of the two genotypes that are involved in most fatalities, namely, EEHV1A and EEHV1B (species Elephantid herpesvirus 1, genus Proboscivirus, subfamily Betaherpesvirinae, family Herpesviridae). The sequences were determined from postmortem tissue samples, despite the data containing tiny proportions of viral reads among reads from a host for which the genome sequence was not available. The EEHV1A genome is 180,421 bp in size and consists of a unique sequence (174,601 bp) flanked by a terminal direct repeat (2,910 bp). The genome contains 116 predicted protein-coding genes, of which six are fragmented, and seven paralogous gene families are present. The EEHV1B genome is very similar to that of EEHV1A in structure, size, and gene layout. Half of the EEHV1A genes lack orthologs in other members of subfamily Betaherpesvirinae, such as human cytomegalovirus (genus Cytomegalovirus) and human herpesvirus 6A (genus Roseolovirus). Notable among these are 23 genes encoding type 3 membrane proteins containing seven transmembrane domains (the 7TM family) and seven genes encoding related type 2 membrane proteins (the EE50 family). The EE50 family appears to be under intense evolutionary selection, as it is highly diverged between the two genotypes, exhibits evidence of sequence duplications or deletions, and contains several fragmented genes. The availability of the genome sequences will facilitate future research on the epidemiology, pathogenesis, diagnosis, and treatment of EEHV-associated disease.     

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.