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.     

Secretory Pattern of Inhibin During Estrous Cycle and Pregnancy in African (Loxodonta africana) and Asian (Elephas maximus) Elephants

The ovary of female elephants has multiple corpora lutea (CL) during the estrous cycle and gestation. The previous reports clearly demonstrated that inhibin was secreted from lutein cells as well as granulosa cells of antral follicles in cyclic Asian elephants. The aim of this study is to investigate the inhibin secretion during the pregnancy in African and Asian elephants. Two African elephants and two Asian elephants were subjected to this study. Circulating levels of immunoreactive (ir‐) inhibin and progesterone were measured by radioimmunoassay. Four pregnant periods of an African elephant and three pregnant periods of an Asian elephant were analyzed in this study. Circulating levels of ir‐inhibin started to increase at 1 or 2 week before the ovulation and reached the peak level 3 or 4 weeks earlier than progesterone during the estrous cycle in both African and Asian elephants. After last luteal phase, the serum levels of ir‐inhibin remained low throughout pregnancy in both an African and an Asian elephant. The mean levels of ir‐inhibin during the pregnancy were lower than the luteal phase in the estrous cycle despite high progesterone levels were maintained throughout the pregnancy. These results strongly suggest that CL secrete a large amount of progesterone but not inhibin during the pregnancy in elephants. Zoo Biol 31:511‐522, 2012. © 2011 Wiley Periodicals, Inc.     

Calculation of longevity and life expectancy in captive elephants

The concepts of longevity (longest lived) and life expectancy (typical age at death) are common demographic parameters that provide insight into a population. Defined as the longest lived individual, longevity is easily calculated but is not representative, as only one individual will live to this extreme. Longevity records for North American Asian elephants (Elephas maximus) and African elephants (Loxodonta africana) have not yet been set, as the oldest individuals (77 and 53 years, respectively) are still alive. One Asian elephant lived to 86 years in the Taipei Zoo. This is comparable to the maximum (though not typical) longevity estimated in wild populations. Calculation of life expectancy, however, must use statistics that are appropriate for the data available, the distribution of the data, and the species' biology. Using a simple arithmetic mean to describe the non‐normally distributed age at death for elephant populations underestimates life expectancy. Use of life‐table analysis to estimate median survivorship or survival analysis to estimate average survivorship are more appropriate for the species' biology and the data available, and provide more accurate estimates. Using a life‐table, the median life expectancy for female Asian elephants (Lx=0.50) is 35.9 years in North America and 41.9 years in Europe. Survival analysis estimates of average life expectancy for Asian elephants are 47.6 years in Europe and 44.8 years in North America. Survival analysis estimates for African elephants are less robust due to less data. Currently the African elephant average life expectancy estimate in North America is 33.0 years, but this is likely to increase with more data, as it has over the past 10 years. Zoo Biol 23:365–373, 2004. © 2004 Wiley‐Liss, Inc.     

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.     

A Novel Objective Method of Estimating the Age of Mandibles from African Elephants (Loxodonta africana Africana)

The importance of assigning an accurate estimate of age and sex to elephant carcasses found in the wild has increased in recent years with the escalation in levels of poaching throughout Africa. Irregularities identified in current ageing techniques prompted the development of a new method to describe molar progression throughout life. Elephant mandibles (n = 323) were studied and a point near the distal dental alveolus was identified as being most useful in ranking each jaw according to molar progression. These ‘Age Reference Lines’ were then associated with an age scale based on previous studies and Zimbabwean mandibles of known age. The new ranking produced a single age scale that proved useful for both male and female mandibles up to the maximum lifespan age of 70–75 years. Methods to aid in molar identification and the sexing of found jaws were also identified.     

Survey of the reproductive cyclicity status of Asian and African elephants in North America

The Asian and African elephant populations in North America are not self‐sustaining, and reproductive rates remain low. One problem identified from routine progestagen analyses is that some elephant females do not exhibit normal ovarian cycles. To better understand the extent of this problem, the Elephant TAG/SSP conducted a survey to determine the reproductive status of the captive population based on hormone and ultrasound evaluations. The survey response rates for facilities with Asian and African elephants were 81% and 71%, respectively, for the studbook populations, and nearly 100% for the SSP facilities. Of the elephants surveyed, 49% of Asian and 62% of African elephant females were being monitored for ovarian cyclicity via serum or urinary progestagen analyses on a weekly basis. Of these, 14% of Asian and 29% of African elephants either were not cycling at all or exhibited irregular cycles. For both species, ovarian inactivity was more prevalent in the older age categories (>30 years); however, acyclicity was found in all age groups of African elephants. Fewer elephant females (～30%) had been examined by transrectal ultrasound to assess reproductive‐tract integrity, and corresponding hormonal data were available for about three‐quarters of these females. Within this subset, most (～75%) cycling females had normal reproductive‐tract morphologies, whereas at least 70% of noncycling females exhibited some type of ovarian or uterine pathology. In summary, the survey results suggest that ovarian inactivity is a significant reproductive problem for elephants held in zoos, especially African elephants. To increase the fecundity of captive elephants, females should be bred at a young age, before reproductive pathologies occur. However, a significant number of older Asian elephants are still not being reproductively monitored. More significantly, many prime reproductive‐age (10–30 years) African females are not being monitored. This lack of information makes it difficult to determine what factors affect the reproductive health of elephants, and to develop mitigating treatments to reinitiate reproductive cyclicity. Zoo Biol 23:309–321, 2004. © 2004 Wiley‐Liss, Inc.     

Myth, marula, and elephant: an assessment of voluntary ethanol intoxication of the African elephant (Loxodonta africana) following feeding on the fruit of the marula tree (Sclerocarya birrea)

Africa can stir wild and fanciful notions in the casual visitor; one of these is the tale of inebriated wild elephants. The suggestion that the African elephant (Loxodonta africana) becomes intoxicated from eating the fruit of the marula tree (Sclerocarya birrea) is an attractive, established, and persistent tale. This idea now permeates the African tourist industry, historical travelogues, the popular press, and even scholastic works. Accounts of ethanol inebriation in animals under natural conditions appear mired in folklore. Elephants are attracted to alcohol, but there is no clear evidence of inebriation in the field. Extrapolating from human physiology, a 3,000-kg elephant would require the ingestion of between 10 and 27 L of 7% ethanol in a short period to overtly affect behavior, which is unlikely in the wild. Interpolating from ecological circumstances and assuming rather unrealistically that marula fruit contain 3% ethanol, an elephant feeding normally might attain an ethanol dose of 0.3 g kg(-1), about half that required. Physiological issues to resolve include alcohol dehydrogenase activity and ethanol clearance rates in elephants, as well as values for marula fruit alcohol content. These models were highly biased in favor of inebriation but even so failed to show that elephants can ordinarily become drunk. Such tales, it seems, may result from "humanizing" elephant behavior.     

Wild Asian elephants distinguish aggressive tiger and leopard growls according to perceived danger

Prey species exhibit antipredator behaviours such as alertness, aggression and flight, among others, in response to predators. The nature of this response is variable, with animals reacting more strongly in situations of increased vulnerability. Our research described here is the first formal study to investigate night-time antipredator behaviour in any species of elephants, Asian or African. We examined the provocative effects of elephant-triggered tiger and leopard growls while elephants attempted to crop-raid. Tigers opportunistically prey on elephant calves, whereas leopards pose no threat; therefore, we predicted that the elephant response would be reflective of this difference. Elephants reacted similarly cautiously to the simulated presence of felids of both species by eventually moving away, but differed markedly in their more immediate behavioural responses. Elephants retreated silently to tiger-growl playbacks, whereas they responded with aggressive vocalizations, such as trumpets and grunts, to leopard-growl playbacks. Elephants also lingered in the area and displayed alert or investigative behaviours in response to leopard growls when compared with tiger growls. We anticipate that the methods outlined here will promote further study of elephant antipredator behaviour in a naturalistic context, with applications for conservation efforts as well.     

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.     

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.     

The African elephant, Loxodonta africana:a field method for the estimation of age

The need for a field method of determining and describing the relative age of African elephants collected in their natural habitat arose during a recent research project, and has led to an attempt to formulate a laminary age standard for use in the field, based upon direct observations and measurements on the lower right molars. For this purpose aseries of 31 African elephants of both sexes, covering almostthe complete potential age range of an elephant's life, and of known body condition, locality and size, has been used as the basis for constructing a reference chart of molar laminary age. Eye lens weights were also obtained for 26 of these specimens, but, although indicativeof a direct correlation with laminary age, they were obtained in insufficient numbers to provide an adequate sequence. Each of the specimens used was first observed alive, then shot and examined post mortem during the course of a research project*on cardiovascular disease, in which the determination of relative age formed an integral part.     

Secretory patterns of serum prolactin in Asian (Elephas maximus) and African (Loxodonta africana) elephants during different reproductive states: Comparison with concentrations in a noncycling African elephant

Serum prolactin was quantified in adult female Asian (Elephas maximus) and African (Loxodonta africana) elephants during various reproductive states and the profiles compared to that in a noncycling African elephant. In reproductively normal elephants, there was no effect of season, estrous cycle stage, or lactational status on quantitative or qualitative prolactin secretion (P > 0.05), nor where there any differences (P > 0.05) in overall prolactin concentrations between species. In pregnant elephants, prolactin concentrations remained at baseline for the first 4–6 months of gestation. Thereafter, concentrations during early pregnancy averaged ∼four-fold higher than those during the estrous cycle, increasing to ∼100-fold over baseline during mid- to late gestation in both species. In contrast to cycling elephants, prolactin concentrations in an African elephant exhibiting chronic anovulation (on the basis of an acyclic serum progesterone profile) and mild galactorrhea were consistently about five-fold higher (P < 0.05), suggesting she is hyperprolactinemic. Other endocrinological assesments confirmed the hypogonadal state of this female. Serum estradiol concentrations were consistently at or below detectable levels. Additionally, no preovulatory luteinizing hormone (LH) surges occurred in daily serum samples analyzed over a 12-month period. The pituitary was not totally refractory, however, and responded with a several-fold increase in serum LH concentration (peak, 3.07 ng/ml) over baseline (0.75 ng/ml) after i.v. injection of gonadotropin-releasing hormone. This study describes normal baseline serum prolactin values for Asian and African elephants and is the first to identify hyperprolactinemia as a possible cause of reproductive acyclicity and galactorrhea in an African elephant. Zoo Biol 16:149–159, 1997. © 1997 Wiley-Liss, Inc.     

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.     

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.     

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.     

Notes on the teeth and ovaries of an African elephant (Loxodonta africana) of known age

A captive female African elephant, known to be 27 years old, died as a result of trauma. Her growth rate was similar to that of other captive African elephants, and slightly greater than that of wild animals. The 5th molar was in full wear, and the 6th was just coming into wear. There was extensive dental caries of the labial, lingual and occlusal surfaces of the 5th molars, presumably due to the unnatural diet. The ovaries contained a number of large cystic follicles, and at least 50 regressing corpora lutea. These abnormalities are probably related to the fact that the elephant had never been mated.     

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 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.     

Contribution of molecular phylogeny and morphometrics to the systematics of African elephants

African elephants are conventionally classified as a single species: Loxodonta africana (Blumenbach 1797). However, the discovery in 1900 of a smaller form of the African elephant, spread throughout the equatorial belt of this land, has given rise to a debate over the relevance of a second species of elephant in Africa. The twentieth century has not provided any definite answer to this question. Actually, recent molecular analyses have sustained this issue by advocating either a division of forest elephants into a valid species, or their inclusion as a subspecies of L. africana. Our work initiated at the National Museum of Natural History of Paris provides new molecular (mitochondrial) and morphological (and morphometrical) evidence making it possible to propose a comprehensive phylogenetic hypothesis. It appears that there is no conclusive argument to keep forest elephants (cyclotis form) and savannah elephants (africana form) apart in two distinct species. A high level of mitochondrial introgression between the two forms, as well as a continuum in the morphology of the skulls of the two morphotypes rather suggests that, despite an ancient division, these two taxa freely interbreed wherever their ranges intersect. We thus adopt a conservative systematic position in considering these two forms as two subspecies, respectively: L. africana africana, the savannah elephant, and L. africana cyclotis, the forest elephant. We finally discuss the conservation topic in the light of this systematic framework.     

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.