Does the 43 bp sequence from an 800,000 year old cretan dwarf elephantid really rewrite the textbook on mammoths?

Pigmy elephants inhabited the islands from the Mediterranean region during the Pleistocene period but became extinct in the course of the Holocene. Despite striking distinctive anatomical characteristics related to insularity, some similarities with the lineage of extant Asian elephants have suggested that pigmy elephants could be most probably seen as members of the genus Elephas. Poulakakis et al (2006) have recently challenged this view by recovering a short mtDNA sequence from an 800 000 year old fossil of the Cretan pigmy elephant (Elephas creticus). According to the authors of this study, a deep taxonomic revision of Cretan dwarf elephants would be needed, as the sequence exhibits clear affinities with woolly mammoth haplotypes. However, we point here many aspects that seriously weaken the strength of the ancient DNA evidence reported.     

Does the 43?bp sequence from an 800?000 year old Cretan dwarf elephantid really rewrite the textbook on mammoths?

Pigmy elephants inhabited the islands from the Mediterranean region during the Pleistocene period but became extinct in the course of the Holocene. Despite striking distinctive anatomical characteristics related to insularity, some similarities with the lineage of extant Asian elephants have suggested that pigmy elephants could be most probably seen as members of the genus Elephas. Poulakakis et al. (2006) have recently challenged this view by recovering a short mtDNA sequence from an 800 000 year old fossil of the Cretan pigmy elephant (Elephas creticus). According to the authors of this study, a deep taxonomic revision of Cretan dwarf elephants would be needed, as the sequence exhibits clear affinities with woolly mammoth haplotypes. However, we point here many aspects that seriously weaken the strength of the ancient DNA evidence reported.     

洛阳首次发现旧石器

本文系记述洛阳市首次发现的旧石器。它发现于距地表约12米的砂土层中,并与似诺氏古菱齿象化石共同出土,其地质时代为更新世晚期。这一发现为研究中原地区旧石器文化和洛阳地区第四纪地层划分提供有意义的资料。     

The amino acid sequence of elephant (Elephas maximus) myoglobin and the phylogeny of Proboscidea

The complete amino acid sequence of skeletal myoglobin from the Asian elephant (Elephas maximus) is reported. The functional significance of variations seen when this sequence is compared with that of sperm whale myoglobin is explored in the light of the crystallographic model available for the latter molecule. The phylogenetic implications of the elephant myoglobin amino acid sequence are evaluated by using the maximum parsimony technique. A similar analysis is also presented which incorporates all of the proteins sequenced from the elephant. These results are discussed with respect to current views on proboscidean phylogeny.     

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.     

Extreme insular dwarfism evolved in a mammoth

The insular dwarfism seen in Pleistocene elephants has come to epitomize the island rule; yet our understanding of this phenomenon is hampered by poor taxonomy. For Mediterranean dwarf elephants, where the most extreme cases of insular dwarfism are observed, a key systematic question remains unresolved: are all taxa phyletic dwarfs of a single mainland species Palaeoloxodon antiquus (straight-tusked elephant), or are some referable to Mammuthus (mammoths)? Ancient DNA and geochronological evidence have been used to support a Mammuthus origin for the Cretan ‘Palaeoloxodon’ creticus, but these studies have been shown to be flawed. On the basis of existing collections and recent field discoveries, we present new, morphological evidence for the taxonomic status of ‘P’. creticus, and show that it is indeed a mammoth, most probably derived from Early Pleistocene Mammuthus meridionalis or possibly Late Pliocene Mammuthus rumanus. We also show that Mammuthus creticus is smaller than other known insular dwarf mammoths, and is similar in size to the smallest dwarf Palaeoloxodon species from Sicily and Malta, making it the smallest mammoth species known to have existed. These findings indicate that extreme insular dwarfism has evolved to a similar degree independently in two elephant lineages.     

Molecular Phylogenetic Inference of the Woolly Mammoth Mammuthus primigenius, Based on Complete Sequences of Mitochondrial Cytochrome b and 12S Ribosomal RNA Genes

Complete sequences of cytochrome b (1,137 bases) and 12S ribosomal RNA (961 bases) genes in mitochondrial DNA were successfully determined from the woolly mammoth (Mammuthus primigenius), African elephant (Loxodonta africana), and Asian elephant (Elephas maximus). From these sequence data, phylogenetic relationships among three genera were examined. Molecular phylogenetic trees reconstructed by the neighbor-joining and the maximum parsimony methods provided an identical topology both for cytochrome b and 12S rRNA genes. These results support the ``Mammuthus-Loxodonta' clade, which is contrary to some previous morphological reports that Mammuthus is more closely related to Elephas than to Loxodonta. Received: 8 April 1997 / Accepted: 23 July 1997     

A new elephant fossil from the late Pleistocene of Alghero: The puzzling question of Sardinian dwarf elephants

Endemic elephants, variously reduced in size, have been reported from a number of Mediterranean islands. Most of these originated from the mainland species Palaeoloxodon antiquus. A few dwarf mammoth remains are recorded from Crete and Sardinia. In Sardinia, a largely incomplete skeleton and a few mammoth teeth have been reported from localities believed to range in age from the late middle to the late Pleistocene. The chronology of colonisation by the ancestral species, the actual persistence through time of Mammuthus lamarmorai on the island, and the morphological and dimensional range of the species are, however, poorly known. This research aims to describe a distal portion of a left tibia of a dwarf elephant found in the Alghero area (NW Sardinia), showing some morphological traits and dimensions consistent with those of the endemic Sardinian mammoth (Mammuthus lamarmorai). The main unanswered questions about chronology, colonisation and population dynamics of endemic Sardinian elephants are highlighted and briefly discussed.     

Social organization of the Asian elephant (Elephas maximus) in southern India inferred from microsatellite DNA

Social organization of the Asian elephant (Elephas maximus) is not well understood in the absence of long-term studies of identified individuals. Adult Asian elephant females and their young offspring of both sexes form matriarchal groups, with pubertal males dispersing from natal groups, but whether these social groups represent families and whether males show locational or social dispersal were unknown. Using nuclear microsatellite loci amplified from dung-extracted DNA of free-ranging elephants in a large southern Indian population, we demonstrate that female-led herds comprise closely related individuals that are indeed families, and that males exhibit non-random locational dispersal.     

The fast life of a dwarfed giant

In the first half of the 1960s, a rich paleontological site was discovered at Spinagallo caves (Eastern Sicily, Southern Italy). A very abundant fossil population (at least 104 specimens) of the dwarf elephant Elephas falconeri, the smallest elephant that ever lived, was recovered. We computed the survivorship curve for this fossil population in order to investigate both the great juvenile abundance and high calf mortality which it shows. Through the analysis of E. falconeri survivorship, of some reconstructed life-history traits, and of its ecology, and taking into account the Island rule (Foster, 1964), we concluded that E. falconeri moved somewhat toward the fast extreme of the slow-fast continuum in life-history traits in regards to its mainland ancestor E. antiquus, that is, it was somehow r-selected. In keeping with our findings, we propose a new explanation for the common occurrence of dwarfism in large mammals living on islands. We suggest the interplay of competition, resource allocation shift and feeding niche width could successfully explain this pattern.     

基于线粒体DNA的中国亚洲象种群遗传多样性及种群遗传结构

亚洲象是我国国家一级保护动物.本文利用非损伤性取样法,以亚洲象粪便中脱落的肠道上皮细胞为DNA来源,选用线粒体DNA作为分子标记,对分布于我国境内的亚洲象种群的遗传结构和种群遗传多样性进行研究.本研究得到mtDNA序列片段长度为556 bp,经对178个个体进行扩增结果分析,共得到24个单倍型.在5个地理种群中,除南滚河种群外,其他4个种群中的114个个体共享同一单倍型,南滚河种群与其他种群间未观察到共享单倍型.系统发生分析,观察到中国境内现有亚洲象种群在进化上分为两大分支,α和β.其中分支α中包含除南滚河种群外的4个地理种群,分支β仅含有南滚河种群,表明南滚河种群与其他4个地理种群间存在明显分化.遗传多样性分析结果表明,中国境内的亚洲象种群的遗传多样性水平较低,分析原因认为是栖息地破碎化阻断了种群间有效的基因交流.     

A diseased Panthera leo spelaea (Goldfuss 1810) lioness from a forest elephant graveyard in the Late Pleistocene (Eemian) interglacial lake at Neumark-Nord,central Germany

A solitary articulated skeleton of a middle-aged and diseased Panthera leo spelaea lioness from the Eemian interglacial has been found amongst numerous articulated skeletons of Palaeoloxodon antiquus forest elephants, in sediments from a small, shallow lake at Neumark-Nord in central Germany, which has Neanderthal settlements along its shoreline. Several pathologies such as a fibula fracture, arthritis in one of the front legs and a lost canine tooth with associated maxillary inflammation and dissolution made the lioness vulnerable to other predators such as hyenas, whose presence is indicated by their bones, coprolites and many scavenging marks on the elephant skeletons and on a femur from a male lion. The scavenging of hyenas and lions at this site is commonly documented by canine bite marks on the joints of elephant bones. Bite and scratch marks on the ventral vertebral columns and pelvises of two P. antiquus forest elephant skeletons suggest that the intestines and inner organs may have been consumed by large predators, as is commonly the case with modern African lions feeding on elephants. The weak and diseased lioness may possibly have been killed during antagonistic battles between hyenas and lions over their larger prey.     

Population differentiation within and among Asian elephant (Elephas maximus) populations in southern India

Southern India, one of the last strongholds of the endangered Asian elephant (Elephas maximus), harbours about one-fifth of the global population. We present here the first population genetic study of free-ranging Asian elephants, examining within- and among-population differentiation by analysing mitochondrial DNA (mtDNA) and nuclear microsatellite DNA differentiation across the Nilgiris-Eastern Ghats, Anamalai, and Periyar elephant reserves of southern India. Low mtDNA diversity and 'normal' microsatellite diversity were observed. Surprisingly, the Nilgiri population, which is the world's single largest Asian elephant population, had only one mtDNA haplotype and lower microsatellite diversity than the two other smaller populations examined. There was almost no mtDNA or microsatellite differentiation among localities within the Nilgiris, an area of about 15,000 km2. This suggests extensive gene flow in the past, which is compatible with the home ranges of several hundred square kilometres of elephants in southern India. Conversely, the Nilgiri population is genetically distinct at both mitochondrial and microsatellite markers from the two more southerly populations, Anamalai and Periyar, which in turn are not genetically differentiated from each other. The more southerly populations are separated from the Nilgiris by only a 40-km-wide stretch across a gap in the Western Ghats mountain range. These results variably indicate the importance of population bottlenecks, social organization, and biogeographic barriers in shaping the distribution of genetic variation among Asian elephant populations in southern India.     

Dental identification and age determination in Elephas maximus

The dentition of an elephant (fossil or extant) can yield clues to the animal's age species identity, provided the teeth are correctly identified. Identifying the serial category of elephant teeth is difficult because the size, shape and position of each tooth changes throughout life, as the teeth form, erupt, wear and move throught the jaw. In the present study, teeth from over 100 museum specimens of the Asian elephant ( Elephas maximus ) were the basis for establishing size ranges for cheek teeth in six serial categories (designated by Roman numerals I to VI). Although the teeth vary greatly and overlap in their dimensions, reliable identifications (as well as estimates of an individual's age in years) can be obtained using three or more measurements. An appreciation for dental variability in Elephas maximus will demand a re-evaluastion of frequently-cited examples of macroevolutionary patterns within the Elephantidae.     

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.     

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.     

Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids

During the Pleistocene pygmy elephantids, some only a quarter of their ancestors' size, were present on Mediterranean islands until about 10,000 years ago (y.a.). Using a new methodology for ancient DNA (aDNA) studies, the whole genomic multiple displacement amplification method, we were able to retrieve cytochrome b (cytb) DNA fragments from 4200 to 800,000 y.a. specimens from island and mainland samples, including pygmy and normal-sized forms. The short DNA sequence (43 bp) retrieved from the 800,000 y.a. sample is one of the oldest DNA fragment ever retrieved. Duplication of the experiments in two laboratories, the occurrence of three diagnostic sites and the results of the phylogenetic analyses strongly support its authenticity. Our results challenge the prevailing view that pygmy elephantids of the eastern Mediterranean originated exclusively from Elephas, suggesting independent histories of dwarfism and the presence of both pygmy mammoths and elephant-like taxa on these islands. Based on our molecular data, the origin of the Tilos and Cyprus elephantids from a lineage within the genus Elephas is confirmed, while the DNA sequence from the Cretan sample falls clearly within the mammoth clade. Thus, the name Mammuthus creticus rather than Elephas creticus, seems to be justified for this form. Our findings also suggest a need to re-evaluate the evolutionary history of the Sicilian/Maltese species, traditionally included in the genus Elephas.     

Paenungulata: a comparison of the hemoglobin sequences from elephant, hyrax, and manatee

Inspection of the amino acid differences among hemoglobin sequences of a wide range of mammalian species suggested that at alpha 19, alpha 110, alpha 111, beta 23, beta 44, and beta 56, synapomorphies group manatee (Trichechus inungius, Sirenia), Indian and African elephant (Elephas maximus and Loxodonta africana, Proboscidea), and rock hyrax (Procavia habessinica, Hyracoidea) into a monophyletic clade. Results obtained by parsimony analysis provide evidence for this grouping--and thus support for the genealogical validity of Simpson's superorder Paenungulata, which contains as the extant orders Proboscidea, Sirenia, and Hyracoidea. All of the 39 most, or nearly most, parsimonious of 10,395 trees constructed from a tandemly combined alpha- and beta- hemoglobin sequence for 103 vertebrate species (of which 79 were mammals from 16 extant orders), depicted Paenungulata as one of the most anciently separated branches of Eutheria. It was found on examining thousands of alternative trees that to not group Proboscidea, Hyracoidea, and Sirenia in a monophyletic clade required at least four additional substitutions.