Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius

The interval since circa 50 Ka has been a period of significant species extinctions among the large mammal fauna. However, the relative roles of an increasing human presence and a synchronous series of complex environmental changes in these extinctions have yet to be fully resolved. Recent analyses of fossil material from Beringia have clarified our understanding of the spatiotemporal pattern of Late Pleistocene extinctions, identifying periods of population turnover well before the last glacial maximum (LGM: circa 21 Ka) or subsequent human expansion. To examine the role of pre-LGM population changes in shaping the genetic structure of an extinct species, we analyzed the mitochondrial DNA of woolly mammoths in western Beringia and across its range. We identify genetic signatures of a range expansion of mammoths, from eastern to western Beringia, after the last interglacial (circa 125 Ka), and then an extended period during which demographic inference indicates no population-size increase. The most marked change in diversity at this time is the loss of one of two major mitochondrial lineages.     

Late Quaternary woolly mammoth (Mammuthus primigenius Blum) remains from southern Transdanubia,Hungary

Six samples of subfossil tusk, bone and tooth remains from the woolly mammoth (Mammuthus primigenius Blum) were discovered in south-western Hungary. The remains are relatively well preserved in a Late Pleistocene loess deposit. The samples have been radiocarbon dated (AMS) and are of Late Weichselian (MIS 2) age (21.8–24.1 ka cal BP). The skull fragments, the tusks and maxillary teeth are in close proximity to associated postcranial remains, indicating that the mammoth died where it was found. The size and characteristics of skeletal elements have allowed us to determine that this was a mature male of about 38 years of age.     

Isolation and characterization of deoxyribonucleic acid from tissue of the woolly mammoth, Mammuthus primigenius

DNA was isolated from tissue samples of several mammoth specimens, radiocarbon dated between 10,000 and 53,000 years old. The DNA was purified by chromatography on hydroxyapatite at 60 degrees C and was characterized as a heterogeneous population of fragments ranging in size from 3000 to 200 base pairs. Thermal denaturation analysis demonstrated that approximately 25% of the DNA had a base composition similar to Asian elephant DNA calculated as 36% G + C. Preliminary analysis by nucleic acid hybridization indicated that only a small fraction of DNA isolated from mammoth tissue (2-5%) was homologous to DNA of Asian elephant, a close living relative of the mammoth. Our results provide the first definitive isolation and characterization of DNA from ancient tissue and suggest a purification strategy that will lead to preparations of DNA from mammoth tissue significantly enriched in elephant-related DNA sequences.     

Specific characters of the mammoth calf (Mammuthus primigenius) from the Khroma River (Yakutia)

The exterior, skeletal morphology, and teeth of a 4- to 5-month-old woolly mammoth calf, Mammuthus primigenius Proboscidea, Elephantidae from the Khroma River (Yakutia, Russia) are described. This is the third and best preserved frozen carcass of the mammoth calves from Yakutia. The calf is male (penis available). The individual age as determined by the degree of wearing of DP2 and the beginning of wear of DP3 corresponds to the stage of transition to combined feeding (milk and vegetal forage). At the same time, formation of the cranial sutures (sutura sagittalis, fronto-temporalis, squamo-temporalis, and the suture between os occipitale superior and os occipitale inferior) testifies to an older juvenile stage. The proximal and distal epiphyses of the humerus and the distal epiphysis of the femur are represented by paired centers of ossification. A comparison of the dimensions of the head, body, and legs with the corresponding parameters of other M. primigenius calves of the same age shows the individual variability (10–15%) of these features. Although of medium size characteristic of M. primigenius calves, the described individual lacks subcutaneous fat deposits in the withers and subdermal areas of the body flanks. Death was caused by a rupture of the body and vertebral column at the level of the pectoral vertebrae 11–12. The deformation of the legs and longitudinal stretching of the soft tissues of the body caused no bone fractures (except for three ribs in the zone of the rupture). The long bones are not dislocated either in the shoulder and pelvic girdles or relative to each other. Possible causes and the timing of the death of the mammoth calves preserved in the permafrost are discussed.     

Hair structure of the Woolly mammoth, Mammuthus primigenius and the modern elephants, Elephas maximus and Loxodonta africana

The structure of overhairs from a Wooly mammoth, Mammuthus primigenius , 10–13 thousand years old, is compared with that of its living relatives, Elephas maximus and Loxodonta africana . The hair profile, cross-sectional appearance, wholeamount and cuticular scale cast of the haris of the three species were examined and a selected array of photographs representing the hair structure of each species are presented. In general there is little variation between the three in the gross structure of the overhairs.     

A simulation of anthropogenic Columbian mammoth (Mammuthus columbi) extinction

The cause of the extinction of the Columbian mammoth (Mammuthus columbi) and other species of megafauna during the end of the Pleistocene epoch is an ongoing debate. In this study, we used mathematical modelling to test the overkill hypothesis first proposed by Martin in 1973. The overkill hypothesis claims that early humans migrating from Asia through Beringia and into North America hunted the majority of the continent’s megafauna to extinction. Previous research has been conducted on the overkill hypothesis for the Columbian mammoth using a continuous differential equations model. We improved on this work by developing a computationally more efficient and more realistic discrete stochastic model. Most model parameters were obtained directly from the literature; migration parameters were informed by the literature and calibrated for the model. Our results provide evidence in support of the overkill hypothesis.     

Increasing and decreasing functional area of the dentition (FAD) of Mammuthus primigenius

The occlusal morphology and continuous molar replacement in elephants provide a very effective functional area for grinding the biomass that is more or less abrasive. Parts of two subsequent molars contribute to the “functional area of the dentition” (FAD). The FAD size, measured in cm², is associated with age and body size. The FAD stage is indicated by the specific teeth contributing to the FAD and represents the individual age. This study concentrates on Mammuthus primigenius and compares the FAD stages, as derived from growth series, with the fossil Elephas antiquus, as well as the extant Elephas maximus and Loxodonta africana. During the life history of the taxa studied, the functional area increases simultaneously with an increase in body size, but decreases severely in senile age stages. In some senile individuals, the FAD is only about 20–50 % of the mean area of an adult animal. The reduction of the FAD beyond a specific size does not mean an immediate starvation of the animal. The general constitution of the individual and the resources of fat accumulation earlier may support the animal for some time but certainly not over a longer period. Nevertheless, the highly reduced functional area was sufficient to keep the animal alive despite its full adult body mass. A much larger FAD in all adult stages provides the energy requirements needed for all additional life functions including competition and reproduction.     

Structural and Functional Organization of the Mitochondrial DNA Control Region in the Woolly Mammoth (Mammuthus primigenius)

Molecular Biology - The woolly mammoth mitochondrial genome (including the Malolyakhovsky mammoth) has been previously sequenced, followed by the annotation of all its genes (MF770243). In this...     

Successful genotyping of microsatellites in the woolly mammoth

Genetic analyses using ancient DNA from Pleistocene and early Holocene fossils have largely relied on mitochondrial DNA (mtDNA) sequences. Among woolly mammoths, Mammuthus primigenius, mtDNA analyses have identified 2 distinct clades (I and II) that diverged 1-2 Ma. Here, we establish that microsatellite markers can be effective on Pleistocene samples, successfully genotyping woolly mammoth specimens at 2 loci. Although significant differentiation at the 2 microsatellite loci was not detected between 16 clade I and 4 clade II woolly mammoths, our results demonstrate that the nuclear population structure of Pleistocene species can be examined using fast-evolving nuclear microsatellite markers.     

ERV-L elements: a family of endogenous retrovirus-like elements active throughout the evolution of mammals

We have previously identified in the human genome a family of 200 endogenous retrovirus-like elements, the HERV-L elements, disclosing similarities with the foamy retroviruses and which might be the evolutionary intermediate between classical intracellular retrotransposons and infectious retroviruses. Southern blot analysis of a large series of mammalian genomic DNAs shows that HERV-L-related elements-so-called ERV-L-are present among all placental mammals, suggesting that ERV-L elements were already present at least 70 million years ago. Most species exhibit a low copy number of ERV-L elements (from 10 to 30), while simians (not prosimians) and mice (not rats) have been subjected to bursts resulting in increases in the number of copies up to 200. The burst of copy number in primates can be dated to shortly after the prosimian and simian branchpoint, 45 to 65 million years ago, whereas murine species have been subjected to two much more recent bursts (less than 10 million years ago), occurring after the Mus/Rattus split. We have amplified and sequenced 360-bp ERV-L internal fragments of the highly conserved pol gene from a series of 22 mammalian species. These sequences exhibit high percentages of identity (57 to 99%) with the murine fully coding MuERV-L element. Phylogenetic analyses allowed the establishment of a plausible evolutionary scheme for ERV-L elements, which accounts for the high level of sequence conservation and the widespread dispersion among mammals.     

Holarctic genetic structure and range dynamics in the woolly mammoth

Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32–34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20–15 kyr BP, when a severe population size decline occurred.     

Adaptation of the woolly mammoth <Emphasis Type="Italic">Mammuthus primigenius</Emphasis> (Blumenbach, 1799) to habitat conditions in the glacial period

An analysis of the available data on the various adaptations of the woolly mammoth to the cryoarid conditions of the Ice Age is presented. Mammuthus primigenius had a set of specific anatomic–morphological (thick long three-row wool, small ears, a short tail, an adipose “hump”, a “hood”-like extension on the trunk, and wide soles of the feet) and physiological (reduced sensitivity to cold and a specific kind of lipid metabolism) ideoadaptations that provided safe existence and wide distribution of this species in the Northern Holarctic for a long time. The current data make it possible to refer the woolly mammoth to a highly specialized species of the Mammoth biome.     

Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth

Background  

Like humans, the living elephants are unusual among mammals in being sparsely covered with hair. Relative to extant elephants, the extinct woolly mammoth, Mammuthus primigenius, had a dense hair cover and extremely long hair, which likely were adaptations to its subarctic habitat. The fibroblast growth factor 5 (FGF5) gene affects hair length in a diverse set of mammalian species. Mutations in FGF5 lead to recessive long hair phenotypes in mice, dogs, and cats; and the gene has been implicated in hair length variation in rabbits. Thus, FGF5 represents a leading candidate gene for the phenotypic differences in hair length notable between extant elephants and the woolly mammoth. We therefore sequenced the three exons (except for the 3' UTR) and a portion of the promoter of FGF5 from the living elephantid species (Asian, African savanna and African forest elephants) and, using protocols for ancient DNA, from a woolly mammoth.     

A biochemical--biophysical study of hemoglobins from woolly mammoth, Asian elephant, and humans

This study is aimed at investigating the molecular basis of environmental adaptation of woolly mammoth hemoglobin (Hb) to the harsh thermal conditions of the Pleistocene ice ages. To this end, we have carried out a comparative biochemical-biophysical characterization of the structural and functional properties of recombinant hemoglobins (rHb) from woolly mammoth (rHb WM) and Asian elephant (rHb AE) in relation to human hemoglobins Hb A and Hb A(2) (a minor component of human blood). We have obtained oxygen equilibrium curves and calculated O(2) affinities, Bohr effects, and the apparent heat of oxygenation (ΔH) in the presence and absence of allosteric effectors [inorganic phosphate and inositol hexaphosphate (IHP)]. Here, we show that the four Hbs exhibit distinct structural properties and respond differently to allosteric effectors. In addition, the apparent heat of oxygenation (ΔH) for rHb WM is less negative than that of rHb AE, especially in phosphate buffer and the presence of IHP, suggesting that the oxygen affinity of mammoth blood was also less sensitive to temperature change. Finally, (1)H NMR spectroscopy data indicates that both α(1)(β/δ)(1) and α(1)(β/δ)(2) interfaces in rHb WM and rHb AE are perturbed, whereas only the α(1)δ(1) interface in Hb A(2) is perturbed compared to that in Hb A. The distinct structural and functional features of rHb WM presumably facilitated woolly mammoth survival in the Arctic environment.     

Evolution of Streptococcus pneumoniae and its close commensal relatives

Streptococcus pneumoniae is a member of the Mitis group of streptococci which, according to 16S rRNA-sequence based phylogenetic reconstruction, includes 12 species. While other species of this group are considered prototypes of commensal bacteria, S. pneumoniae is among the most frequent microbial killers worldwide. Population genetic analysis of 118 strains, supported by demonstration of a distinct cell wall carbohydrate structure and competence pheromone sequence signature, shows that S. pneumoniae is one of several hundred evolutionary lineages forming a cluster separate from Streptococcus oralis and Streptococcus infantis. The remaining lineages of this distinct cluster are commensals previously collectively referred to as Streptococcus mitis and each represent separate species by traditional taxonomic standard. Virulence genes including the operon for capsule polysaccharide synthesis and genes encoding IgA1 protease, pneumolysin, and autolysin were randomly distributed among S. mitis lineages. Estimates of the evolutionary age of the lineages, the identical location of remnants of virulence genes in the genomes of commensal strains, the pattern of genome reductions, and the proportion of unique genes and their origin support the model that the entire cluster of S. pneumoniae, S. pseudopneumoniae, and S. mitis lineages evolved from pneumococcus-like bacteria presumably pathogenic to the common immediate ancestor of hominoids. During their adaptation to a commensal life style, most of the lineages gradually lost the majority of genes determining virulence and became genetically distinct due to sexual isolation in their respective hosts.