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 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.     

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.     

Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths

Although the iconic mammoth of the Late Pleistocene, the woolly mammoth (Mammuthus primigenius), has traditionally been regarded as the end point of a single anagenetically evolving lineage, recent paleontological and molecular studies have shown that successive allopatric speciation events must have occurred within Pleistocene Mammuthus in Asia, with subsequent expansion and hybridization between nominal taxa [1, 2]. However, the role of North American mammoth populations in these events has not been adequately explored from an ancient-DNA standpoint. To undertake this task, we analyzed mtDNA from a large data set consisting of mammoth samples from across Holarctica (n = 160) and representing most of radiocarbon time. Our evidence shows that, during the terminal Pleistocene, haplotypes originating in and characteristic of New World populations replaced or succeeded those endemic to Asia and western Beringia. Also, during the Last Glacial Maximum, mammoth populations do not appear to have suffered an overall decline in diversity, despite differing responses on either side of the Bering land bridge. In summary, the "Out-of-America" hypothesis holds that the dispersal of North American woolly mammoths into other parts of Holarctica created major phylogeographic structuring within Mammuthus primigenius populations, shaping the last phase of their evolutionary history before their demise.     

Temporal genetic change in the last remaining population of woolly mammoth

During the Late Pleistocene, the woolly mammoth (Mammuthus primigenius) experienced a series of local extinctions generally attributed to human predation or environmental change. Some small and isolated populations did however survive far into the Holocene. Here, we investigated the genetic consequences of the isolation of the last remaining mammoth population on Wrangel Island. We analysed 741 bp of the mitochondrial DNA and found a loss of genetic variation in relation to the isolation event, probably caused by a demographic bottleneck or a founder event. However, in spite of ca 5000 years of isolation, we did not detect any further loss of genetic variation. Together with the relatively high number of mitochondrial haplotypes on Wrangel Island near the final disappearance, this suggests a sudden extinction of a rather stable population.     

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.     

Complete Mitochondrial Genome and Phylogeny of Pleistocene MammothMammuthus primigenius

Phylogenetic relationships between the extinct woolly mammoth(Mammuthus primigenius), and the Asian(Elephas maximus) and African savanna(Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch—the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as ~1,600–1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests thatM. primigenius andE. maximus are sister species that diverged soon after their common ancestor split from theL. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population ofM. primigenius throughout the late Pleistocene.     

Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus primigenius

Phylogenetic relationships between the extinct woolly mammoth(Mammuthus primigenius), and the Asian(Elephas maximus) and African savanna(Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch—the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as ~1,600–1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests thatM. primigenius andE. maximus are sister species that diverged soon after their common ancestor split from theL. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population ofM. primigenius throughout the late Pleistocene.     

Complete Mitochondrial Genome and Phylogeny of Pleistocene MammothMammuthus primigenius

Phylogenetic relationships between the extinct woolly mammoth(Mammuthus primigenius), and the Asian(Elephas maximus) and African savanna(Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch—the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as ~1,600–1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests thatM. primigenius andE. maximus are sister species that diverged soon after their common ancestor split from theL. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population ofM. primigenius throughout the late Pleistocene.     

The flickering genes of the last mammoths

Woolly mammoths, Mammuthus primigenius, are arguably the most iconic of the extinct Pleistocene megafauna, and an abundance of large permafrost‐embedded bone and ivory material ( Fig. 1 ) means they were also among the first to yield credible DNA sequences ( Hagelberg et al. 1994 ; Hoss et al. 1994 ). Despite mammoth remains being numerous throughout northern Eurasia and North America, both the earliest and most recent fossils are found in northeast Siberia, with the last known population being confined to Wrangel Island in the Arctic Ocean from around 10,000 years ago until their extinction around 4,000 years ago. The extent to which these Holocene mammoths were descended from the Pleistocene populations of Wrangel Island and the demographic nature of their terminal decline have, until now, remained something of a mystery. In this issue of Molecular Ecology, Nyström et al. (2012) report the first use of autosomal variation to track the decline of the last mammoths and, in doing so, take a significant step towards resolving these questions. The authors genotyped four microsatellite loci in 59 Pleistocene and Holocene mammoths from Wrangel Island and Chukotka in mainland northeastern Siberia and showed that while the Pleistocene‐to‐Holocene transition is associated with a significant reduction in genetic diversity, subsequent levels of variation remain constant until extinction. Such a pattern is somewhat surprising as it indicates that while the last mammoths were confined to only a few Arctic islands, their final extinction on Wrangel Island was not a gradual process resulting from loss of genetic diversity/inbreeding. Instead, it seems they maintained a viable effective population size of around 500 until near their presumably rapid extinction. While the ultimate agent of mammoth extinction remains unknown, the work of Nyström et al. (2012) . suggests that we should be looking for something sudden, like a rapid change in climate/ecology or perhaps the arrival of humans.

Figure 1 Open in figure viewer PowerPoint Sergey Vartanyan during field collection, holding a woolly mammoth tusk found along a river embankment in northeast Siberia (photographer: Diana Solovyeva).     

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.     

An Ice Age spotted hyena Crocuta crocuta spelaea (Goldfuss 1823) population,their excrements and prey from the Late Pleistocene hyena den of the Sloup Cave in the Moravian Karst,Czech Republic

A Late Pleistocene spotted hyena Crocuta crocuta spelaea (Goldfuss 1823) population from the cave bear den Sloup Cave, Moravia (Czech Republic) consists of mainly adult/senior and few cub/juvenile remains and coprolites, and 139 prey bones. Hyenas used the Nicová Cave branch that is connected to the entrance area mainly as a communal den site. Prey bone damage is most visible on the imported woolly rhinoceros remains. The partly excavated prey bone accumulation consists of a single woolly mammoth Mammuthus primigenius (Blumenbach 1799) tooth (2%), mainly Coelodonta antiquitatis (Blumenbach 1807) remains (16%), 4% Bos primigenius (Bojanus 1827) and 1% each of Megaloceros giganteus (Blumenbach 1799) and Rangifer tarandus (Linnaeus 1758). The other carnivores such as Panthera leo spelaea (Goldfuss 1810), Gulo gulo (Linnaeus 1758) and Canis lupus (Linnaeus 1758) subsp. are less represented (1–3%). Wolverines might have been imported also as prey remains, whereas wolves also possibly used this cave on a short-term basis, whereas steppe lions seem to have preyed upon cave bears deeper in the cave periodically, where even skeletons of P. leo spelaea were found in the Elisabeth Cave part.     

Issue Information

Front Cover: Skeleton of a Columbian mammoth (Mammuthus columbi) assembled from bones recovered at the La Brea Tar Pits in Los Angeles, California. Original photograph taken by Jonathan Drury. Reproduced by permission of David A. Gold, Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA.     

Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins

We used high-sensitivity, high-resolution tandem mass spectrometry to shotgun sequence ancient protein remains extracted from a 43?000 year old woolly mammoth ( Mammuthus primigenius ) bone preserved in the Siberian permafrost. For the first time, 126 unique protein accessions, mostly low-abundance extracellular matrix and plasma proteins, were confidently identified by solid molecular evidence. Among the best characterized was the carrier protein serum albumin, presenting two single amino acid substitutions compared to extant African ( Loxodonta africana ) and Indian ( Elephas maximus ) elephants. Strong evidence was observed of amino acid modifications due to post-mortem hydrolytic and oxidative damage. A consistent subset of this permafrost bone proteome was also identified in more recent Columbian mammoth ( Mammuthus columbi ) samples from temperate latitudes, extending the potential of the approach described beyond subpolar environments. Mass spectrometry-based ancient protein sequencing offers new perspectives for future molecular phylogenetic inference and physiological studies on samples not amenable to ancient DNA investigation. This approach therefore represents a further step into the ongoing integration of different high-throughput technologies for identification of ancient biomolecules, unleashing the field of paleoproteomics.     

Attempted DNA extraction from a Rancho La Brea Columbian mammoth (Mammuthus columbi): prospects for ancient DNA from asphalt deposits

Fossil‐bearing asphalt deposits are an understudied and potentially significant source of ancient DNA. Previous attempts to extract DNA from skeletons preserved at the Rancho La Brea tar pits in Los Angeles, California, have proven unsuccessful, but it is unclear whether this is due to a lack of endogenous DNA, or if the problem is caused by asphalt‐mediated inhibition. In an attempt to test these hypotheses, a recently recovered Columbian mammoth (Mammuthus columbi) skeleton with an unusual pattern of asphalt impregnation was studied. Ultimately, none of the bone samples tested successfully amplified M. columbi DNA. Our work suggests that reagents typically used to remove asphalt from ancient samples also inhibit DNA extraction. Ultimately, we conclude that the probability of recovering ancient DNA from fossils in asphalt deposits is strongly (perhaps fatally) hindered by the organic compounds that permeate the bones and that at the Rancho La Brea tar pits, environmental conditions might not have been ideal for the general preservation of genetic material.     

Meet the new mammoth,same as the old? Resurrecting the <Emphasis Type="Italic">Mammuthus primigenius</Emphasis>

Media reporters often announce that we are on the verge of bringing back the woolly mammoth, even while there is growing consensus among scientists that resurrecting the mammoth is unlikely. In fact, current “de-extinction” efforts are not designed to bring back a mammoth, but rather adaptations of the mammoth using close relatives. For example, Harvard scientists are working on creating an Asian elephant with the thick coat of a mammoth by merging mammoth and elephant DNA. But how should such creatures be classified? Are they elephants, mammoths, or both? Answering these questions requires getting clear about the concept of reproduction. What I hope to show is that with an appropriate notion of reproduction—one for which I will argue—resurrecting a member of Mammuthus primigenius is a genuine possibility.     

Phylogenetic Position of Mammoth and Steller's Sea Cow Within Tethytheria Demonstrated by Mitochondrial DNA Sequences

Here we report DNA sequences from mitochondrial cytochrome b gene segments (1,005 base pairs per species) for the extinct woolly mammoth (Mammuthus primigenius) and Steller's sea cow (Hydrodamalis gigas) and the extant Asian elephant (Elephas maximus), the Western Indian manatee (Trichechus manatus), and the hyrax (Procavia capensis). These molecular data have allowed us to construct the phylogeny for the Tethytheria. Our molecular data resolve the trichotomy between the two species of living elephants and the mammoth and confirm that the mammoth was more closely related to the Asian elephant than to the African elephant. Our data also suggest that the sea cow–dugong divergence was likely as ancient as the dugong–manatee split, and it appears to have been much earlier (22 million years ago) than had been previously estimated (4–8 million years ago) by immunological comparison. Received: 8 August 1996 / Accepted: 30 September 1996     

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.     

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     

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.