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At least 19 recordsLinked to original sources

Paleogenomic sex inference of mammoth remains sheds light on the anthropogenic nature of bone accumulations.

Whether large accumulations of woolly mammoth (Mammuthus primigenius) bones reflect natural mortality or deliberate human resource exploitation has long been debated, with major implications for understanding Late Pleistocene human-megafaunal interactions.1,2,3,4,5 Here, we use ancient DNA to investigate site-formation hypotheses by comparing genetic sex ratios from mammoth remains recovered in putative anthropogenic bone accumulations and from geographically dispersed, non-anthropogenic contexts. We studied genome-wide data from 521 woolly mammoths-including 100 mammoths from bone accumulation sites and 421 mammoths from natural depositional settings across Eurasia and North America-of which 448 are newly generated. Genetic sex determination reveals a striking contrast between contexts: mammoths from dispersed sites show a male bias (∼66.5%), which is consistent with the heightened vulnerability of solitary males to hazards such as natural traps, where bones are more likely to be preserved, whereas mammoths from anthropogenic bone accumulations are predominantly female (∼70%). This female bias is pervasive across multiple sites, indicating an anthropogenic origin for these accumulations as a result of Upper Paleolithic hunters preferentially exploiting female mammoths, possibly derived from herd contexts. Together, these results provide population-scale genetic evidence that highlights the central role of mammoths in the subsistence and material economies of some Paleolithic communities.

Animals↗

Genomic and morphological analysis reveals long-term mammoth hybridization in British Columbia, Canada.

Climate changes profoundly impact species distributions and can drastically alter dynamics between formerly isolated taxa. The evolution of mammoths within North America was characterized by repeated cycles of dispersal and putative gene flow between woolly and Columbian mammoths. However, as genome-wide studies on mammoths have predominantly focused on Siberia, the consequences of these North American range shifts remain unclear. Here, we generated genome-wide and morphological data for two Late Pleistocene mammoth molars from British Columbia, Canada (BC), and jointly analysed these with previously published data. Our genome-wide analysis (n = 16) revealed gene flow between woolly and Columbian mammoths that would have gone undiscovered based on morphological (n = 48) and mitochondrial analysis (n = 124) alone. Consistent with their hybrid nature, our analyses suggest that these two BC mammoths had elevated genomic diversity. Our results highlight the importance of combining data types to reconstruct past evolutionary events. These findings demonstrate how the geographical range expansion of woolly mammoths resulted in long-term hybridization with local Columbian mammoths and enhance our understanding of the genomic and morphological consequences of climate-mediated dispersal.

British Columbia↗

Mitochondrial cytochrome b of the Lyakhov mammoth (Proboscidea, Mammalia): new data and phylogenetic analyses of Elephantidae.

The phylogenetic relationships between recent Elephantidae (Proboscidea, Mammalia), that is to say extant elephants (Asian and African) and extinct woolly mammoth, have remained unclear to date. The prevailing morphological scheme (mammoth grouped with Asian elephant) is either supported or questioned by the molecular results. Recently, the monophyly of woolly mammoths on mitochondrial grounds has been demonstrated (Thomas, et al., 2000), but it conflicts with previous studies (Barriel et al., 1999; Derenko et al., 1997). Here, we report the partial sequencing of two mitochondrial genes: 128 bp of 12S rDNA and 561 bp of cytochrome b for the Lyakhov mammoth, a 49,000-year-old Siberian individual. We use the most comprehensive sample of mammoth (11 sequences) to determine whether the sequences achieved by former studies were congruent or not. The monophyly of a major subset of mammoths sequences (including ours) is recovered. Such a result is assumed to be a good criterion for ascertaining the origin of ancient DNA. Our sequence is incongruent with that of Yang et al. (1996), though obtained for the same individual. As far as the latter sequence is concerned, a contamination by non-identified exogenous DNA is suspected. The robustness and reliability of the sister group relation between Mammuthus primigenius and Loxodonta africana are examined: down-weighting saturated substitutions has no impact on the topology; analyzing data partitions proves that the support of this clade can be assigned to the most conservative phylogenetic signal; insufficient taxonomic and/or characters sampling contributed to former discordant conclusions. We therefore assume the monophyly of "real mammoth sequences" and the (Mammuthus, Loxodonta) clade.

Animals↗

Radiocarbon evidence of mid-Holocene mammoths stranded on an Alaskan Bering Sea island.

Island colonization and subsequent dwarfing of Pleistocene proboscideans is one of the more dramatic evolutionary and ecological occurrences, especially in situations where island populations survived end-Pleistocene extinctions whereas those on the nearby mainland did not. For example, Holocene mammoths have been dated from Wrangel Island in northern Russia. In most of these cases, few details are available about the dynamics of how island colonization and extinction occurred. As part of a large radiocarbon dating project of Alaskan mammoth fossils, I addressed this question by including mammoth specimens from Bering Sea islands known to have formed during the end-Pleistocene sea transgression. One date of 7,908 +/- 100 yr bp (radiocarbon years before present) established the presence of Holocene mammoths on St Paul Island, a first Holocene island record for the Americas. Four lines of evidence--265 accelerator mass spectrometer (AMS) radiocarbon dates from Alaskan mainland mammoths, 13 new dates from Alaskan island mammoths, recent reconstructions of bathymetric plots and sea transgression rates from the Bering Sea--made it possible to reconstruct how mammoths became stranded in the Pribilofs and why this apparently did not happen on other Alaskan Bering Sea islands.

Alaska↗

A Million Years of Mammoth Mitogenome Evolution.

The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.

Animals↗

Ancient biodeterioration: an FT-Raman spectroscopic study of mammoth and elephant ivory.

Raman spectra of mammoth ivory specimens have been recorded using near-infrared excitation, and comparisons made with modern Asian and African elephant ivories. Whereas the most ancient mammoth ivory (60-65 ky) showed no evidence for an organic collagen component, more recent samples of mammoth ivory indicated that some preservation had occurred, although with biodeterioration of the protein structure exhibited by the amide I and III bands in the 1200-1700 cm(-1) region of the Raman spectrum. The consequent difficulties encountered when applying chemometrics methods to ancient ivory analysis (which are successful for modern specimens) are noted. In the most ancient mammoth ivory specimens, which are extensively fragmented, evidence of mineralization is seen, with the production of gypsum, calcite and limonite; Raman microscopic analysis of crystalline material inside the fissures of the mammoth ivory shows the presence of gypsum as well as cyanobacterial colonisation. The application of Raman spectroscopy to the nondestructive analysis of archaeological materials in order to gain information of relevance to their preservation or restoration is highlighted.

Animals↗

Mammoth albumin.

Serum albumin was detected immunologically in muscle from a mammoth that died about 40,000 years ago. Rabbits injected with ground mammoth muscle produced antibodies that react strongly with elephant albumin, weakly with sea cow albumin, and still more weakly or not at all with other mammalian albumins. Since elephant albumin elicited antibodies with the same specificity, some of the surviving mammoth albumin molecules evidently have antigenic sites identical to those on native elephant albumin. Much of the mammoth albumin has, however, undergone postmortem change. The small amount of soluble albumin extractable from mammoth muscle is heterogeneous in size, charge, and antigenic properties.

Animals↗

The maryland mammoth allele and rooting both perturb the fate of florally determined apices in Nicotiana tabacum.

The stability of the florally determined state in terminal and axillary buds of two tobacco cultivars was studied. We used Hicks and Hicks Maryland Mammoth, near-isogenic cultivars of Nicotiana tabacum differing at the recessive maryland mammoth locus which confers short-day behavior. The experimental design consisted of growing plants in short-day conditions and subjecting them to three bioassays in long-day conditions: in vitro culture of apices consisting of meristems and three to four leaf primordia; rooting of buds consisting of meristems and 8 to 12 leaves, leaf primordia, and internodes; and release from apical dominance of axillary buds in situ. Cultured terminal and axillary apices expressed floral determination, indicating that meristems can be florally determined. Two lines of evidence indicate that rooting destabilizes an already acquired florally determined state: cultured apices from both axillary and terminal buds produced fewer nodes after excision than homologous buds which were rooted; and a lower percentage of rooted axillary buds from Hicks Maryland Mammoth plants expressed floral determination than did homologous axillary buds grown out in situ in noninductive conditions. Rooted buds from the two genotypes expressed floral determination at different frequencies, but produced abnormal inflorescences at similar frequencies, indicating that roots and the maryland mammoth allele influence common as well as unique processes associated with floral determination.

Alleles↗

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.

Animals↗

Comparison of aspartic acid racemization between mammoth and human dentinal tissues.

OBJECTIVE: Comprehensive research has revealed the complexity and heterogeneity of amino acid racemization (AAR) in biological samples. Therefore, to date, inherent uncertainties in relative dating as well as in determination of age at death have highlighted the significance of further investigations to explore aspartic acid kinetics in biominerals. Here we present data on an archaeological sample obtained from a mammoth tusk, in comparison to a previously well-described biomineral, to modern human dentin. DESIGN: Since no experimental investigations were carried out on this topic earlier, we provide the first estimates on racemization kinetics and time dependent tendencies in mammoth dentin. We analysed our samples using a protocol, which has been adopted for tooth dentin investigation. We measured different racemization rates amongst mammoth dentin layers. RESULTS AND CONCLUSIONS: Significantly, an overall low racemization rate was detected compared to human dentin. Kinetic experiments were performed by heating the samples, and linear correlations were established between racemization rates and heating time. The results allow us to derive racemization rate constants and activation energy for both samples. Extrapolation for ambient temperature showed increased velocity in mammoth dentin, which can be explained by biodeterioration of ancient collagen and by diagenetic changes in amino acid composition influenced by environmental conditions.

Animals↗

Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae.

In studying the genomes of extinct species, two principal limitations are typically the small quantities of endogenous ancient DNA and its degraded condition, even though products of up to 1,600 base pairs (bp) have been amplified in rare cases. Using small overlapping polymerase chain reaction products, longer stretches of sequences or even whole mitochondrial genomes can be reconstructed, but this approach is limited by the number of amplifications that can be performed from rare samples. Thus, even from well-studied Pleistocene species such as mammoths, ground sloths and cave bears, no DNA sequences of more than about 1,000 bp have been reconstructed. Here we report the complete mitochondrial genome sequence of the Pleistocene woolly mammoth Mammuthus primigenius. We used about 200 mg of bone and a new approach that allows the simultaneous retrieval of multiple sequences from small amounts of degraded DNA. Our phylogenetic analyses show that the mammoth was more closely related to the Asian than to the African elephant. However, the divergence of mammoth, African and Asian elephants occurred over a short time, corresponding to only about 7% of the total length of the phylogenetic tree for the three evolutionary lineages.

Africa↗

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.

Animals↗

Estrous cycle characteristics and response to estrus synchronization in mammoth asses (Equus asinus americanus).

Breeding records from a herd of mammoth asses (Equus asinus americanus) maintained on pasture in southeast Texas from 1990 to 1998 were reviewed. Jennies were pasture or hand mated, and estrus was either observed while the jennies were on pasture or when exposed to a jack after being penned. Eighty-one estrus periods and 43 diestrus intervals were recorded in 33 jennies over 4 seasons of the year (January-March, April-June, July-September, and October-December). Estrous cycle length and the duration of estrus were similar among seasons. Over all seasons, estrous cycle length was 23.3 +/- 2.6 d, duration of estrus was 5.9 +/- 2.1 d, and diestrus length was 17.4 +/- 2.6 d (mean +/- SD). During these same 9 yr, 58 injections of PGF2 alpha (5 mg, i.m.) were administered to 38 jennies without regard to stage of estrous cycle. Seventy-six percent (44/58) of the jennies showed signs of estrus after PGF2 alpha treatment, with an interval to estrus of 4.4 +/- 1.6 d and a duration of estrus of 5.6 +/- 1.7 d. Two estrus synchronization schemes were also assessed. Trial 1 was performed in October to November 1996, and Trial 2 was performed in February to March 1998. In Trial 1 (Group PE + PGF, n = 10), each jenny was injected intramuscularly once daily for 10 d with 150 mg progesterone and 10 mg estradiol-17 beta in sesame oil, and PGF2 alpha (10 mg) was injected intramuscularly on the last day of treatment. In Trial 2 (Group PGF-2X, n = 11), each jenny was injected intramuscularly twice, 16 d apart, with 10 mg PGF2 alpha. All Group PE + PGF jennies responded to treatment. One jenny in Group PGF-2X did not respond to either injection of PGF2 alpha, while 2 jennies responded to the first but not the second PGF2 alpha injection (8 of 11 jennies returned to estrus and ovulated after the second PGF2 alpha injection). Duration of estrus was 6.8 +/- 1.9 d for Group PE + PGF and 7.1 +/- 1.8 d for Group PGF-2X jennies. Interval to estrus and interval to ovulation following the last treatment were 9.0 +/- 0.9 d and 14.5 +/- 1.7 d, respectively, in Group PE + PGF jennies, and 4.5 +/- 0.9 d and 10.4 +/- 1.8 d, respectively, for Group PGF-2X jennies. In summary, estrous cycle characteristics of mammoth asses are similar to those reported for standard jennies, and estrus synchronization schemes used in horses are effective in mammoth asses.

Animals↗

Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.

We sequenced 28 million base pairs of DNA in a metagenomics approach, using a woolly mammoth (Mammuthus primigenius) sample from Siberia. As a result of exceptional sample preservation and the use of a recently developed emulsion polymerase chain reaction and pyrosequencing technique, 13 million base pairs (45.4%) of the sequencing reads were identified as mammoth DNA. Sequence identity between our data and African elephant (Loxodonta africana) was 98.55%, consistent with a paleontologically based divergence date of 5 to 6 million years. The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.

Animals↗

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 approximately 1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. 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 of M. primigenius throughout the late Pleistocene.

Animals↗

Studies of collagen in bone and dentin matrix of a Columbian mammoth (late Pleistocene) of central Utah.

A Columbian mammoth, Mammuthus columbi, was excavated at an elevation of 9000 feet in Huntington Canyon, Emery County, Utah. Radiocarbon dates on the skeleton indicated death approximately 11,200 years ago. The skeleton was removed from postglacial, Late Quaternary, lake sediments deposited as glacial runoff approximately 9500 years ago. The bones and teeth were especially well preserved in a saturated lake bed. After excavation the bones and teeth were preserved by controlled desiccation, without hardeners, over a period of 9 months. Microradiography, light and electron microscopy, medium and high angle X-ray diffraction, amino acid analysis and cyanogen bromide peptide mapping were undertaken to evaluate the packing, organization, and preservation of collagen in bone and dentin of this mammoth. Microradiography and light microscopy showed that the bone consisted of especially well preserved compact and trabecular bone, and electron microscopy of demineralized bone and tusk showed that the matrix consisted of lamellae of densely packed cylindrical collagen fibrils. Cell remnants with intact nuclei, with or without a nucleolus, as well as variable lengths of plasma membrane were occasionally present on the surface of bony trabecula. Remnants of odontoblast processes were present in some dentin tubules. High and low angle X-ray diffraction demonstrated that the demineralized matrix contained native collagen molecules and amino acid analysis showed that the composition was comparable to that of type I collagen. Cyanogen bromide peptide mapping indicated that the major peptides of type I collagen were present and had the same electrophoretic mobility as that of type I collagen of demineralized Asian elephant bone and rat tail tendon.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acids↗

Identification of phenolic compounds in tissues of the novel olive cultivar hardy's mammoth.

A methodological approach to phenolic profiling making extensive use of LC-MS with extracted ion chromatograms was applied to extracts of five different olive tissues: pulp, seed, stone, new-season leaves, and old-season leaves. Tissue extracts of the cultivars Hardy's Mammoth, Corregiola, Verdale, and Manzanillo were analyzed by HPLC with UV and ESI MS detection. Chromatograms of samples of green Hardy's Mammoth drupes, a uniquely Australian olive cultivar, were dominated by a large, broad peak. This peak was not attributable to oleuropein, which is usually the dominant phenolic compound in green olive fruit, but the phenolic compound I. This compound was isolated by semipreparative HPLC and characterized by 1D- and 2D-NMR. Extraction studies showed that the compound was not likely to be an artifact of an enzymatic degradation process. Tritium labeling studies were used to establish a possible relationship between the biosynthesis of I and oleuropein.

Chromatography, High Pressure Liquid↗

Pleistocene to Holocene extinction dynamics in giant deer and woolly mammoth.

The extinction of the many well-known large mammals (megafauna) of the Late Pleistocene epoch has usually been attributed to 'overkill' by human hunters, climatic/vegetational changes or to a combination of both. An accurate knowledge of the geography and chronology of these extinctions is crucial for testing these hypotheses. Previous assumptions that the megafauna of northern Eurasia had disappeared by the Pleistocene/Holocene transition were first challenged a decade ago by the discovery that the latest woolly mammoths on Wrangel Island, northeastern Siberia, were contemporaneous with ancient Egyptian civilization. Here we show that another spectacular megafaunal species, the giant deer or 'Irish elk', survived to around 6,900 radiocarbon yr bp (about 7,700 yr ago) in western Siberia-more than three millennia later than its previously accepted terminal date-and therefore, that the reasons for its ultimate demise are to be sought in Holocene not Pleistocene events. Before their extinction, both giant deer and woolly mammoth underwent dramatic shifts in distribution, driven largely by climatic/vegetational changes. Their differing responses reflect major differences in ecology.

Animals↗