The Experts below are selected from a list of 1203 Experts worldwide ranked by ideXlab platform
Johannes Van Der Plicht - One of the best experts on this subject based on the ideXlab platform.
-
‘Semi‐dwarf’ Woolly Mammoths from the East Siberian Sea coast, continental Russia
Boreas, 2020Co-Authors: Irina V. Kirillova, Patricia Pecnerova, Johannes Van Der Plicht, Olga K. Borisova, O. F. Chernova, Thijs Van Kolfschoten, Jeroen H.j.l. Van Der Lubbe, A. V. Panin, Fedor K. Shidlovskiy, Vadim V. TitovAbstract:A pioneer comprehensive study of several diminutive last-generation Woolly Mammoth teeth (M3) found on the coast of the East Siberian Sea between the mouths of the Alazeya and Malaya Kuropatoch'ya ...
-
genome based sexing provides clues about behavior and social structure in the Woolly Mammoth
Current Biology, 2017Co-Authors: Patricia Pecnerova, David Diezdelmolino, Nicolas Dussex, Tatiana R Feuerborn, Johanna Von Seth, Johannes Van Der PlichtAbstract:Summary While present-day taxa are valuable proxies for understanding the biology of extinct species, it is also crucial to examine physical remains in order to obtain a more comprehensive view of their behavior, social structure, and life histories [1, 2]. For example, information on demographic parameters such as age distribution and sex ratios in fossil assemblages can be used to accurately infer socioecological patterns (e.g., [3]). Here we use genomic data to determine the sex of 98 Woolly Mammoth ( Mammuthus primigenius ) specimens in order to infer social and behavioral patterns in the last 60,000 years of the species' existence. We report a significant excess of males among the identified samples (69% versus 31%; p
-
Elevated δ^15N values in Mammoths: a comparison with modern elephants
Archaeological and Anthropological Sciences, 2015Co-Authors: Margot Kuitems, Thijs Van Kolfschoten, Johannes Van Der PlichtAbstract:The extinct Pleistocene Woolly Mammoth bone collagen shows compared with collagen from other contemporaneous large herbivores remarkably high δ^15N values. In order to investigate if the observed discrepancy in δ^15N values between Pleistocene Woolly Mammoths and coeval large ungulates also exists in modern relatives, we investigated the δ^15N (and δ^13C) values in nails of modern proboscideans, rhinoceroses and horses kept in captivity and with a comparable forage. The results of this study show that the nails of the different modern herbivores, supplied with similar diet, have more or less identical δ^15N values, so elephants do not show higher δ^15N values. How to explain the high values in Pleistocene Mammoths? Two different options will be discussed.
-
tracking possible decline of Woolly Mammoth during the gravettian in dordogne france and the ach valley germany using multi isotope tracking 13c 14c 15n 34s 18o
Quaternary International, 2015Co-Authors: Dorothee G Drucker, Susanne C Munzel, Nicholas J Conard, Johannes Van Der Plicht, Thomas Higham, Laurent Chiotti, Roland Nespoulet, Carole Vercoutere, Laurent CrepinAbstract:The Woolly Mammoth (Mammuthus primigenius) was an emblematic and key species of the so-called Mammoth steppe ecosystem between ca. 110,000 and 12,000 years ago. Its contribution to human subsistence during the Gravettian period as source of raw material was documented in southwestern France and southwestern Germany, with some evidence of active hunting in the latter region. However, decreasing genetic diversity and increasing indications of nutritional stress point to a likely decline of this megaherbivore. The specificity of the ecological niche occupied by the Woolly Mammoth is clearly reflected by their collagen 13C and 15N abundances (δ13Ccoll and δ15Ncoll), measured on skeletal remains of the typical Mammoth steppe. The abundances of carbon-13 in Mammoth collagen are comparable to those of other grazers like horse (Equus sp.), while the nitrogen-15 abundances are significantly higher (about 3‰) than in the other herbivores, either horse or reindeer (Rangifer tarandus). During the Aurignacian and Gravettian occupation at Geisenklosterle in the Ach Valley (Germany), the Mammoths had the expected stable isotope signature, but the nitrogen-15 of horses showed an unexpected overlap with those of the Mammoth. This unusual pattern was already occurring during the Aurignacian, while the oxygen-18 abundances in bone phosphate (δ18Obp) of horse and reindeer were unchanged between Aurignacian and Gravettian periods, which rules out significant change in environmental and climatic conditions. Thus, we hypothesize that during the Aurignacian and Gravettian, the ecological niche of Mammoth was intact but not occupied intensively by Mammoths due to a decline in their population. This decline could be tentatively explained by human pressure through hunting. In Dordogne (France), decreasing horse and reindeer δ15Ncoll values coeval to decreasing horse δ18Obp values between the Aurignacian and the Early Gravettian periods reflected a clear change in the environment, while no contrast in δ15Ncoll values was observed between the Early and Final Gravettian at the Abri Pataud. The Mammoth of Dordogne yielded slightly higher δ15Ncoll values than expected, probably as a consequence of the nursing effect since all the analyzed samples were ivory instead of bone. The direct dating and sulphur-34 measurement on the ivory of the Early Gravettian at Pataud showed that almost all of them were of contemporaneous and local origin. Significant contrasts in δ34Scoll values were found between the Dordogne and the Ach Valley for the same herbivores species, which confirms the potential of sulphur-34 in collagen as a mobility tracker.
-
tracking possible decline of Woolly Mammoth during the gravettian in dordogne france and the ach valley germany using
2014Co-Authors: G Drucker, Susanne C Munzel, Nicholas J Conard, Laurent Chiotti, Roland Nespoulet, Johannes Van Der PlichtAbstract:The Woolly Mammoth (Mammuthus primigenius) was an emblematic and key species of the so-called Mammoth steppe ecosystem between ca. 110,000 and 12,000 years ago. Its contribution to human subsistence during the Gravettian period as source of raw material was documented in southwestern France and southwestern Germany, with some evidence of active hunting in the latter region. However, decreasing genetic diversity and increasing indications of nutritional stress point to a likely decline of this megaherbivore. The specificity of the ecological niche occupied by the Woolly Mammoth is clearly reflected by their collagen 13 C and 15 N abundances (d 13 Ccoll and d 15 Ncoll), measured on skeletal remains of the typical Mammoth steppe. The abundances of carbon-13 in Mammoth collagen are comparable to those of other grazers like horse (Equus sp.), while the nitrogen-15 abundances are significantly higher (about 3‰) than in the other herbivores, either horse or reindeer (Rangifer tarandus). During the Aurignacian and Gravettian occupation at Geisenkl€ in the Ach Valley (Germany), the Mammoths had the expected stable isotope signature, but the nitrogen-15 of horses showed an unexpected overlap with those of the Mammoth. This unusual pattern was already occurring during the Aurignacian, while the oxygen-18 abundances in bone phosphate (d 18 Obp) of horse and reindeer were unchanged between Aurignacian and Gravettian periods, which rules out significant change in environmental and climatic conditions. Thus, we hypothesize that during the Aurignacian and Gravettian, the ecological niche of Mammoth was intact but not occupied intensively by Mammoths due to a decline in their population. This decline could be tentatively explained by human pressure through hunting. In Dordogne (France), decreasing horse and reindeer d 15 Ncoll values coeval to decreasing horse d 18 Obp values between the Aurignacian and the Early Gravettian periods reflected a clear change in the environment, while no contrast in d 15 Ncoll values was observed between the Early and Final Gravettian at the Abri Pataud. The
Alex D Greenwood - One of the best experts on this subject based on the ideXlab platform.
-
Short communication A nuclear DNA phylogeny of the Woolly Mammoth (Mammuthus primigenius)
2020Co-Authors: Cristian Capelli, Alfred L Roca, Nicholas J Georgiadis, Francesca Brisighelli, Alex D GreenwoodAbstract:) (e.g., Deb-ruyne et al., 2003; Noro et al., 1998). However, othermtDNA studies (Ozawa et al., 1997), including recentsequencing eVorts that yielded the complete mitochondrialgenomes of two Woolly Mammoths (Krause et al., 2006;Rogaev et al., 2006), suggested that the Asian elephant isthe closest living aYne of Mammoths. However, relation-ships inferred from mtDNA may be misleading due to theabsence of a closely related outgroup species, or to the radi-ation of the three elephantid genera in rapid succession,which can produce discordance between a species tree anda gene (mtDNA) tree due to lineage sorting processes.Another diYculty is that in certain species—includingelephants—the presence of nuclear insertions of mitochon-drial sequences (Numts) can make identifying organellarmtDNA problematic (Greenwood and Paabo, 1999;Thalmann et al., 2004). Moreover, Numt sequences are aroutine, if unwanted, result of the procedures used inancient DNA studies (Greenwood et al., 1999). Recently,cytonuclear genomic dissociation has been observed inAfrican elephants, likely due to past hybridization betweenspecies (Roca et al., 2005). The existence of such dissocia-tion phenomena could also confound mtDNA analysiswithin or among other elephantid species.To date, the only extinct elephantid that has been ame-nable to conWrmable molecular analysis by multipleresearch groups working with diVerent specimens is theWoolly Mammoth (for a recent summary, see Greenwood,2001). Yet, given the lack of consistent results acrossmtDNA phylogenetic studies, and given the possibility ofdiscrepancies between the mtDNA tree and the species treedue to lineage sorting processes or to cytonuclear dissocia-tion, nuclear DNA oVers an alternative approach to study-ing Woolly Mammoth phylogeny. Nuclear DNA sequencesfrom Mammoths and other well-preserved extinct mega-fauna have been reported (Greenwood et al., 1999; Green-wood et al., 2001; Poinar et al., 2003; Poinar et al., 2006),and in principle it should be possible to characterizeMammoth nuclear DNA sequences for the purpose of phy-logenetic analysis. Of additional relevance, several nucleargenes have been investigated in a large number of individu-als from diVerent populations of
-
successful genotyping of microsatellites in the Woolly Mammoth
Journal of Heredity, 2012Co-Authors: Yasuko Ishida, Alfred L Roca, Stephen Fratpietro, Alex D GreenwoodAbstract: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.
-
genetic variation at hair length candidate genes in elephants and the extinct Woolly Mammoth
BMC Evolutionary Biology, 2009Co-Authors: Alfred L Roca, G. G. Boeskorov, Yasuko Ishida, Stephen Fratpietro, Nikolas Nikolaidis, Sergiosorestis Kolokotronis, Kristin Stewardson, Shannon M Hensley, Michele Tisdale, Alex D GreenwoodAbstract: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. Results: Between the extant elephants and the Mammoth, two single base substitutions were observed in FGF5, neither of which alters the amino acid sequence. Modeling of the protein structure suggests that the elephantid proteins fold similarly to the human FGF5 protein. Bioinformatics analyses and DNA sequencing of another locus that has been implicated in hair cover in humans, type I hair keratin pseudogene (KRTHAP1), also yielded negative results. Interestingly, KRTHAP1 is a pseudogene in elephantids as in humans (although fully functional in non-human primates). Conclusion: The data suggest that the coding sequence of the FGF5 gene is not the critical determinant of hair length differences among elephantids. The results are discussed in the context of hairlessness among mammals and in terms of the potential impact of large body size, subarctic conditions, and an aquatic ancestor on hair cover in the Proboscidea.
-
a nuclear dna phylogeny of the Woolly Mammoth mammuthus primigenius
Molecular Phylogenetics and Evolution, 2006Co-Authors: Cristian Capelli, Alfred L Roca, Alex D Greenwood, Nicholas J Georgiadis, Francesca Brisighelli, Ross D E Macphee, Stephen J ObrienAbstract:a Istituto di Medicina Legale, Universita Cattolica del Sacro Cuore, Rome, Italy b Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA c Laboratory of Genomic Diversity, Basic Research Program, SAIC-Frederick, Frederick, MD 21702, USA d Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA e Mpala Research Center, P.O. Box 555, Nanyuki, Kenya f GSF-National Research Centre for Environment and Health, Institute of Molecular Virology, Neuherberg, Germany g Technical University of Munich, Institute of Virology, Munich, Germany
Sergey Vartanyan - One of the best experts on this subject based on the ideXlab platform.
-
thriving or surviving the isotopic record of the wrangel island Woolly Mammoth population
Quaternary Science Reviews, 2019Co-Authors: Laura Arppe, Dorothee G Drucker, Sergey Vartanyan, Juha A Karhu, Heli Etusihvola, Herve BocherensAbstract:Abstract The world's last population of Woolly Mammoths (Mammuthus primigenius) lived on Wrangel Island persisting well into the Holocene, going extinct at ca. 4000 cal BP. According to the frequency of radiocarbon dated Mammoth remains from the island, the extinction appears fairly abrupt. This study investigates the ecology of the Wrangel Island Mammoth population by means of carbon, nitrogen and sulfur isotope analyses. We report new isotope data on 77 radiocarbon dated Mammoth specimens from Wrangel Island and Siberia, and evaluate them in relation to previously published isotope data for Pleistocene Mammoths from Beringia and lower latitude Eurasia, and the other insular Holocene Mammoth population from St. Paul Island. Contrary to prior suggestions of gradual habitat deterioration, the nitrogen isotope values of the Wrangel Island Mammoths do not support a decline in forage quality/quantity, and are in fact very similar to their north Beringian forebears right to the end. However, compared to Siberian Mammoths, those from Wrangel Island show a difference in their energy economy as judged by the carbon isotope values of structural carbonate, possibly representing a lower need of adaptive strategies for survival in extreme cold. Increased mid-Holocene weathering of rock formations in the central mountains is suggested by sulfur isotope values. Scenarios related to water quality problems stemming from increased weathering, and a possibility of a catastrophic starvation event as a cause of, or contributing factor in their demise are discussed.
-
changes in variation at the mhc class ii dqa locus during the final demise of the Woolly Mammoth
Scientific Reports, 2016Co-Authors: Patricia Pecnerova, Sergey Vartanyan, David Diezdelmolino, Love DalenAbstract:According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck. In this study, we analyse three fragments of the MHC DQA gene in Woolly Mammoth samples radiocarbon dated to before and after a well-documented bottleneck that took place about ten thousand years ago. Our results indicate a decrease in observed heterozygosity and number of alleles, suggesting that genetic drift had an impact on the variation on MHC. Based on coalescent simulations, we found no evidence of balancing selection maintaining MHC diversity during the Holocene. However, strong trans-species polymorphism among Mammoths and elephants points to historical effects of balancing selection on the Woolly Mammoth lineage.
-
genome wide signatures of demographic change and holocene genetic decline in the extinct Woolly Mammoth
2014Co-Authors: Eleftheria Palkopoulou, Sergey Vartanyan, Anders Gotherstrom, Swapan Mallick, Pontus Skoglund, Nadin Rohland, Heng Li, Ayca Omrak, Hendrik N Poinar, David ReichAbstract:In light of current climate change it is critical to understand how different species have been affected in the past by well-known climatic events. In this thesis, DNA was retrieved from ancient material to study the population dynamics of two cold-adapted taxa that capture the extremes of body size range in mammals: the collared lemming (Dicrostonyx sp.) and the Woolly Mammoth (Mammuthus primigenius). The aim was to reconstruct their histories to investigate possible associations between past population events and changes in climate. Mitochondrial DNA sequences from collared lemming fossil remains in western Europe suggested that the history of this small mammal was characterized by repeated population extinctions followed by recolonizations, and that these were related to millennial-scale climatic fluctuations. Further genetic sampling of more than 300 mitochondrial DNA sequences, covering a large part of the collared lemming’s historical distribution, showed that these population turnovers were not site-specific but widespread, occurring across Europe and western Russia. Extant populations were found to harbor only a small fraction of the historical genetic diversity demonstrating an extensive loss of genetic variation in this small mammal during the last 50,000 years. For the Woolly Mammoth, a comprehensive dataset of novel and publicly available mitochondrial DNA sequences was compiled, covering a broad geographical and temporal range. In addition, complete genome sequencing was performed on two Mammoth specimens, the first representing one of the last surviving individuals from Wrangel Island and the second representing the ancestral Late Pleistocene Siberian population. Genome-wide as well as mitochondrial DNA data revealed that climatic changes have played a major role in shaping the demographic history of the Woolly Mammoth. For example, two severe population reductions were identified, with the first one encompassing the last warm interglacial period (~130,000 – 116,000 years ago) and the second coinciding with the end of the last Ice Age (~11,000 years ago). Moreover, climate-driven sea level changes appear to have had considerable impact by enabling increased gene flow across the Bering land bridge, as well as the isolation of Mammoths on Wrangel Island. When comparing the two complete genomes, the one from Wrangel Island displayed 20% lower genome-wide diversity and a markedly higher fraction of runs of homozygosity. Consequently, loss of genetic variation and inbreeding may have contributed to the extinction of the Woolly Mammoth. Overall, the findings presented in this thesis illustrate the power of ancient DNA in providing unique insights into past evolutionary processes.
-
holarctic genetic structure and range dynamics in the Woolly Mammoth
Proceedings of The Royal Society B: Biological Sciences, 2013Co-Authors: Love Dalen, Sergey Vartanyan, Andrei Sher, Eleftheria Palkopoulou, Adrian M Lister, Mikhail V Sablin, Veronica Nystrom Edmark, Mikael BrandstromAbstract: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.
-
validation of radiocarbon dates of Woolly Mammoth remains from northwestern chukotka russia
Radiocarbon, 2013Co-Authors: Sergey VartanyanAbstract:This paper presents the results of cross-dating of Mammoth remains from northwestern Chukotka, northeastern Siberia. Our results suggest that several dates obtained by the radiocarbon laboratory at the Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk (laboratory code SOAN) appear to be too recent. Cross-dating in different laboratories revealed significant differences in the ages obtained compared to SOAN. This highlights the need to critically assess 14C dates, and where necessary, confirm results in independent laboratories. DOI: 10.2458/azu_js_rc.v55i1.16465
Love Dalen - One of the best experts on this subject based on the ideXlab platform.
-
changes in variation at the mhc class ii dqa locus during the final demise of the Woolly Mammoth
Scientific Reports, 2016Co-Authors: Patricia Pecnerova, Sergey Vartanyan, David Diezdelmolino, Love DalenAbstract:According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck. In this study, we analyse three fragments of the MHC DQA gene in Woolly Mammoth samples radiocarbon dated to before and after a well-documented bottleneck that took place about ten thousand years ago. Our results indicate a decrease in observed heterozygosity and number of alleles, suggesting that genetic drift had an impact on the variation on MHC. Based on coalescent simulations, we found no evidence of balancing selection maintaining MHC diversity during the Holocene. However, strong trans-species polymorphism among Mammoths and elephants points to historical effects of balancing selection on the Woolly Mammoth lineage.
-
holarctic genetic structure and range dynamics in the Woolly Mammoth
Proceedings of The Royal Society B: Biological Sciences, 2013Co-Authors: Love Dalen, Sergey Vartanyan, Andrei Sher, Eleftheria Palkopoulou, Adrian M Lister, Mikhail V Sablin, Veronica Nystrom Edmark, Mikael BrandstromAbstract: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.
-
population level genotyping of coat colour polymorphism in Woolly Mammoth mammuthus primigenius
Quaternary Science Reviews, 2011Co-Authors: Claire Workman, Love Dalen, Sergey Vartanyan, Beth Shapiro, Pavel A Kosintsev, Andrei Sher, Anders Gotherstrom, Ian BarnesAbstract:Population-level genotyping of coat colour polymorphism in Woolly Mammoth (Mammuthus primigenius)
-
temporal genetic change in the last remaining population of Woolly Mammoth
Proceedings of The Royal Society B: Biological Sciences, 2010Co-Authors: Veronica Nystrom, Love Dalen, Sergey Vartanyan, Kerstin Liden, Nils Ryman, Anders AngerbjornAbstract: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.
-
Intraspecific phylogenetic analysis of Siberian Woolly Mammoths using complete mitochondrial genomes
Proceedings of the National Academy of Sciences of the United States of America, 2008Co-Authors: M. Thomas P. Gilbert, Love Dalen, Andrei Sher, Daniela I Drautz, Aakrosh Ratan, Ji Qi, Arthur M Lesk, Simon Y. W. Ho, Anders GotherstromAbstract:We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian Woolly Mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of Mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, ≈1–2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the 14C ages of these and previously identified members of the two Mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.
Nadin Rohland - One of the best experts on this subject based on the ideXlab platform.
-
complete genomes reveal signatures of demographic and genetic declines in the Woolly Mammoth
Current Biology, 2015Co-Authors: Eleftheria Palkopoulou, Swapan Mallick, Pontus Skoglund, Nadin RohlandAbstract:Summary The processes leading up to species extinctions are typically characterized by prolonged declines in population size and geographic distribution, followed by a phase in which populations are very small and may be subject to intrinsic threats, including loss of genetic diversity and inbreeding [1]. However, whether such genetic factors have had an impact on species prior to their extinction is unclear [2, 3]; examining this would require a detailed reconstruction of a species' demographic history as well as changes in genome-wide diversity leading up to its extinction. Here, we present high-quality complete genome sequences from two Woolly Mammoths ( Mammuthus primigenius ). The first Mammoth was sequenced at 17.1-fold coverage and dates to ∼4,300 years before present, representing one of the last surviving individuals on Wrangel Island. The second Mammoth, sequenced at 11.2-fold coverage, was obtained from an ∼44,800-year-old specimen from the Late Pleistocene population in northeastern Siberia. The demographic trajectories inferred from the two genomes are qualitatively similar and reveal a population bottleneck during the Middle or Early Pleistocene, and a more recent severe decline in the ancestors of the Wrangel Mammoth at the end of the last glaciation. A comparison of the two genomes shows that the Wrangel Mammoth has a 20% reduction in heterozygosity as well as a 28-fold increase in the fraction of the genome that comprises runs of homozygosity. We conclude that the population on Wrangel Island, which was the last surviving Woolly Mammoth population, was subject to reduced genetic diversity shortly before it became extinct.
-
genome wide signatures of demographic change and holocene genetic decline in the extinct Woolly Mammoth
2014Co-Authors: Eleftheria Palkopoulou, Sergey Vartanyan, Anders Gotherstrom, Swapan Mallick, Pontus Skoglund, Nadin Rohland, Heng Li, Ayca Omrak, Hendrik N Poinar, David ReichAbstract:In light of current climate change it is critical to understand how different species have been affected in the past by well-known climatic events. In this thesis, DNA was retrieved from ancient material to study the population dynamics of two cold-adapted taxa that capture the extremes of body size range in mammals: the collared lemming (Dicrostonyx sp.) and the Woolly Mammoth (Mammuthus primigenius). The aim was to reconstruct their histories to investigate possible associations between past population events and changes in climate. Mitochondrial DNA sequences from collared lemming fossil remains in western Europe suggested that the history of this small mammal was characterized by repeated population extinctions followed by recolonizations, and that these were related to millennial-scale climatic fluctuations. Further genetic sampling of more than 300 mitochondrial DNA sequences, covering a large part of the collared lemming’s historical distribution, showed that these population turnovers were not site-specific but widespread, occurring across Europe and western Russia. Extant populations were found to harbor only a small fraction of the historical genetic diversity demonstrating an extensive loss of genetic variation in this small mammal during the last 50,000 years. For the Woolly Mammoth, a comprehensive dataset of novel and publicly available mitochondrial DNA sequences was compiled, covering a broad geographical and temporal range. In addition, complete genome sequencing was performed on two Mammoth specimens, the first representing one of the last surviving individuals from Wrangel Island and the second representing the ancestral Late Pleistocene Siberian population. Genome-wide as well as mitochondrial DNA data revealed that climatic changes have played a major role in shaping the demographic history of the Woolly Mammoth. For example, two severe population reductions were identified, with the first one encompassing the last warm interglacial period (~130,000 – 116,000 years ago) and the second coinciding with the end of the last Ice Age (~11,000 years ago). Moreover, climate-driven sea level changes appear to have had considerable impact by enabling increased gene flow across the Bering land bridge, as well as the isolation of Mammoths on Wrangel Island. When comparing the two complete genomes, the one from Wrangel Island displayed 20% lower genome-wide diversity and a markedly higher fraction of runs of homozygosity. Consequently, loss of genetic variation and inbreeding may have contributed to the extinction of the Woolly Mammoth. Overall, the findings presented in this thesis illustrate the power of ancient DNA in providing unique insights into past evolutionary processes.
-
genomic dna sequences from mastodon and Woolly Mammoth reveal deep speciation of forest and savanna elephants
PLOS Biology, 2010Co-Authors: Nadin Rohland, Alfred L Roca, Swapan Mallick, David Reich, Matthias Meyer, Richard E Green, Nicholas J Georgiadis, Michael HofreiterAbstract: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.
-
substitutions in Woolly Mammoth hemoglobin confer biochemical properties adaptive for cold tolerance
Nature Genetics, 2010Co-Authors: Kevin L Campbell, Jeremy R H Tame, Nadin Rohland, Jason E E Roberts, Laura N Watson, Jorg Stetefeld, Angela M Sloan, Anthony V Signore, Jesse W Howatt, Tongjian ShenAbstract:Wehavegeneticallyretrieved, � resurrectedandperformed � detailedstructure-functionanalysesonauthenticWoolly � Mammothhemoglobintorevealforthefirsttimeboth � theevolutionaryoriginsandthestructuralunderpinnings � ofakeyadaptivephysiochemicaltraitinanextinct � species. � HemoglobinbindsandcarriesO2;� however, � its � abilitytooffloadO2�torespiringcellsishamperedat � lowtemperatures, � ashemedeoxygenationisinherently � endothermic � (thatis, � hemoglobin-O2�affinityincreasesas � temperaturedecreases). � Weidentifyaminoacidsubstitutions � withlargephenotypiceffectonthechimericb/d-globin � subunitofMammothhemoglobinthatprovideaunique � solutiontothisproblemandtherebyminimizeenergetically � costlyheatloss. � Thisbiochemicalspecializationmay � havebeeninvolvedintheexploitationofhigh-latitude � environmentsbythisAfrican-derivedelephantidlineage � duringthePleistoceneperiod. � Thispowerfulnewapproach �
