Eske Willerslev, Enrico Cappellini, Wouter Boomsma, Rasmus Nielsen, Martin B Hebsgaard, Tina B Brand, Michael Hofreiter, Michael Bunce, Hendrik N Poinar, Dorthe Dahl-Jensen, Sigfus Johnsen, Jørgen Peder Steffensen, Ole Bennike, Jean-Luc Schwenninger, Roger Nathan, Simon Armitage, Cees-Jan de Hoog, Vasily Alfimov, Marcus Christl, Juerg Beer, Raimund Muscheler, Joel Barker, Martin Sharp, Kirsty E H Penkman, James Haile, Pierre Taberlet, M Thomas P Gilbert, Antonella Casoli, Elisa Campani, Matthew J Collins
It is difficult to obtain fossil data from the 10% of Earth's terrestrial surface that is covered by thick glaciers and ice sheets, and hence, knowledge of the paleoenvironments of these regions has remained limited. We show that DNA and amino acids from buried organisms can be recovered from the basal sections of deep ice cores, enabling reconstructions of past flora and fauna. We show that high-altitude southern Greenland, currently lying below more than 2 kilometers of ice, was inhabited by a diverse array of conifer trees and insects within the past million years. The results provide direct evidence in support of a forested southern Greenland and suggest that many deep ice cores may contain genetic records of paleoenvironments in their basal sections.
Mol Ecol. 2012 Apr ;21 (8):1806-15 21988749
Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA.
Sanne Boessenkool, Laura S Epp, James Haile, Eva Bellemain, Mary Edwards, Eric Coissac, Eske Willerslev, Christian Brochmann
National Centre for Biosystematics, Natural History Museum, University of Oslo, Oslo, Norway. email@example.com
Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results because of competition, or bias, during the PCR. In this study, we test the utility of human-specific blocking primers in mammal diversity analyses of ancient permafrost samples from Siberia. Using quantitative PCR (qPCR) on human and mammoth DNA, we first optimized the design and concentration of blocking primer in the PCR. Subsequently, 454 pyrosequencing of ancient permafrost samples amplified with and without the addition of blocking primer revealed that DNA sequences from a diversity of mammalian representatives of the Beringian megafauna were retrieved only when the blocking primer was added to the PCR. Notably, we observe the first retrieval of woolly rhinoceros (Coelodonta antiquitatis) DNA from ancient permafrost cores. In contrast, reactions without blocking primer resulted in complete dominance by human DNA sequences. These results demonstrate that in ancient environmental analyses, the PCR can be biased towards the amplification of contaminant sequences to such an extent that retrieval of the endogenous DNA is severely restricted. The application of blocking primers is a promising tool to avoid this bias and can greatly enhance the quantity and the diversity of the endogenous DNA sequences that are amplified.
Tony Dejean, Alice Valentini, Antoine Duparc, Stéphanie Pellier-Cuit, François Pompanon, Pierre Taberlet, Claude Miaud
SPYGEN, Savoie Technolac - BP 274, Le Bourget-du-Lac, France.
The precise knowledge of species distribution is a key step in conservation biology. However, species detection can be extremely difficult in many environments, specific life stages and in populations at very low density. The aim of this study was to improve the knowledge on DNA persistence in water in order to confirm the presence of the focus species in freshwater ecosystems. Aquatic vertebrates (fish: Siberian sturgeon and amphibian: Bullfrog tadpoles) were used as target species. In control conditions (tanks) and in the field (ponds), the DNA detectability decreases with time after the removal of the species source of DNA. DNA was detectable for less than one month in both conditions. The density of individuals also influences the dynamics of DNA detectability in water samples. The dynamics of detectability reflects the persistence of DNA fragments in freshwater ecosystems. The short time persistence of detectable amounts of DNA opens perspectives in conservation biology, by allowing access to the presence or absence of species e.g. rare, secretive, potentially invasive, or at low density. This knowledge of DNA persistence will greatly influence planning of biodiversity inventories and biosecurity surveys.
Ludovic Orlando, Aurelien Ginolhac, Maanasa Raghavan, Julia Vilstrup, Morten Rasmussen, Kim Magnussen, Kathleen E Steinmann, Philipp Kapranov, John F Thompson, Grant Zazula, Duane Froese, Ida Moltke, Beth Shapiro, Michael Hofreiter, Khaled A S Al-Rasheid, M Thomas P Gilbert, Eske Willerslev
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, Copenhagen DK-1350, Denmark. Lorlando@snm.ku.dk
Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences that do not reflect the original DNA template composition. This is particularly true for ancient DNA, where templates have undergone extensive damage post-mortem. Here, we report the results of the first "true single molecule sequencing" of ancient DNA. We generated 115.9 Mb and 76.9 Mb of DNA sequences from a permafrost-preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous DNA sequences derived from the horse is higher among the Helicos data than Illumina data. This result indicates that the molecular biology tools used to generate sequencing libraries of ancient DNA molecules, as required for second-generation sequencing, introduce biases into the data that reduce the efficiency of the sequencing process and limit our ability to fully explore the molecular complexity of ancient DNA extracts. We demonstrate that simple modifications to the standard Helicos DNA template preparation protocol further increase the proportion of horse DNA for this sample by threefold. Comparison of Helicos-specific biases and sequence errors in modern DNA with those in ancient DNA also reveals extensive cytosine deamination damage at the 3' ends of ancient templates, indicating the presence of 3'-sequence overhangs. Our results suggest that paleogenomes could be sequenced in an unprecedented manner by combining current second- and third-generation sequencing approaches.
Sr-Nd-Pb isotope evidence for ice-sheet presence on southern Greenland during the Last Interglacial.
Elizabeth J Colville, Anders E Carlson, Brian L Beard, Robert G Hatfield, Joseph S Stoner, Alberto V Reyes, David J Ullman
Department of Geoscience, University of Wisconsin, Madison, WI 53706, USA.
To ascertain the response of the southern Greenland Ice Sheet (GIS) to a boreal summer climate warmer than at present, we explored whether southern Greenland was deglaciated during the Last Interglacial (LIG), using the Sr-Nd-Pb isotope ratios of silt-sized sediment discharged from southern Greenland. Our isotope data indicate that no single southern Greenland geologic terrane was completely deglaciated during the LIG, similar to the Holocene. Differences in sediment sources during the LIG relative to the early Holocene denote, however, greater southern GIS retreat during the LIG. These results allow the evaluation of a suite of GIS models and are consistent with a GIS contribution of 1.6 to 2.2 meters to the ≥4-meter LIG sea-level highstand, requiring a significant sea-level contribution from the Antarctic Ice Sheet.
To clone or not to clone: method analysis for retrieving consensus sequences in ancient DNA samples.
School of Biological Sciences, Washington State University, Pullman, Washington, United States of America.
The challenges associated with the retrieval and authentication of ancient DNA (aDNA) evidence are principally due to post-mortem damage which makes ancient samples particularly prone to contamination from "modern" DNA sources. The necessity for authentication of results has led many aDNA researchers to adopt methods considered to be "gold standards" in the field, including cloning aDNA amplicons as opposed to directly sequencing them. However, no standardized protocol has emerged regarding the necessary number of clones to sequence, how a consensus sequence is most appropriately derived, or how results should be reported in the literature. In addition, there has been no systematic demonstration of the degree to which direct sequences are affected by damage or whether direct sequencing would provide disparate results from a consensus of clones.To address this issue, a comparative study was designed to examine both cloned and direct sequences amplified from ∼3,500 year-old ancient northern fur seal DNA extracts. Majority rules and the Consensus Confidence Program were used to generate consensus sequences for each individual from the cloned sequences, which exhibited damage at 31 of 139 base pairs across all clones. In no instance did the consensus of clones differ from the direct sequence. This study demonstrates that, when appropriate, cloning need not be the default method, but instead, should be used as a measure of authentication on a case-by-case basis, especially when this practice adds time and cost to studies where it may be superfluous.
Am J Bot. 2010 Sep ;97 (9):1579-84 21616909
Evidence of a high-Andean, mid-Holocene plant community: An ancient DNA analysis of glacially preserved remains.
Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14850 USA.
• Premise of the study: Around the world, tropical glaciers and ice caps are retreating at unprecedented rates because of climate change. In at least one location, along the margin of the Quelccaya Ice Cap in southeastern Peru, ancient plant remains have been continually uncovered since 2002. We used genetic analysis to identify plants that existed at these sites during the mid-Holocene. • Methods: We examined remains between 4576 and 5222 yr old, using PCR amplification, cloning, and sequencing of a fragment of the chloroplast trnL intron. We then matched these sequences to sequences in GenBank. • Key results: We found evidence of at least five taxa characteristic of wetlands, which occur primarily at lower elevations in the region today. • Conclusions: A diverse community most likely existed at these locations the last time they were ice-free and thus has the potential to reestablish with time. This is the first genetic analysis of vegetation uncovered by receding glacial ice, and it may become one of many as ancient plant materials are newly uncovered in a changing climate.
Detection and structural identification of dissolved organic matter in Antarctic glacial ice at natural abundance by SPR-W5-WATERGATE 1H NMR spectroscopy.
Brent G Pautler, André J Simpson, Myrna J Simpson, Li-Hong Tseng, Manfred Spraul, Ashley Dubnick, Martin J Sharp, Sean J Fitzsimons
Environmental NMR Centre and Department of Chemistry, University of Toronto, Toronto, Ontario, M1C 1A4 Canada.
Dissolved organic matter (DOM) is ubiquitous in aquatic ecosystems and is derived from various inputs that control its turnover. Glaciers and ice sheets are the second largest water reservoir in the global hydrologic cycle, but little is known about glacial DOM composition or contributions to biogeochemical cycling. Here we employ SPR-W5-WATERGATE (1)H NMR spectroscopy to elucidate and quantify the chemical structures of DOM constituents in Antarctic glacial ice as they exist in their natural state (average DOC of 8 mg/L) without isolation or preconcentration. This Antarctic glacial DOM is predominantly composed of a mixture of small recognizable molecules differing from DOM in marine, lacustrine, and other terrestrial environments. The major constituents detected in three distinct types of glacial ice include lactic and formic acid, free amino acids, and a mixture of simple sugars and amino sugars with concentrations that vary between ice types. The detection of free amino acid and amino sugar monomer components of peptidoglycan within the ice suggests that Antarctic glacial DOM likely originates from in situ microbial activity. As these constituents are normally considered to be biologically labile (fast cycling) in nonglacial environments, accelerated glacier melt and runoff may result in a flux of nutrients into adjacent ecosystems.
Department of Biology, The Pennsylvania State University, PA, USA. firstname.lastname@example.org
Heterochronous data sets comprise molecular sequences sampled at different points in time. If the temporal range of the sampled sequences is large relative to the rate of mutation, the sampling times can directly calibrate evolutionary rates to calendar time. Here, we extend this calibration process to provide a full probabilistic method that utilizes temporal information in heterochronous data sets to estimate sampling times (leaf-ages) for sequenced for which this information unavailable. Our method is similar to relaxing the constraints of the molecular clock on specific lineages within a phylogenetic tree. Using a combination of synthetic and empirical data sets, we demonstrate that the method estimates leaf-ages reliably and accurately. Potential applications of our approach include incorporating samples of uncertain or radiocarbon-infinite age into ancient DNA analyses, evaluating the temporal signal in a particular sequence or data set, and exploring the reliability of sequence ages that are somehow contentious.
Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia. email@example.com
Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. firstname.lastname@example.org
High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering.
Other papers by authors:
Eline D Lorenzen, David Nogués-Bravo, Ludovic Orlando, Jaco Weinstock, Jonas Binladen, Katharine A Marske, Andrew Ugan, Michael K Borregaard, M Thomas P Gilbert, Rasmus Nielsen, Simon Y W Ho, Ted Goebel, Kelly E Graf, David Byers, Jesper T Stenderup, Morten Rasmussen, Paula F Campos, Jennifer A Leonard, Klaus-Peter Koepfli, Duane Froese, Grant Zazula, Thomas W Stafford Jr, Kim Aaris-Sørensen, Persaram Batra, Alan M Haywood, Joy S Singarayer, Paul J Valdes, Gennady Boeskorov, James A Burns, Sergey P Davydov, James Haile, Dennis L Jenkins, Pavel Kosintsev, Tatyana Kuznetsova, Xulong Lai, Larry D Martin, H Gregory McDonald, Dick Mol, Morten Meldgaard, Kasper Munch, Elisabeth Stephan, Mikhail Sablin, Robert S Sommer, Taras Sipko, Eric Scott, Marc A Suchard, Alexei Tikhonov, Rane Willerslev, Robert K Wayne, Alan Cooper, Michael Hofreiter, Andrei Sher, Beth Shapiro, Carsten Rahbek, Eske Willerslev
Centre for GeoGenetics, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.
Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.
Charlotte L Oskam, James Haile, Emma McLay, Paul Rigby, Morten E Allentoft, Maia E Olsen, Camilla Bengtsson, Gifford H Miller, Jean-Luc Schwenninger, Chris Jacomb, Richard Walter, Alexander Baynes, Joe Dortch, Michael Parker-Pearson, M Thomas P Gilbert, Richard N Holdaway, Eske Willerslev, Michael Bunce
Ancient DNA Laboratory, School of Biological Sciences, Murdoch University, Perth, Western Australia, Australia.
Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes.
M Thomas P Gilbert, Toomas Kivisild, Bjarne Grønnow, Pernille K Andersen, Ene Metspalu, Maere Reidla, Erika Tamm, Erik Axelsson, Anders Götherström, Paula F Campos, Morten Rasmussen, Mait Metspalu, Thomas F G Higham, Jean-Luc Schwenninger, Roger Nathan, Cees-Jan De Hoog, Anders Koch, Lone Nukaaraq Møller, Claus Andreasen, Morten Meldgaard, Richard Villems, Christian Bendixen, Eske Willerslev
Center for Ancient Genetics, Department of Biology, Universitetsparken 15, DK-2100, Copenhagen, Denmark.
The Paleo-Eskimo Saqqaq and Independence I cultures, documented from archaeological remains in Northern Canada and Greenland, represent the earliest human expansion into the New World's northern extremes. However, their origin and genetic relationship to later cultures is unknown. We sequenced a mitochondrial genome from a Paleo-Eskimo human, using 3400- to 4500-year-old frozen hair excavated from an early Greenlandic Saqqaq settlement. The sample is distinct from modern Native Americans and Neo-Eskimos, falling within haplogroup D2a1, a group previously observed among modern Aleuts and Siberian Sireniki Yuit. This suggests that the earliest migrants into the New World's northern extremes derived from populations in the Bering Sea area, and were neither directly related to Native Americans nor the later Neo-Eskimos that replaced them.
Sarah Stewart Johnson, Martin B Hebsgaard, Torben R Christensen, Mikhail Mastepanov, Rasmus Nielsen, Kasper Munch, Tina Brand, M Thomas P Gilbert, Maria T Zuber, Michael Bunce, Regin Rønn, David Gilichinsky, Duane Froese, Eske Willerslev
Recent claims of cultivable ancient bacteria within sealed environments highlight our limited understanding of the mechanisms behind long-term cell survival. It remains unclear how dormancy, a favored explanation for extended cellular persistence, can cope with spontaneous genomic decay over geological timescales. There has been no direct evidence in ancient microbes for the most likely mechanism, active DNA repair, or for the metabolic activity necessary to sustain it. In this paper, we couple PCR and enzymatic treatment of DNA with direct respiration measurements to investigate long-term survival of bacteria sealed in frozen conditions for up to one million years. Our results show evidence of bacterial survival in samples up to half a million years in age, making this the oldest independently authenticated DNA to date obtained from viable cells. Additionally, we find strong evidence that this long-term survival is closely tied to cellular metabolic activity and DNA repair that over time proves to be superior to dormancy as a mechanism in sustaining bacteria viability.
Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?
James Haile, Richard Holdaway, Karen Oliver, Michael Bunce, M Thomas P Gilbert, Rasmus Nielsen, Kasper Munch, Simon Y W Ho, Beth Shapiro, Eske Willerslev
Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom.
In recent years, several studies have reported the successful extraction of ancient DNA (aDNA) from both frozen and nonfrozen sediments (even in the absence of macrofossils) in order to obtain genetic "profiles" from past environments. One of the hazards associated with this approach, particularly in nonfrozen environments, is the potential for vertical migration of aDNA across strata. To assess the extent of this problem, we extracted aDNA from sediments up to 3300 years old at 2 cave sites in the North Island of New Zealand. These sites are ideal for this purpose as the presence or absence of DNA from nonindigenous fauna (such as sheep) in sediments deposited prior to European settlement can serve as an indicator of DNA movement. Additionally, these strata are well defined and dated. DNA from sheep was found in strata that also contained moa DNA, indicating that genetic material had migrated downwards. Quantitative polymerase chain reaction analyses demonstrated that the amount of sheep DNA decreased as the age of sediments increased. Our results suggest that sedimentary aDNA is unlikely to be deposited from wind-borne DNA and that physical remains of organisms or their ejecta need to have been incorporated in the sediments for their DNA to be detected. Our study indicates that DNA from sediments can still offer a rich source of information on past environments, provided that the risk from vertical migration can be controlled for.
Mol Ecol. 2012 Apr ;21 (8):1989-2003 22590727
A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability.
Tina Jørgensen, James Haile, Per Möller, Andrei Andreev, Sanne Boessenkool, Morten Rasmussen, Frank Kienast, Eric Coissac, Pierre Taberlet, Christian Brochmann, Nancy H Bigelow, Kenneth Andersen, Ludovic Orlando, M Thomas P Gilbert, Eske Willerslev
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Although ancient DNA from sediments (sedaDNA) has been used to investigate past ecosystems, the approach has never been directly compared with the traditional methods of pollen and macrofossil analysis. We conducted a comparative survey of 18 ancient permafrost samples spanning the Late Pleistocene (46-12.5 thousand years ago), from the Taymyr Peninsula in northern Siberia. The results show that pollen, macrofossils and sedaDNA are complementary rather than overlapping and, in combination, reveal more detailed information on plant palaeocommunities than can be achieved by each individual approach. SedaDNA and macrofossils share greater overlap in plant identifications than with pollen, suggesting that sedaDNA is local in origin. These two proxies also permit identification to lower taxonomic levels than pollen, enabling investigation into temporal changes in species composition and the determination of indicator species to describe environmental changes. Combining data from all three proxies reveals an area continually dominated by a mosaic vegetation of tundra-steppe, pioneer and wet-indicator plants. Such vegetational stability is unexpected, given the severe climate changes taking place in the Northern Hemisphere during this time, with changes in average annual temperatures of >22 °C. This may explain the abundance of ice-age mammals such as horse and bison in Taymyr Peninsula during the Pleistocene and why it acted as a refugium for the last mainland woolly mammoth. Our finding reveals the benefits of combining sedaDNA, pollen and macrofossil for palaeovegetational reconstruction and adds to the increasing evidence suggesting large areas of the Northern Hemisphere remained ecologically stable during the Late Pleistocene.
Laura Parducci, Tina Jørgensen, Mari Mette Tollefsrud, Ellen Elverland, Torbjørn Alm, Sonia L Fontana, K D Bennett, James Haile, Irina Matetovici, Yoshihisa Suyama, Mary E Edwards, Kenneth Andersen, Morten Rasmussen, Sanne Boessenkool, Eric Coissac, Christian Brochmann, Pierre Taberlet, Michael Houmark-Nielsen, Nicolaj Krog Larsen, Ludovic Orlando, M Thomas P Gilbert, Kurt H Kjær, Inger Greve Alsos, Eske Willerslev
Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
It is commonly believed that trees were absent in Scandinavia during the last glaciation and first recolonized the Scandinavian Peninsula with the retreat of its ice sheet some 9000 years ago. Here, we show the presence of a rare mitochondrial DNA haplotype of spruce that appears unique to Scandinavia and with its highest frequency to the west-an area believed to sustain ice-free refugia during most of the last ice age. We further show the survival of DNA from this haplotype in lake sediments and pollen of Trøndelag in central Norway dating back ~10,300 years and chloroplast DNA of pine and spruce in lake sediments adjacent to the ice-free Andøya refugium in northwestern Norway as early as ~22,000 and 17,700 years ago, respectively. Our findings imply that conifer trees survived in ice-free refugia of Scandinavia during the last glaciation, challenging current views on survival and spread of trees as a response to climate changes.
Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins.
Enrico Cappellini, Lars J Jensen, Damian Szklarczyk, Aurélien Ginolhac, Rute A R da Fonseca, Thomas W Stafford, Steven R Holen, Matthew J Collins, Ludovic Orlando, Eske Willerslev, M Thomas P Gilbert, Jesper V Olsen
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen , Øster Voldgade 5-7, 1350, Copenhagen, Denmark. email@example.com
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.
Mol Ecol. 2012 Apr ;21 (8):1980-8 21951625
Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding.
Tina Jørgensen, Kurt H Kjaer, James Haile, Morten Rasmussen, Sanne Boessenkool, Kenneth Andersen, Eric Coissac, Pierre Taberlet, Christian Brochmann, Ludovic Orlando, M Thomas P Gilbert, Eske Willerslev
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Nunataks are isolated bedrocks protruding through ice sheets. They vary in age, but represent island environments in 'oceans' of ice through which organism dispersals and replacements can be studied over time. The J.A.D. Jensen's Nunataks at the southern Greenland ice sheet are the most isolated nunataks on the northern hemisphere - some 30 km from the nearest biological source. They constitute around 2 km(2) of ice-free land that was established in the early Holocene. We have investigated the changes in plant composition at these nunataks using both the results of surveys of the flora over the last 130 years and through reconstruction of the vegetation from the end of the Holocene Thermal Maximum (5528 ± 75 cal year BP) using meta-barcoding of plant DNA recovered from the nunatak sediments (sedaDNA). Our results show that several of the plant species detected with sedaDNA are described from earlier vegetation surveys on the nunataks (in 1878, 1967 and 2009). In 1967, a much higher biodiversity was detected than from any other of the studied periods. While this may be related to differences in sampling efforts for the oldest period, it is not the case when comparing the 1967 and 2009 levels where the botanical survey was exhaustive. As no animals and humans are found on the nunataks, this change in diversity over a period of just 42 years must relate to environmental changes probably being climate-driven. This suggests that even the flora of fairly small and isolated ice-free areas reacts quickly to a changing climate.
Morten Rasmussen, Xiaosen Guo, Yong Wang, Kirk E Lohmueller, Simon Rasmussen, Anders Albrechtsen, Line Skotte, Stinus Lindgreen, Mait Metspalu, Thibaut Jombart, Toomas Kivisild, Weiwei Zhai, Anders Eriksson, Andrea Manica, Ludovic Orlando, Francisco M De La Vega, Silvana Tridico, Ene Metspalu, Kasper Nielsen, María C Ávila-Arcos, J Víctor Moreno-Mayar, Craig Muller, Joe Dortch, M Thomas P Gilbert, Ole Lund, Agata Wesolowska, Monika Karmin, Lucy A Weinert, Bo Wang, Jun Li, Shuaishuai Tai, Fei Xiao, Tsunehiko Hanihara, George van Driem, Aashish R Jha, François-Xavier Ricaut, Peter de Knijff, Andrea B Migliano, Irene Gallego Romero, Karsten Kristiansen, David M Lambert, Søren Brunak, Peter Forster, Bernd Brinkmann, Olaf Nehlich, Michael Bunce, Michael Richards, Ramneek Gupta, Carlos D Bustamante, Anders Krogh, Robert A Foley, Marta M Lahr, Francois Balloux, Thomas Sicheritz-Pontén, Richard Villems, Rasmus Nielsen, Jun Wang, Eske Willerslev
Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.
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Comparison of the microbial diversity at different depths of the GISP2 Greenland ice core in relationship to deposition climates.
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA. firstname.lastname@example.org
This study presents comparative geochemical, microbiological and molecular analyses of Greenland GISP2 ice core samples representing different depths, ages, deposition climates, in situ temperatures, and gas and ionic compositions. Our goal was to determine whether specific organisms, preserved at different depths, correlate with past climate characteristics recorded chronologically in ice layers. Three clear ice samples were selected from 2495, 2545 and 2578 m to represent distinct climatic periods with milder (-45 degrees C), colder (-51 degrees C) and warmer (-39 degrees C) deposition temperatures, and two Marine Isotope Stages, MIS3 (2495 m) and MIS4 (2545 and 2578 m). Results showed higher microbial abundance in ice deposited during colder climates with higher in situ ion content. The constructed universal SSU rRNA gene clone libraries were dominated by Gram-positive sequences (55-65%), and had fewer Proteobacteria (6-9%) and Archaea (1%). The 2495 m library differed from the other two by being dominated by Actinobacteria (55%) rather than Firmicutes. Fungi were more prevalent in the colder climate (40%). For comparison, a library was constructed from an older silty ice sample (3044 m) possibly originating from underlying permafrost with different in situ characteristics (high temperature, high methane and higher cell numbers). It showed significantly different diversity not found in the clear ice libraries. The bacterial and fungal isolates from the clear ice samples were related to organisms originating from Asian deserts, marine aerosols and volcanic dust, suggesting these environments as sources of deposited microorganisms. The observed differences in microbial diversity patterns, especially with the 2495 m library, support the idea that local climate conditions and global atmospheric circulations at different time periods have influenced the origin and composition of the microbial populations preserved at different depths of Greenland ice. Further investigations may lead to the development of microbial 'markers' for identifying specific deposition climates.
An ultra-clean technique for accurately analysing Pb isotopes and heavy metals at high spatial resolution in ice cores with sub-pg g(-1) Pb concentrations.
Laurie J Burn, Kevin J R Rosman, Jean-Pierre Candelone, Paul Vallelonga, Graeme R Burton, Andrew M Smith, Vin I Morgan, Carlo Barbante, Sungmin Hong, Claude F Boutron
Department of Imaging and Applied Physics, Curtin University of Technology, GPO Box U1987, Perth 6845, Western Australia, Australia.
Measurements of Pb isotope ratios in ice containing sub-pg g(-1) concentrations are easily compromised by contamination, particularly where limited sample is available. Improved techniques are essential if Antarctic ice cores are to be analysed with sufficient spatial resolution to reveal seasonal variations due to climate. This was achieved here by using stainless steel chisels and saws and strict protocols in an ultra-clean cold room to decontaminate and section ice cores. Artificial ice cores, prepared from high purity water were used to develop and refine the procedures and quantify blanks. Ba and In, two other important elements present at pg g(-1) and fg g(-1) concentrations in Polar ice, were also measured. The final blank amounted to 0.2+/-0.2 pg of Pb with (206)Pb/(207)Pb and (208)Pb/(207)Pb ratios of 1.16+/-0.12 and 2.35+/-0.16, respectively, 1.5+/-0.4 pg of Ba and 0.6+/-2.0 fg of In, most of which probably originates from abrasion of the steel saws by the ice. The procedure was demonstrated on a Holocene Antarctic ice core section and was shown to contribute blanks of only approximately 5%, approximately 14% and approximately 0.8% to monthly resolved samples with respective Pb, Ba and In concentrations of 0.12 pg g(-1), 0.3 pg g(-1) and 2.3 fg g(-1). Uncertainties in the Pb isotopic ratio measurements were degraded by only approximately 0.2%.
Patrik R Kaufmann, Urs Federer, Manuel A Hutterli, Matthias Bigler, Simon Schüpbach, Urs Ruth, Jochen Schmitt, Thomas F Stocker
Climate and Environmental Physics, Physics Institute, University of Bern, Bern, Switzerland. email@example.com
Continuous flow analysis (CFA) is a well-established method to obtain information about impurity contents in ice cores as indicators of past changes in the climate system. A section of an ice core is continuously melted on a melter head supplying a sample water flow which is analyzed online. This provides high depth and time resolution of the ice core records and very efficient sample decontamination as only the inner part of the ice sample is analyzed. Here we present an improved CFA system which has been totally redesigned in view of a significantly enhanced overall efficiency and flexibility, signal quality, compactness, and ease of use. These are critical requirements especially for operations of CFA during field campaigns, e.g., in Antarctica or Greenland. Furthermore, a novel deviceto measure the total air content in the ice was developed. Subsequently, the air bubbles are now extracted continuously from the sample water flow for subsequent gas measurements.
Climate and Environmental Physics, Physics Institute, University of Bern, Bern, Switzerland. firstname.lastname@example.org
Ice cores are a widely used archive to reconstruct past changes of the climate system. This is done by measuring the concentration of substances in the ice and in the air of bubbles enclosed in ice. Some species pertaining to the carbon cycle (e.g., CO2, CH4) are routinely measured. However, information about the organic fraction of the impurities in polar ice is still very limited. Therefore, we developed a new method to determine the content of total organic carbon (TOC) in ice cores using a continuous flow analysis (CFA) system. The method is based on photochemical oxidation of TOC and the electrolytic quantification of the CO2 produced during oxidation. The TOC instrument features a limit of detection of 2 ppbC and a response time of 60 s at a sample flow rate of 0.7 mL/min and a linear measurement range of 2-4000 ppbC. First measurements on the ice core from Talos Dome, Antarctica, reveal TOC concentrations varying between 80 and 360 ppbC in the 20 m section presented.
Talanta. 2001 Oct 31;55 (4):765-72 18968423
Determination of trace amounts of heavy metals in arctic ice core samples using inductively coupled plasma mass spectrometry.
Nagaoka Institute of Snow and Ice Studies, National Research Institute for Earth Science and Disaster Prevention, Nagaoka, Niigata 940-0821, Japan.
Trace amounts of heavy metals in the ice cores from Canadian Arctic were analyzed using inductively coupled plasma mass spectrometry (ICP-MS). A custom made plastic device and ceramic knives were used to remove the contamination on the ice core surface. Ice cores could be broken into small sections (2-3 cm thick) after decontamination with the plastic device and ceramic knives. High-resolution depth profiles of various elements, i.e. As, Cd, Co, Cu, Ni, Pb, Zn and U, were thus attained. Concentrations in 518 ice core samples range from 0.1 (U) to 673.3 (Zn) pg g(-1).
R S W van de Wal, W Boot, M R van den Broeke, C J P P Smeets, C H Reijmer, J J A Donker, J Oerlemans
Institute for Marine and Atmospheric research Utrecht, Utrecht University, Netherlands. email@example.com
Continuous Global Positioning System observations reveal rapid and large ice velocity fluctuations in the western ablation zone of the Greenland Ice Sheet. Within days, ice velocity reacts to increased meltwater production and increases by a factor of 4. Such a response is much stronger and much faster than previously reported. Over a longer period of 17 years, annual ice velocities have decreased slightly, which suggests that the englacial hydraulic system adjusts constantly to the variable meltwater input, which results in a more or less constant ice flux over the years. The positive-feedback mechanism between melt rate and ice velocity appears to be a seasonal process that may have only a limited effect on the response of the ice sheet to climate warming over the next decades.
GEOTOP Geochemistry and Geodynamics Research Center-Université du Québec à Montréal, Case Postale 8888, succursale Centre-Ville, Montréal, Québec H3C 3P8, Canada. firstname.lastname@example.org
The response of the Greenland ice sheet to global warming is a source of concern notably because of its potential contribution to changes in the sea level. We demonstrated the natural vulnerability of the ice sheet by using pollen records from marine sediment off southwest Greenland that indicate important changes of the vegetation in Greenland over the past million years. The vegetation that developed over southern Greenland during the last interglacial period is consistent with model experiments, suggesting a reduced volume of the Greenland ice sheet. Abundant spruce pollen indicates that boreal coniferous forest developed some 400,000 years ago during the "warm" interval of marine isotope stage 11, providing a time frame for the development and decline of boreal ecosystems over a nearly ice-free Greenland.
J P Steffensen, K K Andersen, M Bigler, H B Clausen, D Dahl-Jensen, H Fischer, K Goto-Azuma, M Hansson, S J Johnsen, J Jouzel, V Masson-Delmotte, T Popp, S O Rasmussen, R Rothlisberger, U Ruth, B Stauffer, M-L Siggaard-Andersen, A E Sveinbjörnsdóttir, A Svensson, J W C White
Centre for Ice and Climate, Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, DK-2100 Copenhagen OE, Denmark.
The last two abrupt warmings at the onset of our present warm interglacial period, interrupted by the Younger Dryas cooling event, are investigated in high temporal resolution from the Greenland NGRIP ice core. The deuterium excess, a proxy of Greenland precipitation moisture source, switches mode within 1 to 3 years over these transitions and initiates a more gradual change (50 years) of the Greenland air temperature as recorded by water stable isotopes. The onsets of both abrupt Greenland warmings are slightly preceded by decreasing Greenland dust deposition, reflecting wetting of Asian deserts. A northern shift of the ITCZ could be the trigger of these abrupt shifts of northern hemisphere atmospheric circulation resulting in 2 to 4K changes in Greenland moisture source temperature from one year to the next.
School of Earth, Ocean and Planetary Sciences, Cardiff University, Main Building, Park Place, Cardiff CF10 3YE, United Kingdom. email@example.com
A numerical algorithm is applied to the Greenland Ice Sheet Project 2 (GISP2) dust record from Greenland to remove the abrupt changes in dust flux associated with the Dansgaard-Oeschger (D-O) oscillations of the last glacial period. The procedure is based on the assumption that the rapid changes in dust are associated with large-scale changes in atmospheric transport and implies that D-O oscillations (in terms of their atmospheric imprint) are more symmetric in form than can be inferred from Greenland temperature records. After removal of the abrupt shifts the residual, dejumped dust record is found to match Antarctic climate variability with a temporal lag of several hundred years. It is argued that such variability may reflect changes in the source region of Greenland dust (thought to be the deserts of eastern Asia). Other records from this region and more globally also reveal Antarctic-style variability and suggest that this signal is globally pervasive. This provides the potential basis for suggesting a more important role for gradual changes in triggering more abrupt transitions in the climate system.