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Source
Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660)
Publication Type
Article
Date
Jan-19-2015
Author
Mikkel Winther Pedersen
Søren Overballe-Petersen
Luca Ermini
Clio Der Sarkissian
James Haile
Micaela Hellstrom
Johan Spens
Philip Francis Thomsen
Kristine Bohmann
Enrico Cappellini
Ida Bærholm Schnell
Nathan A Wales
Christian Carøe
Paula F Campos
Astrid M Z Schmidt
M Thomas P Gilbert
Anders J Hansen
Ludovic Orlando
Eske Willerslev
Author Affiliation
Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark.
Source
Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660)
Date
Jan-19-2015
Language
English
Publication Type
Article
Abstract
DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.
PubMed ID
25487334 View in PubMed
Less detail

Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics.

https://arctichealth.org/en/permalink/ahliterature97786
Source
Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5675-80
Publication Type
Article
Date
Mar-23-2010
Author
Paula F Campos
Eske Willerslev
Andrei Sher
Ludovic Orlando
Erik Axelsson
Alexei Tikhonov
Kim Aaris-Sørensen
Alex D Greenwood
Ralf-Dietrich Kahlke
Pavel Kosintsev
Tatiana Krakhmalnaya
Tatyana Kuznetsova
Philippe Lemey
Ross MacPhee
Christopher A Norris
Kieran Shepherd
Marc A Suchard
Grant D Zazula
Beth Shapiro
M Thomas P Gilbert
Author Affiliation
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK 1350 Copenhagen, Denmark.
Source
Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5675-80
Date
Mar-23-2010
Language
English
Publication Type
Article
Keywords
Animals
DNA - genetics - history
DNA, Mitochondrial - genetics - history
Extinction, Biological
Fossils
Genetic Variation
History, Ancient
Humans
Molecular Sequence Data
Phylogeny
Population Dynamics
Ruminants - genetics
Abstract
The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population dynamics throughout the late Pleistocene and Holocene. Our results reveal that musk ox genetic diversity was much higher during the Pleistocene than at present, and has undergone several expansions and contractions over the past 60,000 years. Northeast Siberia was of key importance, as it was the geographic origin of all samples studied and held a large diverse population until local extinction at approximately 45,000 radiocarbon years before present ((14)C YBP). Subsequently, musk ox genetic diversity reincreased at ca. 30,000 (14)C YBP, recontracted at ca. 18,000 (14)C YBP, and finally recovered in the middle Holocene. The arrival of humans into relevant areas of the musk ox range did not affect their mitochondrial diversity, and both musk ox and humans expanded into Greenland concomitantly. Thus, their population dynamics are better explained by a nonanthropogenic cause (for example, environmental change), a hypothesis supported by historic observations on the sensitivity of the species to both climatic warming and fluctuations.
PubMed ID
20212118 View in PubMed
Less detail

Ancient DNA reveals lack of continuity between neolithic hunter-gatherers and contemporary Scandinavians.

https://arctichealth.org/en/permalink/ahliterature148346
Source
Curr Biol. 2009 Nov 3;19(20):1758-62
Publication Type
Article
Date
Nov-3-2009
Author
Helena Malmström
M Thomas P Gilbert
Mark G Thomas
Mikael Brandström
Jan Storå
Petra Molnar
Pernille K Andersen
Christian Bendixen
Gunilla Holmlund
Anders Götherström
Eske Willerslev
Author Affiliation
Department of Evolutionary Biology, Uppsala University, Sweden.
Source
Curr Biol. 2009 Nov 3;19(20):1758-62
Date
Nov-3-2009
Language
English
Publication Type
Article
Keywords
Agriculture - history
Anthropology, Physical
DNA, Mitochondrial - chemistry
Emigration and Immigration - history
Genetic Variation
History, Ancient
Humans
Scandinavia
Abstract
The driving force behind the transition from a foraging to a farming lifestyle in prehistoric Europe (Neolithization) has been debated for more than a century [1-3]. Of particular interest is whether population replacement or cultural exchange was responsible [3-5]. Scandinavia holds a unique place in this debate, for it maintained one of the last major hunter-gatherer complexes in Neolithic Europe, the Pitted Ware culture [6]. Intriguingly, these late hunter-gatherers existed in parallel to early farmers for more than a millennium before they vanished some 4,000 years ago [7, 8]. The prolonged coexistence of the two cultures in Scandinavia has been cited as an argument against population replacement between the Mesolithic and the present [7, 8]. Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern Scandinavians (including the Saami people of northern Scandinavia) but are more closely related to contemporary populations of the eastern Baltic region. Our findings support hypotheses arising from archaeological analyses that propose a Neolithic or post-Neolithic population replacement in Scandinavia [7]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations.
Notes
Comment In: Curr Biol. 2009 Nov 3;19(20):R948-919889371
PubMed ID
19781941 View in PubMed
Less detail

Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene.

https://arctichealth.org/en/permalink/ahliterature100381
Source
Mol Ecol. 2010 Nov;19(22):4863-75
Publication Type
Article
Date
Nov-2010
Author
Paula F Campos
Tommy Kristensen
Ludovic Orlando
Andrei Sher
Marina V Kholodova
Anders Götherström
Michael Hofreiter
Dorothée G Drucker
Pavel Kosintsev
Alexei Tikhonov
Gennady F Baryshnikov
Eske Willerslev
M Thomas P Gilbert
Author Affiliation
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Source
Mol Ecol. 2010 Nov;19(22):4863-75
Date
Nov-2010
Language
English
Publication Type
Article
Abstract
Prior to the Holocene, the range of the saiga antelope (Saiga tatarica) spanned from France to the Northwest Territories of Canada. Although its distribution subsequently contracted to the steppes of Central Asia, historical records indicate that it remained extremely abundant until the end of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species' genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two well-supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49,500 (14) C ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals and includes samples dating from between 40,400 to 10,250 (14) C ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate Bayesian Computation analyses show the observed data is more compatible with a drastic population size reduction (c. 66-77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition.
PubMed ID
20874761 View in PubMed
Less detail

Ancient genomes from Iceland reveal the making of a human population.

https://arctichealth.org/en/permalink/ahliterature294280
Source
Science. 2018 06 01; 360(6392):1028-1032
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
06-01-2018
Author
S Sunna Ebenesersdóttir
Marcela Sandoval-Velasco
Ellen D Gunnarsdóttir
Anuradha Jagadeesan
Valdís B Guðmundsdóttir
Elísabet L Thordardóttir
Margrét S Einarsdóttir
Kristjan H S Moore
Ásgeir Sigurðsson
Droplaug N Magnúsdóttir
Hákon Jónsson
Steinunn Snorradóttir
Eivind Hovig
Pål Møller
Ingrid Kockum
Tomas Olsson
Lars Alfredsson
Thomas F Hansen
Thomas Werge
Gianpiero L Cavalleri
Edmund Gilbert
Carles Lalueza-Fox
Joe W Walser
Steinunn Kristjánsdóttir
Shyam Gopalakrishnan
Lilja Árnadóttir
Ólafur Þ Magnússon
M Thomas P Gilbert
Kári Stefánsson
Agnar Helgason
Author Affiliation
deCODE Genetics/AMGEN, Inc., Reykjavik Iceland. sunna@decode.is kstefan@deocde.is agnar@decode.is.
Source
Science. 2018 06 01; 360(6392):1028-1032
Date
06-01-2018
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Biological Evolution
DNA, Ancient
Female
Founder Effect
Gene Pool
Genetic Drift
Genome, Human
Genotype
Humans
Iceland
Male
Phenotype
Population - genetics
Abstract
Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of Norse, Gaelic, and admixed individuals. We further show that these ancient Icelanders are markedly more similar to their source populations in Scandinavia and the British-Irish Isles than to contemporary Icelanders, who have been shaped by 1100 years of extensive genetic drift. Finally, we report evidence of unequal contributions from the ancient founders to the contemporary Icelandic gene pool. These results provide detailed insights into the making of a human population that has proven extraordinarily useful for the discovery of genotype-phenotype associations.
Notes
CommentIn: Science. 2018 Jun 1;360(6392):964-965 PMID 29853673
PubMed ID
29853688 View in PubMed
Less detail

Ancient human genome sequence of an extinct Palaeo-Eskimo.

https://arctichealth.org/en/permalink/ahliterature98088
Source
Nature. 2010 Feb 11;463(7282):757-62
Publication Type
Article
Date
Feb-11-2010
Author
Morten Rasmussen
Yingrui Li
Stinus Lindgreen
Jakob Skou Pedersen
Anders Albrechtsen
Ida Moltke
Mait Metspalu
Ene Metspalu
Toomas Kivisild
Ramneek Gupta
Marcelo Bertalan
Kasper Nielsen
M Thomas P Gilbert
Yong Wang
Maanasa Raghavan
Paula F Campos
Hanne Munkholm Kamp
Andrew S Wilson
Andrew Gledhill
Silvana Tridico
Michael Bunce
Eline D Lorenzen
Jonas Binladen
Xiaosen Guo
Jing Zhao
Xiuqing Zhang
Hao Zhang
Zhuo Li
Minfeng Chen
Ludovic Orlando
Karsten Kristiansen
Mads Bak
Niels Tommerup
Christian Bendixen
Tracey L Pierre
Bjarne Grønnow
Morten Meldgaard
Claus Andreasen
Sardana A Fedorova
Ludmila P Osipova
Thomas F G Higham
Christopher Bronk Ramsey
Thomas V O Hansen
Finn C Nielsen
Michael H Crawford
Søren Brunak
Thomas Sicheritz-Pontén
Richard Villems
Rasmus Nielsen
Anders Krogh
Jun Wang
Eske Willerslev
Author Affiliation
Centre for GeoGenetics, Natural History Museum of Denmark and Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
Source
Nature. 2010 Feb 11;463(7282):757-62
Date
Feb-11-2010
Language
English
Geographic Location
Russia
Publication Type
Article
Keywords
Cryopreservation
Emigration and Immigration - history
Extinction, Biological
Genetics, Population
Genome, Human - genetics
Genomics
Genotype
Greenland
Hair
History, Ancient
Humans
Inuits - genetics
Male
Phenotype
Phylogeny
Polymorphism, Single Nucleotide - genetics
Sequence Analysis, DNA
Siberia - ethnology
Abstract
We report here the genome sequence of an ancient human. Obtained from approximately 4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20x, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.
Notes
RefSource: Nature. 2010 Feb 11;463(7282):739-40
PubMed ID
20148029 View in PubMed
Less detail

Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process.

https://arctichealth.org/en/permalink/ahliterature265418
Source
Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130373
Publication Type
Article
Date
Jan-19-2015
Author
Helena Malmström
Anna Linderholm
Pontus Skoglund
Jan Storå
Per Sjödin
M Thomas P Gilbert
Gunilla Holmlund
Eske Willerslev
Mattias Jakobsson
Kerstin Lidén
Anders Götherström
Source
Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130373
Date
Jan-19-2015
Language
English
Publication Type
Article
Keywords
Agriculture - history
Base Sequence
Computational Biology
DNA Primers - genetics
DNA, Mitochondrial - genetics - history
Gene Flow
Genetic Variation
Genetics, Population
High-Throughput Nucleotide Sequencing
History, Ancient
Human Migration - history
Humans
Models, Genetic
Molecular Sequence Data
Population Dynamics
Real-Time Polymerase Chain Reaction
Sweden
Abstract
The European Neolithization process started around 12 000 years ago in the Near East. The introduction of agriculture spread north and west throughout Europe and a key question has been if this was brought about by migrating individuals, by an exchange of ideas or a by a mixture of these. The earliest farming evidence in Scandinavia is found within the Funnel Beaker Culture complex (Trichterbecherkultur, TRB) which represents the northernmost extension of Neolithic farmers in Europe. The TRB coexisted for almost a millennium with hunter-gatherers of the Pitted Ware Cultural complex (PWC). If migration was a substantial part of the Neolithization, even the northerly TRB community would display a closer genetic affinity to other farmer populations than to hunter-gatherer populations. We deep-sequenced the mitochondrial hypervariable region 1 from seven farmers (six TRB and one Battle Axe complex, BAC) and 13 hunter-gatherers (PWC) and authenticated the sequences using postmortem DNA damage patterns. A comparison with 124 previously published sequences from prehistoric Europe shows that the TRB individuals share a close affinity to Central European farmer populations, and that they are distinct from hunter-gatherer groups, including the geographically close and partially contemporary PWC that show a close affinity to the European Mesolithic hunter-gatherers.
Notes
Cites: Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18255-922042855
Cites: Mol Ecol. 2012 Jan;21(1):45-5622117930
Cites: Ann Anat. 2012 Jan 20;194(1):138-4521596538
Cites: PLoS One. 2012;7(3):e3247322427842
Cites: Science. 2012 Apr 27;336(6080):466-922539720
Cites: PLoS One. 2012;7(4):e3441722563371
Cites: Curr Biol. 2012 Aug 21;22(16):1494-922748318
Cites: Science. 2014 May 16;344(6185):747-5024762536
Cites: Mol Biol Evol. 2001 Feb;18(2):262-511158385
Cites: Nucleic Acids Res. 2001 Dec 1;29(23):4793-911726688
Cites: Bioinformatics. 2004 Jan 22;20(2):289-9014734327
Cites: Proc Natl Acad Sci U S A. 1989 Mar;86(6):1939-432928314
Cites: Genetics. 1992 Oct;132(2):583-91427045
Cites: Am J Hum Genet. 1998 Feb;62(2):488-929463326
Cites: Nat Genet. 1999 Oct;23(2):14710508508
Cites: PLoS Biol. 2004 Dec;2(12):e42115562317
Cites: Science. 2005 Jul 22;309(5734):597-915933159
Cites: Science. 2005 Nov 11;310(5750):1016-816284177
Cites: Proc Biol Sci. 2007 Sep 7;274(1622):2161-717609193
Cites: J Mol Evol. 2007 Jul;65(1):92-10217593420
Cites: Curr Biol. 2008 Nov 11;18(21):1687-9318976917
Cites: Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18226-3119015520
Cites: Hum Mutat. 2009 Feb;30(2):E386-9418853457
Cites: PLoS One. 2009;4(5):e554119440242
Cites: Science. 2009 Oct 2;326(5949):137-4019729620
Cites: Curr Biol. 2009 Nov 3;19(20):1758-6219781941
Cites: Int J Legal Med. 2010 Mar;124(2):91-819590886
Cites: Nature. 2010 Apr 8;464(7290):894-720336068
Cites: Science. 2010 May 7;328(5979):710-2220448178
Cites: PLoS Biol. 2010;8(11):e100053621085689
Cites: Hum Mutat. 2011 Jan;32(1):25-3220960467
Cites: C R Biol. 2011 Mar;334(3):182-921377612
Cites: Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):9788-9121628562
Cites: Trends Genet. 2012 Oct;28(10):496-50522889475
Cites: PLoS Genet. 2013;9(2):e100329623459685
Cites: Cell Mol Life Sci. 2013 Jul;70(14):2473-8723052219
Cites: Nature. 2013 Jul 4;499(7456):74-823803765
Cites: Science. 2013 Oct 11;342(6155):257-6124115443
Cites: Science. 2013 Oct 25;342(6157):479-8124114781
Cites: Mol Biol Evol. 2014 May;31(5):1248-6024497031
PubMed ID
25487325 View in PubMed
Less detail

Biological adaptations in the Arctic cervid, the reindeer (Rangifer tarandus).

https://arctichealth.org/en/permalink/ahliterature301069
Source
Science. 2019 06 21; 364(6446):
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
06-21-2019
Author
Zeshan Lin
Lei Chen
Xianqing Chen
Yingbin Zhong
Yue Yang
Wenhao Xia
Chang Liu
Wenbo Zhu
Han Wang
Biyao Yan
Yifeng Yang
Xing Liu
Kjersti Sternang Kvie
Knut Håkon Røed
Kun Wang
Wuhan Xiao
Haijun Wei
Guangyu Li
Rasmus Heller
M Thomas P Gilbert
Qiang Qiu
Wen Wang
Zhipeng Li
Author Affiliation
Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Source
Science. 2019 06 21; 364(6446):
Date
06-21-2019
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Abstract
The reindeer is an Arctic species that exhibits distinctive biological characteristics, for which the underlying genetic basis remains largely unknown. We compared the genomes of reindeer against those of other ruminants and nonruminant mammals to reveal the genetic basis of light arrhythmicity, high vitamin D metabolic efficiency, the antler growth trait of females, and docility. We validate that two reindeer vitamin D metabolic genes (CYP27B1 and POR) show signs of positive selection and exhibit higher catalytic activity than those of other ruminants. A mutation upstream of the reindeer CCND1 gene endows an extra functional binding motif of the androgen receptor and thereby may result in female antlers. Furthermore, a mutation (proline-1172?threonine) in reindeer PER2 results in loss of binding ability with CRY1, which may explain circadian arrhythmicity in reindeer.
Notes
CommentIn: Science. 2019 Jun 21;364(6446):1130-1131 PMID 31221843
PubMed ID
31221829 View in PubMed
Less detail

The genetic prehistory of the New World Arctic.

https://arctichealth.org/en/permalink/ahliterature256691
Source
Science. 2014 Aug 29;345(6200):1255832
Publication Type
Article
Date
Aug-29-2014
Author
Maanasa Raghavan
Michael DeGiorgio
Anders Albrechtsen
Ida Moltke
Pontus Skoglund
Thorfinn S Korneliussen
Bjarne Grønnow
Martin Appelt
Hans Christian Gulløv
T Max Friesen
William Fitzhugh
Helena Malmström
Simon Rasmussen
Jesper Olsen
Linea Melchior
Benjamin T Fuller
Simon M Fahrni
Thomas Stafford
Vaughan Grimes
M A Priscilla Renouf
Jerome Cybulski
Niels Lynnerup
Marta Mirazon Lahr
Kate Britton
Rick Knecht
Jette Arneborg
Mait Metspalu
Omar E Cornejo
Anna-Sapfo Malaspinas
Yong Wang
Morten Rasmussen
Vibha Raghavan
Thomas V O Hansen
Elza Khusnutdinova
Tracey Pierre
Kirill Dneprovsky
Claus Andreasen
Hans Lange
M Geoffrey Hayes
Joan Coltrain
Victor A Spitsyn
Anders Götherström
Ludovic Orlando
Toomas Kivisild
Richard Villems
Michael H Crawford
Finn C Nielsen
Jørgen Dissing
Jan Heinemeier
Morten Meldgaard
Carlos Bustamante
Dennis H O'Rourke
Mattias Jakobsson
M Thomas P Gilbert
Rasmus Nielsen
Eske Willerslev
Author Affiliation
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Source
Science. 2014 Aug 29;345(6200):1255832
Date
Aug-29-2014
Language
English
Publication Type
Article
Keywords
Alaska - ethnology
Arctic regions - ethnology
Base Sequence
Bone and Bones
Canada - ethnology
DNA, Mitochondrial - genetics
Genome, Human - genetics
Greenland - ethnology
Hair
History, Ancient
Human Migration
Humans
Inuits - ethnology - genetics - history
Molecular Sequence Data
Siberia - ethnology
Survivors - history
Tooth
Abstract
The New World Arctic, the last region of the Americas to be populated by humans, has a relatively well-researched archaeology, but an understanding of its genetic history is lacking. We present genome-wide sequence data from ancient and present-day humans from Greenland, Arctic Canada, Alaska, Aleutian Islands, and Siberia. We show that Paleo-Eskimos (~3000 BCE to 1300 CE) represent a migration pulse into the Americas independent of both Native American and Inuit expansions. Furthermore, the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population, representing the ancestors of present-day Inuit, with evidence of past gene flow between these lineages. Despite periodic abandonment of major Arctic regions, a single Paleo-Eskimo metapopulation likely survived in near-isolation for more than 4000 years, only to vanish around 700 years ago.
Notes
Comment In: Science. 2014 Aug 29;345(6200):1004-525170138
PubMed ID
25170159 View in PubMed
Less detail

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.

https://arctichealth.org/en/permalink/ahliterature258009
Source
Genome Res. 2014 Mar;24(3):454-66
Publication Type
Article
Date
Mar-2014
Author
Jakob Skou Pedersen
Eivind Valen
Amhed M Vargas Velazquez
Brian J Parker
Morten Rasmussen
Stinus Lindgreen
Berit Lilje
Desmond J Tobin
Theresa K Kelly
Søren Vang
Robin Andersson
Peter A Jones
Cindi A Hoover
Alexei Tikhonov
Egor Prokhortchouk
Edward M Rubin
Albin Sandelin
M Thomas P Gilbert
Anders Krogh
Eske Willerslev
Ludovic Orlando
Author Affiliation
Department of Molecular Medicine (MOMA), Aarhus University Hospital, Skejby, DK-8200 Aarhus N, Denmark;
Source
Genome Res. 2014 Mar;24(3):454-66
Date
Mar-2014
Language
English
Publication Type
Article
Keywords
Animals
Chromosome Mapping
Cytosine - metabolism
DNA Methylation
Epigenesis, Genetic
Epigenomics
Evolution, Molecular
Gene Expression
Gene Expression Regulation
Genome, Human
Humans
Inuits - genetics
Nucleosomes - genetics
Phylogeny
Promoter Regions, Genetic
Sequence Analysis, DNA
Abstract
Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery of the expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues. Using ancient methylation information, we estimated the age at death of the Saqqaq individual and illustrate how epigenetic information can be used to infer ancient gene expression. Similar epigenetic signatures were found in other fossil material, such as 110,000- to 130,000-yr-old bones, supporting the contention that ancient epigenomic information can be reconstructed from a deep past. Our findings lay the foundation for extracting epigenomic information from ancient samples, allowing shifts in epialleles to be tracked through evolutionary time, as well as providing an original window into modern epigenomics.
Notes
Cites: PLoS Genet. 2012;8(11):e100303623166509
Cites: Nature. 2011 Jun 23;474(7352):516-2021602827
Cites: Nat Genet. 2011 Jul;43(7):630-821685913
Cites: Bioinformatics. 2011 Aug 1;27(15):2153-521659319
Cites: Nucleic Acids Res. 2011 Sep 1;39(16):6956-6921622955
Cites: PLoS One. 2011;6(8):e2416121904610
Cites: Science. 2011 Oct 7;334(6052):94-821940856
Cites: BMC Med Genomics. 2011;4:6821958464
Cites: Nature. 2011 Oct 27;478(7370):506-1021993626
Cites: Genome Res. 2011 Nov;21(11):1863-7121750105
Cites: Aging (Albany NY). 2011 Oct;3(10):1018-2722067257
Cites: Nature. 2011 Nov 17;479(7373):359-6422048313
Cites: PLoS One. 2012;7(1):e3022622276161
Cites: Nat Methods. 2012 Feb;9(2):145-5122290186
Cites: J Proteome Res. 2012 Feb 3;11(2):917-2622103443
Cites: Biotechniques. 2012 Feb;52(2):87-9422313406
Cites: PLoS One. 2010;5(6):e1093320532171
Cites: PLoS One. 2010;5(6):e1121720585459
Cites: PLoS Genet. 2010 Sep;6(9):e100113420885785
Cites: Nat Commun. 2012;3:69822426219
Cites: Mol Cell. 2012 Mar 30;45(6):814-2522387027
Cites: Genome Res. 2012 Apr;22(4):623-3222300631
Cites: Nucleic Acids Res. 2012 May;40(10):e7222323520
Cites: Nature. 2012 Jun 28;486(7404):496-50122722846
Cites: Biophys J. 2012 May 2;102(9):2140-822824278
Cites: Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):E2382-9022826254
Cites: Science. 2012 Oct 12;338(6104):222-622936568
Cites: Genome Res. 2012 Dec;22(12):2497-50622960375
Cites: Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2223-723341637
Cites: Nat Struct Mol Biol. 2013 Mar;20(3):267-7323463311
Cites: Epigenomics. 2013 Apr;5(2):205-2723566097
Cites: Elife. 2013;2:e0073123741619
Cites: Nature. 2013 Jul 4;499(7456):74-823803765
Cites: Science. 2013 Jul 12;341(6142):179-8323765279
Cites: Nat Commun. 2013;4:217223863894
Cites: Nature. 2014 Jan 2;505(7481):87-9124256729
Cites: Nucleic Acids Res. 2001 Dec 1;29(23):4793-911726688
Cites: Genes Dev. 2002 Jan 1;16(1):6-2111782440
Cites: Mol Phylogenet Evol. 2003 Sep;28(3):485-9912927133
Cites: Nature. 1984 Nov 15-21;312(5991):282-46504142
Cites: Proc Natl Acad Sci U S A. 1989 Mar;86(6):1939-432928314
Cites: Science. 1997 Mar 21;275(5307):1793-69065404
Cites: Am J Pathol. 1997 Nov;151(5):1205-139358745
Cites: Nature. 1998 Jan 1;391(6662):43-509422506
Cites: Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8544-99671714
Cites: Science. 2004 Nov 26;306(5701):1561-515567864
Cites: Science. 2005 Jul 22;309(5734):597-915933159
Cites: J Invest Dermatol. 2006 Feb;126(2):258-6416418734
Cites: Nature. 2006 Feb 9;439(7077):724-716362058
Cites: Mol Cell Proteomics. 2006 May;5(5):789-80016446289
Cites: Ann Clin Lab Sci. 2006 Spring;36(2):115-2616682506
Cites: J Biomol Struct Dyn. 2006 Aug;24(1):43-816780374
Cites: Nature. 2006 Aug 17;442(7104):772-816862119
Cites: Science. 2006 Nov 17;314(5802):1113-817110569
Cites: Nat Biotechnol. 2007 Feb;25(2):244-817220878
Cites: Genome Res. 2007 Jun;17(6):928-3917568008
Cites: Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14616-2117715061
Cites: Cell. 2008 Mar 7;132(5):887-9818329373
Cites: Histochem Cell Biol. 2008 Jun;129(6):705-3318461349
Cites: PLoS Genet. 2008;4(7):e100013818654629
Cites: Nature. 2008 Aug 7;454(7205):766-7018600261
Cites: Nature. 2008 Nov 20;456(7220):387-9019020620
Cites: Nat Biotechnol. 2009 Apr;27(4):361-819329998
Cites: Nat Struct Mol Biol. 2009 May;16(5):564-7119377480
Cites: Genome Res. 2009 Jun;19(6):959-6619273618
Cites: Bioinformatics. 2009 Jul 15;25(14):1754-6019451168
Cites: Genome Res. 2009 Aug;19(8):1419-2819478138
Cites: Nature. 2001 Feb 8;409(6821):704-711217857
Cites: Science. 2001 Jan 19;291(5503):447-5011228144
Cites: Nucleic Acids Res. 2009 Nov;37(20):6701-1519740762
Cites: Differentiation. 2009 Dec;78(5):292-30019683850
Cites: J Invest Dermatol. 2010 Jan;130(1):55-7319587698
Cites: Curr Biol. 2010 Feb 9;20(3):231-620045327
Cites: Nature. 2010 Feb 11;463(7282):757-6220148029
Cites: Genome Res. 2010 Mar;20(3):320-3120133333
Cites: Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5675-8020212118
Cites: Nucleic Acids Res. 2010 Apr;38(6):e8720028723
Cites: Genome Res. 2010 Apr;20(4):440-620219944
Cites: Science. 2010 May 7;328(5979):710-2220448178
Cites: Nat Protoc. 2009;4(1):44-5719131956
Cites: Nature. 2010 Dec 23;468(7327):1053-6021179161
Cites: PLoS One. 2010;5(12):e1575421206756
Cites: PLoS One. 2011;6(1):e1452421267076
Cites: Genes Dev. 2011 May 15;25(10):1010-2221576262
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