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137 ancient human genomes from across the Eurasian steppes.

https://arctichealth.org/en/permalink/ahliterature291698
Source
Nature. 2018 May; 557(7705):369-374
Publication Type
Journal Article
Date
May-2018
Author
Peter de Barros Damgaard
Nina Marchi
Simon Rasmussen
Michaël Peyrot
Gabriel Renaud
Thorfinn Korneliussen
J Víctor Moreno-Mayar
Mikkel Winther Pedersen
Amy Goldberg
Emma Usmanova
Nurbol Baimukhanov
Valeriy Loman
Lotte Hedeager
Anders Gorm Pedersen
Kasper Nielsen
Gennady Afanasiev
Kunbolot Akmatov
Almaz Aldashev
Ashyk Alpaslan
Gabit Baimbetov
Vladimir I Bazaliiskii
Arman Beisenov
Bazartseren Boldbaatar
Bazartseren Boldgiv
Choduraa Dorzhu
Sturla Ellingvag
Diimaajav Erdenebaatar
Rana Dajani
Evgeniy Dmitriev
Valeriy Evdokimov
Karin M Frei
Andrey Gromov
Alexander Goryachev
Hakon Hakonarson
Tatyana Hegay
Zaruhi Khachatryan
Ruslan Khaskhanov
Egor Kitov
Alina Kolbina
Tabaldiev Kubatbek
Alexey Kukushkin
Igor Kukushkin
Nina Lau
Ashot Margaryan
Inga Merkyte
Ilya V Mertz
Viktor K Mertz
Enkhbayar Mijiddorj
Vyacheslav Moiyesev
Gulmira Mukhtarova
Bekmukhanbet Nurmukhanbetov
Z Orozbekova
Irina Panyushkina
Karol Pieta
Václav Smrcka
Irina Shevnina
Andrey Logvin
Karl-Göran Sjögren
Tereza Ć tolcová
Kadicha Tashbaeva
Alexander Tkachev
Turaly Tulegenov
Dmitriy Voyakin
Levon Yepiskoposyan
Sainbileg Undrakhbold
Victor Varfolomeev
Andrzej Weber
Nikolay Kradin
Morten E Allentoft
Ludovic Orlando
Rasmus Nielsen
Martin Sikora
Evelyne Heyer
Kristian Kristiansen
Eske Willerslev
Author Affiliation
Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Source
Nature. 2018 May; 557(7705):369-374
Date
May-2018
Language
English
Publication Type
Journal Article
Abstract
For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers. Later, Scythians admixed with the eastern steppe nomads who formed the Xiongnu confederations, and moved westward in about the second or third century BC, forming the Hun traditions in the fourth-fifth century AD, and carrying with them plague that was basal to the Justinian plague. These nomads were further admixed with East Asian groups during several short-term khanates in the Medieval period. These historical events transformed the Eurasian steppes from being inhabited by Indo-European speakers of largely West Eurasian ancestry to the mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry.
PubMed ID
29743675 View in PubMed
Less detail
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
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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
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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 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
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Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing.

https://arctichealth.org/en/permalink/ahliterature278532
Source
Mol Ecol Resour. 2016 Mar;16(2):459-69
Publication Type
Article
Date
Mar-2016
Author
Cristina Gamba
Kristian Hanghøj
Charleen Gaunitz
Ahmed H Alfarhan
Saleh A Alquraishi
Khaled A S Al-Rasheid
Daniel G Bradley
Ludovic Orlando
Source
Mol Ecol Resour. 2016 Mar;16(2):459-69
Date
Mar-2016
Language
English
Publication Type
Article
Keywords
Alaska
Bone and Bones
DNA - isolation & purification
Fossils
High-Throughput Nucleotide Sequencing - methods
Molecular Biology - methods
South America
Abstract
The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost-effective solution for downstream applications, including DNA sequencing on HTS platforms.
PubMed ID
26401836 View in PubMed
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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
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The genome of a Late Pleistocene human from a Clovis burial site in western Montana.

https://arctichealth.org/en/permalink/ahliterature104987
Source
Nature. 2014 Feb 13;506(7487):225-9
Publication Type
Article
Date
Feb-13-2014
Author
Morten Rasmussen
Sarah L Anzick
Michael R Waters
Pontus Skoglund
Michael DeGiorgio
Thomas W Stafford
Simon Rasmussen
Ida Moltke
Anders Albrechtsen
Shane M Doyle
G David Poznik
Valborg Gudmundsdottir
Rachita Yadav
Anna-Sapfo Malaspinas
Samuel Stockton White
Morten E Allentoft
Omar E Cornejo
Kristiina Tambets
Anders Eriksson
Peter D Heintzman
Monika Karmin
Thorfinn Sand Korneliussen
David J Meltzer
Tracey L Pierre
Jesper Stenderup
Lauri Saag
Vera M Warmuth
Margarida C Lopes
Ripan S Malhi
Søren Brunak
Thomas Sicheritz-Ponten
Ian Barnes
Matthew Collins
Ludovic Orlando
Francois Balloux
Andrea Manica
Ramneek Gupta
Mait Metspalu
Carlos D Bustamante
Mattias Jakobsson
Rasmus Nielsen
Eske Willerslev
Author Affiliation
1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark [2].
Source
Nature. 2014 Feb 13;506(7487):225-9
Date
Feb-13-2014
Language
English
Publication Type
Article
Keywords
Archaeology
Asia - ethnology
Bone and Bones
Burial
Chromosomes, Human, Y - genetics
DNA, Mitochondrial - genetics
Emigration and Immigration - history
Europe - ethnology
Gene Flow - genetics
Genome, Human - genetics
Haplotypes - genetics
History, Ancient
Humans
Indians, North American - genetics
Infant
Male
Models, Genetic
Molecular Sequence Data
Montana
Phylogeny
Population Dynamics
Radiometric Dating
Abstract
Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 (14)C years before present (bp) (13,000 to 12,600 calendar years?bp). Nearly 50?years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705?±?35 (14)C years?bp (approximately 12,707-12,556 calendar years?bp) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4×?and show that the gene flow from the Siberian Upper Palaeolithic Mal'ta population into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years?bp. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.
Notes
Comment In: Nature. 2014 Feb 13;506(7487):162-324522593
PubMed ID
24522598 View in PubMed
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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
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PubMed ID
24299735 View in PubMed
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Mitochondrial Genetic Diversity of Eurasian Red Squirrels (Sciurus vulgaris) from Denmark.

https://arctichealth.org/en/permalink/ahliterature271703
Source
J Hered. 2015 Nov-Dec;106(6):719-27
Publication Type
Article
Author
Corrie L Madsen
Julia T Vilstrup
Ruth Fernández
Nina Marchi
Bo Håkansson
Mogens Krog
Tommy Asferg
Hans Baagøe
Ludovic Orlando
Source
J Hered. 2015 Nov-Dec;106(6):719-27
Language
English
Publication Type
Article
Keywords
Animals
Bayes Theorem
Conservation of Natural Resources
DNA, Mitochondrial - genetics
Denmark
Genetic Variation
Genetics, Population
Molecular Sequence Data
Sciuridae - genetics
Sequence Analysis, DNA
Abstract
Melanistic Eurasian red squirrels Sciurus vulgaris are commonly found on the Danish island of Funen. They are thought to represent native Danish squirrel types and are presently under threat from admixture with introduced red squirrels. In response, a conservation program was started in 2009 that involves the translocation of melanistic squirrels from Funen to the squirrel-free island of Langeland. Using mitochondrial DNA of 101 historical and modern samples from throughout Denmark, we assess for the first time population structure and mitochondrial genetic diversity of Danish squirrels compared to its larger pan-Eurasian distribution. We find that Danish squirrels have low levels of genetic diversity, especially melanistic individuals. Bayesian skyline reconstructions show that Danish squirrels have most probably experienced a severe bottleneck within the last 200 years. Also, fine-scale genetic structure was found between squirrels from the regions of Funen, Zealand and Jutland, which mimics the insular geography of Denmark. Additional nuclear DNA analyses will be required to determine the precise admixture levels between original Danish and introduced squirrels and to locate unmixed candidate populations for specific conservation efforts.
PubMed ID
26519513 View in PubMed
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