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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
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Species-specific responses of Late Quaternary megafauna to climate and humans.

https://arctichealth.org/en/permalink/ahliterature129951
Source
Nature. 2011 Nov 17;479(7373):359-64
Publication Type
Article
Date
Nov-17-2011
Author
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
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
Author Affiliation
Centre for GeoGenetics, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.
Source
Nature. 2011 Nov 17;479(7373):359-64
Date
Nov-17-2011
Language
English
Publication Type
Article
Keywords
Animals
Bayes Theorem
Biota
Bison
Climate Change - history
DNA, Mitochondrial - analysis - genetics
Europe
Extinction, Biological
Fossils
Genetic Variation
Geography
History, Ancient
Horses
Human Activities - history
Humans
Mammals - genetics - physiology
Mammoths
Molecular Sequence Data
Population Dynamics
Reindeer
Siberia
Species Specificity
Time Factors
Abstract
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.
Notes
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PubMed ID
22048313 View in PubMed
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Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings.

https://arctichealth.org/en/permalink/ahliterature278309
Source
Glob Chang Biol. 2016 May;22(5):1710-21
Publication Type
Article
Date
May-2016
Author
Eleftheria Palkopoulou
Mateusz Baca
Natalia I Abramson
Mikhail Sablin
Pawel Socha
Adam Nadachowski
Stefan Prost
Mietje Germonpré
Pavel Kosintsev
Nickolay G Smirnov
Sergey Vartanyan
Dmitry Ponomarev
Johanna Nyström
Pavel Nikolskiy
Christopher N Jass
Yuriy N Litvinov
Daniela C Kalthoff
Semyon Grigoriev
Tatyana Fadeeva
Aikaterini Douka
Thomas F G Higham
Erik Ersmark
Vladimir Pitulko
Elena Pavlova
John R Stewart
Piotr Weglenski
Anna Stankovic
Love Dalén
Source
Glob Chang Biol. 2016 May;22(5):1710-21
Date
May-2016
Language
English
Publication Type
Article
Keywords
Animals
Arctic Regions
Arvicolinae - genetics
DNA, Ancient - analysis
DNA, Mitochondrial - analysis
Europe
Extinction, Biological
Fossils
Genetic Variation
Grassland
North America
Phylogeny
Population Dynamics
Russia
Sequence Analysis, DNA
Tundra
Abstract
Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings (Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D. torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next-generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D. torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50 000 years. The observation of repeated extinctions across such a vast geographical range indicates large-scale changes in the steppe-tundra environment in western Eurasia during the last glaciation. All Holocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D. torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D. groenlandicus and D. richardsoni were recovered from a Late Pleistocene site in south-western Canada. This suggests that D. groenlandicus had a more southern and D. richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical history, which could have had bottom-up effects in the Late Pleistocene steppe-tundra ecosystem.
PubMed ID
26919067 View in PubMed
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