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Admixture and gene flow from Russia in the recovering Northern European brown bear (Ursus arctos).

https://arctichealth.org/en/permalink/ahliterature259339
Source
PLoS One. 2014;9(5):e97558
Publication Type
Article
Date
2014
Author
Alexander Kopatz
Hans Geir Eiken
Jouni Aspi
Ilpo Kojola
Camilla Tobiassen
Konstantin F Tirronen
Pjotr I Danilov
Snorre B Hagen
Source
PLoS One. 2014;9(5):e97558
Date
2014
Language
English
Publication Type
Article
Keywords
Animals
Finland
Gene Flow - genetics
Genetic Variation
Microsatellite Repeats
Norway
Russia
Scandinavian and Nordic Countries
Sweden
Ursidae - genetics
Abstract
Large carnivores were persecuted to near extinction during the last centuries, but have now recovered in some countries. It has been proposed earlier that the recovery of the Northern European brown bear is supported by migration from Russia. We tested this hypothesis by obtaining for the first time continuous sampling of the whole Finnish bear population, which is located centrally between the Russian and Scandinavian bear populations. The Finnish population is assumed to experience high gene flow from Russian Karelia. If so, no or a low degree of genetic differentiation between Finnish and Russian bears could be expected. We have genotyped bears extensively from all over Finland using 12 validated microsatellite markers and compared their genetic composition to bears from Russian Karelia, Sweden, and Norway. Our fine masked investigation identified two overlapping genetic clusters structured by isolation-by-distance in Finland (pairwise FST = 0.025). One cluster included Russian bears, and migration analyses showed a high number of migrants from Russia into Finland, providing evidence of eastern gene flow as an important driver during recovery. In comparison, both clusters excluded bears from Sweden and Norway, and we found no migrants from Finland in either country, indicating that eastern gene flow was probably not important for the population recovery in Scandinavia. Our analyses on different spatial scales suggest a continuous bear population in Finland and Russian Karelia, separated from Scandinavia.
Notes
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PubMed ID
24839968 View in PubMed
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Agroecosystems shape population genetic structure of the greenhouse whitefly in Northern and Southern Europe.

https://arctichealth.org/en/permalink/ahliterature258712
Source
BMC Evol Biol. 2014;14:165
Publication Type
Article
Date
2014
Author
Irina Ovcarenko
Despoina Evripidis Kapantaidaki
Leena Lindström
Nathalie Gauthier
Anastasia Tsagkarakou
Karelyn Emily Knott
Irene Vänninen
Source
BMC Evol Biol. 2014;14:165
Date
2014
Language
English
Publication Type
Article
Keywords
Animals
Climate change
Ecosystem
Female
Finland
Gene Flow
Genetics, Population
Greece
Hemiptera - classification - genetics
Microsatellite Repeats
Abstract
To predict further invasions of pests it is important to understand what factors contribute to the genetic structure of their populations. Cosmopolitan pest species are ideal for studying how different agroecosystems affect population genetic structure within a species at different climatic extremes. We undertook the first population genetic study of the greenhouse whitefly (Trialeurodes vaporariorum), a cosmopolitan invasive herbivore, and examined the genetic structure of this species in Northern and Southern Europe. In Finland, cold temperatures limit whiteflies to greenhouses and prevent them from overwintering in nature, and in Greece, milder temperatures allow whiteflies to inhabit both fields and greenhouses year round, providing a greater potential for connectivity among populations. Using nine microsatellite markers, we genotyped 1274 T. vaporariorum females collected from 18 greenhouses in Finland and eight greenhouses as well as eight fields in Greece.
Populations from Finland were less diverse than those from Greece, suggesting that Greek populations are larger and subjected to fewer bottlenecks. Moreover, there was significant population genetic structure in both countries that was explained by different factors. Habitat (field vs. greenhouse) together with longitude explained genetic structure in Greece, whereas in Finland, genetic structure was explained by host plant species. Furthermore, there was no temporal genetic structure among populations in Finland, suggesting that year-round populations are able to persist in greenhouses.
Taken together our results show that greenhouse agroecosystems can limit gene flow among populations in both climate zones. Fragmented populations in greenhouses could allow for efficient pest management. However, pest persistence in both climate zones, coupled with increasing opportunities for naturalization in temperate latitudes due to climate change, highlight challenges for the management of cosmopolitan pests in Northern and Southern Europe.
Notes
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PubMed ID
25266268 View in PubMed
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Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe.

https://arctichealth.org/en/permalink/ahliterature115842
Source
PLoS Genet. 2013;9(2):e1003296
Publication Type
Article
Date
2013
Author
Clio Der Sarkissian
Oleg Balanovsky
Guido Brandt
Valery Khartanovich
Alexandra Buzhilova
Sergey Koshel
Valery Zaporozhchenko
Detlef Gronenborn
Vyacheslav Moiseyev
Eugen Kolpakov
Vladimir Shumkin
Kurt W Alt
Elena Balanovska
Alan Cooper
Wolfgang Haak
Author Affiliation
Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia.
Source
PLoS Genet. 2013;9(2):e1003296
Date
2013
Language
English
Publication Type
Article
Keywords
Archaeology
DNA, Mitochondrial - genetics
Europe
European Continental Ancestry Group - genetics
Gene Flow
Genetic Variation
Genetics, Population
Genome, Mitochondrial
Genotype
Haplotypes
Humans
Population Dynamics
Russia
Scandinavia
Siberia
Abstract
North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans.
Notes
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PubMed ID
23459685 View in PubMed
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Ancient gene flow from early modern humans into Eastern Neanderthals.

https://arctichealth.org/en/permalink/ahliterature270960
Source
Nature. 2016 Feb 25;530(7591):429-33
Publication Type
Article
Date
Feb-25-2016
Author
Martin Kuhlwilm
Ilan Gronau
Melissa J Hubisz
Cesare de Filippo
Javier Prado-Martinez
Martin Kircher
Qiaomei Fu
Hernán A Burbano
Carles Lalueza-Fox
Marco de la Rasilla
Antonio Rosas
Pavao Rudan
Dejana Brajkovic
Željko Kucan
Ivan Gušic
Tomas Marques-Bonet
Aida M Andrés
Bence Viola
Svante Pääbo
Matthias Meyer
Adam Siepel
Sergi Castellano
Source
Nature. 2016 Feb 25;530(7591):429-33
Date
Feb-25-2016
Language
English
Publication Type
Article
Keywords
Altitude
Animals
Bayes Theorem
Chromosomes, Human, Pair 21 - genetics
Croatia - ethnology
Gene Flow - genetics
Genome, Human - genetics
Genomics
Haplotypes - genetics
Heterozygote
Humans
Hybridization, Genetic - genetics
Neanderthals - genetics
Phylogeny
Population Density
Siberia
Spain - ethnology
Time Factors
Abstract
It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000-65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.
PubMed ID
26886800 View in PubMed
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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
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PubMed ID
25487325 View in PubMed
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Assessing pre- and post-zygotic barriers between North Atlantic eels (Anguilla anguilla and A. rostrata).

https://arctichealth.org/en/permalink/ahliterature283605
Source
Heredity (Edinb). 2017 Mar;118(3):266-275
Publication Type
Article
Date
Mar-2017
Author
M W Jacobsen
L. Smedegaard
S R Sørensen
J M Pujolar
P. Munk
B. Jónsson
E. Magnussen
M M Hansen
Source
Heredity (Edinb). 2017 Mar;118(3):266-275
Date
Mar-2017
Language
English
Publication Type
Article
Keywords
Anguilla - classification - genetics
Animals
Atlantic Ocean
Gene Flow
Gene Frequency
Genetic Speciation
Genotype
Hybridization, Genetic
Iceland
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
Zygote
Abstract
Elucidating barriers to gene flow is important for understanding the dynamics of speciation. Here we investigate pre- and post-zygotic mechanisms acting between the two hybridizing species of Atlantic eels: Anguilla anguilla and A. rostrata. Temporally varying hybridization was examined by analyzing 85 species-diagnostic single-nucleotide polymorphisms (SNPs; FST ?0.95) in eel larvae sampled in the spawning region in the Sargasso Sea in 2007 (N=92) and 2014 (N=460). We further investigated whether genotypes at these SNPs were nonrandomly distributed in post-F1 hybrids, indicating selection. Finally, we sequenced the mitochondrial ATP6 and nuclear ATP5c1 genes in 19 hybrids, identified using SNP and restriction site associated DNA (RAD) sequencing data, to test a previously proposed hypothesis of cytonuclear incompatibility leading to adenosine triphosphate (ATP) synthase dysfunction and selection against hybrids. No F1 hybrids but only later backcrosses were observed in the Sargasso Sea in 2007 and 2014. This suggests that interbreeding between the two species only occurs in some years, possibly controlled by environmental conditions at the spawning grounds, or that interbreeding has diminished through time as a result of a declining number of spawners. Moreover, potential selection was found at the nuclear and the cytonuclear levels. Nonetheless, one glass eel individual showed a mismatch, involving an American ATP6 haplotype and European ATP5c1 alleles. This contradicted the presence of cytonuclear incompatibility but may be explained by that (1) cytonuclear incompatibility is incomplete, (2) selection acts at a later life stage or (3) other genes are important for protein function. In total, the study demonstrates the utility of genomic data when examining pre- and post-zyotic barriers in natural hybrids.
Notes
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PubMed ID
27827390 View in PubMed
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Asymmetric isolating barriers between different microclimatic environments caused by low immigrant survival.

https://arctichealth.org/en/permalink/ahliterature269611
Source
Proc Biol Sci. 2015 Mar 7;282(1802)
Publication Type
Article
Date
Mar-7-2015
Author
Thomas P Gosden
John T Waller
Erik I Svensson
Source
Proc Biol Sci. 2015 Mar 7;282(1802)
Date
Mar-7-2015
Language
English
Publication Type
Article
Keywords
Adaptation, Physiological
Animals
Copulation
Ecosystem
Female
Fertility
Gene Flow
Longevity
Male
Microclimate
Odonata - genetics - physiology
Sweden
Abstract
Spatially variable selection has the potential to result in local adaptation unless counteracted by gene flow. Therefore, barriers to gene flow will help facilitate divergence between populations that differ in local selection pressures. We performed spatially and temporally replicated reciprocal field transplant experiments between inland and coastal habitats using males of the common blue damselfly (Enallagma cyathigerum) as our study organism. Males from coastal populations had lower local survival rates than resident males at inland sites, whereas we detected no differences between immigrant and resident males at coastal sites, suggesting asymmetric local adaptation in a source-sink system. There were no intrinsic differences in longevity between males from the different environments suggesting that the observed differences in male survival are environment-dependent and probably caused by local adaptation. Furthermore, the coastal environment was found to be warmer and drier than the inland environment, further suggesting local adaptation to microclimatic factors has lead to differential survival of resident and immigrant males. Our results suggest that low survival of immigrant males mediates isolation between closely located populations inhabiting different microclimatic environments.
Notes
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PubMed ID
25631994 View in PubMed
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Brief communication: Evolution of a specific O allele (O1vG542A) supports unique ancestry of Native Americans.

https://arctichealth.org/en/permalink/ahliterature108611
Source
Am J Phys Anthropol. 2013 Aug;151(4):649-57
Publication Type
Article
Date
Aug-2013
Author
Fernando A Villanea
Deborah A Bolnick
Cara Monroe
Rosita Worl
Rosemary Cambra
Alan Leventhal
Brian M Kemp
Author Affiliation
School of Biological Sciences, Washington State University, Pullman, WA 99164-4910, USA.
Source
Am J Phys Anthropol. 2013 Aug;151(4):649-57
Date
Aug-2013
Language
English
Publication Type
Article
Keywords
ABO Blood-Group System - genetics
Alaska
Alleles
Base Sequence
Biological Evolution
California
DNA Primers - genetics
DNA, Mitochondrial - genetics
Demography
Gene Flow - genetics
Genetics, Population
Haplotypes - genetics
Humans
Indians, North American - genetics
Molecular Sequence Data
Sequence Analysis, DNA
Abstract
In this study, we explore the geographic and temporal distribution of a unique variant of the O blood group allele called O1v(G542A) , which has been shown to be shared among Native Americans but is rare in other populations. O1v(G542A) was previously reported in Native American populations in Mesoamerica and South America, and has been proposed as an ancestry informative marker. We investigated whether this allele is also found in the Tlingit and Haida, two contemporary indigenous populations from Alaska, and a pre-Columbian population from California. If O1v(G542A) is present in Na-Dene speakers (i.e., Tlingits), it would indicate that Na-Dene speaking groups share close ancestry with other Native American groups and support a Beringian origin of the allele, consistent with the Beringian Incubation Model. If O1v(G542A) is found in pre-Columbian populations, it would further support a Beringian origin of the allele, rather than a more recent introduction of the allele into the Americas via gene flow from one or more populations which have admixed with Native Americans over the past five centuries. We identified this allele in one Na-Dene population at a frequency of 0.11, and one ancient California population at a frequency of 0.20. Our results support a Beringian origin of O1v(G542A) , which is distributed today among all Native American groups that have been genotyped in appreciable numbers at this locus. This result is consistent with the hypothesis that Na-Dene and other Native American populations primarily derive their ancestry from a single source population.
PubMed ID
23868176 View in PubMed
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Brief communication: mitochondrial DNA variation suggests extensive gene flow from Polynesian ancestors to indigenous Melanesians in the northwestern Bismarck Archipelago.

https://arctichealth.org/en/permalink/ahliterature171091
Source
Am J Phys Anthropol. 2006 Aug;130(4):551-6
Publication Type
Article
Date
Aug-2006
Author
Jun Ohashi
Izumi Naka
Katsushi Tokunaga
Tsukasa Inaoka
Yuji Ataka
Minato Nakazawa
Yasuhiro Matsumura
Ryutaro Ohtsuka
Author Affiliation
Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan. juno-tky@umin.ac.jp
Source
Am J Phys Anthropol. 2006 Aug;130(4):551-6
Date
Aug-2006
Language
English
Publication Type
Article
Keywords
African Continental Ancestry Group - genetics
Base Pairing - genetics
Base Sequence - genetics
Cluster analysis
DNA, Mitochondrial - chemistry - genetics
Electron Transport Complex IV - genetics
European Continental Ancestry Group - genetics
Female
Gene Flow
Genetics, Population
Humans
Lysine - genetics
Male
Melanesia
Molecular Sequence Data
Phylogeny
Polymerase Chain Reaction
Polymorphism, Genetic - genetics
Polynesia
RNA, Transfer - genetics
Sequence Deletion - genetics
Abstract
Archaeological, linguistic, and genetic studies show that Austronesian (AN)-speaking Polynesian ancestors came from Asia/Taiwan to the Bismarck Archipelago in Near Oceania more than 3,600 years ago, and then expanded into Remote Oceania. However, it remains unclear whether they extensively mixed with indigenous Melanesians who had populated the Bismarck Archipelago before their arrival. To examine the extent of admixture between Polynesian ancestors and indigenous Melanesians, mitochondrial DNA (mtDNA) variations in the D-loop region and the cytochrome oxidase and lysine transfer RNA (COII/tRNA(Lys)) intergenic 9-bp deletion were analyzed in the following three Oceanian populations: 1) Balopa Islanders as AN-speaking Melanesians living in the northwestern end of the Bismarck Archipelago, 2) Tongans as AN-speaking Polynesians, and 3) Gidra as non-Austronesian-speaking Melanesians in the southwestern lowlands of Papua New Guinea. Phylogenetic analysis of mtDNA sequences revealed that more than 60% of mtDNA sequences in the Balopa Islanders were very similar to those in Tongans, suggesting an extensive gene flow from Polynesian ancestors to indigenous Melanesians. Furthermore, analysis of pairwise difference distributions for the D-loop sequences with the 9-bp deletion and the Polynesian motif (i.e., T16217C, A16247G, and C16261T) suggested that the expansion of Polynesian ancestors possessing these variations occurred approximately 7,000 years ago.
PubMed ID
16425188 View in PubMed
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Causes and consequences of fine-scale population structure in a critically endangered freshwater seal.

https://arctichealth.org/en/permalink/ahliterature257095
Source
BMC Ecol. 2014;14:22
Publication Type
Article
Date
2014
Author
Mia Valtonen
Jukka U Palo
Jouni Aspi
Minna Ruokonen
Mervi Kunnasranta
Tommi Nyman
Author Affiliation
Department of Biology, University of Eastern Finland, Joensuu, Finland. mia.valtonen@uef.fi.
Source
BMC Ecol. 2014;14:22
Date
2014
Language
English
Publication Type
Article
Keywords
Animal Distribution
Animals
Bayes Theorem
Cluster analysis
DNA, Mitochondrial - genetics
Endangered Species
Female
Finland
Fresh Water
Gene Flow
Genetic Variation
Genetics, Population
Male
Microsatellite Repeats
Models, Genetic
Population Density
Seals, Earless - genetics
Sequence Analysis, DNA
Abstract
Small, genetically uniform populations may face an elevated risk of extinction due to reduced environmental adaptability and individual fitness. Fragmentation can intensify these genetic adversities and, therefore, dispersal and gene flow among subpopulations within an isolated population is often essential for maintaining its viability. Using microsatellite and mtDNA data, we examined genetic diversity, spatial differentiation, interregional gene flow, and effective population sizes in the critically endangered Saimaa ringed seal (Phoca hispida saimensis), which is endemic to the large but highly fragmented Lake Saimaa in southeastern Finland.
Microsatellite diversity within the subspecies (HE?=?0.36) ranks among the lowest thus far recorded within the order Pinnipedia, with signs of ongoing loss of individual heterozygosity, reflecting very low effective subpopulation sizes. Bayesian assignment analyses of the microsatellite data revealed clear genetic differentiation among the main breeding areas, but interregional structuring was substantially weaker in biparentally inherited microsatellites (FST?=?0.107) than in maternally inherited mtDNA (FST?=?0.444), indicating a sevenfold difference in the gene flow mediated by males versus females.
Genetic structuring in the population appears to arise from the joint effects of multiple factors, including small effective subpopulation sizes, a fragmented lacustrine habitat, and behavioural dispersal limitation. The fine-scale differentiation found in the landlocked Saimaa ringed seal is especially surprising when contrasted with marine ringed seals, which often exhibit near-panmixia among subpopulations separated by hundreds or even thousands of kilometres. Our results demonstrate that population structures of endangered animals cannot be predicted based on data on even closely related species or subspecies.
Notes
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PubMed ID
25005257 View in PubMed
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