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Source
Nature. 2005 Oct 6;437(7060):794-5
Publication Type
Article
Date
Oct-6-2005
Source
Nature. 2005 Oct 6;437(7060):794-5
Date
Oct-6-2005
Language
English
Publication Type
Article
Keywords
Alaska
Biomedical Research - ethics - legislation & jurisprudence
Bioterrorism - prevention & control
Evolution, Molecular
Female
History, 20th Century
Humans
Influenza, Human - epidemiology - history - prevention & control - virology
Orthomyxoviridae - genetics - pathogenicity
Publishing
Time Factors
Virulence - genetics
Virulence Factors
Notes
Comment In: Nature. 2006 Jan 19;439(7074):26616421546
Comment On: Nature. 2005 Oct 6;437(7060):889-9316208372
Erratum In: Nature. 2005 Oct 13;437(7061):940
PubMed ID
16208326 View in PubMed
Less detail

The adaptation of polar fishes to climatic changes: Structure, function and phylogeny of haemoglobin.

https://arctichealth.org/en/permalink/ahliterature86911
Source
IUBMB Life. 2008 Jan;60(1):29-40
Publication Type
Article
Date
Jan-2008
Author
Verde Cinzia
Giordano Daniela
di Prisco Guido
Author Affiliation
Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, Naples, Italy.
Source
IUBMB Life. 2008 Jan;60(1):29-40
Date
Jan-2008
Language
English
Publication Type
Article
Keywords
Adaptation, Physiological
Animals
Antarctic Regions
Antifreeze Proteins - genetics
Arctic Regions
Cold Climate
Evolution, Molecular
Fishes - physiology
Hemoglobins - chemistry - genetics - physiology
Oxygen - blood
Phylogeny
Abstract
In the Antarctic, fishes of dominant suborder Notothenioidei have evolved in a unique thermal scenario. Phylogenetically related taxa of the suborder live in a wide range of latitudes, in Antarctic, sub-Antarctic and temperate oceans. Consequently, they offer a remarkable opportunity to study the physiological and biochemical characters gained and, conversely, lost during their evolutionary history. The evolutionary perspective has also been pursued by comparative studies of some features of the heme protein devoted to O(2) transport in fish living in the other polar region, the Arctic. The two polar regions differ by age and isolation. Fish living in each habitat have undergone regional constraints and fit into different evolutionary histories. The aim of this contribution is to survey the current knowledge of molecular structure, functional features, phylogeny and adaptations of the haemoglobins of fish thriving in the Antarctic, sub-Antarctic and Arctic regions (with some excursions in the temperate latitudes), in search of insights into the convergent processes evolved in response to cooling. Current climate change may disturb adaptation, calling for strategies aimed at neutralising threats to biodiversity.
PubMed ID
18379990 View in PubMed
Less detail

Adaptive evolution of HIV at HLA epitopes is associated with ethnicity in Canada.

https://arctichealth.org/en/permalink/ahliterature123483
Source
PLoS One. 2012;7(5):e36933
Publication Type
Article
Date
2012
Author
Manon Ragonnet-Cronin
Stéphane Aris-Brosou
Isabelle Joanisse
Harriet Merks
Dominic Vallee
Kyna Caminiti
Paul Sandstrom
James Brooks
Author Affiliation
National HIV and Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, Canada.
Source
PLoS One. 2012;7(5):e36933
Date
2012
Language
English
Publication Type
Article
Keywords
Adaptation, Physiological - genetics
Adult
Alleles
Canada - ethnology
Epitopes - immunology
Evolution, Molecular
Female
HIV Infections - ethnology - immunology - virology
HIV-1 - genetics - pathogenicity
HLA Antigens - genetics - immunology
Humans
Male
Middle Aged
Selection, Genetic
Young Adult
Abstract
Host immune selection pressure influences the development of mutations that allow for HIV escape. Mutation patterns induced in HIV by the human leukocyte antigen (HLA) are HLA-allele specific. As ethnic groups have distinct and characteristic HLA allele frequencies, we can expect divergent viral evolution within ethnicities. Here, we have sequenced and analyzed the HIV pol gene from 1248 subtype B infected, treatment-na?ve individuals in Canada. Phylogenetic analysis showed no separation between pol sequences from five self-identified ethnic groups, yet fixation index (F(ST)) values showed significant divergence between ethnicities. A total of 17 amino acid sites showed an ethnic-specific fixation pattern (0.015
Notes
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PubMed ID
22693560 View in PubMed
Less detail

Adler hantavirus, a new genetic variant of Tula virus identified in Major's pine voles (Microtus majori) sampled in southern European Russia.

https://arctichealth.org/en/permalink/ahliterature265932
Source
Infect Genet Evol. 2015 Jan;29:156-63
Publication Type
Article
Date
Jan-2015
Author
Evgeniy A Tkachenko
Peter T Witkowski
Lukas Radosa
Tamara K Dzagurova
Nataliya M Okulova
Yulia V Yunicheva
Ludmila Vasilenko
Vyacheslav G Morozov
Gennadiy A Malkin
Detlev H Krüger
Boris Klempa
Source
Infect Genet Evol. 2015 Jan;29:156-63
Date
Jan-2015
Language
English
Publication Type
Article
Keywords
Animals
Arvicolinae - classification - virology
Black Sea
DNA, Mitochondrial - genetics
Evolution, Molecular
Genetic Variation
Hantavirus - classification - genetics - isolation & purification
Humans
Phylogeny
Phylogeography
RNA, Viral - analysis
Russia
Sequence Analysis, RNA
Abstract
Although at least 30 novel hantaviruses have been recently discovered in novel hosts such as shrews, moles and even bats, hantaviruses (family Bunyaviridae, genus Hantavirus) are primarily known as rodent-borne human pathogens. Here we report on identification of a novel hantavirus variant associated with a rodent host, Major's pine vole (Microtus majori). Altogether 36 hantavirus PCR-positive Major's pine voles were identified in the Krasnodar region of southern European Russia within the years 2008-2011. Initial partial L-segment sequence analysis revealed novel hantavirus sequences. Moreover, we found a single common vole (Microtusarvalis) infected with Tula virus (TULV). Complete S- and M-segment coding sequences were determined from 11 Major's pine voles originating from 8 trapping sites and subjected to phylogenetic analyses. The data obtained show that Major's pine vole is a newly recognized hantavirus reservoir host. The newfound virus, provisionally called Adler hantavirus (ADLV), is closely related to TULV. Based on amino acid differences to TULV (5.6-8.2% for nucleocapsid protein, 9.4-9.5% for glycoprotein precursor) we propose to consider ADLV as a genotype of TULV. Occurrence of ADLV and TULV in the same region suggests that ADLV is not only a geographical variant of TULV but a host-specific genotype. High intra-cluster nucleotide sequence variability (up to 18%) and geographic clustering indicate long-term presence of the virus in this region.
PubMed ID
25433134 View in PubMed
Less detail

Allelic imbalance at rs6983267 suggests selection of the risk allele in somatic colorectal tumor evolution.

https://arctichealth.org/en/permalink/ahliterature159495
Source
Cancer Res. 2008 Jan 1;68(1):14-7
Publication Type
Article
Date
Jan-1-2008
Author
Sari Tuupanen
Iina Niittymäki
Kari Nousiainen
Sakari Vanharanta
Jukka-Pekka Mecklin
Kyösti Nuorva
Heikki Järvinen
Sampsa Hautaniemi
Auli Karhu
Lauri A Aaltonen
Author Affiliation
Department of Medical Genetics, Genome-Scale Biology Research Program, Biomedicum Helsinki, University of Helsinki, P.O. Box 63, FIN-00014 Helsinki, Finland.
Source
Cancer Res. 2008 Jan 1;68(1):14-7
Date
Jan-1-2008
Language
English
Publication Type
Article
Keywords
Aged
Alleles
Allelic Imbalance
Chromosomes, Human, Pair 8 - genetics
Colorectal Neoplasms - genetics
DNA, Neoplasm
European Continental Ancestry Group - genetics
Evolution, Molecular
Female
Finland
Heterozygote
Humans
Male
Middle Aged
Polymorphism, Single Nucleotide
Risk
Selection, Genetic
Sequence Analysis, DNA
Abstract
A common single nucleotide polymorphism (SNP), rs6983267, at 8q24.21 has recently been shown to associate with colorectal cancer (CRC). Three independent SNP association studies showed that rs6983267 contributes to CRC with odds ratios (OR) of 1.17 to 1.22. Here, we genotyped a population-based series of 1,042 patients with CRC and 1,012 healthy controls for rs6983267 and determined the contribution of SNP to CRC in Finland, using germ line DNA, as well as the respective cancer DNA in heterozygous patients. The comprehensive clinical data available from the 1,042 patients and their first-degree relatives enabled us to thoroughly examine the possible association of this variant with different clinical features. As expected, a significant association between the G allele of rs6983267 and CRC [OR, 1.22; 95% confidence interval (CI), 1.08-1.38; P = 0.0018] was found, confirming the previous observations. A trend towards association of the G allele with microsatellite-stable cancer (OR, 1.37; 95% CI, 1.02-1.85; P = 0.04) and family history of cancers other than CRC was seen (OR, 1.20; 95% CI, 1-1.43; P = 0.05). Four hundred and sixty-six GT heterozygotes identified in this study were analyzed for allelic imbalance at rs6983267 in the respective cancer DNA. One hundred and one tumors showed allelic imbalance (22%). The risk allele G was favored in 67 versus 34 tumors (P = 0.0007). This finding implicates that the underlying germ line genetic defect in 8q24.21 is a target in the somatic evolution of CRC.
PubMed ID
18172290 View in PubMed
Less detail

An AFLP clock for the absolute dating of shallow-time evolutionary history based on the intraspecific divergence of southwestern European alpine plant species.

https://arctichealth.org/en/permalink/ahliterature90263
Source
Mol Ecol. 2009 Feb;18(4):697-708
Publication Type
Article
Date
Feb-2009
Author
Kropf Matthias
Comes Hans Peter
Kadereit Joachim W
Author Affiliation
Institut für Botanik, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Applied Life Sciences, A-1180 Vienna, Austria. matthias.kropf@boku.ac.at
Source
Mol Ecol. 2009 Feb;18(4):697-708
Date
Feb-2009
Language
English
Publication Type
Article
Keywords
Amplified Fragment Length Polymorphism Analysis
Brassicaceae - genetics
Caryophyllaceae - genetics
DNA, Plant - genetics
Ecosystem
Europe
Evolution, Molecular
Genetics, Population
Gentiana - genetics
Models, Genetic
Mutation
Phylogeny
Plants - genetics
Regression Analysis
Sequence Analysis, DNA
Species Specificity
Abstract
The dating of recent events in the history of organisms needs divergence rates based on molecular fingerprint markers. Here, we used amplified fragment length polymorphisms (AFLPs) of three distantly related alpine plant species co-occurring in the Spanish Sierra Nevada, the Pyrenees and the southwestern Alps/Massif Central to establish divergence rates. Within each of these species (Gentiana alpina, Kernera saxatilis and Silene rupestris), we found that the degree of AFLP divergence (D(N72)) between mountain phylogroups was significantly correlated with their time of divergence (as inferred from palaeoclimatic/palynological data), indicating constant AFLP divergence rates. As these rates did not differ significantly among species, a regression analysis based on the pooled data was utilized to generate a general AFLP rate. The application of this latter rate to AFLP data from other herbaceous plant species (Minuartia biflora: Schönswetter et al. 2006; Nigella degenii: Comes et al. 2008) resulted in a plausible timing of the recolonization of the Svalbard Islands and the separation of populations from the Alps and Scandinavia (Minuartia), and of island population separation in the Aegean Archipelago (Nigella). Furthermore, the AFLP mutation rate obtained in our study is of the same magnitude as AFLP mutation rates published previously. The temporal limits of our AFLP rate, which is based on intraspecific vicariance events at shallow (i.e. late glacial/Early Holocene) time scales, remains to be tested.
PubMed ID
19175503 View in PubMed
Less detail

Analysis of echovirus 30 isolates from Russia and new independent states revealing frequent recombination and reemergence of ancient lineages.

https://arctichealth.org/en/permalink/ahliterature159831
Source
J Clin Microbiol. 2008 Feb;46(2):665-70
Publication Type
Article
Date
Feb-2008
Author
Alexander N Lukashev
Olga E Ivanova
Tatiana P Eremeeva
Larisa V Gmyl
Author Affiliation
Institute of Poliomyelitis and Viral Encephalitides RAMS, Moscow, Russia. Alexander_lukashev@hotmail.com
Source
J Clin Microbiol. 2008 Feb;46(2):665-70
Date
Feb-2008
Language
English
Publication Type
Article
Keywords
Enterovirus B, Human - classification - genetics - isolation & purification
Enterovirus Infections - epidemiology - virology
Evolution, Molecular
Humans
Molecular Epidemiology
Molecular Sequence Data
Phylogeny
Recombination, Genetic
Russia - epidemiology
Sequence Analysis, DNA
Sequence Homology
Viral Proteins - genetics
Abstract
We studied two genome regions, VP1 and 3D, of 48 echovirus 30 (E30) isolates from Russia and the new independent states. In VP1, most isolates were similar to European strains reported earlier, and frequent change of circulating subgroups was noticed. We also observed, in 2003-2006, the reemergence of a group of E30 strains with a VP1 region very distant from most modern E30 strains and remotely similar to E30 isolates from the 1960s and the 1970s. A study of the 3D genome region detected multiple recombination events among the studied strains. Recombination presumably occurred every few years, and therefore, the study of a single VP1 genome region cannot accurately describe the phylogenetic history of the virus or predict pathogenetic properties of an isolate. In general, a comparison of the VP1 and 3D genome region phylogenies revealed, in some instances, virtually independent circulation of enterovirus genome fragments on a scale of years.
Notes
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PubMed ID
18077646 View in PubMed
Less detail

Analysis of mitochondrial DNA diversity in the aleuts of the commander islands and its implications for the genetic history of beringia.

https://arctichealth.org/en/permalink/ahliterature6718
Source
Am J Hum Genet. 2002 Aug;71(2):415-21
Publication Type
Article
Date
Aug-2002
Author
Olga A Derbeneva
Rem I Sukernik
Natalia V Volodko
Seyed H Hosseini
Marie T Lott
Douglas C Wallace
Author Affiliation
Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, 10 Lavrent'ev Avenue, Novosibirsk 630090, Russia.
Source
Am J Hum Genet. 2002 Aug;71(2):415-21
Date
Aug-2002
Language
English
Publication Type
Article
Keywords
DNA, Mitochondrial
Evolution, Molecular
Humans
Inuits
Phylogeny
Point Mutation
Polymorphism, Genetic
Research Support, U.S. Gov't, P.H.S.
Variation (Genetics)
Abstract
The Aleuts are aboriginal inhabitants of the Aleutian archipelago, including Bering and Copper (Medny) Islands of the Commanders, and seem to be the survivors of the inhabitants of the southern belt of the Bering Land Bridge that connected Chukotka/Kamchatka and Alaska during the end of the Ice Age. Thirty mtDNA samples collected in the Commanders, as well as seven mtDNA samples from Sireniki Eskimos in Chukotka who belong to the Beringian-specific subhaplogroup D2, were studied through complete sequencing. This analysis has provided evidence that all 37 of these mtDNAs are closely related, since they share the founding haplotype for subhaplogroup D2. We also demonstrated that, unlike the Eskimos and Na-Dene, the Aleuts of the Commanders were founded by a single lineage of haplogroup D2, which had acquired the novel transversion mutation 8910A. The phylogeny of haplogroup D complete sequences showed that (1) the D2 root sequence type originated among the latest inhabitants of Beringia and (2) the Aleut 8910A sublineage of D2 is a part of larger radiation of rooted D2, which gave rise to D2a (Na-Dene), D2b (Aleut), and D2c (Eskimo) sublineages. The geographic specificity and remarkable intrinsic diversity of D2 lineages support the refugial hypothesis, which assumes that the founding population of Eskimo-Aleut originated in Beringan/southwestern Alaskan refugia during the early postglacial period, rather than having reached the shores of Alaska as the result of recent wave of migration from interior Siberia.
PubMed ID
12082644 View in PubMed
Less detail

Analysis of Puumala hantavirus in a bank vole population in northern Finland: evidence for co-circulation of two genetic lineages and frequent reassortment between strains.

https://arctichealth.org/en/permalink/ahliterature151379
Source
J Gen Virol. 2009 Aug;90(Pt 8):1923-31
Publication Type
Article
Date
Aug-2009
Author
Maria Razzauti
Angelina Plyusnina
Tarja Sironen
Heikki Henttonen
Alexander Plyusnin
Author Affiliation
Department of Virology, Infection Biology Research Program, University of Helsinki, FI-00014 Helsinki, Finland. maria.razzauti@hwlsinki.fi
Source
J Gen Virol. 2009 Aug;90(Pt 8):1923-31
Date
Aug-2009
Language
English
Publication Type
Article
Keywords
Amino Acid Sequence
Animals
Arvicolinae - virology
Cluster analysis
Evolution, Molecular
Finland
Genotype
Hemorrhagic Fever with Renal Syndrome - veterinary - virology
Humans
Lung - virology
Molecular Epidemiology
Molecular Sequence Data
Phylogeny
Puumala virus - classification - genetics - isolation & purification
RNA, Viral - genetics
Reassortant Viruses - genetics - isolation & purification
Sequence Analysis, DNA
Sequence Homology
Abstract
In this study, for the first time, two distinct genetic lineages of Puumala virus (PUUV) were found within a small sampling area and within a single host genetic lineage (Ural mtDNA) at Pallasjärvi, northern Finland. Lung tissue samples of 171 bank voles (Myodes glareolus) trapped in September 1998 were screened for the presence of PUUV nucleocapsid antigen and 25 were found to be positive. Partial sequences of the PUUV small (S), medium (M) and large (L) genome segments were recovered from these samples using RT-PCR. Phylogenetic analysis revealed two genetic groups of PUUV sequences that belonged to the Finnish and north Scandinavian lineages. This presented a unique opportunity to study inter-lineage reassortment in PUUV; indeed, 32 % of the studied bank voles appeared to carry reassortant virus genomes. Thus, the frequency of inter-lineage reassortment in PUUV was comparable to that of intra-lineage reassortment observed previously (Razzauti, M., Plyusnina, A., Henttonen, H. & Plyusnin, A. (2008). J Gen Virol 89, 1649-1660). Of six possible reassortant S/M/L combinations, only two were found at Pallasjärvi and, notably, in all reassortants, both S and L segments originated from the same genetic lineage, suggesting a non-random pattern for the reassortment. These findings are discussed in connection to PUUV evolution in Fennoscandia.
PubMed ID
19386780 View in PubMed
Less detail

Ancestral components of admixed genomes in a Mexican cohort.

https://arctichealth.org/en/permalink/ahliterature128519
Source
PLoS Genet. 2011 Dec;7(12):e1002410
Publication Type
Article
Date
Dec-2011
Author
Nicholas A Johnson
Marc A Coram
Mark D Shriver
Isabelle Romieu
Gregory S Barsh
Stephanie J London
Hua Tang
Author Affiliation
Department of Statistics, Stanford University, Stanford, California, United States of America.
Source
PLoS Genet. 2011 Dec;7(12):e1002410
Date
Dec-2011
Language
English
Publication Type
Article
Keywords
African Americans - genetics
African Continental Ancestry Group - genetics
American Native Continental Ancestry Group - genetics
Cohort Studies
Demography
Ethnic Groups - genetics
European Continental Ancestry Group - genetics
Evolution, Molecular
Genome, Human
Haplotypes - genetics
Hispanic Americans - genetics
Humans
Mexico
Polymorphism, Single Nucleotide
Population - genetics
Principal Component Analysis
Selection, Genetic
Abstract
For most of the world, human genome structure at a population level is shaped by interplay between ancient geographic isolation and more recent demographic shifts, factors that are captured by the concepts of biogeographic ancestry and admixture, respectively. The ancestry of non-admixed individuals can often be traced to a specific population in a precise region, but current approaches for studying admixed individuals generally yield coarse information in which genome ancestry proportions are identified according to continent of origin. Here we introduce a new analytic strategy for this problem that allows fine-grained characterization of admixed individuals with respect to both geographic and genomic coordinates. Ancestry segments from different continents, identified with a probabilistic model, are used to construct and study "virtual genomes" of admixed individuals. We apply this approach to a cohort of 492 parent-offspring trios from Mexico City. The relative contributions from the three continental-level ancestral populations-Africa, Europe, and America-vary substantially between individuals, and the distribution of haplotype block length suggests an admixing time of 10-15 generations. The European and Indigenous American virtual genomes of each Mexican individual can be traced to precise regions within each continent, and they reveal a gradient of Amerindian ancestry between indigenous people of southwestern Mexico and Mayans of the Yucatan Peninsula. This contrasts sharply with the African roots of African Americans, which have been characterized by a uniform mixing of multiple West African populations. We also use the virtual European and Indigenous American genomes to search for the signatures of selection in the ancestral populations, and we identify previously known targets of selection in other populations, as well as new candidate loci. The ability to infer precise ancestral components of admixed genomes will facilitate studies of disease-related phenotypes and will allow new insight into the adaptive and demographic history of indigenous people.
Notes
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PubMed ID
22194699 View in PubMed
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216 records – page 1 of 22.