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Accumulation and exchange of parasites during adaptive radiation in an ancient lake.

https://arctichealth.org/en/permalink/ahliterature301785
Source
Int J Parasitol. 2018 03; 48(3-4):297-307
Publication Type
Journal Article
Date
03-2018
Author
Joseph E Ironside
Toby J Wilkinson
Author Affiliation
Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion SY23 3DA, United Kingdom. Electronic address: jei@aber.ac.uk.
Source
Int J Parasitol. 2018 03; 48(3-4):297-307
Date
03-2018
Language
English
Publication Type
Journal Article
Keywords
Adaptation, Biological
Amphipoda - classification - parasitology - physiology
Animals
Bayes Theorem
Biodiversity
Cloning, Molecular
DNA, Fungal - chemistry
DNA, Ribosomal - chemistry
Europe
Host Specificity
Lakes - parasitology
Microsporidia - classification - genetics - growth & development
Phylogeny
Ponds - parasitology
Rivers - parasitology
Russia
Abstract
In the ancient Lake Baikal, Russia, amphipod crustaceans have undergone a spectacular adaptive radiation, resulting in a diverse community of species. A survey of microsporidian parasites inhabiting endemic and non-endemic amphipod host species at the margins of Lake Baikal indicates that the endemic amphipods harbour many microsporidian parasite groups associated with amphipods elsewhere in Eurasia. While these parasites may have undergone a degree of adaptive radiation within the lake, there is little evidence of host specificity. Furthermore, a lack of reciprocal monophyly indicates that exchanges of microsporidia between Baikalian and non-Baikalian hosts have occurred frequently in the past and may be ongoing. Conversely, limitations to parasite exchange between Baikalian and non-Baikalian host populations at the margins of the lake are implied by differences in parasite prevalence and lack of shared microsporidian haplotypes between the two host communities. While amphipod hosts have speciated sympatrically within Lake Baikal, the parasites appear instead to have accumulated, moving into the lake from external amphipod populations on multiple occasions to exploit the large and diverse community of endemic amphipods in Lake Baikal.
PubMed ID
29273284 View in PubMed
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A Bayesian network for assessing the collision induced risk of an oil accident in the Gulf of Finland.

https://arctichealth.org/en/permalink/ahliterature268276
Source
Environ Sci Technol. 2015 May 5;49(9):5301-9
Publication Type
Article
Date
May-5-2015
Author
Annukka Lehikoinen
Maria Hänninen
Jenni Storgård
Emilia Luoma
Samu Mäntyniemi
Sakari Kuikka
Source
Environ Sci Technol. 2015 May 5;49(9):5301-9
Date
May-5-2015
Language
English
Publication Type
Article
Keywords
Accidents - statistics & numerical data
Bayes Theorem
Estonia
Finland
Models, Theoretical
Oceans and Seas
Oil and Gas Industry - statistics & numerical data
Risk assessment
Russia
Ships
Abstract
The growth of maritime oil transportation in the Gulf of Finland (GoF), North-Eastern Baltic Sea, increases environmental risks by increasing the probability of oil accidents. By integrating the work of a multidisciplinary research team and information from several sources, we have developed a probabilistic risk assessment application that considers the likely future development of maritime traffic and oil transportation in the area and the resulting risk of environmental pollution. This metamodel is used to compare the effects of two preventative management actions on the tanker collision probabilities and the consequent risk. The resulting risk is evaluated from four different perspectives. Bayesian networks enable large amounts of information about causalities to be integrated and utilized in probabilistic inference. Compared with the baseline period of 2007-2008, the worst-case scenario is that the risk level increases 4-fold by the year 2015. The management measures are evaluated and found to decrease the risk by 4-13%, but the utility gained by their joint implementation would be less than the sum of their independent effects. In addition to the results concerning the varying risk levels, the application provides interesting information about the relationships between the different elements of the system.
PubMed ID
25780862 View in PubMed
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Efficient maximum likelihood pedigree reconstruction.

https://arctichealth.org/en/permalink/ahliterature148349
Source
Theor Popul Biol. 2009 Dec;76(4):285-91
Publication Type
Article
Date
Dec-2009
Author
Robert G Cowell
Author Affiliation
Faculty of Actuarial Science and Insurance, Cass Business School, 106 Bunhill Row, London EC1Y 8TZ, UK. rgc@city.ac.uk
Source
Theor Popul Biol. 2009 Dec;76(4):285-91
Date
Dec-2009
Language
English
Publication Type
Article
Keywords
Algorithms
Bayes Theorem
DNA, Satellite - genetics
Female
Forensic Anthropology
Forensic Genetics
Genotype
Humans
Likelihood Functions
Male
Microsatellite Repeats
Pedigree
Russia
Abstract
A simple and efficient algorithm is presented for finding a maximum likelihood pedigree using microsatellite (STR) genotype information on a complete sample of related individuals. The computational complexity of the algorithm is at worst (O(n(3)2(n))), where n is the number of individuals. Thus it is possible to exhaustively search the space of all pedigrees of up to thirty individuals for one that maximizes the likelihood. A priori age and sex information can be used if available, but is not essential. The algorithm is applied in a simulation study, and to some real data on humans.
PubMed ID
19781561 View in PubMed
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Evaluation of uncertainties in 90Sr-body-burdens obtained by whole-body count: application of Bayes' rule to derive detection limits by analysis of a posteriori data.

https://arctichealth.org/en/permalink/ahliterature188305
Source
Appl Radiat Isot. 2002 Oct;57(4):525-35
Publication Type
Article
Date
Oct-2002
Author
V P Kozheurov
V I Zalyapin
N B Shagina
E E Tokarevaa
M O Degteva
E I Tolstykh
L R Anspaugh
B A Napier
Author Affiliation
Urals Research Center for Radiation Medicine, Chelyabinsk, Russia.
Source
Appl Radiat Isot. 2002 Oct;57(4):525-35
Date
Oct-2002
Language
English
Publication Type
Article
Keywords
Bayes Theorem
Body Burden
Humans
Radioactive Hazard Release
Radiobiology
Radiometry - instrumentation - methods
Russia
Strontium Radioisotopes - adverse effects - analysis
Abstract
A whole body counter (WBC) designed to measure bremsstrahlung from 90Y, the short-lived daughter of 90Sr, has been used since 1974 to measure 90Sr-body burdens in residents along the Techa River, which was contaminated by releases from the Mayak Production Association. Bayes' rule has been applied to the a posteriori WBC data in order to derive the uncertainties associated with the data: The lower limit of reliable detection is 2.0 kBq and the uncertainty of routine measurements is 1.6 kBq.
PubMed ID
12361332 View in PubMed
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The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west?

https://arctichealth.org/en/permalink/ahliterature283312
Source
Mol Ecol. 2016 Jun;25(12):2773-89
Publication Type
Article
Date
Jun-2016
Author
Yoshiaki Tsuda
Jun Chen
Michael Stocks
Thomas Källman
Jørn Henrik Sønstebø
Laura Parducci
Vladimir Semerikov
Christoph Sperisen
Dmitry Politov
Tiina Ronkainen
Minna Väliranta
Giovanni Giuseppe Vendramin
Mari Mette Tollefsrud
Martin Lascoux
Source
Mol Ecol. 2016 Jun;25(12):2773-89
Date
Jun-2016
Language
English
Publication Type
Article
Keywords
Bayes Theorem
DNA, Mitochondrial - genetics
DNA, Plant - genetics
Genetics, Population
Genotyping Techniques
Hybridization, Genetic
Microsatellite Repeats
Models, Genetic
Picea - classification - genetics
Population Dynamics
Refugium
Russia
Scandinavian and Nordic Countries
Abstract
Boreal species were repeatedly exposed to ice ages and went through cycles of contraction and expansion while sister species alternated periods of contact and isolation. The resulting genetic structure is consequently complex, and demographic inferences are intrinsically challenging. The range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata) covers most of northern Eurasia; yet their geographical limits and histories remain poorly understood. To delineate the hybrid zone between the two species and reconstruct their joint demographic history, we analysed variation at nuclear SSR and mitochondrial DNA in 102 and 88 populations, respectively. The dynamics of the hybrid zone was analysed with approximate Bayesian computation (ABC) followed by posterior predictive structure plot reconstruction and the presence of barriers across the range tested with estimated effective migration surfaces. To estimate the divergence time between the two species, nuclear sequences from two well-separated populations of each species were analysed with ABC. Two main barriers divide the range of the two species: one corresponds to the hybrid zone between them, and the other separates the southern and northern domains of Norway spruce. The hybrid zone is centred on the Urals, but the genetic impact of Siberian spruce extends further west. The joint distribution of mitochondrial and nuclear variation indicates an introgression of mitochondrial DNA from Norway spruce into Siberian spruce. Overall, our data reveal a demographic history where the two species interacted frequently and where migrants originating from the Urals and the West Siberian Plain recolonized northern Russia and Scandinavia using scattered refugial populations of Norway spruce as stepping stones towards the west.
PubMed ID
27087633 View in PubMed
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Source
Sov Zdravookhr. 1990;(10):25-30
Publication Type
Article
Date
1990
Author
L F Molchanova
Source
Sov Zdravookhr. 1990;(10):25-30
Date
1990
Language
Russian
Publication Type
Article
Keywords
Adult
Attitude to Health
Bayes Theorem
Child
Child, Preschool
Family
Female
Health status
Health Surveys
Humans
Life Style
Male
Morbidity
Prognosis
Russia
Socioeconomic Factors
Abstract
The article provides the findings of a complex socio-hygienic survey of the lifestyle and health status of 350 families of workers and employees of Izhevsk. The identified differences in the conditions and lifestyle of families with high and low rates of morbidity permitted to calculate the values of relative risk for the formation of pathology among family members. It made it possible on the basis of the theorem of hypotheses (the Bayes' formula) and the algorithm of sequential statistical procedures to develop a screening prognostic table for early identification of families with risk for frequent diseases and providing them with primary prevention measures that would contribute to the reduction of morbidity.
PubMed ID
2148650 View in PubMed
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Genetic differentiation of southeast Baltic populations of sea trout inferred from single nucleotide polymorphisms.

https://arctichealth.org/en/permalink/ahliterature261446
Source
Anim Genet. 2014 Feb;45(1):96-104
Publication Type
Article
Date
Feb-2014
Author
A. Pocwierz-Kotus
R. Bernas
P. Debowski
M P Kent
S. Lien
M. Kesler
S. Titov
E. Leliuna
H. Jespersen
A. Drywa
R. Wenne
Source
Anim Genet. 2014 Feb;45(1):96-104
Date
Feb-2014
Language
English
Publication Type
Article
Keywords
Animals
Bayes Theorem
Denmark
Estonia
Gene Frequency
Genetics, Population
Genotype
Lithuania
Models, Genetic
Poland
Polymorphism, Single Nucleotide
Russia
Trout - genetics
Abstract
Sea trout (Salmo trutta m. trutta) is a migratory form of brown trout common in the Baltic Sea. Nine populations from the southeast Baltic (Poland; Lithuania; Denmark, Bornholm; Estonia and Russia) were genotyped using iPLEX Gold technology (Sequenom) with 62 informative SNPs. A diagnostic panel of 23 SNPs was applied to estimate genetic differentiation and assess the population structure of Baltic sea trout. The highest level of pairwise FST differences was observed between the Russian (East Gulf of Finland) and Polish (Baltic main basin) populations. The lowest differences were between the two Polish and the Polish and Lithuanian populations. A genetic similarity was noted between the Estonian Riguldi River and Danish Bornholm populations, and this finding was supported by a Bayesian and factorial correspondence analysis. Diversity within populations was highest for populations from Estonia and lowest for the Lithuanian population. Genetic structure analysis indicated that individuals from the nine populations were clustered into four groups.
Notes
Erratum In: Anim Genet. 2014 Feb;45(1):155
PubMed ID
24236931 View in PubMed
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The genetic structure of cattle populations (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions: implications for breeding strategies and conservation.

https://arctichealth.org/en/permalink/ahliterature84352
Source
Mol Ecol. 2007 Sep;16(18):3839-53
Publication Type
Article
Date
Sep-2007
Author
Li Meng-Hua
Tapio Ilma
Vilkki Johanna
Ivanova Zoya
Kiselyova Tatyana
Marzanov Nurby
Cinkulov Mirjana
Stojanovic Srdjan
Ammosov Innokenty
Popov Ruslan
Kantanen Juha
Author Affiliation
Biotechnology and Food Research, MTT Agrifood Research Finland, FIN-31600 Jokioinen, Finland.
Source
Mol Ecol. 2007 Sep;16(18):3839-53
Date
Sep-2007
Language
English
Publication Type
Article
Keywords
Analysis of Variance
Animals
Bayes Theorem
Breeding - methods
Cattle - classification - genetics - physiology
Cluster analysis
Conservation of Natural Resources
Europe, Eastern
Geography
Microsatellite Repeats
Phylogeny
Population Dynamics
Russia
Sequence Analysis, DNA
Variation (Genetics)
Abstract
We investigated the genetic structure and variation of 21 populations of cattle (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions of the Balkan, the Caucasus and Ukraine employing 30 microsatellite markers. By analyses of population relationships, as well as by a Bayesian-based clustering approach, we identified a genetic distinctness between populations of modern commercial origin and those of native origin. Our data suggested that northern European Russia represents the most heavily colonized area by modern commercial cattle. Further genetic mixture analyses based on individual assignment tests found that native Red Steppe cattle were also employed in the historical breeding practices in Eastern Europe, most probably for incorporating their strong and extensive adaptability. In analysis of molecular variance, within-population differences accounted for approximately 90% of the genetic variation. Despite some correspondence between geographical proximity and genetic similarity, genetic differentiation was observed to be significantly associated with the difference in breeding purpose among the European populations (percentage of variance among groups and significance: 2.99%, P = 0.02). Our findings give unique genetic insight into the historical patterns of cattle breeding practices in the former Soviet Union. The results identify the neighbouring Near Eastern regions such as the Balkan, the Caucasus and Ukraine, and the isolated Far Eastern Siberia as areas of 'genetic endemism', where cattle populations should be given conservation priority. The results will also be of importance for cost-effective management of their future utilization.
PubMed ID
17850550 View in PubMed
Less detail

Genetic structure of Sakhalin spruce (Picea glehnii) in northern Japan and adjacent regions revealed by nuclear microsatellites and mitochondrial gene sequences.

https://arctichealth.org/en/permalink/ahliterature269464
Source
J Plant Res. 2015 Jan;128(1):91-102
Publication Type
Article
Date
Jan-2015
Author
Mineaki Aizawa
Hiroshi Yoshimaru
Makoto Takahashi
Takayuki Kawahara
Hisashi Sugita
Hideyuki Saito
Renat N Sabirov
Source
J Plant Res. 2015 Jan;128(1):91-102
Date
Jan-2015
Language
English
Publication Type
Article
Keywords
Base Sequence
Bayes Theorem
Cell Nucleus - genetics
Cluster analysis
DNA, Mitochondrial - genetics
Genes, Mitochondrial
Genetic Loci
Genetic Variation
Geography
Haplotypes - genetics
Introns - genetics
Japan
Microsatellite Repeats - genetics
Picea - genetics
Principal Component Analysis
Russia
Sequence Analysis, DNA
Abstract
The genetic structure of Sakhalin spruce (Picea glehnii) was studied across the natural range of the species, including two small isolated populations in south Sakhalin and Hayachine, by using six microsatellite loci and maternally inherited mitochondrial gene sequences. We also analyzed P. jezoensis, a sympatric spruce in the range. Genetic diversity of P. glehnii was higher in central Hokkaido and the lowest in the Hayachine. Bayesian clustering and principal coordinate analysis by using the microsatellites indicated that the Hayachine was clearly distinct from other populations, implying that it had undergone strong genetic drift since the last glacial period. P. glehnii harbored four mitochondrial haplotypes, two of which were shared with P. jezoensis. One of the two was observed without geographical concentration, suggesting its derivation from ancestral polymorphism. Another was observed in south Sakhalin and in P. jezoensis across Sakhalin. The Bayesian clustering--by using four microsatellite loci, including P. jezoensis populations--indicated unambiguous species delimitation, but with possible admixture of P. jezoensis genes into P. glehnii in south Sakhalin, where P. glehnii is abundantly overwhelmed by P. jezoensis; this might explain the occurrence of introgression of the haplotype of P. jezoensis into P. glehnii.
PubMed ID
25421922 View in PubMed
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20 records – page 1 of 2.