scholarly journals Using Statistical Phylogenetics for Investigation of Enterovirus 71 Genotype A Reintroduction into Circulation

Viruses ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 895 ◽  
Author(s):  
Yulia Vakulenko ◽  
Andrei Deviatkin ◽  
Alexander Lukashev
Keyword(s):  
Natural Circulation ◽  
Enterovirus 71 ◽  
Genetic Distances ◽  
Bayesian Phylogenetic Analysis ◽  
Spread Pattern ◽  
The Mean ◽  
Event Based ◽  
Tree Branch ◽  
Artificial Introduction ◽  
Genotype A

Neurovirulent enterovirus 71 (EV-A71) caused a massive epidemic in China in 2008–2011. While subgenotype C4 was the major causative agent, a few isolates were almost identical to the prototype EV-A71 strain and belonged to genotype A. This variant was allegedly extinct since 1970, and its identification in this epidemic suggests reintroduction of the archive virus. Regression analysis of genetic distances (TempEst software) was of moderate utility due to the low resolution of classical phylogenetic methods. Bayesian phylogenetic analysis (BEAST software) suggested artificial introduction event based on highly aberrant phylogenetic tree branch rates that differed by over three standard deviations from the mean substitution rate for EV71. Manual nucleotide-level analysis was used to further explore the virus spread pattern after introduction into circulation. Upon reintroduction, the virus accumulated up to seven substitutions in VP1, most of them non-synonymous and located within the capsid’s canyon or at its rims, compatible with readaptation of a lab strain to natural circulation.

scholarly journals Attenuation of peak ground accelerations in some recent New Zealand earthquakes

1993 ◽  
Vol 26 (1) ◽  
pp. 3-13 ◽  
Author(s):  
D. J. Dowrick ◽  
S. Sritharan
Keyword(s):  
New Zealand ◽  
Strong Motion ◽  
Medium Size ◽  
Data Sets ◽  
Fault Rupture ◽  
Motion Data ◽  
Peak Ground Accelerations ◽  
The Mean ◽  
Using Data ◽  
Event Based

The attenuation of peak ground accelerations was studied for eight New Zealand earthquakes which occurred in the period 1987 to 1991. These events were of medium size with moment magnitudes in the range Mw = 5.8 - 6.7, with depth to centroids of the fault rupture ranging from 4 to 60 km. Attenuation of peak ground accelerations was examined for each event, based on the slope distance from the rupture surface to each strong motion data site. The mean regression attenuation curve for each event was compared with those derived by others using data sets from other parts of the world, allowance being made for source mechanism and depth. Excepting the 1988 Te Anau event, the other seven New Zealand events as a set closely match a Japanese model, but give significantly stronger accelerations than those predicted by the models from western USA and Europe.

scholarly journals Assessment of genetic diversity among surian Toona sinensis Roem in progenies test using random amplified polymorphic DNA markers

2018 ◽  
Vol 22 (1) ◽  
pp. 22
Author(s):  
Jayusman Jayusman ◽  
Muhammad Na’iem ◽  
Sapto Indrioko ◽  
Eko Bhakti Hardiyanto ◽  
ILG Nurcahyaningsih
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Management Strategies ◽  
Genetic Distances ◽  
Sampled Data ◽  
Toona Sinensis ◽  
The Mean ◽  
Individual Trees

Surian Toona sinensis Roem is one of the most widely planted species in Indonesia. This study aimed to estimate the genetic diversity between a number of surian populations in a progeny test using RAPD markers, with the goal of proposing management strategies for a surian breeding program. Ninety-six individual trees from 8 populations of surian were chosen as samples for analysis. Eleven polymorphic primers (OP-B3, OP-B4, OP-B10, OP-H3, OP-Y6, OP-Y7, OP-Y8, OP-Y10, OP-Y11, OP-Y14, and OP-06) producing reproducible bands were analyzed for the 96 trees, with six trees per family sampled. Data were analyzed using GenAlEx 6.3, NTSYS 2.02. The observed percentage of polymorphic loci ranged from 18.2% to 50%. The mean level of genetic diversity among the surian populations was considered to be moderate (He 0.304). Cluster analysis grouped the genotypes into two main clusters, at similarity levels of 0.68 and 0.46. The first two axes of the PCoA explained 46.16% and 25.54% of the total variation, respectively. The grouping of samples into clusters and subclusters did not correspond with family and their distances, but the grouping was in line with the genetic distances of the samples.

Reassignment of 'Triplophysa' jiarongensis (Cypriniformes: Nemacheilidae) to Oreonectes Günther, 1868

Zootaxa ◽  
2019 ◽  
Vol 4565 (3) ◽  
pp. 398 ◽  
Author(s):  
XUAN LIU ◽  
HUAIQING DENG ◽  
ZHIJIN LIU ◽  
JIANG ZHOU
Keyword(s):  
Phylogenetic Analysis ◽  
Short Distance ◽  
River System ◽  
Genetic Distances ◽  
Molecular Evidence ◽  
Karst Cave ◽  
Bayesian Phylogenetic Analysis ◽  
As Species ◽  
Secondary Sexual Dimorphism ◽  
Underground River

Specimens identified as Oreonectes jiarongensis (Cypriniformes: Nemacheilidae) were collected from a karst cave in Jiarong Town and Banzhai Township, Libo County, Guizhou, China. Several lines of morphological and molecular evidence suggested that this species was similar to species of Oreonectes Günther 1868 and not closely related to species of Triplophysa Rendal, 1933. The anterior and posterior nostrils of 'Triplophysa' jiarongensis were separated by a short distance, and there was no secondary sexual dimorphism in male specimens. The Bayesian phylogenetic analysis based on cytochrome b recovered 'T.' jiarongensis in a well-supported clade with Oreonectes daqikongensis, O. shuilongensis, O. furcocaudalis and O. platycephalus, sister to the Triplophysa clade. In addition, the genetic distances between 'T.' jiarongensis and species of Oreonectes were low (O. daqikongensis: 0.114; O. shuilongensis: 0.106; O. platycephalus: 0.180), while distances to species of Triplophysa were higher (T. dorsalis: 0.233; T. yarkandensis: 0.282). Therefore, we reassign 'T.' jiarongensis to Oreonectes. Based on this result, it is now clear that species of both Oreonectes and Triplophysa inhabit the same underground river system in Guizhou. However, as species of Oreonectes are only known from the southern part of Guizhou, it may be that O. jiarongensis inhabits the most northerly part of the range of this genus. 

scholarly journals Ampelographic and molecular diversity among grapevine (Vitis spp.) cultivars

2009 ◽  
Vol 45 (No. 4) ◽  
pp. 160-168 ◽  
Author(s):  
A. Sabir ◽  
S. Tangolar ◽  
S. Buyukalaca ◽  
S. Kafkas
Keyword(s):  
Molecular Characterization ◽  
Molecular Diversity ◽  
Genetic Distances ◽  
Mean Values ◽  
Issr Analysis ◽  
Geographic Origins ◽  
The Mean ◽  
Vitis Spp

This study presents the ampelographic and molecular characterization of 44 grapevine cultivars. Ampelographic data were obtained during two vegetation periods using the latest version of the descriptors. Based on the mean values transformed by the method indicated in IBPGR publications, a dendrogram was constructed. ISSR analysis was also employed to characterize the genotypes at the DNA level. Twenty primers, selected on the basis of their discriminating potential, generated a total of 157 bands, of which 140 were polymorphic. The dendrograms constructed by the two approaches were largely similar in both the clustering position and divergence of varietal groups. The least distance was observed between Yuvarlak Cekirdeksiz and Superior Seedless. The clustering position of cultivars throughout the dendrograms was basically related to the genetic distances and main uses, as well as to geographic origins.

Admixture analysis and stocking impact assessment in brown trout (Salmo trutta), estimated with incomplete baseline data

2001 ◽  
Vol 58 (9) ◽  
pp. 1853-1860 ◽  
Author(s):  
Michael M Hansen ◽  
Einar E Nielsen ◽  
Dorte Bekkevold ◽  
Karen-Lise D Mensberg
Keyword(s):  
Brown Trout ◽  
Salmo Trutta ◽  
Population Level ◽  
Genetic Distances ◽  
Scaling Analysis ◽  
Genetic Contribution ◽  
Multidimensional Scaling Analysis ◽  
Genetic Impact ◽  
Brown Trout Salmo Trutta ◽  
The Mean

Studies of genetic interactions between wild and domesticated fish are often hampered by unavailability of samples from wild populations prior to population admixture. We assessed the utility of a new Bayesian method, which can estimate individual admixture coefficients even with data missing from the populations contributing to admixture. We applied the method to analyse the genetic contribution of domesticated brown trout (Salmo trutta) in samples of anadromous trout from two stocked populations with no genetic data available before stocking. Further, we estimated population level admixture proportions by the mean of individual admixture coefficients. This method proved more informative than a multidimensional scaling analysis of individual-based genetic distances and assignment tests. The results showed almost complete absence of stocked, domesticated trout in samples of trout from the rivers. Consequently, stocking had little effect on improving fisheries. In one population, the genetic contribution by domesticated trout was small, whereas in the other population, some genetic impact was suggested. Admixture in this sample of anadromous trout despite absence of stocked domesticated trout could be because of introgression by domesticated trout adopting a resident life history.

scholarly journals An Attenuated Strain of Enterovirus 71 Belonging to Genotype A Showed a Broad Spectrum of Antigenicity with Attenuated Neurovirulence in Cynomolgus Monkeys

2007 ◽  
Vol 81 (17) ◽  
pp. 9386-9395 ◽  
Author(s):  
Minetaro Arita ◽  
Noriyo Nagata ◽  
Naoko Iwata ◽  
Yasushi Ami ◽  
Yuriko Suzaki ◽  
...  
Keyword(s):  
Broad Spectrum ◽  
Tissue Specificity ◽  
Virulent Strain ◽  
Enterovirus 71 ◽  
Infection Model ◽  
Intravenous Route ◽  
Lethal Challenge ◽  
Neutralization Activity ◽  
Cynomolgus Monkeys ◽  
Genotype A

ABSTRACT Enterovirus 71 (EV71) is a causative agent of hand, foot, and mouth disease and is also sometimes associated with serious neurological disorders. In this study, we characterized the antigenicity and tissue specificity of an attenuated strain of EV71 [EV71(S1-3′)], which belongs to genotype A, in a monkey infection model. Three cynomolgus monkeys were inoculated with EV71(S1-3′), followed by lethal challenge with the parental virulent strain EV71(BrCr-TR) via an intravenous route on day 45 postinoculation of EV71(S1-3′). Monkeys inoculated with EV71(S1-3′) showed a mild neurological symptom (tremor) but survived lethal challenge by virulent EV71(BrCr-TR) without exacerbation of the symptom. The immunized monkey sera showed a broad spectrum of neutralizing activity against different genotypes of EV71, including genotypes A, B1, B4, C2, and C4. For the strains examined, the sera showed the highest neutralization activity against the homotype (genotype A) and the lowest neutralization activity against genotype C2. The order of decreasing neutralization activity of sera was as follows: A > B1 > C4 > B4 > C2. To examine the tissue specificity of EV71(S1-3′), two monkeys were intravenously inoculated with EV71(S1-3′), followed by examination of virus distribution in the central nervous system (CNS) and extraneural tissues. In the CNS, EV71(S1-3′) was isolated only from the spinal cord. These results indicate that EV71(S1-3′) acts as an effective antigen, although this attenuated strain was still neurotropic when inoculated via the intravenous route.

scholarly journals Genetic Diversity and Variability in Endangered Pantesco and Two Other Sicilian Donkey Breeds Assessed by Microsatellite Markers

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Salvatore Bordonaro ◽  
Anna Maria Guastella ◽  
Andrea Criscione ◽  
Antonio Zuccaro ◽  
Donata Marletta
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Genetic Information ◽  
Gene Diversity ◽  
Genetic Distances ◽  
Conservation Strategies ◽  
Population Structure Analysis ◽  
The Mean ◽  
Differentiation Index

The genetic variability of Pantesco and other two Sicilian autochthonous donkey breeds (Ragusano and Grigio Siciliano) was assessed using a set of 14 microsatellites. The main goals were to describe the current differentiation among the breeds and to provide genetic information useful to safeguard the Pantesco breed as well as to manage Ragusano and Grigio Siciliano. In the whole sample, that included 108 donkeys representative of the three populations, a total of 85 alleles were detected. The mean number of alleles was lower in Pantesco (3.7), than in Grigio Siciliano and Ragusano (4.4 and 5.9, resp.). The three breeds showed a quite low level of gene diversity (He) ranging from 0.471 in Pantesco to 0.589 in Grigio. The overall genetic differentiation index (Fst) was quite high; more than 10% of the diversity was found among breeds. Reynolds’ () genetic distances, correspondence, and population structure analysis reproduced the same picture, revealing that, (a) Pantesco breed is the most differentiated in the context of the Sicilian indigenous breeds, (b) within Ragusano breed, two well-defined subgroups were observed. This information is worth of further investigation in order to provide suitable data for conservation strategies.

First record of Pampus minor (Actinopterygii: Perciformes: Stromateidae) from the coastal waters of Wenzhou, China

2020 ◽  
Vol 33 ◽  
pp. 5
Author(s):  
Cheng Liu ◽  
Zhijin Yang ◽  
Pan Liu ◽  
Shen Ye ◽  
Fozia Khan Siyal ◽  
...  
Keyword(s):  
Coastal Waters ◽  
First Record ◽  
Genetic Distances ◽  
Valid Species ◽  
Cytochrome Oxidase Subunit ◽  
Morphometric Measurements ◽  
Meristic Counts ◽  
Commercial Species ◽  
The Mean ◽  
Cytochrome Oxidase Subunit 1

Pampus fishes (Perciformes: Stromateidae) are important commercial species and include six valid species in China. The southern lesser pomfret (Pampus minor Liu and Li, 1998) is a species of Pampus for which knowledge is incomplete. This report confirms the occurrence of P. minor in the coastal waters of Wenzhou, China, by analyzing five specimens of P. minor obtained in Wenzhou in March 2019. Morphometric measurements and meristic counts were performed. The diagnostic morphological features of these species were consistent with those of the neotype specimen of P. minor and sufficient for separating the examined specimens from other Pampus species. This study was based on the Cytochrome Oxidase Subunit 1 (CO1) gene, which was sequenced for the purpose of identification. The genetic distances between P. minor and other Pampus species ranged from 13.4% to 15.5%, and the mean genetic distance within the P. minor group was 0.2%. Given that P. minor has not been reported in this region, our findings represent the first record from the coastal waters of Wenzhou and extend the distribution range of this species to the central and northern East China Sea. The reason for the observed northward migration of some P. minor individuals from their northernmost recorded habitat (Taiwan Strait) might be global warming. The collection of additional specimens is needed to further study the geographic limits of P. minor and its presumed northern expansion.

A partial cpDNA trnL sequence from the extinct legume Streblorrhiza speciosa confirms its placement in the tribe Coluteae (Fabaceae)

Phytotaxa ◽  
2018 ◽  
Vol 374 (1) ◽  
pp. 87
Author(s):  
PETER B. HEENAN ◽  
JAMIE R. WOOD ◽  
THERESA L. COLE
Keyword(s):  
Phylogenetic Analysis ◽  
New Zealand ◽  
Pacific Ocean ◽  
Genetic Distances ◽  
Morphological Features ◽  
Western Pacific ◽  
Herbarium Specimens ◽  
Western Pacific Ocean ◽  
Base Pairs ◽  
Bayesian Phylogenetic Analysis

We report a partial cpDNA trnL sequence of 203 base pairs from the extinct legume Streblorrhiza speciosa that was obtained from herbarium specimens collected from Phillip Island, south-western Pacific Ocean, in 1836. Bayesian phylogenetic analysis of the trnL sequence of S. speciosa and those of other Fabaceae species placed S. speciosa as a member of the tribe Coluteae, along with the Australian and New Zealand genera Carmichaelia, Clianthus, Montigena and Swainsona. Smaller genetic distances and shared morphological features indicate stronger links within this group may exist between S. speciosa and Carmichaelia.

scholarly journals Intra-line and inter-line genetic diversity in sire lines of the Old Kladruber horse based on microsatellite analysis of DNA

2011 ◽  
Vol 56 (No. 4) ◽  
pp. 163-175 ◽  
Author(s):  
L. Vostrý ◽  
O. Kracíková ◽  
B. Hofmanová ◽  
V. Czerneková ◽  
T. Kott ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Analysis ◽  
Genetic Difference ◽  
Principal Component ◽  
Genetic Distances ◽  
Mean Value ◽  
Pedigree Information ◽  
Mean Values ◽  
The Mean ◽  
Coefficient Of Relationship

The Old Kladruber horse is the oldest original Czech horse breed &ndash; gene resource, with pedigree records spanning three centuries. Because the population is closed, there is a concern about the loss of genetic variation. The genetic diversity within and amongst sire lines was evaluated using microsatellite markers and based on pedigree information. The DNA analysis, covering 16 microsatellite loci, revealed that the genetic diversity (observed heterozygosity = 0.637, genetic diversity = 0.678 and the mean number of alleles = 8.25) for the Old Kladruber horse is consistent with other populations of horses. Inter-line genetic difference in sire lines reached the mean value (the F<sub>ST</sub> values ranged from 0.020 to 0.017). Differences amongst the sire lines were identified using genetic distances and principal component analysis. One gene cluster comprised black variation sire lines, while the second cluster included the sire lines of the grey variation. In the subjects monitored, the average inbreeding coefficient of 0.076 was estimated on the basis of pedigree information. The highest mean values of the coefficient of relationship were estimated within the colour variations. When comparing the genetic distance and the average coefficient of relationship, differences were found out. These results are useful for the development of breeding strategies which consider classical horse breeding as well as recent achievements of population and conservation genetics.

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