Patterns of nucleotide substitutions in influenza A virus genes

Saitou, Naruya

doi:10.1266/jjg.62.439

Cited by 12 publications

(4 citation statements)

References 9 publications

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“…The average numbers of synonymous (s S ) and nonsynonymous (s N ) sites were computed by taking into account the transition/transversion rate ratio for the mutation pattern of H3N2 human influenza A virus, which has been estimated to be 7.5 in large-scale genomic analyses (Saitou, 1987;Suzuki, 2006). The null hypothesis of selective neutrality was tested by Fig.…”

Section: Discussionmentioning

confidence: 99%

Positive selection operates continuously on hemagglutinin during evolution of H3N2 human influenza A virus

Suzuki

2008

Gene

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Section: Discussionmentioning

confidence: 99%

Positive selection operates continuously on hemagglutinin during evolution of H3N2 human influenza A virus

Suzuki

2008

Gene

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“…The phylogeny reconstruction was performed in MEGA 7 [28] using the maximum-likelihood [29] and Neighbour-Joining [30] methods. Clade credibility was assessed using bootstrap tests with 1,000 replicates [31].…”

Section: Methodsmentioning

confidence: 99%

Parasites, pathogens and commensals in the “low-impact” non-native amphipod host Gammarus roeselii

et al. 2017

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BackgroundWhilst vastly understudied, pathogens of non-native species (NNS) are increasingly recognised as important threats to native wildlife. This study builds upon recent recommendations for improved screening for pathogens in NNS by focusing on populations of Gammarus roeselii in Chojna, north-western Poland. At this location, and in other parts of continental Europe, G. roeselii is considered a well-established and relatively ‘low-impact’ invader, with little understanding about its underlying pathogen profile and even less on potential spill-over of these pathogens to native species.ResultsUsing a combination of histological, ultrastructural and phylogenetic approaches, we define a pathogen profile for non-native populations of G. roeselii in Poland. This profile comprised acanthocephalans (Polymorphus minutus Goese, 1782 and Pomphorhynchus sp.), digenean trematodes, commensal rotifers, commensal and parasitic ciliated protists, gregarines, microsporidia, a putative rickettsia-like organism, filamentous bacteria and two viral pathogens, the majority of which are previously unknown to science. To demonstrate potential for such pathogenic risks to be characterised from a taxonomic perspective, one of the pathogens, a novel microsporidian, is described based upon its pathology, developmental cycle and SSU rRNA gene phylogeny. The novel microsporidian Cucumispora roeselii n. sp. displayed closest morphological and phylogenetic similarity to two previously described taxa, Cucumispora dikerogammari (Ovcharenko & Kurandina, 1987), and Cucumispora ornata Bojko, Dunn, Stebbing, Ross, Kerr & Stentiford, 2015.ConclusionsIn addition to our discovery extending the host range for the genus Cucumispora Ovcharenko, Bacela, Wilkinson, Ironside, Rigaud & Wattier, 2010 outside of the amphipod host genus Dikerogammarus Stebbing, we reveal significant potential for the co-transfer of (previously unknown) pathogens alongside this host when invading novel locations. This study highlights the importance of pre-invasion screening of low-impact NNS and, provides a means to document and potentially mitigate the additional risks posed by previously unknown pathogens.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-017-2108-6) contains supplementary material, which is available to authorized users.

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“…The mutation matrices for these schemes are shown in Table 2. 1. Influenza virus gene mutation scheme: A substitution matrix at the third position of codons for human influenza A virus gene was estimated by Saitou (1987).…”

Section: Mutation Schemementioning

confidence: 99%

New methods for estimating the numbers of synonymous and nonsynonymous substitutions

1995

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New methods for estimating the numbers of synonymous and nonsynonymous substitutions per site were developed. The methods are unweighted pathway methods based on Kimura's two-parameter model. Computer simulations were conducted to evaluate the accuracies of the new methods, Nei and Gojobori's (NG) method, Miyata and Yasunaga's (MY) method, Li, Wu, and Luo's (LWL) method, and Pamilo, Bianchi, and Li's (PBL) method. The following results were obtained: (1) The NG, MY, and LWL methods give overestimates of the number of synonymous substitutions and underestimates of the number of nonsynonymous substitutions. The major cause for the biased estimation is that these three methods underestimate the number of synonymous sites and overestimate the number of nonsynonymous sites. (2) The PBL method gives better estimates of the numbers of synonymous and nonsynonymous substitutions than those obtained by the NG, MY, and LWL methods. (3) The new methods also give better estimates of the numbers of synonymous and nonsynonymous substitutions than those obtained by the NG, MY, and LWL methods. In addition, estimates of the numbers of synonymous and nonsynonymous sites obtained by the new methods are reasonably accurate. (4) In some cases, the new methods and the PBL method give biased estimates of substitution numbers. However, from the number of nucleotide substitutions at the third position of codons, we can examine whether estimates obtained by the new methods are good or not, whereas we cannot make an examination of estimates obtained by the PBL method. (5) When there are strong transition/transversion and nucleotide-frequency biases like mitochondrial genes, all of the above methods give biased estimates of substitution numbers. In such cases, Kondo et al.'s method is recommended to be used for estimating the number of synonymous substitutions, although their method cannot estimate the number of nonsynonymous substitutions and is time-consuming. These results, particularly result (1), call for reexaminations of some genes. This is because evolutionary pictures of genes have often been discussed on the basis of results obtained by the NG, MY, and LWL methods, which are favorable for the neutral theory of molecular evolution.

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Patterns of nucleotide substitutions in influenza A virus genes

Cited by 12 publications

References 9 publications

Positive selection operates continuously on hemagglutinin during evolution of H3N2 human influenza A virus

Positive selection operates continuously on hemagglutinin during evolution of H3N2 human influenza A virus

Parasites, pathogens and commensals in the “low-impact” non-native amphipod host Gammarus roeselii

New methods for estimating the numbers of synonymous and nonsynonymous substitutions

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