Sister-Scanning: a Monte Carlo procedure for assessing signals
  in recombinant sequences

Gibbs, Mark J.; Armstrong, J. Scott; Gibbs, Adrian

doi:10.1093/bioinformatics/16.7.573

Cited by 978 publications

(669 citation statements)

References 22 publications

Supporting

Mentioning

661

Contrasting

Unclassified

Order By: Relevance

“…A total of seven methods were applied, including GENECONV,46 RDP,47 Chimaera,48 SiScan,49 3Seq,50 MaxChi,51 LARD 52. Recombination had to be confirmed by at least four of the seven methods with p value cut‐off of 0.05.…”

Section: Methodsmentioning

confidence: 99%

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

et al. 2018

View full text Add to dashboard Cite

Porcine circovirus 3 (PCV3) is a novel virus associated with acute PDNS (porcine dermatitis and nephropathy syndrome)‐like clinical signs identified by metagenomic sequencing from swine. Its high occurrence may pose a potential threat to the swine industry worldwide. The processes resulting in the emergence and spread of PCV3 remain poorly understood. Herein, the possible origin, genotypes, and evolutionary dynamics of PCV3 based on available genomic sequences are determined. The closest ancestor of PCV3 is found to be within the clade 1 bat CVs. Using different phylogenetic methods, two major genotypes are identified, PCV3a and PCV3b. It is found that the effective population size of PCV3 increased rapidly during late 2013 to early 2014 and this is associated with the diversification of PCV3a and PCV3b. A relatively high effective reproductive number (Re) value and higher evolutionary rate were found compared to other single‐stranded DNA viruses, and positive selection on codons 122 and 320 (24 of ORF2) is identified. It is hypothesized that this, together with the prediction of a potential change of an antigenic epitope at position 320, might have allowed PCV3 to escape from the host immune response. Overall, this study has important implications for understanding the ongoing PCV3 cases worldwide and will guide future efforts to develop effective preventive and control measures.

show abstract

Section: Methodsmentioning

confidence: 99%

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Comment citer ce document : Desbiez, C. (Auteur de correspondance), Wipf-Scheibel, C., Millot, P., Verdin, E., Dafalla, G., (Holmes, Worobey, and Rambaut 1999), and SISCAN (Gibbs, Armstrong, and Gibbs 2000). Only recombination signals detected by more than four methods were used to determine approximate breakpoint positions.…”

Section: Version Postprintmentioning

confidence: 99%

New species in the papaya ringspot virus cluster: Insights into the evolution of the PRSV lineage

Desbiez¹,

Wipf-Scheibel²,

Millot³

et al. 2017

Virus Research

View full text Add to dashboard Cite

Please cite this article as: Desbiez, C., Wipf-Scheibel, C., Millot, P., Verdin, E., Dafalla, G., Lecoq, H., New species in the papaya ringspot virus cluster: insights into the evolution of the PRSV lineage.Virus Research http://dx.doi.org/10. 1016/j.virusres.2017.06.022 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. SuWMV appeared 10 times more frequent than WMVBV in that country (14.6% vs. 1.5% of the samples tested). The geographic structure and molecular diversity patterns of the putative and acknowledged species suggest that the PRSV-like cluster originated in the Old World about 3600 years ago, with an important diversification in Africa.

show abstract

“…The frequency with which V D exceeds V e can be used to provide an estimate as to the significance of the difference. Further evidence of recombination was sought using six additional recombination detection tests, implemented under the RDP package version 2.08: RDP (Martin & Rybicki, 2000) detects recombined fragments by statistical analysis of the composition of aligned sequence triplets; GENECONV (Padidam et al, 1999) seeks aligned segments for which a pair of sequences are sufficiently similar to be suggestive of recombination; Bootscan (Salminen et al, 1995) detects recombination breakpoint using bootstrapping of phylogenetic trees generated from sequence fragments; MaxChi (Smith, 1992) compares the composition of windows within pairs of aligned sequences in order to identify recombination breakpoints; Chimaera (Posada & Crandall, 2001) is a variant of the MaxChi method; and SiScan (Gibbs et al, 2000) is a method for measuring variations in the relatedness of aligned nucleotide sequences; the significance of detected variations is tested in the program using Monte Carlo randomization procedures.The non-synonymous to synonymous nucleotide substitution ratio (d N /d S ) of each SBT locus fragment was estimated using the modified Nei and Gojobori method (Nei & Gojobori, 1986) using START2; estimates of positive/purifying selection for individual amino acid residues at each locus were carried out using Selecton (Stern et al, Phylogenetic analysis. Genealogies were created using ClonalFrame (Didelot & Falush, 2007).…”

mentioning

confidence: 99%

Clonal population structure of Legionella pneumophila inferred from allelic profiling

Edwards

Fry²,

Harrison³

2008

Microbiology

View full text Add to dashboard Cite

The population structure of Legionella pneumophila was investigated by analysing nucleotide sequences from six loci (flaA, pilE, asd, mip, mompS and proA) of 335 globally distributed isolates from clinical and environmental sources over a 29-year period (1977-2006). Data were obtained from unrelated isolates from Europe (n5270), Japan (n531), Canada (n57), the USA (n524) and Australia (n51). The country of origin of two strains was unknown. Analysis of these isolates indicated significant linkage disequilibrium between the six loci. Application of six sequence-based recombination detection tests did not reveal evidence of recombination, but estimates of rates of recombination and mutation made by a seventh test suggested that recombination could have occurred at a rate similar to, but probably lower than, that of mutation.Genealogies inferred under models with and without recombination were congruent with each other, providing no definitive evidence regarding recombination, and were in agreement with sequence clusters identified by graph methods. Further evidence supporting the distinct nature of two of the three subspecies of L. pneumophila, subsp. fraseri and subsp. pascullei, was also found. The ratios of non-synonymous to synonymous nucleotide polymorphisms for each of the allele sets were examined and revealed that the putative virulence loci mompS and pilE are under diversifying pressure, while the allelic regions of three other loci linked to virulence (flaA, proA and mip) do not appear to be. INTRODUCTIONFollowing the recognition of the aetiological agent of Legionnaires' disease in 1977(McDade et al., 1977, phenotypic and genotypic analyses of Legionella pneumophila have mainly focused on the short-term epidemiology of the bacterium. In this scenario, the aim has been to demonstrate potential environmental sources of infection, thereby allowing timely intervention, in order to prevent further infection. Many such methods have been developed and applied with the purpose of discriminating between epidemiologically unrelated strains of L. pneumophila, particularly those belonging to serogroup (sg) 1 (Edelstein et al., 1986;Fry et al., 1999; Saunders et al., 1990;Schoonmaker et al., 1992;van Ketel et al., 1984).The utility of the multi-locus sequence typing (MLST) approach, in which sequences from five to 10 housekeeping genes are determined, in the identification of major bacterial lineages associated with invasive disease was first described in 1998 (Enright & Spratt, 1998;Maiden et al., 1998). Since then, this robust and portable technique (or variations of it) has been applied to the study of genetic diversity and clonal expansion, and to the long-term epidemiological analysis of microbial populations (see http://pubmlst.org/ and http://www.mlst.net/) (Giske et al., 2006;Paraskevopoulos et al., 2006;Vassileva et al., 2006).Recently, a similar approach, termed sequence-based typing (SBT), developed by members of the European Working Group for Legionella Infections (EWGLI), was applied to the epidemiolo...

show abstract

Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences

Cited by 978 publications

References 22 publications

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

New species in the papaya ringspot virus cluster: Insights into the evolution of the PRSV lineage

Clonal population structure of Legionella pneumophila inferred from allelic profiling

Contact Info

Product

Resources

About