GARD: A genetic algorithm for recombination detection
ABSTRACT Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments.
We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection.
Freely available http://www.datamonkey.org/GARD/
Full-textDOI: · Available from: Simon D W Frost, Aug 11, 2015
- SourceAvailable from: Zaharoula Kyriakopoulou
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- "In order to increase the effective sample size (ESS > 200), the analysis was run in duplicate for each dataset, with 50 million chain lengths and sampled every 1000 states. In order to estimate the rate dN/dS and to investigate the selective pressure acting on specific codons in VP1 gene, SLAC, FEL (Kosakovsky Pond and Frost, 2005), FUBAR (Murrell et al., 2013) and IFEL (Pond et al., 2006) methods were used, provided from Datamonkey website. Almost the complete genome sequence of strain EIS6B (from 1 to 7365 nt) has been deposited to GenBank under the accession number KM024043. "
ABSTRACT: Echovirus 3 (E3) serotype has been related with several neurologic diseases, although it constitutes one of the rarely isolated serotypes, with no report of epidemics in Europe. The aim of the present study was to provide insights into the molecular epidemiology and evolution of this enterovirus serotype, while an E3 strain was isolated from sewage in Greece, four years after the initial isolation of the only reported E3 strain in the same geographical region. Phylogenetic analysis of the complete VP1 genomic region of that E3 strain and of those available in GenBank suggested three main genogroups that were further subdivided into seven subgenogroups. Further evolutionary analysis suggested that VP1 genomic region of E3 was dominated by purifying selection, as the vast majority of genetic diversity presumably occurred through synonymous nucleotide substitutions and the substitution rate for complete and partial VP1 sequences was calculated to be 8.13 x 10(-3)and 7.72 x 10(-3) substitutions/ site/ year respectively. The partial VP1 sequence analysis revealed the composite epidemiology of this serotype, as the strains of the three genogroups presented different epidemiological characteristics. Copyright © 2015. Published by Elsevier B.V.Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 03/2015; 32. DOI:10.1016/j.meegid.2015.03.008 · 3.26 Impact Factor
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- "There were too few sequences available for CpYDV, CpRLV and CpYV for us to perform selection analyses on these species. Accounting for recombination breakpoints identified with the GARD method (Kosakovsky Pond et al., 2006) these "
ABSTRACT: In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 147 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species. Copyright © 2014 Elsevier B.V. All rights reserved.Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 01/2015; 29:203-2015. DOI:10.1016/j.meegid.2014.11.024 · 3.26 Impact Factor
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- "Sergei et al., 2005b). As recombination can break the linkage and could be falsely interpreted as adaptive selection significant recombination events were tested by genetic algorithm for recombination detection (GARD; Sergei et al., 2006) implemented in Datamonkey. 2.4. "
ABSTRACT: Mutations in the Plasmodium falciparum multidrug resistance (pfmdr1) gene are known to provide compensatory fitness benefits to the chloroquine (CQ)-resistant malaria parasites and are often associated with specific mutations in the P. falciparum CQ resistant transporter (pfcrt) gene. Prevalence of the specific mutations in these two genes across different malaria endemic regions was mostly studies. However, reports on mutations in the pfmdr1 gene and their genetic associations with mutations in the pfcrt gene in Indian P. falciparum field isolates are scarce. We have sequenced a 560 bp region of pfmdr1 coding sequence in 64 P. falciparum isolates collected from different malaria endemic populations in India. Twenty out of these 64 isolates were laboratory cultured with known in vitro CQ sensitiveness (10 sensitive and 10 resistant). Three low frequency mutations (two non-synonymous and one synonymous) in the pfmdr1 gene were segregating in Indian isolates in addition to the predominant Y86 and Y184 ones, with high haplotype and nucleotide diversity in the field isolates in comparison to the cultured ones. No statistically significant genetic association between the mutations in the pfmdr1 and pfcrt gene could be detected; almost all observed associations were intragenic in nature. The results on the genetic diversity of the pfmdr1 gene were discussed in term of evolutionary perspectives in Indian P. falciparum, with possible future potential of gaining further insights on this gene in view of evolving malaria parasites resistant to artemisinin partner drugs.Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 08/2014; 26(1):213-222. DOI:10.1016/j.meegid.2014.05.033 · 3.26 Impact Factor