The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data

Duchêne, Sebastián; Duchêne, David A.; Holmes, Edward C.; Ho, Simon Y. W.

doi:10.1093/molbev/msv056

Cited by 174 publications

(202 citation statements)

References 49 publications

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“…An uncorrelated exponential relaxed-clock model 28 provided a better fit than the strict-clock model, indicating the presence of rate variation among lineages. All data sets passed date-randomization tests for temporal structure 8–10, 29, 30 .…”

Section: Resultsmentioning

confidence: 99%

The Timescale of Emergence and Spread of Turnip Mosaic Potyvirus

Yasaka

Fukagawa

Ikematsu

et al. 2017

Sci Rep

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Plant viruses have important global impacts on crops, and identifying their centre and date of emergence is important for planning control measures. Turnip mosaic virus (TuMV) is a member of the genus Potyvirus in the family Potyviridae and is a major worldwide pathogen of brassica crops. For two decades, we have collected TuMV isolates, mostly from brassicas, in Turkey and neighbouring countries. This region is thought to be the centre of emergence of this virus. We determined the genomic sequences of 179 of these isolates and used these to estimate the timescale of the spread of this virus. Our Bayesian coalescent analyses used synonymous sites from a total of 417 novel and published whole-genome sequences. We conclude that TuMV probably originated from a virus of wild orchids in Germany and, while adapting to wild and domestic brassicas, spread via Southern Europe to Asia Minor no more than 700 years ago. The population of basal-B group TuMVs in Asia Minor is older than all other populations of this virus, including a newly discovered population in Iran. The timescale of the spread of TuMV correlates well with the establishment of agriculture in these countries.

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Section: Resultsmentioning

confidence: 99%

The Timescale of Emergence and Spread of Turnip Mosaic Potyvirus

Yasaka

Fukagawa

Ikematsu

et al. 2017

Sci Rep

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“…These provided the TMRCAs, and other dates were obtained from the ‘maximum clade credibility tree’, namely the tree that was commonest among those observed. The adequacy of the temporal signal in our data was also checked by using ten independently date-randomized replicates in both the least squared dating (LSD) and BEAST analyses (Ramsden, Holmes and Charleston, 2009; Duchêne 2015). …”

Section: Methods and Data Sourcesmentioning

confidence: 99%

The phylogenetics of the global population of potato virus Y and its necrogenic recombinants

et al. 2017

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Potato virus Y (PVY) is a major pathogen of potatoes and other solanaceous crops worldwide. It is most closely related to potyviruses first or only found in the Americas, and it almost certainly originated in the Andes, where its hosts were domesticated. We have inferred the phylogeny of the published genomic sequences of 240 PVY isolates collected since 1938 worldwide, but not the Andes. All fall into five groupings, which mostly, but not exclusively, correspond with groupings already devised using biological and taxonomic data. Only 42 percent of the sequences are not recombinant, and all these fall into one or other of three phylogroups; the previously named C (common), O (ordinary), and N (necrotic) groups. There are also two other distinct groups of isolates all of which are recombinant; the R-1 isolates have N (5′ terminal minor) and O (major) parents, and the R-2 isolates have R-1 (major) and N (3′ terminal minor) parents. Many isolates also have additional minor intra- and inter-group recombinant genomic regions. The complex interrelationships between the genomes were resolved by progressively identifying and removing recombinants using partitioned sequences of synonymous codons. Least squared dating and BEAST analyses of two datasets of gene sequences from non-recombinant heterochronously-sampled isolates (seventy-three non-recombinant major ORFs and 166 partial ORFs) found the 95% confidence intervals of the TMRCA estimates overlap around 1,000 CE (Common Era; AD). We attempted to identify the most accurate datings by comparing the estimated phylogenetic dates with historical events in the worldwide adoption of potato and other PVY hosts as crops, but found that more evidence from gene sequences of non-potato isolates, especially from South America, was required.

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“…Each BEAST analysis was run for 50,000,000 to 100,000,000 generations until convergence was achieved, and at least two independent runs were performed for each set of priors. A maximum clade credibility (MCC) tree with mean node (73) and the BEAST analysis repeated. This date randomization test was repeated nine times and compared to the BEAST results with the correctly dated sequences described above.…”

Section: Methodsmentioning

confidence: 99%

Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives

Mahar

Nicholson

Eden

et al. 2016

J Virol

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Two closely related caliciviruses cocirculate in Australia: rabbit hemorrhagic disease virus (RHDV) and rabbit calicivirus Australia 1 (RCV-A1). RCV-A1 causes benign enteric infections in the European rabbit (Oryctolagus cuniculus) in Australia and New Zealand, while its close relative RHDV causes a highly pathogenic infection of the liver in the same host. The comparison of these viruses provides important information on the nature and trajectory of virulence evolution, particularly as highly virulent strains of RHDV may have evolved from nonpathogenic ancestors such as RCV-A1. To determine the evolution of RCV-A1 we sequenced the full-length genomes of 44 RCV-A1 samples isolated from healthy rabbits and compared key evolutionary parameters to those of its virulent relative, RHDV. Despite their marked differences in pathogenicity and tissue tropism, RCV-A1 and RHDV have evolved in a very similar manner. Both viruses have evolved at broadly similar rates, suggesting that their dynamics are largely shaped by high background mutation rates, and both exhibit occasional recombination and an evolutionary environment dominated by purifying selection. In addition, our comparative analysis revealed that there have been multiple changes in both virulence and tissue tropism in the evolutionary history of these and related viruses. Finally, these new genomic data suggest that either RCV-A1 was introduced into Australia after the introduction of myxoma virus as a biocontrol agent in 1950 or there was drastic reduction of the rabbit population, and hence of RCV-A1 genetic diversity, perhaps coincident with the emergence of myxoma virus. IMPORTANCEThe comparison of closely related viruses that differ profoundly in propensity to cause disease in their hosts offers a powerful opportunity to reveal the causes of changes in virulence and to study how such changes alter the evolutionary dynamics of these pathogens. Here we describe such a novel comparison involving two closely related RNA viruses that cocirculate in Australia, the highly virulent rabbit hemorrhagic disease virus (RHDV) and the nonpathogenic rabbit calicivirus Australia 1 (RCV-A1). Both viruses infect the European rabbit, but they differ in virulence, tissue tropism, and mechanisms of transmission. Surprisingly, and despite these fundamental differences, RCV-A1 and RHDV have evolved at very similar (high) rates and with strong purifying selection. Furthermore, candidate key mutations were identified that may play a role in virulence and/or tissue tropism and therefore warrant further investigation. R evealing the factors that determine the evolution of virulence in viruses and identifying how changes in virulence might impact viral evolutionary dynamics are key queries in the study of infectious disease evolution. Although there is a large body of work on revealing the relationship between virulence and transmissibility, most studies of virulence evolution involve the retrospective analysis of single viruses (1-4). However, the comparison of closely related...

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The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data

Cited by 174 publications

References 49 publications

The Timescale of Emergence and Spread of Turnip Mosaic Potyvirus

The Timescale of Emergence and Spread of Turnip Mosaic Potyvirus

The phylogenetics of the global population of potato virus Y and its necrogenic recombinants

Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives

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