PhyloSTemS: a new graphical tool to investigate temporal signal of heterochronous sequences at various evolutionary scales

Doizy, Anna; Prin, Amaury; Cornu, Guillaume; Chiroleu, Frédéric; Rieux, Adrien

doi:10.22541/au.159050344.45788558

Cited by 6 publications

(3 citation statements)

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“…We tested for the presence of a significant temporal signal over the recombination filtered core phylogeny, subset to include only those HSV-1 genomes with associated collection dates, using PhyloStems (74) and BactDating (75). Where a range in sampling date was provided in the associated metadata, we set the date of sampling to the midpoint.…”

Section: Phylogenetic Datingmentioning

confidence: 99%

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

et al. 2022

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Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, infects a majority of adults globally. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups has suggested the virus codiverged with human migrations out of Africa, although a much younger origin has also been proposed. We present three full ancient European HSV-1 genomes and one partial genome, dating from the 3rd to 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. Considering a dataset of modern and ancient genomes, we apply phylogenetic methods to estimate the age of sampled modern Eurasian HSV-1 diversity to 4.68 (3.87 to 5.65) ka. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60 to 6.12) ka, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations.

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Section: Phylogenetic Datingmentioning

confidence: 99%

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

et al. 2022

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“…In order to examine the degree of temporal signal in the CP gene dataset, we first used an exploratory linear regression approach (Duchêne et al, 2015; Murray et al, 2016). Based on ML phylogenetic tree reconstructed from the CP gene dataset, the temporal signal of this sequence dataset was visualized and tested in PhyloStemS (Doizy et al, 2020) to regress phylogenetic root-to-tip distances against sampling date using the root that minimized the residual mean squares. In addition, the significance of the temporal signal was evaluated by a date-randomization test.…”

Section: Methodsmentioning

confidence: 99%

Dynamics of the rice yellow mottle disease in western Burkina Faso: epidemic monitoring, spatio-temporal variation of viral diversity and pathogenicity in a disease hotspot

Billard¹,

Barro²,

Sérémé³

et al. 2023

Preprint

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The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology and phylogeography, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at local scale remain scarce, in spite of potential implications for crop protection. Here we describe a five-years monitoring of RYMV prevalence in six sites from western Burkina Faso. This study confirmed one irrigated site as a disease hotspot, and found two rainfed lowland sites with occasional high prevalence levels. Within studied field, a pattern of disease aggregation was evidenced at a five-meter distance, as expected for a mechanically transmitted virus. Next, we monitored RYMV genetic diversity in the irrigated disease hotspot site, revealing a high viral diversity, with the current coexistence of various distinct genetic groups at the site-scale (irrigated perimeter of ca. 520 ha), and also within various specific fields (25 meters side). One genetic lineage, named S1bzn, is the most recently introduced group and increased in frequency over the studied period. Its genome results from a recombination between two other lineages. Finally, experimental work evidenced no differences between three rice varieties cultivated in Burkina Faso in terms of resistance level, and no statistical effect of RYMV genetic group on symptom expression and viral load. We found however, that infection outcome depended on the specific RYMV isolate, with various isolates from the lineage S1bzn found to be particularly aggressive, including one accumulating at highest level. Overall, this study documents a case of high viral prevalence and high viral diversity, with the co-occurrence of divergent genetic lineages at small geographic scale. A recently introduced lineage, that includes viral isolates with high symptoms and accumulation in controlled conditions, could be recently rising though natural selection. Following up the monitoring of RYMV genetic and pathogenic diversity in the area is required to confirm this trend and further understand the factors driving the maintenance of viral diversity at local scale.

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“…The tree was instead rooted with TempEst(52) so as to maximise the temporal signal. Measurable temporal evolution over the phylogeny was inspected using Phylo STemS (53). Initially, testing an unfiltered alignment, no statistically significant temporal regression was observed at the base of any of the four major clades likely due to extensive recombination in the history of HAdV-C (Fig.…”

Section: Phylogenetic Reconstruction and Datingmentioning

confidence: 99%

31,600-year-old human virus genomes support a Pleistocene origin for common childhood infections

Nielsen

et al. 2021

Preprint

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The origins of viral pathogens and the age of their association with humans remains largely elusive. To date, there is no direct evidence about the diversity of viral infections in early modern humans pre-dating the Holocene. We recovered two near-complete genomes (5.2X and 0.7X) of human adenovirus C (HAdV-C), as well as low-coverage genomes from four distinct species of human herpesvirus obtained from two 31,630-year-old milk teeth excavated at Yana, in northeastern Siberia. Phylogenetic analysis of the two HAdV-C genomes suggests an evolutionary origin around 700,000 years ago consistent with a common evolutionary history with hominin hosts. Our findings push back the earliest direct molecular evidence for human viral infections by ~25,000 years, and demonstrate that viral species causing common childhood viral infections today have been in circulation in humans at least since the Pleistocene.

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PhyloSTemS: a new graphical tool to investigate temporal signal of heterochronous sequences at various evolutionary scales

Cited by 6 publications

References 0 publications

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Dynamics of the rice yellow mottle disease in western Burkina Faso: epidemic monitoring, spatio-temporal variation of viral diversity and pathogenicity in a disease hotspot

31,600-year-old human virus genomes support a Pleistocene origin for common childhood infections

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