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      Time scale evolution of avipoxviruses

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          Highlights

          • Avipoxviruses evolution rate: 2–8 × 10 −5  substitution/site/year.

          • Mean time of divergence from common ancestor: 10,000–30,000 years.

          • Purifying selection in avipoxviruses P4b, cnpv186 and DNA polymerase genes.

          Abstract

          Avipoxviruses are divided into three clades: canarypox-like viruses, fowlpox-like viruses, and psittacinepox-like viruses. Several molecular clock and demographic models available in the BEAST package were compared on three avipoxvirus genes (P4b, cnpv186 and DNA polymerase genes), which enabled to determine that avipoxviruses evolved at a rate of 2–8 × 10 −5 substitution/site/year, in the range of poxviruses previously reported evolution rates. In addition, the date of mean time of divergence of avipoxviruses from a common ancestor was extrapolated to be about 10,000–30,000 years ago, at the same period as modern poxvirus species. Our findings will facilitate epidemiological investigations on avipoxviruses’ spread, origin and circulation.

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          Most cited references19

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          Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses

          Abstract Double-stranded (ds) DNA viruses are often described as evolving through long-term codivergent associations with their hosts, a pattern that is expected to be associated with low rates of nucleotide substitution. However, the hypothesis of codivergence between dsDNA viruses and their hosts has rarely been rigorously tested, even though the vast majority of nucleotide substitution rate estimates for dsDNA viruses are based upon this assumption. It is therefore important to estimate the evolutionary rates of dsDNA viruses independent of the assumption of host-virus codivergence. Here, we explore the use of temporally structured sequence data within a Bayesian framework to estimate the evolutionary rates for seven human dsDNA viruses, including variola virus (VARV) (the causative agent of smallpox) and herpes simplex virus-1. Our analyses reveal that although the VARV genome is likely to evolve at a rate of approximately 1 × 10−5 substitutions/site/year and hence approaching that of many RNA viruses, the evolutionary rates of many other dsDNA viruses remain problematic to estimate. Synthetic data sets were constructed to inform our interpretation of the substitution rates estimated for these dsDNA viruses and the analysis of these demonstrated that given a sequence data set of appropriate length and sampling depth, it is possible to use time-structured analyses to estimate the substitution rates of many dsDNA viruses independently from the assumption of host-virus codivergence. Finally, the discovery that some dsDNA viruses may evolve at rates approaching those of RNA viruses has important implications for our understanding of the long-term evolutionary history and emergence potential of this major group of viruses.
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            Evidence for time dependency of molecular rate estimates.

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              Extensive gene gain associated with adaptive evolution of poxviruses.

              Previous studies of genome evolution usually have involved one or two genomes and have thus been limited in their ability to detect the direction and rate of evolutionary change. Here, we use complete genome data from 20 poxvirus genomes to build a robust phylogeny of the Poxviridae and to study patterns of genome evolution. We show that, although there has been little gene order evolution, there are substantial differences between poxviruses in terms of genome content. Furthermore, we show that the rate of gene acquisition is not constant over time and that it has increased in the orthopox lineage (which includes smallpox and vaccinia). We also tested for positive selection on 204 groups of genes and show that a disproportionately high proportion of genes in the orthopox clade are under positive selection. The association of an increased rate of gene gain and positive selection is indicative of adaptive genome evolution. Many of the genes involved in these processes are likely to be associated with host-parasite coevolution.
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                Author and article information

                Contributors
                Journal
                Infect Genet Evol
                Infect. Genet. Evol
                Infection, Genetics and Evolution
                The Authors. Published by Elsevier B.V.
                1567-1348
                1567-7257
                29 July 2015
                October 2015
                29 July 2015
                : 35
                : 75-81
                Affiliations
                [a ]RENECO Wildlife Consultants LLC, Abu Dhabi, United Arab Emirates
                [b ]Université de Toulouse, INP, ENVT, UMR1225, IHAP, F-31076 Toulouse, France
                [c ]INRA, UMR1225, IHAP, F-31076 Toulouse, France
                Author notes
                [* ]Corresponding author at: Université de Toulouse, INP, ENVT, UMR1225, IHAP, F-31076 Toulouse, France. g.leloch@ 123456hotmail.fr
                Article
                S1567-1348(15)00308-1
                10.1016/j.meegid.2015.07.031
                7106339
                26231721
                17ac93fb-95eb-4bcb-9e46-e29bd029e8e7
                © 2015 The Authors

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

                History
                : 25 March 2015
                : 16 July 2015
                : 24 July 2015
                Categories
                Article

                Genetics
                avipoxvirus,evolution,molecular clock,dna virus
                Genetics
                avipoxvirus, evolution, molecular clock, dna virus

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