The Prehistory of Potyviruses: Their Initial Radiation Was during the Dawn of Agriculture

Abstract

BackgroundPotyviruses are found world wide, are spread by probing aphids and cause considerable crop damage. Potyvirus is one of the two largest plant virus genera and contains about 15% of all named plant virus species. When and why did the potyviruses become so numerous? Here we answer the first question and discuss the other.Methods and FindingsWe have inferred the phylogenies of the partial coat protein gene sequences of about 50 potyviruses, and studied in detail the phylogenies of some using various methods and evolutionary models. Their phylogenies have been calibrated using historical isolation and outbreak events: the plum pox virus epidemic which swept through Europe in the 20th century, incursions of potyviruses into Australia after agriculture was established by European colonists, the likely transport of cowpea aphid-borne mosaic virus in cowpea seed from Africa to the Americas with the 16th century slave trade and the similar transport of papaya ringspot virus from India to the Americas.Conclusions/SignificanceOur studies indicate that the partial coat protein genes of potyviruses have an evolutionary rate of about 1.15×10−4 nucleotide substitutions/site/year, and the initial radiation of the potyviruses occurred only about 6,600 years ago, and hence coincided with the dawn of agriculture. We discuss the ways in which agriculture may have triggered the prehistoric emergence of potyviruses and fostered their speciation.

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

“…In the coreCP region, patristic distances between the members of the same species reached 0.2 for ZTMV, ZYFV and MWMV, and 0.17 for PRSV as already estimated by Gibbs et al (Gibbs et al, 2008a). The average divergence between the PRSV cluster and the other potyviruses was 0.9.…”

“…The coherently-evolving region of the CP sequences (Gibbs et al, 2008a), i.e. the core and C-terminal regions minus the repetitive N domain, of 45 isolates in the PRSV cluster were aligned with ClustalW included in MEGA6.…”

“…These include 36 virus species and isolates in the PRSV cluster, 11 viruses in the bean common mosaic virus (BCMV) cluster (Gibbs et al, 2008b), 26 potyviruses outside these two (Supplementary table S1). Patristic distances were calculated using PATRISTIC v1.0 (Fourment and Gibbs, 2006;Gibbs et al, 2008b), and times of divergence were estimated using a substitution rate of 1.25 nt/site/year (Gibbs et al, 2008a). A Bayesian coalescent framework by a Markov Chain Monte Carlo (MCMC) method was applied to the aligned coreCP dataset using the Bayesian Evolutionary Analysis by Sampling Trees (BEAST v1.8.3) program (http://beast.bio.ed.ac.uk/) (Drummond et al, 2012), with an uncorrelated relaxed clock model.…”

“…Potyvirus star-like phylogeny suggests an initial radiation in the genus that, based on a molecular clock calibration using historical isolation and outbreak events, took place about 6600 years ago, i.e at the dawn of agriculture (Gibbs et al, 2008a). Several "clusters" of closely related species have been defined within the Potyvirus genus with viruses in a cluster sharing 70 to 80% sequence identity in the coat protein coding region (Gibbs et al, 2008b;Romay et al, 2014;Spetz et al, 2003).…”

Analysis of Simple and Imperfect Microsatellites in Ebolavirus Species and Other Genomes of Filoviridae Family

“…The distribution of microsatellite in the viral genome is organism specific rather than host specific. This is supported by the fact that the taxonomy of Filoviridae family shows no comparable congruence with host taxonomy, and species from the same lineage may have quite unrelated hosts (38). Interestingly, each Filoviridae family species possesses at least one cSSR, which might be causing their variation and evolution.…”