The Prehistory of Potyviruses: Their Initial Radiation Was during the Dawn of Agriculture Adrian J. Gibbs1*, Kazusato Ohshima 2 , Matthew J. Phillips3, Mark J. Gibbs4 1 Yarralumla, Australian Capital Territory (ACT), Australia, 2 Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga, Japan, 3 School of Botany and Zoology, Faculty of Science, Australian National University, Canberra, Australia, 4 Curtin, Australian Capital Territory (ACT), Australia Abstract Background: Potyviruses 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 Findings: We 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/Significance: Our studies indicate that the partial coat protein genes of potyviruses have an evolutionary rate of about 1.1561024 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. Citation: Gibbs AJ, Ohshima K, Phillips MJ, Gibbs MJ (2008) The Prehistory of Potyviruses: Their Initial Radiation Was during the Dawn of Agriculture. PLoS ONE 3(6): e2523. doi:10.1371/journal.pone.0002523 Editor: Brett Lindenbach, Yale University, United States of America Received March 5, 2008; Accepted May 19, 2008; Published June 25, 2008 Copyright: 2008 Gibbs et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The authors have no support or funding to report. Competing Interests: The authors have declared that no competing interests exist. * E-mail: adrian_j_gibbs@hotmail.com. Introduction Two of the 73 genera of plant viruses share equally more than 30% of all recognized species [1]; Potyvirus is one of them and Begomovirus the other. Potyvirus is the largest of six genera in the family Potyviridae [1,2], and is named after its type species, potato virus Y. Many potyviruses are damaging crop pathogens. They infect species of most angiosperm taxa in all temperate and tropical climes. They are transmitted by aphids, especially species of Aphidinae, when aphids move from plant to plant and probe them in search of their preferred host species, and some are also transmitted in seeds to the progeny of infected plants. Why are there so many potyviruses? Is their dominance recent or ancient? To answer such questions we first need to know when the present day plague of potyviruses originated. Viruses leave no fossils and their evolutionary rates can only be estimated by linking features of their phylogenies to dates obtained in other ways. A few viruses of animals, notably some orthomyxoviruses and lentiviruses, sometimes evolve so quickly that their evolutionary rates can be estimated by comparing samples collected at different times during an epidemic [3,4]. Other viruses have phylogenies that are congruent with those of their hosts implying that they have co-evolved [5–10], and the co- evolutionary congruence is sometimes complete suggesting that the virus group is as old as its hosts. One genus of plant viruses, the tobamoviruses, shows this sort of relationship [11,12] suggesting that it first radiated about 100 million years ago, when the asterid and rosid lineages of plants diverged. The taxonomy of potyviruses shows no comparable congruence with host taxonomy, and species from the same lineage may have quite unrelated hosts. For example, the principal hosts of different species of the bean common mosaic lineage are aroids, cucurbits, legumes, orchids and passifloras. The only other published estimates of the rates of evolution of plant viruses are those of wheat streak mosaic tritimovirus (WSMV), which was found to be 1.161024 nucleotide substitutions/site/year (ns/s/yr) [13], of rice yellow mottle virus, 4–861024 ns/s/yr [14], and of tomato yellow leaf curl begomo- virus 4.661024 ns/s/yr [15]. These rates are similar to those reported for some populations of viruses of animals [16]. In this paper we report a study of the timescale of potyvirus evolution. The development of methods for inferring and dating phylogenies from gene sequences is currently an active area of research. We have therefore used several different methods, and made limited comparisons between them, to search for a consensus of estimates that will provide a credible timescale for the prehistory of potyviruses. Materials and Methods Potyvirus gene sequences were obtained from the Genbank database using its ENTREZ and BLAST search facilities, and PLoS ONE | www.plosone.org 1 June 2008 | Volume 3 | Issue 6 | e2523