Table 2. Potyviruses found only in Australia. Name Carrot virus Y3 Ceratobium mosaic virus Hardenbergia mosaic virus Passionfruit woodiness virus-NSW Passionfruit woodiness virus-WA Pterostylis virus Y mean 30 3 5 3 5 2 8 Number of Australian sequences Divergence1 of Australian sequences 0.007 0.109 0.297 0.037 0.049 0.011 0.085 Prehistory of Potyviruses Nearest viral sequence Celery mosaic virus Tricyrtis virus Y Passionfruit woodiness virus-WA Siratro 1 virus Y Clitoria virus Y Ornithogalum mosaic virus - Maximum identity2 81% 77% 80% 85% 84% 90% 82.8% 1divergences calculated from ML trees (GTR+I+G) of the cCP sequences as the mean pairwise nucleotide substitutions/site of sequences linked through the basal node. 2Maximum identity in BLAST searches of the Genbank database. 3Carrot virus Y infects carrot crops throughout southern Australia, and has all the features of a recent immigrant rather than an endemic. Note: Single cCP sequences are also known for Clitoria virus Y, Diuris virus Y, Eustrephus virus Y, Hibbertia virus Y, Kennedya virus Y, Passiflora foetida virusY, Rhopalanthe virus Y, Sarcochilus virus Y, Siratro 1 virus Y and Siratro 2 virus Y. The nearest sequences to these had 84%, 78%, 83%, 82%, 74%, 89%, 80%, 83%, 86% and 84% maximum identities respectively in BLAST searches of the Genbank database. Single partial cCP sequences also available for Dianella chlorotic mottle virus and Glycine virus Y and the nearest sequences to these had 82% and 84% identities respectively in BLAST searches of the Genbank database. doi:10.1371/journal.pone.0002523.t002 1.17361024 ns/s/yr and hence the potyvirus radiation occurred 6353 YBP. Maritime trade and the great plant diaspora. The discovery of America by Columbus in 1492 is traditionally taken to be the event that initiated long distance maritime trade. This linked all parts of the world and over the following two centuries dispersed most cultivated plants from the restricted regions where they had been independently domesticated and grown during the previous 10 to 13 millenia [41–43]. Of the quarter million or so species of flowering plants, only about 1,800 of them have been ‘‘brought into cultivation’’ [44], and ‘‘only about 100 yielded valuable domesticates’’ [43]. More than five centuries ago only the calabash gourd, Lagenaria siceraria, and the coconut, Cocos nucifera, were present in both the Old and New Worlds, and the sweet potato or kumara, Ipomoea batatas, was grown in both the Americas and Polynesia [44]. Maritime trade carried most of the others to all corners of the world, and viruses that could travel with them probably did. We therefore searched phylogenies of potyviruses present in both the Old and New Worlds to find those with sub- lineages found only in either the New or Old World. We presume that such disjunct populations were probably transported between the Old and New Worlds and are at most around 500 years old. So far we have examined phylogenies of more than 50 species and found two of this sort, namely those of cowpea aphid-borne mosaic (CAbMV) (Fig. 4) and papaya ringspot (PRSV) viruses (Fig. 5). CAbMV infects various species and cultivars of cowpea, and also many other species, and is transmitted to a large proportion of the seed of infected cowpea plants. Cowpeas were first domesticated in West Africa [45], and were taken from there to south and east Asia [46], where their name, catjang, is from the ancient Indian language Sanskrit and hence at least 3,000 years old. They were also grown by the Romans and Greeks. Several published CAbMV cCP sequences are from African isolates and one from passion fruit with woodiness disease in South Africa [47], but the majority are from South American isolates from passion fruit and a few from Arachis hypogaea and Crotalaria spp. [48]. A phylogeny of the 25 reported CAbMV cCP sequences (Fig. 4 and List S6) shows that the ten isolates from Africa are the most diverse and closest to the potyvirus radiation, whereas the 15 from South America form a monophyletic subcluster within the CAbMV tree; two South American sequences (DQ397525/6) are recombinants with sequence regions from an unknown potyvirus and were not included in the analysis, and one isolate found in plants grown in the USA from African seed [49] clusters with African isolates. The basal node of the 16 South American cCP sequences linked sequences that differed by a mean of 0.1397+/20.024 ns/s. CAbMV is a member of the bean common mosaic lineage of potyviruses, so all ten other members of that lineage were excluded from the PhyML analysis that showed that the 16 South American CAbMV cCPs differed from the outgroup potyviruses by a mean of 1.555+/20.143 ns/s. Travel between Africa and the Americas started around 1500 AD; Brazil was discovered inadvertently in 1502 and slaves taken there from Africa soon afterwards [50,51]. It is very likely that seeds of cowpea, a staple food of tropical Africans, were taken too [35,52]. So if we assume that the South American CAbMV lineage was established by infected seed Figure 4. Radial neighbor-joining tree of the cCP genes of 149 isolates of different species of the bean common mosaic virus (BCMV) group (green branches), with 36 outgroup potyviruses and ryegrass mosaic rymovirus (RGMV) (black branches) as an outgroup; the other 11 ‘outgroup potyviruses’ were of the BCMV group. The BCMV group isolates included 24 isolates of cowpea aphid-borne mosaic virus, eight of which came from Africa (blue branches) and 16 of which came from South America (red branches); it also included single isolates of 11 species in the outgroup potyviruses. doi:10.1371/journal.pone.0002523.g004 PLoS ONE | www.plosone.org 5 June 2008 | Volume 3 | Issue 6 | e2523