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Figure 1 The branches of NJ phylogenies calculated from the main genomic ORFs of (A) 240 isolates of PVY and (B) 103 of the isolates that showed no significant.

Published byMercy Fitzgerald Modified over 6 years ago

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Presentation on theme: "Figure 1 The branches of NJ phylogenies calculated from the main genomic ORFs of (A) 240 isolates of PVY and (B) 103 of the isolates that showed no significant."— Presentation transcript:

1 Figure 1 The branches of NJ phylogenies calculated from the main genomic ORFs of (A) 240 isolates of PVY and (B) 103 of the isolates that showed no significant evidence of recombination (see text). The marked clusters are of groups named in Kehoe and Jones (2016); cluster C is of groups C1(II) and C2(III); O is of O(I) and O5(X); N is of N(IV), XIII and NA-N(IX); NTN-1 is of NTN-NW, SYR-I(XII), NTN-B(VI), NTN-NW, SYR-II(XI), N-Wi(VII), and N:O(VIII); and NTN-2 of NTN-A(V). Chile 3 is isolate Accession Code FJ From: The phylogenetics of the global population of potato virus Y and its necrogenic recombinants Virus Evol. Published online March 02, doi: /ve/vex002 Virus Evol | © The Author Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact

2 Figure 2 The branches of SplitsTree phylogenies of the main genomic ORFs of (A) 240 isolates of PVY and (B) 103 of those isolates that showed no significant evidence of recombination. The marked clusters are the same as those in Fig. 1. From: The phylogenetics of the global population of potato virus Y and its necrogenic recombinants Virus Evol. Published online March 02, doi: /ve/vex002 Virus Evol | © The Author Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact

3 Figure 3 A cartoon summarizing the relationships and genomic maps of the five major phylogroups of the PVY isolates shown in Figs 1 and 2. From: The phylogenetics of the global population of potato virus Y and its necrogenic recombinants Virus Evol. Published online March 02, doi: /ve/vex002 Virus Evol | © The Author Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact

4 Figure 4 A cartoon summarizing the divergence dates of a ML phylogeny of seventy-three dated n-rec ORF sequences (Table 1 - line 1) estimated by the LSD method, and the dates from the MCC tree of a BEAST analysis of the same data. Bars indicate the 95% CI ranges for both analyses. Arrows indicate the period, 1935 CE–2016 CE, during which the isolates were collected. From: The phylogenetics of the global population of potato virus Y and its necrogenic recombinants Virus Evol. Published online March 02, doi: /ve/vex002 Virus Evol | © The Author Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact

5 Figure 6 A cartoon summarizing the TMRCA dates and 95% CIs (vertical scale) of PVY estimated by TempEst, LSD (ML and NJ trees) and BEAST (MCC tree) analyses of the seventy-three n-rec ORF and 161-core sequences, together with historical events that may have influenced the evolution of the virus. From: The phylogenetics of the global population of potato virus Y and its necrogenic recombinants Virus Evol. Published online March 02, doi: /ve/vex002 Virus Evol | © The Author Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact

6 Figure 5 The NJ phylogeny of the central core regions of the genomes of 166 dated C, O, N, R-1, and R-2 isolates. (A) the Accession Codes of the C isolates are blue, O red, R-1 green, R-2 orange, and N yellow. (B) Summary of the phylogroup composition of the collapsed clusters a–f. The node dates are from LSD estimates of MJ and NJ phylogenies and from the MCC phylogeny of a BEAST analysis. These node dates were used to calculate the date scales assuming linearity. Labeled arrows indicate the dates of the likely origins of the O, R-1, and R-2 populations. From: The phylogenetics of the global population of potato virus Y and its necrogenic recombinants Virus Evol. Published online March 02, doi: /ve/vex002 Virus Evol | © The Author Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact

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