# Molecular Population Genetics of Aspen Mosaic-Associated Virus in Finland and Sweden
## 3 Results and Discussion
### Genetic Diversity and Phylogeny of AsMaV Isolates Based on Partial RNA1  
Based on the consensus maximum parsimony tree generated from 25 partial AsMaV RNA1 nt 20-1588 sequenced in this study (18 from Finland and 7 from Sweden) and one previously reported isolate (GenBank Acc. No. LR742461) at the nucleotide level, AsMaV isolates were placed in five main groups (Figure 3). Swedish isolates clustered in one clade (R1-G6) with the exception of E58213 which was grouped with the two Finnish isolates of E58632 and E58491 in the clade R1-G1. Interestingly, two Finnish isolates, E58632 and E58491, were clustered with the Swedish isolates in R1-G6. The isolates E58426, E58433, E58434, E57260, and E58385 in group R1-G2, isolates E58386, E58389, and E58446 in group R1-G3, isolates E58397 and E58398 in the group R1-G4, and the isolates E58413, E58421, and E58439 in the group R1-G5 (Figure 3). The phylogenetic tree based on the first 517 deduced aa sequences of AsMaV-ORF1 was not phylogenetically informative.  
Among the generated phylogenetic trees for RAN3, RNA4, partial RNA1 at nt level, ORF3, ORF4, and partial ORF1 at both nucleotide and amino acid levels, phylogenetic trees constructed for AsMaV-RNA3 were in accordance with each other with one difference: isolates E58632 and E58227 remained ungrouped. There was no difference between phylogenetic trees generated based on the ORF3 or almost full length of the RNA3 at the nt levels. Therefore, it might be concluded that among investigated regions RNA3-based trees, regardless of full length (at nt level) or coding regions (at nt or aa level), produce almost the same results. AsMaV isolates were better discriminated in constructed phylogenetic trees  
Figure 3: The consensus maximum parsimony trees constructed based on the nucleotide sequences of partial RNA1 (**left**) and RNA4 (**right**). Nodes with bootstrap support less than 70% were collapsed. Corresponding regions of RNA1 sequences of PPSMV-2, FMV, and PiVB with the accession numbers NC_030660, NC_029560, and MH727572, respectively, as well as those of full-length RNA4 with the accession numbers NC_030663, NC_029564, and MH727575, were used as out-groups in the analyses. The geographical origin and accession number of each isolate are presented next to the isolate name, as well as in Supplementary Table S3. Isolates from Sweden and Finland are shown in red and black colors, respectively. The out-groups are in blue.  
based on the nt level of the AsMaV-RNA4 and partial RNA1 rather than aa-based trees, because approximately 57% (15 out of 26) and 30% (8 out of 26) of the isolates used for these analyses remained ungrouped in the mentioned phylogenetic trees, respectively. The phylogenetic trees based on the ORF4 in comparison to the almost full-length RNA4-based tree at nt levels had ungrouped isolates (six out of twenty-six). As mentioned before, both CMP trees constructed based on the partial nt sequence of RNA1 were identical. Therefore, using the nt sequences of almost full-length RNA3-4 and longer region(s) of RNA1 to generate phylogenetic trees was more informative than amino acid sequences of related ORFs (Figures 2 and 3).