# Molecular Population Genetics of Aspen Mosaic-Associated Virus in Finland and Sweden
## 3 Results and Discussion
### Recombination Analysis  
The unstable position of a few isolates in phylogenetic trees raised the idea that there may be recombination events between the sequenced isolates. Searching for recombination \begin{table}
\begin{tabular}{c c c c c c c c c c c} \hline \hline
**Genomic** & **Populations** & **KST* & \(p\)-Value** & **Z* & \(p\)-Value** & **Snn** & \(p\)**-Value** & **Hs** & \(p\)**-Value** & **FST** \\ \hline
**RNA3** & S. vs. F & 0.07092 & 0.0000 *** & 4.51006 & 0.0000 *** & 0.85185 & 0.0010 ** & 0.99545 & 0.5330 [FOOTNOTE:]Footnote : not significant, * 0.01 \(<\)\(p\)-value \(<\) 0.05; **, 0.001 \(<\)\(p\)-value \(<\) 0.01; ***, \(p\)-value \(<\) 0.001.[ENDFOOTNOTE] & 0.22767 \\
**RNA4** & S. vs. F & 0.02288 & 0.0080 ** & 4.63422 & 0.0050 ** & 0.88462 & 0.0030 ** & 1.00000 & 1.0000 [FOOTNOTE:]Footnote : not significant, * 0.01 \(<\)\(p\)-value \(<\) 0.05; **, 0.001 \(<\)\(p\)-value \(<\) 0.01; ***, \(p\)-value \(<\) 0.001.[ENDFOOTNOTE] & 0.06408 \\
**RNA1** & S. vs. F & 0.03890 & 0.0000 *** & 4.44027 & 0.0000 *** & 0.92308 & 0.0010 * & 1.00000 & 1.0000 [FOOTNOTE:]Footnote : not significant, * 0.01 \(<\)\(p\)-value \(<\) 0.05; **, 0.001 \(<\)\(p\)-value \(<\) 0.01; ***, \(p\)-value \(<\) 0.001.[ENDFOOTNOTE] & 0.23698 \\ \hline \hline \end{tabular}
\end{table} 
Table 4: Geneflow and genetic differentiation parameters. \begin{table}
\begin{tabular}{c c c c c c c c c c} \hline \hline
**Genomic** & **Geographical** & **m** & **S** & **\(\theta_{w}\)** & **PiT** & **Pi\({}_{\text{s}}\)** & **Pi\({}_{\text{a}}\)** & **Pi\({}_{\text{a}}\)/Pi\({}_{\text{s}}\)** & **[PERSON]’s D** & **Fu and LI’s D** \\ \hline  & Sweden & 9 & 275 & 0.06347 \(\pm\) (0.02651) & 0.04735 \(\pm\) (0.01764) & 0.11984 & 0.02115 & 0.176 & \(-\)1.322703 & \(-\)1.56810 \\  & Finland & 18 & 298 & 0.05435 \(\pm\) (0.01881) & 0.04207 \(\pm\) (0.01138) & 0.11180 & 0.02432 & 0.217 & \(-\)0.961799 & \(-\)0.47563 \\  & Total & 27 & 361 & 0.05876 \(\pm\) (0.01844) & 0.04994 \(\pm\) (0.00834) & 0.12843 & 0.02695 & 0.210 & \(-\)0.579852 & \(-\)0.60644 \\ \hline  & & & & & & & & & & \\ \hline  & Sweden & 8 & 119 & 0.02948 \(\pm\) (0.01286) & 0.03048 \(\pm\) (0.00391) & 0.09485 & 0.00542 & 0.057 & 0.186391 & \(-\)0.14740 \\  & Finland & 18 & 141 & 0.02633 \(\pm\) (0.000929) & 0.02497 \(\pm\) (0.00237) & 0.08977 & 0.00418 & 0.047 & \(-\)0.246562 & \(-\)0.29650 \\  & Total & 26 & 190 & 0.03198 \(\pm\) (0.01032) & 0.02738 \(\pm\) (0.01087) & 0.09406 & 0.00460 & 0.049 & \(-\)0.568813 & \(-\)0.66359 \\ \hline  & & & & & & & & & & \\ \hline  & & & & & & & & & & & \\ \hline  & & & & & & & & & & & \\ \hline \end{tabular}
\end{table} 
Table 3: Results from population parameters estimated based on demographic trends. events in the RNA4, RNA3, and partial RNA1 of AsMaV (nucleotides 20-1570) using RDP5 software revealed that there were no recombinant events in RNA4 and RNA3. However, a recombination event with a low probability has been detected by RDP (_E_-value \(3.956\times 10^{-3}\)), MaxChi (_E_-value \(1.118\times 10^{-2}\)), and Phylopro (_E_-value \(2.545\times 10^{-2}\)) in the isolate E58213 (Sweden) with the major parent of E58627 (Finland) and minor parent of E58299 (Sweden) in nts 581-631 and nts 647-915. It should be mentioned again that the E-value and the number of methods that supported this event were not strong. The isolate E58213 was placed in a different clade when the tree was based on the MP. The grouping profile of few isolates such as E58299, E58405, E58413, E58421, and E58434 were different. Since there were no recombination events reported for these isolates, two different scenarios would be possible: (i) there were insufficient data from AsMaV isolates especially from different geographical regions or (ii) the other mechanisms rather than recombination, for example, reassortment or genetic drift, were responsible for the evolution of these isolates. Several recombination events have been reported in the HPWMoV-RNA3, especially in Australian isolates.