# Molecular Population Genetics of Aspen Mosaic-Associated Virus in Finland and Sweden
## 3 Results and Discussion
### Relation of Distant Isolates of AsMaV with Clade A Emaraviruses  
AsMaV isolates shared a max. of 76%, 50%, 81%, and 80% identity in the pairwise alignment of RdRP, GPP, NP, and MP protein of clade A species of emaravirus in the RdRP, GPP, NP, and MP at the aa level being PiVB, PPSMV-1, PPSMV-2 the closest virus as confirmed with CMP trees. Therefore, the divergent isolates also belong to the AsMaV and did not belong to a new species. In the phylogenetic tree based on the aa sequences of the encoded protein of AsMaV with corresponding proteins, the sequenced isolates of AsMaV were clustered in a distinct sub-cluster next to the PiVB. The GPP was not parsimoniously informative, since most of the species remained ungrouped. The RdRP-based tree had better discrimination of the species (Figure 5). To study the phylogeny and genetic diversity of emaraviruses, researchers have utilized different regions of the emaravirus genome, each exhibiting varying degrees of variation among different emaravirus isolates. One particular region of interest is the NP due to its correspondence to the coat protein in non-enveloped viruses [29; 30; 31; 32; 33; 34; 35; 36; 37; 38; 39]. In certain emaraviruses, such as HPWMoV, the RNA3 or NP region has been identified as the most divergent genomic region, leading to the division of HPWMoV isolates into subgroups based on this region [28; 39; 65]. Similarly, for EMARaV, RNA3 exhibited more diversity than RNA4, and a phylogenetic tree based on RNA3 provided better discrimination among EMARaV isolates [38]. The NP has also been effectively used to assess genetic diversity and phylogenetic relationships among Serbian and Finnish isolates of RLBV, revealing a minimum of 93% identity [34]. In our study on AsMaV, our results indicate that the RNA3 or NP region is a promising candidate for investigating genetic diversity, followed by RdRP, which was found to be more phylogenetically informative than RNA4. For FMV, partial sequences of RNA1 to RNA4 were used to assess genetic diversity, revealing that RNA1 and RNA3 exhibited more variation than RNA4 [30]. Partial sequences of RNA1, RNA3,  
Figure 5: Constructed maximum parsimony trees based on the amino acid sequences of RdRP (**A**), GPP (**B**), NP (**C**), and MP (**D**) proteins. The evolutionary history was inferred using the Minimum Evolution method. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed. Branches corresponding to partitions reproduced in less than 70% of bootstrap replicates are collapsed. Trees were constructed by MEGA11 [49]. The AsMaV isolates are presented in red color. and RNA4 of MaMaV showed limited diversity, with RNA1 having a maximum of 2% variation and no diversity observed in the amplicons of RNA3 and RNA4 [32]. In contrast of our findings, it has been shown that the BLMaV-MP region displayed more variation than NP, possibly due to several detected recombination events in the coding region of BLMaV-MP [31]. Additionally, pairwise nucleotide comparisons of ORF1 to ORF6 of six JYMaV isolates revealed that RNA2 and RNA1 were the most divergent genomic regions when compared to ORF3 to ORF6 [36]. In the case of RRV, sequencing several full-length isolates demonstrated a conserved core genome, with RNA5 and RNA7 being the most divergent RNAs [35]. Notably, it is important to acknowledge that RRV-RNA5 is not equivalent to AsMaV-RNA5 due to inconsistencies in the nomenclature of genomic RNAs and proteins in emaraviruses [6]. The parsimony-based trees of the core genomic proteins of clade A species of emaraviruses indicated that RdRP is a better candidate for higher taxonomic levels (Figure 5). Partial RdRP at the nt level was also able to discriminate the AsMaV isolates. Similarly, most but not all of emaraviruses species could be grouped by amino acid sequences of NP. Therefore, it could be concluded that NP and RdRP are the best candidates for phylogenetic studies of emaraviruses for intra- and inter-species relationships, respectively.