Quantitative Delineation of Herpesviruses in Bats for use in Ecological Studies

Anna R. Sjodin; Michael R. Willig; Simon J. Anthony

We gratefully acknowledge Armando Rodriguez-Duran for invaluable logistical help in the field, as well as the intrepid field team, including Sarah Stankavich, Jose Rivera, Melanie Figure 1 : Percent Identity (PID) histograms of herpesviruses using the alignment of all clones (a) and pairwise alignment of clones (b). The x-axis represents the percent identity of clone sequences compared pairwise. The y-axis represents the number of clone sequences. Vertical lines represent cutoff points corresponding to two distinct peaks, with blue lines representing the higher-level cutoff and the red lines representing the lower-level cutoff. Solid lines represent the low end of the cutoff ranges, and the dashed lines represent the upper end of the cutoff ranges. The distinct peaks are consistent regardless of alignment method. . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/856518 doi: bioRxiv preprint Figure 2 : Neighbor-joining trees of betaherpesvirine (a) and gammaherpesvirine (b) exemplars, as defined using affinity propagation. OTUs are named to reflect manual refinement of OTUs after affinity propagation. For example, affinity propagation separated OTU 28, a gammaherpesvirus, into four separate clusters. However, the similarity of the exemplars suggested that these clusters should all be grouped into a single OTU. These trees provide biological support for the manual refinement of OTUs. OTUs 39-41, all betaherpesviruses, were not included in the tree. These OTUs were represented by three highly divergent sequences (< 50% genetic similarity), and their inclusion in the tree impaired visualization of all other relationships.