Quantitative Delineation of Herpesviruses in Bats for use in Ecological Studies

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

To refine the exact number of OTUs, two neighbor-joining trees were generated from the exemplar sequences, as determined using affinity propagation, one for the gammaherpesviruses and one for the betaherpesviruses. (Figure 2 ). When exemplar sequences were greater than 90% similar (the most conservative cutoff within the lower taxonomic range), clusters were merged to represent a single OTU. Additionally, each OTU represented by a single occurrence (i.e. a single clone sequence) was examined individually. If the singleton sequence was greater than 74% similar to the exemplar of another OTU, the least conservative cutoff point demonstrated by PID histograms, it was clustered with that OTU. Singleton sequences less than or equal to 74% similar to each of the other exemplars were considered to be unique OTUs. After refinement, 41 OTUs remained. Preliminary data collected The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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