Figure S1 - Tick-Borne Encephalitis Virus Sequenced Directly from Questing and Blood-Feeding Ticks Reveals Quasispecies Variance

Phylogenetic analysis based on open reading frame sequences of TBEV. Nucleotide sequences of 90 strains were analyzed by the Maximum Likelihood (ML) method with a total of 10237 positions in the final dataset. The evolutionary history was tested by using the ML method based on the GTR +G+I as the best-fit substitution model. The bootstrap confidence is based on 500 replicates of the ML analysis. Omsk sequences were used as outgroup. Evolutionary analysis was conducted in MEGA5 and the Genbank accession numbers are indicated. (EPS)

基于蜱传脑炎病毒（Tick-borne Encephalitis Virus, TBEV）开放阅读框序列的系统发育分析：本研究采用最大似然（Maximum Likelihood, ML）法对90个毒株的核苷酸序列进行分析，最终数据集共包含10237个比对位点。进化历史的推断采用以GTR+G+I为最优替换模型的最大似然法完成，自举置信度（bootstrap confidence）通过500次最大似然分析重复抽样计算获得。本研究以鄂木斯克序列作为外类群（outgroup），进化分析借助MEGA5软件完成，GenBank登录号已在文中标注。(EPS)