Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes - Supplementary Files S1-S5

Supplementary File S1: Simulation parameter files and guide trees (ZIP archive) Supplementary File S2: PCA plot based on diversity of bi-allelic SNPs (PDF file). Same projection as in Figure S5, with samples distinguished by different metadata: country of isolation, year of isolation, host immune status, body compartment of isolation ('respiratory' pools BAL and nasal rinse, 'blood' pools whole blood and plasma). Supplementary File S3: Posterior probability and compatibility matrices of bipartitions in gene trees (XLSX spreadsheet) Supplementary File S4: Local LD index values along HCMV whole-genome alignment. (XLSX spreadsheet) Supplementary File S5: Trees of hyper-variable loci with episodes of positive selection highlighted (PDF file)

补充文件S1：模拟参数文件与引导树（ZIP压缩归档）。补充文件S2：基于双等位基因单核苷酸多态性（bi-allelic SNPs）多样性的主成分分析（PCA）图（PDF文件），该图与图S5采用相同的投影方式，样本按以下不同元数据进行区分：分离来源国、分离年份、宿主免疫状态、样本采集的身体部位（「呼吸道」组包含支气管肺泡灌洗液（BAL）与鼻腔冲洗液，「血液」组包含全血与血浆）。补充文件S3：基因树二分划分的后验概率与兼容性矩阵（XLSX电子表格）。补充文件S4：人类巨细胞病毒（HCMV）全基因组比对区域的局部连锁不平衡（LD）指数值（XLSX电子表格）。补充文件S5：带有正选择事件标注的高变基因座进化树（PDF文件）