C2_1clock - MrBayes file

File_C2 (plain text). MrBayes executable file for a total-evidence dating analysis of all 86 taxa in the matrix in [6], using a single relaxed (independent gamma rates) clock for all traits (morphological and molecular). The sampled ancestor birth-death tree prior [17], and the Markov model of morphological evolution [18,19], were used. Optimal substitution models and substitution-model-partitions were found with PartitionFinder for molecular data (see C1) and with stepping-stone analysis in MrBayes for morphological data as implemented in [10]. Numerous (>20) MCMC runs were initially performed for 5 million generations to investigate tuning, mixing and convergence. The final analysis was then performed with 4 runs of 20 million generations, with the first 30% of samples discarded as burnin.

文件C2（纯文本格式）：用于对文献[6]矩阵中全部86个分类单元开展总证据定年（total-evidence dating）分析的MrBayes可执行文件，本次分析为所有性状（形态学与分子性状）采用单一松弛（独立伽马速率）分子钟。本分析采用采样祖先出生-死亡树先验[17]与形态演化马尔可夫模型[18,19]。分子数据的最优替换模型及替换模型分区通过PartitionFinder确定（详见文件C1），形态数据的最优模型与分区则通过MrBayes中的阶梯式抽样分析实现，具体实现方法参见文献[10]。初始阶段共开展20余次马尔可夫链蒙特卡洛（MCMC）试运行，每条链运行500万代，用于参数调优、链混合效果评估与收敛性检验。最终分析设置4条并行运行链，每条链运行2000万代，并将前30%的样本作为预烧样本予以舍弃。