C7_8clocks MrBayes file

File_C7 (plain text). MrBayes executable file for a total-evidence dating analysis of all 86 taxa in the matrix in [6], using 8 separate relaxed clocks (independent gamma rates; 7 for morphology and 1 for molecular data), as found in analysis B-3. 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 [10]. Numerous (>20) MCMC runs were initially performed for 20 million generations to investigate tuning, mixing and convergence. The final analysis was then performed with 4 runs and the trees from 10 million post-burnin generations retained Note: The burnin for each run varies considerably due to variation in time to reach (apparent) stationarity, from 20 million to 50 million. For computational efficiency, the 4 runs were performed separately and in all cases, the last 10 million steps (after stationarity) were retained. However, the step numbers have been readjusted in file C8 below so they are all identical across runs (ie to a common burnin of 50 million), to facilitate downstream analyses e.g. generating summary statistics in MrBayes.文件C7（纯文本格式），为文献[6]中矩阵内全部86个分类群的总证据定年分析所用的MrBayes可执行文件，对应分析B-3的设置：采用8个独立松弛分子钟（独立伽马速率模型，其中7个用于形态学数据，1个用于分子数据）。本分析使用了采样祖先出生-死亡树先验分布[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），形态学数据的相关最优设置则通过MrBayes中的阶梯石采样分析完成[10]。 初始阶段共开展20余次（>20）马尔可夫链蒙特卡洛（Markov Chain Monte Carlo, MCMC）运行，每条运行链迭代2000万代，用于调试参数、评估链混合效果与收敛性。最终分析设置为4条并行运行链，保留预烧期后的1000万代树形文件。 注：由于各运行链达到（表观）平稳性所需时长存在差异，每条运行链的预烧期跨度较大，介于2000万至5000万代之间。为提升计算效率，4条运行链均独立执行，且均仅保留平稳期后的最后1000万步迭代结果。但为便于后续分析（如在MrBayes中生成汇总统计量），下文的文件C8已对迭代步数进行重新校准，使所有运行链的有效步数保持一致（即统一设置预烧期为5000万代）。