Data from: Can we build it? Yes we can, but should we use it? Assessing the quality and value of a very large phylogeny of campanulid angiosperms

The study of very large and very old clades holds the promise of greater insights into evolution across the tree of life. However, there has been a fair amount of criticism regarding the interpretations and quality of studies to date, with some suggesting that detailed studies carried out on smaller, tractable scales should be preferred over the increasingly grand syntheses of these data.
Methods - We provided in detail our trials and tribulations of compiling a large, sparsely sampled matrix from GenBank data and inferring a well-supported, time-calibrated phylogeny of Campanulidae. We also used a simulation approach to assess tree quality, and to study the value of using very large, comprehensive phylogenies in a comparative context.
Key results - A robust and well-supported phylogeny can be produced as long as automated procedures are supplemented with some human intervention. In the case of campanulids, the overall topology may be driven not only by particular genes, but also particular sequences for a gene. We also determined that estimates of divergence times should be fairly robust to issues related to clade-specific heterogeneity. Finally, we demonstrated how relying on results from smaller, younger clades are prone to produce biased interpretations of tropical to temperate evolution across campanulids as a whole.
Conclusions - While we were both surprised and encouraged by the robust and fairly well-resolved, comprehensive phylogeny of campanulids, challenges still remain. Nevertheless, large phylogenies are inherently valuable in a comparative context if only to attenuate the issue of ascertainment bias.

对超大型、超古老演化支的研究，有望为生命之树各分支的演化研究带来更深刻的洞见。然而，截至目前的相关研究在解读逻辑与数据质量层面饱受诸多诟病，部分学者主张应优先开展规模更小、更易把控的细致研究，而非一味追求此类数据日益宏大的综合分析。
研究方法——本文详细阐明了从GenBank（基因银行）数据库中汇编大型稀疏采样矩阵，并推断得到桔梗类群（Campanulidae）高支持度时间校准系统发育树的全部尝试历程与所遇挑战。此外，我们采用模拟方法评估系统发育树质量，并探究在比较研究语境下使用超大型综合系统发育树的研究价值。
核心研究结果——只要自动化流程辅以一定的人工干预，即可构建出稳健且高支持度的系统发育树。就桔梗类群而言，其整体拓扑结构不仅可能受特定基因的影响，还会受到同一基因特定序列的作用。我们还证实，分化时间估算结果对演化支特异性异质性相关问题具备较强的稳健性。最后，我们证明了仅依赖小型、年轻演化支的研究结果，极易对桔梗类群整体从热带到温带的演化过程产生带有偏差的解读。
研究结论——尽管我们对桔梗类群稳健且分辨率较高的综合系统发育树感到惊喜与鼓舞，但相关挑战依然存在。即便如此，只要能够减轻确定性偏差（ascertainment bias）的影响，大型系统发育树在比较研究语境下仍具备与生俱来的学术价值。