Data from: Phylotranscriptomic consolidation of the jawed vertebrate timetree

Phylogenomics is extremely powerful but introduces new challenges as no
agreement exists on “standards” for data selection, curation and tree
inference. We use jawed vertebrates (Gnathostomata) as model to address
these issues. Despite considerable efforts in resolving their evolutionary
history and macroevolution, few studies have included a full phylogenetic
diversity of gnathostomes and some relationships remain controversial. We
tested a novel bioinformatic pipeline to assemble large and accurate
phylogenomic datasets from RNA sequencing and find this
phylotranscriptomic approach successful and highly cost-effective.
Increased sequencing effort up to ca. 10Gbp allows recovering more genes,
but shallower sequencing (1.5Gbp) is sufficient to obtain thousands of
full-length orthologous transcripts. We reconstruct a robust and strongly
supported timetree of jawed vertebrates using 7,189 nuclear genes from 100
taxa, including 23 new transcriptomes from previously unsampled key
species. Gene jackknifing supports the robustness of our tree and allows
calculating genome-wide divergence times by overcoming gene sampling bias.
Mitochondrial genomes prove insufficient to resolve the deepest
relationships due to limited signal and among-lineage rate heterogeneity.
Our analyses emphasize the importance of large curated nuclear datasets to
increase the accuracy of phylogenomics and provide a reference framework
for the evolutionary history of jawed vertebrates.

系统发育基因组学（Phylogenomics）极具威力，但由于数据选择、整理及系统发育树推断的"标准"尚未达成共识，也带来了新的挑战。我们以有颌脊椎动物（Gnathostomata）为模型来解决这些问题。尽管在解析其进化历史与宏观进化方面已付出大量努力，但鲜有研究涵盖有颌脊椎动物完整的系统发育多样性，且部分亲缘关系仍存争议。我们测试了一套新颖的生物信息学流程，用于从RNA测序数据中组装大型且准确的系统发育基因组数据集，发现这种转录组系统发育学（phylotranscriptomic）方法成效显著且极具成本效益。测序量提升至约10Gbp可恢复更多基因，但低深度测序（1.5Gbp）已足以获得数千条全长直系同源转录本。我们利用来自100个分类单元的7189个核基因，重建了有颌脊椎动物稳健且支持度高的时间树，其中包含23个来自此前未取样关键物种的新转录组数据。基因刀切法（gene jackknifing）支持了我们系统发育树的稳健性，并通过克服基因取样偏差，实现了全基因组分歧时间的计算。线粒体基因组因信号有限及谱系间速率异质性，被证明不足以解析最深层的亲缘关系。我们的分析强调了大型经过整理的核数据集对于提升系统发育基因组学准确性的重要性，并为有颌脊椎动物的进化历史提供了参考框架。