Data from: Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary

The timing of the diversification of placental mammals relative to the Cretaceous–Paleogene (KPg) boundary mass extinction remains highly controversial. In particular, there have been seemingly irreconcilable differences in the dating of the early placental radiation not only between fossil-based and molecular datasets but also among molecular datasets. To help resolve this discrepancy, we performed genome-scale analyses using 4,388 loci from 90 taxa, including representatives of all extant placental orders and transcriptome data from flying lemurs (Dermoptera) and pangolins (Pholidota). Depending on the gene partitioning scheme, molecular clock model, and genic deviation from molecular clock assumptions, extensive sensitivity analyses recovered widely varying diversification scenarios for placental mammals from a given gene set, ranging from a deep Cretaceous origin and diversification to a scenario spanning the KPg boundary, suggesting that the use of suboptimal molecular clock markers and methodologies is a major cause of controversies regarding placental diversification timing. We demonstrate that reconciliation between molecular and paleontological estimates of placental divergence times can be achieved using the appropriate clock model and gene partitioning scheme while accounting for the degree to which individual genes violate molecular clock assumptions. A birth-death-shift analysis suggests that placental mammals underwent a continuous radiation across the KPg boundary without apparent interruption by the mass extinction, paralleling a genus-level radiation of multituberculates and ecomorphological diversification of both multituberculates and therians. These findings suggest that the KPg catastrophe evidently played a limited role in placental diversification, which, instead, was likely a delayed response to the slightly earlier radiation of angiosperms.

胎盘类哺乳动物（placental mammals）的多样化事件与白垩纪-古近纪（KPg）界线大规模灭绝事件的相对时间节点，至今仍存在高度争议。具体而言，早期胎盘类辐射演化的定年分歧不仅存在于化石数据集与分子数据集之间，甚至在不同分子数据集内部也存在看似无法调和的差异。为解决这一争议，我们利用涵盖所有现存胎盘类目级类群代表的90个分类单元的4388个基因座，并结合鼯猴（皮翼目，Dermoptera）与穿山甲（鳞甲目，Pholidota）的转录组数据，开展了全基因组尺度分析。根据所采用的基因分区方案（gene partitioning scheme）、分子钟模型（molecular clock model）以及基因偏离分子钟假设的程度，我们开展了大量敏感性分析。结果显示，针对同一基因集得到的胎盘类哺乳动物多样化演化场景差异显著，时间跨度从晚白垩世的起源与多样化，到跨越KPg界线的各类场景均有覆盖。这表明，使用次优的分子钟标记与研究方法，是导致胎盘类多样化时间争议的主要诱因。我们证实，通过选用合适的分子钟模型与基因分区方案，并考虑单个基因偏离分子钟假设的程度，可实现分子数据与古生物学数据在胎盘类类群分化时间估算上的一致性。生灭漂移分析（birth-death-shift analysis）结果显示，胎盘类哺乳动物在KPg界线前后经历了连续的辐射演化，并未因此次大规模灭绝事件出现明显中断，这与多瘤齿兽类（multituberculates）的属级辐射演化、多瘤齿兽类与兽类（therians）的生态形态多样化相呼应。上述研究结果表明，KPg大灾变对胎盘类哺乳动物的多样化进程影响有限；相反，胎盘类的辐射演化很可能是对稍早前被子植物（angiosperms）辐射演化的滞后响应。