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.胎盘类哺乳动物的演化辐射时间与白垩纪-古近纪（KPg）界线大灭绝事件的相对时序，迄今仍存在高度争议。具体而言，早期胎盘类演化辐射的定年结果不仅在基于化石与分子的两类数据集之间存在看似不可调和的分歧，在不同分子数据集内部也存在差异。为助力解决这一争议，我们依托涵盖90个分类群的4388个基因座开展全基因组分析，所涉类群包含所有现存胎盘类目的代表类群，同时纳入鼯猴（皮翼目，Dermoptera）与穿山甲（鳞甲目，Pholidota）的转录组数据。根据基因分区方案、分子钟模型以及基因偏离分子钟假设的程度，我们通过大量敏感性分析发现，基于同一组基因可得到差异极大的胎盘类哺乳动物演化辐射场景：从白垩纪早期的起源与辐射，到跨越KPg界线的演化场景——这表明使用次优的分子钟标记与研究方法，是导致胎盘类演化辐射时间争议的主要原因。我们证实，通过选用合适的分子钟模型与基因分区方案，并考量单个基因偏离分子钟假设的程度，可实现分子与古生物学对胎盘类分化时间估算结果的统一。生灭-转移分析显示，胎盘类哺乳动物在KPg界线前后持续发生演化辐射，并未因此次大灭绝事件出现明显中断，这一结果与多瘤齿兽类的属级辐射以及多瘤齿兽类与兽亚纲动物的生态形态多样化相呼应。上述研究结果表明，KPg大灭绝事件对胎盘类哺乳动物演化辐射的影响实则有限；相较而言，胎盘类的辐射更可能是对稍早时期被子植物演化辐射的滞后响应。