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.