Novel integrative modeling of molecules and morphology across evolutionary timescales

Evolutionary models account for either population or
species-level processes, but usually not both. We introduce a new model,
the FBD-MSC, which makes it possible for the first time to integrate both
the genealogical and fossilization phenomena, by means of the multispecies
coalescent (MSC) and the fossilized birth-death (FBD) processes. Using
this model, we reconstruct the phylogeny representing all extant and many
fossil Caninae, recovering both the relative and absolute time of
speciation events. We quantify known inaccuracy issues with divergence
time estimates using the popular strategy of concatenating molecular
alignments, and show that the FBD-MSC solves them. Our new integrative
method and empirical results advance the paradigm and practice of
probabilistic total evidence analyses in evolutionary biology.