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.

The input files contain the dataset and model specifications required for FBD-MSC, FBD-concatenation and BD-MSC methods implemented in BEAST2 (the msc-fbd-correctness repository contains code and analyses verifying the correctness of those methods). The output files of those methods are themselves a dataset of samples from the posterior distribution of trees and other evolutionary parameters. For our article we used the code in the caninae-scripts repository to analyze and visualize the output.