Fast Bayesian inference of phylogenies from multiple continuous characters

Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remains challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counterparts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods' properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method's behavior, and suggest future research venues.

Methods
1. The data for well-calibrated validation and simulation studies can be simulated by running R scripts inside corresponding folders (i.e., 01validation, 02simulation and 03carnivora).

2. The XML files are used for Carnivoran analyses. The molecular and continuous traits data can be obtained from Sandra Álvarez-Carretero et al., 2019. The discrete trait data can be obtained from Paul Z. Barrett et al., 2021.

3. Data processing details can be found on the Github repository https://github.com/Rong419/MorphologyDocument.git.