Unifying Fossils and Phylogenies for Comparative Analyses of Diversification and Trait Evolution
A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa
Correspondence author. E-mail: email@example.com
- Applying phylogeny-based analyses of trait evolution and diversification in the fossil record generally involves transforming an unscaled cladogram into a phylogeny scaled to geologic time. Current methods produce single time-scaled phylogenies with no indication of the uncertainty in the temporal relationships and, under some methods, artificial zero-length branches.
- Here, I present a stochastic algorithm for time-scaling phylogenies of fossil taxa by randomly sampling node ages from a constrained distribution, with the ultimate goal of producing large samples of time-scaled phylogenies for a given data set as the basis for phylogeny-based analyses. I describe how this stochastic approach can be extended to consider potential ancestral relationships and resolve polytomies.
- The stochastic selection of node ages in this algorithm is weighted by the probability density of the total inferable unobserved evolutionary history at single divergence events in a tree, a distribution dependent on rates of branching, extinction and sampling in the fossil record.
- The combined time-scaling method must be calibrated with explicit estimates of three rates: branching, extinction and sampling, and thus is named the cal3 time-scaling method, included in the r library paleotree. I test the time-scaling capabilities of the cal3 and older time-scaling methods in simulations. cal3 produces samples of time-scaled trees that better bracket the uncertainty in the true node ages than existing time-scaling methods. This is true even in simulations under a ‘terminal-taxon’ model of differentiation that violates many of the assumptions of the cal3 method.
- The cal3 method provides a new approach for time-scaling palaeontological cladograms, calibrated to estimated sampling and diversification rates, allowing for better estimates of uncertainty in the phylogenetic time-scaling. The cal3 method is robust to relaxation of at least some model assumptions. Additional work is needed to analyse the impact of time-scaling approaches on macroevolutionary analyses and to integrate time-scaling with phylogenetic inference.