Timetrees: Incorporating Fossils and Molecules

Calibrating phylogenies to time is central to addressing many questions in evolutionary biology and macroevolution. The fossil record once provided our only source for establishing a timeline for evolution. However, the incompleteness of the fossil record and the non-uniformity of fossil recovery rate make it challenging to obtain precise estimates of divergence times from fossil evidence alone. Molecular dating, which combines evidence from the geological and molecular records, enables us to generate a much more complete and precise timeline of events. The molecular clock can be time-calibrated using temporal evidence from fossils and used to estimate divergence times based on the assumption that the rate of sequence evolution will be approximately constant over time and among lineages. Methodological challenges to applying this concept in practice have been to relax the assumption of constant evolutionary rates and to model the uncertainty associated with paleontological and geological calibrations. To this end, available statistical methods have become increasingly complex in order to capture key features of empirical data. These are typically applied using Bayesian inference, which provides a powerful framework for incorporating multiple sources of uncertainty.

Although overall more effort has been expended in developing models of molecular sequence evolution, critical advances have also included approaches to modeling taxonomic diversification and fossilization. In particular, recent advances in birth-death process models have allowed for continuous sampling along lineages, enabling more information from the fossil record to be incorporated into dating analyses in a statistically coherent way. In addition, available dating methods can now be applied to scenarios in which no molecular data may be available, allowing for novel insights into the evolution of entirely extinct clades. Other recent innovations enable us to date divergence times among taxa that have no fossil record, including the use of gene duplication events or biogeographic evidence.
Furthermore, time-calibrated trees are necessary for obtaining phylogenetic estimates of taxonomic diversification and extinction rates, which can now be jointly inferred along with lineage divergence times. These approaches offer an exciting opportunity to understand the evolution of life in deep time, although key challenges remain, especially with regards to modeling the processes of genome evolution, taxonomic diversification and fossil recovery.

In this Research Topic, we focus on recent advances in methodology, outstanding challenges, and the application of molecular and paleontological dating methods to empirical case studies across the Tree of Life.