Advances in Time Estimation Methods for Molecular Data

Abstract

Molecular dating has become central to placing a temporal dimension on the tree of life. Methods for estimating divergence times have been developed for over 50 years, beginning with the proposal of molecular clock in 1962. We categorize the chronological development of these methods into four generations based on the timing of their origin. In the first generation approaches (1960s-1980s), a strict molecular clock was assumed to date divergences. In the second generation approaches (1990s), the equality of evolutionary rates between species was first tested and then a strict molecular clock applied to estimate divergence times. The third generation approaches (since ∼2000) account for differences in evolutionary rates across the tree by using a statistical model, obviating the need to assume a clock or to test the equality of evolutionary rates among species. Bayesian methods in the third generation require a specific or uniform prior on the speciation-process and enable the inclusion of uncertainty in clock calibrations. The fourth generation approaches (since 2012) allow rates to vary from branch to branch, but do not need prior selection of a statistical model to describe the rate variation or the specification of speciation model. With high accuracy, comparable to Bayesian approaches, and speeds that are orders of magnitude faster, fourth generation methods are able to produce reliable timetrees of thousands of species using genome scale data. We found that early time estimates from second generation studies are similar to those of third and fourth generation studies, indicating that methodological advances have not fundamentally altered the timetree of life, but rather have facilitated time estimation by enabling the inclusion of more species. Nonetheless, we feel an urgent need for testing the accuracy and precision of third and fourth generation methods, including their robustness to misspecification of priors in the analysis of large phylogenies and data sets.

Mammal madness: is the mammal tree of life not yet resolved?

“…New approaches for molecular dating include total evidence or tip dating, but these approaches are dependent on accurate phylogenies and should be used cautiously given potential problems with morphological and palaeontological character data for placental mammals (e.g. correlated homoplasy, taphonomic biases, incompleteness) that are surpassed by the quantity, quality and unambiguity of molecular data [109][110][111]. Future clever and novel integrative research based on molecules, fossils and timetree estimation methods will be required to resolve the timing of origination and diversification of mammals.…”

Reliable confidence intervals for RelTime estimates of evolutionary divergence times

“…Reliable inference of the confidence intervals around the estimates of divergence times is essential for testing biological hypotheses (Burbrink and Pyron 2008;Kumar and Hedges 2016).…”

Evolution of a dextral lineage by left-right reversal inCristataria(Gastropoda, Pulmonata, Clausiliidae)

“…Due to the lack of fossil calibration points, a direct estimation of the divergence times of species and genera within Alopiinae is currently not attainable. However, fourth generation time estimation methods in molecular data do not require a priori selection of a statistical model for rate variation or the specification of speciation mode (Kumar & Hedges, ; Tamura et al.,). The results of our RelTime analysis estimated that the earliest speciation events within the genus Cristataria occurred between those of the two subgenera of Carinigera , and nearly 2.5 times earlier than divergence within the genus Alopia .…”