Abstract
Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two nonexclusive alternative approaches have recently been developed, the “fossilized birth–death” (FBD) model and “total-evidence dating.” While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher level taxa. We here develop a flexible new approach to Bayesian age estimation that combines advantages of node dating and the FBD model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated data sets, and compare its performance to that of the FBD model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the FBD model. By applying our approach to a large data set including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for transoceanic dispersal of cichlids and other groups of teleost fishes.
Highlights
Drummond (2012), calibration densities interact with each other and with the tree prior to produce marginal prior distributions of node ages that may differ substantially and in unpredictable ways from the specified calibration density
Using a wide range of simulations, we assess the optimal scheme by which to select clades for calibration, and we show that the application of CladeAge calibration densities can result in age estimates comparable or better than those produced with the FBD model if the input rate estimates are correctly specified and only the oldest fossil of each clade is used for calibration
Comparisons for all other tested clade age thresholds are shown in Supplementary Figure S1. These results show that waiting time frequency distributions deviate from the respective CladeAge distribution in most comparisons, and the degree of disagreement depends on sampling rate ψ, on the clade age threshold, and on the applied scheme (A-D)
Summary
Drummond (2012), calibration densities interact with each other and with the tree prior to produce marginal prior distributions of node ages that may differ substantially and in unpredictable ways from the specified calibration density. In “total-evidence” dating, fossils are not explicitely assigned to any clades, but are instead included as terminal taxa The position of these tips is determined as part of the phylogenetic analysis, based on morphological character data that are required for all included fossils and at least some of the extant taxa (Pyron 2011; Ronquist et al 2012). The total-evidence approach is conceptually appealing as it is able to account for uncertainty in the phylogenetic position of fossils, and allows a more complete representation of the fossil record than node dating This approach has been found to result in ancient age estimates and long “ghost lineages” when applied to empirical data sets, leading some authors to question the suitability of morphological clocks for phylogenetic time calibration (Beck and Lee. 2014; Arcila et al 2015; O’Reilly et al 2015). The developments of more realistic sampling schemes (Höhna et al 2011) and advanced models of morphological character evolution (Wright et al 2016) are likely to improve age estimates obtained with total-evidence dating, but have so far been applied only rarely (Klopfstein et al 2015; Zhang et al 2016)
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