Molecular and morphological clocks for estimating evolutionary divergence times

Jose Barba-Montoya,Sudhir Kumar,Qiqing Tao

doi:10.1186/s12862-021-01798-6

Jose Barba-Montoya, Sudhir Kumar

Open Access

https://doi.org/10.1186/s12862-021-01798-6

Copy DOI

Abstract

BackgroundMatrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference.ResultsWe systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur as some intermediate nodes may show large time differences between these two types of data.ConclusionsOur findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before any dating analysis using combined datasets.

Highlights

Matrices of morphological characters are frequently used for dating species divergence times in sys‐ tematics
Overall, our study allows us to conclude that (1) relative maximum likelihood (ML) branch lengths between morphological and molecular characters were very different, but relative node-to-tip distances were considerably more concordant, suggesting a much more concordant time structure in the morphological and molecular dataset than that captured in the comparison of branch lengths
(2) When no internal calibrations were applied, morphological and molecular clock produced time estimates with a high correlation, which may be caused by the same speciation tree prior applied in the joint consideration of molecular and morphological data in the Bayesian analyses

Summary

Introduction

Matrices of morphological characters are frequently used for dating species divergence times in sys‐ tematics. It is important to evaluate whether the time structure in morphological data is concordant with the time structure in the molecular data Such concordance will greatly enhance the utility of total-evidence methods in which morphological characters from extinct taxa are combined [10, 12, 13]. It has implications for FBD dating approaches when molecular and morphological data are jointly used [17] (Fig. 1)

Methods

Results

Conclusion