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The Concept of the Modern Molecular Clock and Experience in Estimating Divergence Times of Eulipotyphla and Rodentia

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Abstract

Almost 60 years have passed since the degree of DNA difference between two species was discovered to be a function of the time since their divergence. Later, it became clear that there is no universal molecular clock and the rate of molecular evolution varies greatly depending on the gene and phylogenetic lineage, correlating with biological characteristics (generation length, body size, and fertility) and features of the genome. The development of the molecular clock concept is associated with progress in methods that allow the degree of inconstancy of the rate of molecular evolution to be taken into account and measured. Currently, dating is mostly performed using Relaxed Clock methods, which rely on various models of the evolution rate (for example, with or without autocorrelation of rates in adjacent branches). Another relevant factor that allows reduction of the errors of molecular dating is the increase in the amount of data up to the genomic level, which enhances the requirements for computationally efficient algorithms and the methods of data partitioning. A separate problem is the time dependence of evolutionary rate estimates (the phenomenon of rate decay), which is especially important for the analysis of recent history. In the absence of an adequate sequence evolution model, time estimates can be significantly biased, which often affects the results obtained with mtDNA. One of the most important trends is the development of methods for obtaining calibration information: the more complete use of the constantly and rapidly growing volume of paleontological data, the analysis of paleoDNA, and other variants of heterochronous data. Despite the fact that the accuracy of estimates of the levels of molecular divergences continues to grow, the uncertainty in dating persists, largely due to the ambiguity of calibrations and the shortcomings of existing models of DNA sequence evolution.

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Funding

The study was supported by the Russian Foundation for Basic Research, project no. 20-14-50062.

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  1. Faculty of Biology, Moscow State University, 119991, Moscow, Russia

    A. A. Bannikova

  2. Zoological Museum, Moscow State University, 125009, Moscow, Russia

    V. S. Lebedev

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  1. A. A. Bannikova
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Bannikova, A.A., Lebedev, V.S. The Concept of the Modern Molecular Clock and Experience in Estimating Divergence Times of Eulipotyphla and Rodentia. Biol Bull Rev 12, 459–482 (2022). https://doi.org/10.1134/S2079086422050024

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