Trends in Genetics
Volume 19, Issue 4, April 2003, Pages 200-206
Journal home page for Trends in Genetics

Genomic clocks and evolutionary timescales

https://doi.org/10.1016/S0168-9525(03)00053-2Get rights and content

Abstract

For decades, molecular clocks have helped to illuminate the evolutionary timescale of life, but now genomic data pose a challenge for time estimation methods. It is unclear how to integrate data from many genes, each potentially evolving under a different model of substitution and at a different rate. Current methods can be grouped by the way the data are handled (genes considered separately or combined into a ‘supergene’) and the way gene-specific rate models are applied (global versus local clock). There are advantages and disadvantages to each of these approaches, and the optimal method has not yet emerged. Fortunately, time estimates inferred using many genes or proteins have greater precision and appear to be robust to different approaches.

Section snippets

Tests of rate variation among lineages

One of the first steps in estimating time is to test for rate variation between lineages, keeping in mind that some variation is expected by chance 5, 15 (Box 1; Fig. 2). Because the probability of rejecting the null hypothesis (rate constancy) is low for slow evolving and/or small genes and proteins, some rate variation could go undetected (type ii error), possibly resulting in biased time estimates. But the stringency of the relative rate test can be increased by tightening the statistical

Global clock methods

Global clock methods use a constant rate model of nucleotide or amino acid substitution in a given gene or genomic segment (not between genes). Although they are often characterized as assuming (a priori) rate constancy, relative rate tests are used in almost all global clock studies. Genes and lineages that are rejected in the rate tests are usually removed from later analyses if they cause an overall bias 16, 19, 21, 22. Each gene that is not rejected in relative rate tests can be considered

Local clock methods

Local clock methods use a model of nucleotide or amino acid substitution in which rate is not constant among all branches of the tree, but can vary from one ‘local’ branch to another. Although these methods ‘relax’ one parameter (constant rate), they impose others, and therefore they are neither model-free nor assumption-free. An immediate advantage of local clock methods is that they can make use of genes discarded by rate tests in the global methods. However, smaller portions (e.g. branches)

Evolutionary timescales

Global and local clock methods have been used with large numbers of genes and proteins to estimate divergence time in a diversity of organisms. The results have shown that fossil and molecular clock based estimates are in much better agreement than often appreciated. This is evident from a scatter plot (Fig. 1b) and a timeline of organismal evolution (Fig. 6) based on time estimates from large numbers of nuclear genes and corresponding dates from the fossil record. Fossil-based estimates of

Conclusions

The availability of genomic data from an increasing number of species, especially model organisms, has created a demand for improved methods of divergence time estimation to help understand the temporal component of the tree of life [3]. Here, we have focused on the development and comparison of new molecular clock methods that can be used with large numbers of genes. There is a surprising diversity of methods available and no clear evidence that any particular approach is superior. Additional

Acknowledgements

We thank Jaime Blair, Robert Friedman, Sankar Subramanian, and Koichiro Tamura for comments on the manuscript. Supported by the NASA Astrobiology Institute (S.B.H.), National Science Foundation (S.B.H., S.K.), National Institutes of Health (S.K.), and Burroughs Wellcome Fund (S.K.).

Glossary

Glossary

Adaptive radiation:
the rapid diversification of a group of species into various habitats over a relatively short period of geological time.
Lineage:
a single branch, or series of connected branches, in an evolutionary tree usually leading to living species or group of species.
Mutation rate:
the number of mutations occurring in germ-line cells per nucleotide site, per gene or genome, or per unit of time or cell division.
Outgroup:
a species or group of species known to be outside of the group under

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