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Review
. 2015 Sep;11(9):20150194.
doi: 10.1098/rsbl.2015.0194.

Biogeographic calibrations for the molecular clock

Simon Y W Ho  1 , K Jun Tong  2 , Charles S P Foster  2 , Andrew M Ritchie  2 , Nathan Lo  2 , Michael D Crisp  3
Affiliations
Review

Biogeographic calibrations for the molecular clock

Simon Y W Ho et al. Biol Lett. 2015 Sep.

Abstract

Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses.

Keywords: Bayesian phylogenetics; biogeography; calibration; divergence dating; molecular clock.

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Figures

Figure 1.
Figure 1.
Biogeographic calibrations can be used in a number of ways. If a geological or climatic event has had an evolutionary or demographic impact, it can be used to calibrate molecular clocks. The age of the biogeographic event must be estimated by independent means, with the associated uncertainty being taken into account. Based on this information, an age constraint or prior distribution can be applied to (a) a divergence event in a phylogenetic tree or genealogy; (b) an estimated shift in diversification rate, as shown here in a lineages-through-time plot; or (c) an inferred change in the population size of a species. (Online version in colour.)
Figure 2.
Figure 2.
Three biogeographic processes that can be used to provide calibrations for molecular clocks. (a) Vicariance involves the formation of a barrier that causes a reduction in gene flow. Here, the fragmentation of a landmass causes a population of palms to split into two. (b) Geodispersal involves the removal of a barrier to gene flow, allowing movement into a new area. Here, the emergence of an isthmus allows a shrew to colonize a new land mass. (c) Biological dispersal involves the movement of an organism across a barrier. In this example, a passerine on the mainland disperses to an island and establishes a new population. (Online version in colour.)
See this image and copyright information in PMC

References

    1. Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu. Rev. Ecol. Syst. 33, 707–740. ( 10.1146/annurev.ecolsys.33.010802.150500) - DOI
    1. Zuckerkandl E, Pauling L. 1962. Molecular disease, evolution, and genic heterogeneity. In Horizons in biochemistry (eds Kasha M, Pullman B), pp. 189–225. New York, NY: Academic Press.
    1. Ho SYW, Duchêne S. 2014. Molecular-clock methods for estimating evolutionary rates and timescales. Mol. Ecol. 23, 5947–5965. ( 10.1111/mec.12953) - DOI - PubMed
    1. Donoghue PC, Benton MJ. 2007. Rocks and clocks: calibrating the tree of life using fossils and molecules. Trends Ecol. Evol. 22, 424–431. ( 10.1016/j.tree.2007.05.005) - DOI - PubMed
    1. Heath TA, Huelsenbeck JP, Stadler T. 2014. The fossilized birth-death process for coherent calibration of divergence-time estimates. Proc. Natl Acad. Sci. USA 111, E2957–E2966. ( 10.1073/pnas.1319091111) - DOI - PMC - PubMed

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