Biogeographic calibrations for the molecular clock

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.

Transoceanic origin of microendemic and flightless New Caledonian weevils

“…We also reject an ancient origin of New Caledonian Trigonopterus and thus the museum hypothesis, as their main diversification was fast and during the past 10 Myr, whereas the museum hypothesis would require a crown and a diversification of New Caledonian Trigonopterus over at least 80 Ma [31]. Even if our biogeographic dating analysis is not optimal (but see [50]), the differences between our estimates and the requirements for a Gondwanan origin are so distinct that we can here reject such a scenario. Instead, we suggest a recent long-distance dispersal with a Melanesian origin for the New Caledonian Trigonopterus .…”

Bayesian spatio‐temporal reconstruction reveals rapid diversification and Pleistocene range expansion in the widespread columnar cactus Pilosocereus

“…Comparable divergence time estimates in Cereus hildmannianus Mill. (Silva et al., ) and the Pilosocereus aurisetus species complex (Bonatelli et al., ) are probably upwardly biased due to the use of distant fossil calibrations and improper tree priors when there is ongoing gene flow (Ho et al., ). If our age estimates are right, species divergence was rapid with a net diversification rate resembling those exhibited by some island radiations (Vitales et al., ).…”

Temperature gradient affects differentiation of gene expression and SNP allele frequencies in the dominant Lake Baikal zooplankton species

“…The only estimate of divergence from the non‐Baikal relatives is available from the internal transcribed spacer (ITS) and COI sequences from E. baikalensis and E. chankensis from the Far‐East Lake Khanka (I. Zaidykov, unpublished data ), showing, respectively, 5.9% and 19.3% divergence between the two species for the ITS and COI sequences, respectively. Biogeography‐based calibrations are difficult, and few of the necessary assumptions (Ho et al., ) can be met for this comparison, but, as a very rough estimate, one can use the calibration of Lee () who estimated divergence time among East Atlantic, West Atlantic and Pacific populations/cryptic species of Epischura's marine relative Eurytemora affinis . She observed a similar level of differentiation in COI sequences (~10%–25%) and was able to calibrate the divergence time using established 16S calibration, with the same populations showing ~5% 16S divergence, at approximately 5.1 My.…”