The effect of inappropriate calibration: three case studies in molecular ecology - PubMed (original) (raw)

The effect of inappropriate calibration: three case studies in molecular ecology

Simon Y W Ho et al. PLoS One. 2008.

Abstract

Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Phylogenetic tree illustrating the impact of using extraspecific and intraspecific calibration points.

The tree shows the locations of nucleotide changes (small vertical bars). The nucleotide changes within the study species represent segregating sites, some of which will be fixed in the long term, but most of which will be removed by drift or selection. The changes between the study species and outgroup species represent substitutions. If an estimate of the evolutionary rate is calibrated using an external calibration point, such as the split between the study and outgroup species, then the intraspecific rate will be underestimated. This will lead to an overestimation of times to divergence, including the age of the most recent common ancestor of the study species.

Figure 2

Figure 2. Bayesian skyline plots showing the recent demographic history of bowhead whales, estimated using phylogenetic analysis of three alignments of the mitochondrial control region: (a) combined alignment of 68 modern haplotypes and 99 radiocarbon-dated, ancient DNA sequences; (b) modern sequences only; and (c) ancient sequences only.

All three plots are drawn to the vertical and horizontal scales.

Figure 3

Figure 3. Maximum clade credibility tree from Bayesian analysis of mitochondrial control region sequences from 56 modern and 51 ancient brown bear samples, with a time scale calibrated using the radiocarbon dates of the ancient sequences.

Major clades and their geographic localities are given. Posterior probabilities are given for the nodes A-N, which are referred to in the text and in Table 2.

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