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.
Highlights
Evolutionary time-scales estimated from molecular data form the foundation for a diverse range of molecular ecological studies, including those of biogeography, speciation, conservation genetics, and population biology
Cyclical glacial advance and retreat produced dramatic changes in local environmental conditions over the past 250 kyr [33], leading to the view that these changes were conducive to an increased rate of avian speciation, a concept embodied in the ‘‘Late Pleistocene Origins’’ (LPO) hypothesis [for a recent review, see 1]
This hypothesis readily lends itself to testing because it makes specific predictions about divergence times, which can be estimated from molecular data
Summary
Evolutionary time-scales estimated from molecular data form the foundation for a diverse range of molecular ecological studies, including those of biogeography, speciation, conservation genetics, and population biology. We can measure the phylogenetic distinctiveness of a species or the antiquity of a specific population [7,8], while past and present effective population sizes can be inferred in studies of population biology [9,10]. All of these studies depend on accurate estimates of molecular time-scales and substitution rates which, primarily due to methodological limitations, have been made with varying degrees of rigour in the past. A third calibration method is the inclusion of heterochronous sequences of known age, such as ancient DNA sequences extracted from radiocarbon-dated samples [16,17]
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