Abstract
The fossil record is well known to be incomplete. Read literally, it provides a distorted view of the history of species divergence and extinction, because different species have different propensities to fossilize, the amount of rock fluctuates over geological timescales, as does the nature of the environments that it preserves. Even so, patterns in the fossil evidence allow us to assess the incompleteness of the fossil record. While the molecular clock can be used to extend the time estimates from fossil species to lineages not represented in the fossil record, fossils are the only source of information concerning absolute (geological) times in molecular dating analysis. We review different ways of incorporating fossil evidence in modern clock dating analyses, including node-calibrations where lineage divergence times are constrained using probability densities and tip-calibrations where fossil species at the tips of the tree are assigned dates from dated rock strata. While node-calibrations are often constructed by a crude assessment of the fossil evidence and thus involves arbitrariness, tip-calibrations may be too sensitive to the prior on divergence times or the branching process and influenced unduly affected by well-known problems of morphological character evolution, such as environmental influence on morphological phenotypes, correlation among traits, and convergent evolution in disparate species. We discuss the utility of time information from fossils in phylogeny estimation and the search for ancestors in the fossil record.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.
Highlights
Approaches to inference of evolutionary history have a patchy record, punctuated as much by the discovery of new types of data, as by changing philosophies in which data are interpreted
Molecular clock methodology is undergoing a period of development unparalleled in the half century since the molecular clock hypothesis was first formulated
There is a broader palate of methods and approaches to divergence time estimation than there has been at any time in the past and these may be assembled in a combination that best suits the testing of the hypothesis at hand
Summary
Approaches to inference of evolutionary history have a patchy record, punctuated as much by the discovery of new types of data, as by changing philosophies in which data are interpreted. For many palaeontologists, stratigraphic time has little role in phylogeny estimation, except in providing minimum ages to calibrate morphology-based cladograms to time, or in discriminating among multiple trees of equal likelihood or parsimony [14] This is not to say that ancestors do not exist in the fossil record [15,16,17] and failure to accommodate fossil species will result in the perception of gaps in the fossil record where there are none [18,19,20]. We highlight challenges confronting the latest methodological developments in divergence time estimation and show that these retread long-standing debates associated with phylogeny and timescale estimation in palaeontology, from which insights might be gained for the future development of molecular clock methodology
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