Try out PMC Labs and tell us what you think. Learn More. Molecular-based divergence dating methods, or molecular clocks, are the primary neontological tool for estimating the temporal origins of clades. While the appropriate use of vertebrate fossils as external clock calibrations has stimulated heated discussions in the paleontological community, less attention has been given to the quality and implementation of other calibration types. In lieu of appropriate fossils, many studies rely on alternative sources of age constraints based on geological events, substitution rates and heterochronous sampling, as well as dates secondarily derived from analyses.
After ing for publications with multiple investigations, a total of individual analyses were scored. Calibrations were categorized as: 1 Fossil.
To illustrate the breadth and frequency of calibration types currently employed, we conducted a literature survey of over articles published from to Current patterns in calibration practices were disproportionate to the of discussions on their proper use, particularly regarding plants and secondarily derived dates, which are both relatively neglected in methodological evaluations. We finally stress that divergence dating is a dynamic science, and that a realistic approach to dating one's clade of interest may involve a possibly suboptimal combination of the methods described below.
Summary of subjects of review-like articles published from to on the proper use of molecular clock calibrations. Calibration of the molecular clock has been shown to be the most ificant factor influencing divergence dates Inoue et al. Our goal is to identify and draw attention to areas of molecular dating research deserving of increased attention, with the hope that their respective workers will formulate a consensus on the best practices regarding choice and implementation of alternative calibration types.
Figure 1. Trends in calibration use for each type as percent of the total analyses published per year.
Original research article
Current patterns in calibration use were assessed by a survey of relevant literature published in the past seven years. Within Metazoa, arthropods were the most commonly studied group, while molluscs and other invertebrates like annelids, sponges and jellyfish were the least.
Our survey shows that from divergence dating analyses are now incorporated into an astounding array of biological and geological investigations Table 2making the accuracy and precision of divergence estimates of paramount importance to our understanding of evolutionary history. The earliest known fossil ased to a lineage provides a minimum age constraint on the divergence event i.
Figure 4. A superior alternative may be to treat fossils as non-contemporaneous terminal taxa, thus allowing direct asment of ages to fossil tips Pyron, ; Ronquist et al. While the appropriate use of vertebrate fossils as external clock calibrations has stimulated heated discussions in the paleontological community, Cary NC durden dating attention has been given to the quality and implementation of other calibration types. Based on our literature survey, below we summarize recent patterns in clock calibration use, and discuss potential pitfalls associated with each methodology.
This is particularly alarming regarding the application of secondarily derived dates as node age priors see discussion belowa practice that has more than tripled in the past seven years Figure 5. Geological calibrations are ased to internal nodes based on the assumption that phylogenetic divergence was caused by vicariance. In the absence of external calibrations, a known substitution rate may be applied to sequence data to convert genetic distance into time.
Dangers of phylogenetic misplacement have also stimulated novel approaches, in which molecular and morphological data are combined to assess uncertainty in fossil position, which is then used to determine confidence intervals surrounding dates derived from those calibrations Lee et al. Comparison of patterns in molecular clock analyses and review-like discussions regarding A calibration type and B taxonomic focus, published between and Figure 5.
As above, review-like Cary NC durden dating discussing multiple calibration types or groups were scored separately for each. Mammals were the most commonly investigated vertebrates, followed by fish, reptiles, birds and amphibians in decreasing order.
In lieu of appropriate fossils, many studies rely on alternative sources of age constraints based on geological events, substitution rates and heterochronous sampling, as well as dates secondarily derived from analyses. A list of all literature included in the survey is available in Supplementary Material.
Trend in calibration use also vary by year Figure 3with fossil and secondary calibrations showing a relative increase over time, while geological events and substitution rates show a slight decrease. These dates are now integrated into a wide array of biological investigations, including studies of ancient dispersal mechanisms, adaptive radiations and species interactions.
Fortunately, recent methods have been developed for the objective quantification of prior distributions based on stratigraphic occurrence and preservation rates of focal taxa Dornburg et al. Fifty-one publications from the past seven years were considered review-like, as they concentrated primarily on the selection and implementation of calibration data in divergence dating analyses. They are not required to present a phylogenetic tree, although they may include examples based on simulated or empirical data. The majority of discussions concentrated on fossil calibrations, with relatively few mentions of secondary calibrations or sampling dates Table 1.
Our goal is not to single out any individual study or author for criticism, but to draw attention to areas of dating research deserving of greater attention. Figure 2.
The purpose of the present study is therefore to review current patterns in calibration types employed within the major taxonomic groups e. After controlling for quality according to the conditions above, unique publications were available for survey. of distinct calibration types e.
Review-like papers should be general in taxonomic scope, i. Both empirical and theoretical work shows that the addition of fossil taxa can improve branch length estimation and phylogenetic support Wiens, ; Pyron,suggesting that combined evidence analyses may supplant purely molecular frameworks in the near future.
This issue is particularly relevant now, as time-calibrated phylogenies are used for more than dating evolutionary origins, but often serve as the backbone of investigations into biogeography, diversity dynamics and rates of phenotypic evolution. of analyses published per year Cary NC durden dating secondarily derived dates as molecular clock calibrations, showing a recent upward trend. This critique should serve as a call to action for researchers across multiple communities, particularly those working on clades for which fossil records are poor, to develop their own guidelines regarding selection and implementation of alternative calibration types.
Five analyses used anthropological events as external calibrations, which were considered unique from the other types. Patterns of molecular clock calibration types applied among major taxonomic groups from to Figure 3. As with fossils, the degree of uncertainty surrounding correspondence between the geological event and date of divergence may be expressed probabilistically. Incorporation of temporal uncertainty into dating analyses is now common practice Heled and Drummond,although parameterization of node age priors is often arbitrary or idiosyncratic at best.
Indeed, the high of citations for many review-like papers on the subject as well as the high impacts of the journals in which they are published indicates a large audience for discussions on proper calibration use. Treatment of paleontological calibrations has been discussed extensively in recent years e. This is likely because many soft-bodied organisms, including some invertebrates, plants and fungi, leave little to no fossil evidence of their ancient existences, making it impossible to implement specimen-based calibrations in reconstructions of their temporal pasts.
Therefore, explicit justification and proper implementation of clock calibrations are essential to ensuring accurate reconstructions of the evolutionary past. For single papers analyzing multiple independent data sets e. When comparing the subjects of these discussions to current divergence dating practices, some disproportion is observed regarding calibration type Figure 4A and taxonomic group Figure 4Bparticularly for plants and secondary calibrations which are both underrepresented in methodological evaluations.
Table 1. We found that although some taxonomic groups and calibration types were neglected in these discussions e. For inclusion in our survey, each paper was required to include an original phylogenetic analysis based on molecular data but could also integrate morphological characters in a total evidence approach and include an ultrametric time-calibrated tree or table or figure providing node age estimates.
The focal taxonomic group of each analysis was recorded, as well as calibration type see below. Papers focusing on the setting of parametric distributions describing calibration uncertainty e. Data sets containing sequences isolated at different times, i. Dating the Tree of Life View all 7 Articles. Temporal information is based on the date of sequence isolation for rapidly evolving organisms like viruses and bacteria, or on radiocarbon dating of preserved material from which ancient DNA is extracted Shapiro et al.
Our initial search resulted in records. The remaining 97 publications included multiple analyses, either on independent data sets or on the same data set using combinations or comparisons of two or more calibration types Figure 1. This imbalance of dialogue between researchers using alternative non-fossil-based calibrations and those focusing on paleontological material is not only detrimental to researchers wishing to reliably date their clades of interest, but also to the of many studies relying on divergence estimates as a backbone for independent analyses of, among other things, diversification dynamics, biogeography, rates of phenotypic evolution, and character correlation.
While each of these calibration types has its strengths and weaknesses, the attention they have garnered in the scientific community seems small compared to the large of commentaries, reviews and databases dedicated to the use of fossil calibrations Cary NC durden dating Parham et al.
Substitution rates may also be calculated indirectly from dated molecular phylogenies, in which case rate estimates depend on the calibration s applied in the original study Ho and Phillips, Secondary calibrations are node ages derived from analyses, applied to an independent data set without reference to the original calibration s used to generate them Shaul and Graur, This category was also reserved for studies citing a specific calibration date but no source.
Although the study mainly focuses on the vertebrate fossil record and its major divergences e. This imbalance is most dramatic for the latter, as the use of secondary calibrations has increased dramatically since Figure 5independent of the yearly increase in s of divergence dating studies in general Figure 3. Of those, were considered for clock calibration, the majority of which included a single analysis with one calibration type e.
This rate can be estimated by direct observation of genetic change, provided that the temporal range Cary NC durden dating which sequences are sampled is large relative to the rate of mutation Drummond et al. In lieu of appropriate fossils, many workers instead rely on geological events, substitution rates, known sampling dates, or secondarily and even tertiarily derived node ages to calibrate the molecular clock.
Examples include the appearance of land bridges generating barriers to gene flow in aquatic organisms minimum age constraintor the emergence of an island on which a clade is inferred to have diversified maximum age constraint Ho et al. Despite major advances in phylogenetic methods e. Surveyed patterns in calibration use are summarized in Figure 2.
Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology
Depending on the quality of the fossil record, the probability that the actual divergence falls around the fossil date may be expressed as a parametric distribution between minimum and maximum bounds i. Divergence dates estimated from molecular phylogenies provide critical information on the timing of historical evolutionary events, including the temporal origins of clades.
For serially sampled sequences, node ages are treated as exact, i.
Other advances regarding paleontological calibrations involve selection of the fossils themselves, either through single-fossil cross-validation Near et al. Molecular-based divergence dating methods, or molecular clocks, are the primary neontological tool for estimating the temporal origins of clades.
Just over one-third of discussions were general in taxonomic scope, although the majority of those citing empirical data used vertebrate examples. This article, co-written by 25 paleontologists and molecular biologists, outlines a rigorous protocol for selecting and reporting fossil-based calibrations. Based on our survey, we provide a comprehensive overview of the latest approaches in clock calibration, and outline strengths and weaknesses associated with each.
Although our list is not exhaustive, we attempt to provide a reasonable overview of calibration implementation, while focusing on progress made in the past seven years.