Accurate timetrees require accurate calibrations

Tao, Qiqing; Walker, Mark; Kumar, Sudhir

doi:10.1073/pnas.1812558115

Cited by 28 publications

(35 citation statements)

References 5 publications

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“…Hedges et al (3) argue that the results of our study are not robust to dating strategies since removal of maximum constraints (maxima) results in significantly older clade age estimates. They conducted experiments by removing Paleozoic maxima and all clade age constraints bar for spermatophytes.…”

contrasting

confidence: 57%

Reply to Hedges et al.: Accurate timetrees do indeed require accurate calibrations

Morris

Puttick

Clark

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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contrasting

confidence: 57%

Reply to Hedges et al.: Accurate timetrees do indeed require accurate calibrations

Morris

Puttick

Clark

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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“…Node dating with fossils is thus still the standard in the field of molecular dating, but its reputation has suffered considerably due to reports of limited reproducibility: several studies that have used identical molecular datasets and the same suite of fossils repeatedly arrive at drastically different age estimates. This has been demonstrated in various taxonomic groups, such as insects (Tong et al 2014), arthropods (Warnock et al 2012), metazoans (dos Reis et al 2015) and land plants (Hedges et al 2018; Morris et al 2018b). The reason for these discrepancies lies in the way that node calibrations are derived from the fossil record.…”

Section: Introductionmentioning

confidence: 94%

“…If it is true that the geological conditions during that time were particularly adverse to fossilisation processes, or if the respective strata simply have not survived to the present day, then the microfossil record of early land plants might not be very complete after all. Indeed, a recent molecular dating study on the age of land plants inferred ages between 473 and 515 Ma ago (Morris et al 2018b), and if anything, these results were themselves criticised as being too young (Hedges et al 2018; Morris et al 2018a).…”

Section: How Old Are Land Plants?mentioning

confidence: 99%

The age of insects and the revival of the minimum age tree

Klopfstein

2020

Austral Entomology

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Deriving node calibrations from fossils remains by far the most common method for attaching an absolute timescale to a molecular tree. But this 'node dating' approach has a credibility problem: different studies using the same molecular data and even the same sets of fossils regularly arrive at drastically different age estimates. A major reason for these differences is well known: even well‐dated and firmly placed fossils can only provide a minimum age for a particular node. The time lag between that node and the fossil (or in other words: between the origin of a clade and its first appearance in the fossil record) is on the other hand notoriously difficult to quantify. Using recent studies on the age of the insect tree of life as an example, I discuss different rationales for choosing calibration priors based on fossils and argue that none of them is entirely convincing. I thus suggest shifting the objective of node dating analyses back to what can be achieved in a scientifically justifiable way: a dated tree that reflects the minimum ages of its constituent taxa. While this interpretation of time trees was followed widely in the early years of molecular dating, its conceptual advantages seem to have been suppressed over the promises of methods that allow integrating more complex node‐age constraints, even when those are difficult to justify. I argue that ‘minimum age trees’ should be revived for groups for which more sophisticated approaches, such as total‐evidence dating, are currently infeasible. Although minimum age trees do not provide mean estimates for the age of a group, they hold a lot of information in their own right and allow the testing of various hypotheses from the areas of biogeography and co‐evolution, while avoiding reliance on ad hoc assumptions about calibration densities.

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“…However, it is essential to note that the use of incorrect calibration constraints or densities can significantly impact the precision of time estimates (Warnock et al 2017). Therefore, one needs to examine the reliability of calibrations before conducting dating analyses (Andújar et al 2014;Battistuzzi et al 2015;Hedges et al 2018).…”

Section: Reltime Produces Cis Comparable To Bayesian Hpd Intervals Inmentioning

confidence: 99%

Reliable confidence intervals for RelTime estimates of evolutionary divergence times

Tao

Tamura

Mello

et al. 2019

Preprint

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Confidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated with clock calibrations. Reliable tests of biological hypotheses demand reliable CIs. However, current non-Bayesian methods may produce unreliable CIs because they do not incorporate rate variation among lineages and interactions among clock calibrations properly. Here, we present a new analytical method to calculate CIs of divergence times estimated using the RelTime method, along with an approach to utilize multiple calibration uncertainty densities in these analyses. Empirical data analyses showed that the new methods produce CIs that overlap with Bayesian highest posterior density (HPD) intervals. In the analysis of computersimulated data, we found that RelTime CIs show excellent average coverage probabilities, i.e., the true time is contained within the CIs with a 95% probability. These developments will encourage broader use of computationally-efficient RelTime approach in molecular dating analyses and biological hypothesis testing.

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Accurate timetrees require accurate calibrations

Cited by 28 publications

References 5 publications

Reply to Hedges et al.: Accurate timetrees do indeed require accurate calibrations

Reply to Hedges et al.: Accurate timetrees do indeed require accurate calibrations

The age of insects and the revival of the minimum age tree

Reliable confidence intervals for RelTime estimates of evolutionary divergence times

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