Skip to content

The impact of fossil stratigraphic ranges on tip-calibration, and the accuracy and precision of divergence time estimates

Research output: Contribution to journalArticle

Standard

The impact of fossil stratigraphic ranges on tip-calibration, and the accuracy and precision of divergence time estimates. / Püschel, Hans; O'Reilly, Joseph; Pisani, Davide; Donoghue, Philip.

In: Palaeontology, 09.05.2019.

Research output: Contribution to journalArticle

Harvard

APA

Vancouver

Author

Bibtex

@article{04b0c77b7d074555aec09c19161e1770,
title = "The impact of fossil stratigraphic ranges on tip-calibration, and the accuracy and precision of divergence time estimates",
abstract = "The molecular clock currently provides the only viable means of establishing realistic evolutionary timescales but it remains unclear how best to calibrate divergence time analyses. Calibrations can be applied to the tips and/ or to the nodes of a phylogeny. Tip-calibration is an attractive approach since it allows fossil species to be included alongside extant relatives in molecular clock analyses. However, most fossil species are known from multiple stratigraphic horizons and it remains unclear how such age ranges should be interpreted to codify tip-calibrations. We use simulations and empirical data to explore the impact on precision and accuracy of different approaches to informing tip-calibrations. In particular, we focus on the effect of using tip-calibrations defined using the oldest versus youngest stratigraphic occurrences, the full stratigraphic range, as well as confidence intervals on these data points. The results of our simulations show that using different calibration approaches leads to different divergence-time estimates and demonstrate that concentrating tip-calibrations near the root of the dated phylogeny improves both precision and accuracy of estimated divergence times. Finally, our results indicate that the highest levels of accuracy and precision are achieved when fossil tips are calibrated based on the fossil occurrence from which the morphological data was derived. These trends were corroborated by analysis of an empirical dataset for Ursidae. Overall, we conclude that tip-dating analyses should, in particular, employ tip calibrations close to the root of the tree and they should be calibrated based on the age of the fossil used to inform the morphological data used in Total Evidence Dating.",
keywords = "molecular clock, simulation, fossil, divergence time, tip-calibration, Ursidae",
author = "Hans P{\"u}schel and Joseph O'Reilly and Davide Pisani and Philip Donoghue",
year = "2019",
month = "5",
day = "9",
language = "English",
journal = "Palaeontology",
issn = "0031-0239",
publisher = "Wiley",

}

RIS - suitable for import to EndNote

TY - JOUR

T1 - The impact of fossil stratigraphic ranges on tip-calibration, and the accuracy and precision of divergence time estimates

AU - Püschel, Hans

AU - O'Reilly, Joseph

AU - Pisani, Davide

AU - Donoghue, Philip

PY - 2019/5/9

Y1 - 2019/5/9

N2 - The molecular clock currently provides the only viable means of establishing realistic evolutionary timescales but it remains unclear how best to calibrate divergence time analyses. Calibrations can be applied to the tips and/ or to the nodes of a phylogeny. Tip-calibration is an attractive approach since it allows fossil species to be included alongside extant relatives in molecular clock analyses. However, most fossil species are known from multiple stratigraphic horizons and it remains unclear how such age ranges should be interpreted to codify tip-calibrations. We use simulations and empirical data to explore the impact on precision and accuracy of different approaches to informing tip-calibrations. In particular, we focus on the effect of using tip-calibrations defined using the oldest versus youngest stratigraphic occurrences, the full stratigraphic range, as well as confidence intervals on these data points. The results of our simulations show that using different calibration approaches leads to different divergence-time estimates and demonstrate that concentrating tip-calibrations near the root of the dated phylogeny improves both precision and accuracy of estimated divergence times. Finally, our results indicate that the highest levels of accuracy and precision are achieved when fossil tips are calibrated based on the fossil occurrence from which the morphological data was derived. These trends were corroborated by analysis of an empirical dataset for Ursidae. Overall, we conclude that tip-dating analyses should, in particular, employ tip calibrations close to the root of the tree and they should be calibrated based on the age of the fossil used to inform the morphological data used in Total Evidence Dating.

AB - The molecular clock currently provides the only viable means of establishing realistic evolutionary timescales but it remains unclear how best to calibrate divergence time analyses. Calibrations can be applied to the tips and/ or to the nodes of a phylogeny. Tip-calibration is an attractive approach since it allows fossil species to be included alongside extant relatives in molecular clock analyses. However, most fossil species are known from multiple stratigraphic horizons and it remains unclear how such age ranges should be interpreted to codify tip-calibrations. We use simulations and empirical data to explore the impact on precision and accuracy of different approaches to informing tip-calibrations. In particular, we focus on the effect of using tip-calibrations defined using the oldest versus youngest stratigraphic occurrences, the full stratigraphic range, as well as confidence intervals on these data points. The results of our simulations show that using different calibration approaches leads to different divergence-time estimates and demonstrate that concentrating tip-calibrations near the root of the dated phylogeny improves both precision and accuracy of estimated divergence times. Finally, our results indicate that the highest levels of accuracy and precision are achieved when fossil tips are calibrated based on the fossil occurrence from which the morphological data was derived. These trends were corroborated by analysis of an empirical dataset for Ursidae. Overall, we conclude that tip-dating analyses should, in particular, employ tip calibrations close to the root of the tree and they should be calibrated based on the age of the fossil used to inform the morphological data used in Total Evidence Dating.

KW - molecular clock

KW - simulation

KW - fossil

KW - divergence time

KW - tip-calibration

KW - Ursidae

M3 - Article

JO - Palaeontology

JF - Palaeontology

SN - 0031-0239

ER -