Assessing Calibration Uncertainty in Molecular Dating: The Assignment of Fossils to Alternative Calibration Points

Rutschmann, Frank; Eriksson, Torsten; Salim, Kamariah Abu; Conti, Elena

doi:10.1080/10635150701491156

Cited by 128 publications

(113 citation statements)

References 113 publications

(148 reference statements)

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“…One way to improve the accuracy of molecular time estimates is to use multiple fossil constraints (Graur and Martin 2004;Hedges and Kumar 2004;Rutschmann et al, 2007;Sauquet et al 2012). However, the very small number of well-preserved and identifiable lichen fossils is a limiting factor in dating studies, and in our particular case there are currently no more available fossils.…”

Section: Divergence Time Estimatesmentioning

confidence: 99%

Phylogeny, taxonomy and diversification events in the Caliciaceae

Prieto

Wedin

2016

Fungal Diversity

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Although the high degree of non-monophyly and parallel evolution has long been acknowledged within the mazaediate Caliciaceae (Lecanoromycetes, Ascomycota), a natural re-classification of the group has not yet been accomplished. Here we constructed a multigene phylogeny of the Caliciaceae-Physciaceae clade in order to resolve the detailed relationships within the group, to propose a revised classification, and to perform a dating study. The few characters present in the available fossil and the complex character evolution of the group affects the interpretation of morphological traits and thus influences the assignment of the fossil to specific nodes in the phylogeny, when divergence time analyses are carried out. Alternative fossil assignments resulted in very different time estimates and the comparison with the analysis based on a secondary calibration demonstrates that the most likely placement of the fossil is close to a terminal node rather than a basal placement in the Calicium clade. Our dating analysis show two successive events giving rise to main clades of mazaediate taxa within the Caliciaceae, in the Upper-Lower Cretaceous boundary and in the Paleocene. As a result of this study, Cyphelium is synonymized with Calicium, Acolium is resurrected, and the new genera Allocalicium and Pseudothelomma are described. Twelve new combinations are proposed: Acolium karelicum, Acolium marcianum, Allocalicium adaequatum, Calicium carolinianum, Calicium lecideinum, Calicium lucidum, Calicium notarisii, Calicium pinicola, Calicium trachyliodes, Pseudothelomma occidentale, Pseudothelomma ocellatum and Thelomma brunneum. A key for the mazaedium-producing Caliciaceae is included.

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Section: Divergence Time Estimatesmentioning

confidence: 99%

Phylogeny, taxonomy and diversification events in the Caliciaceae

Prieto

Wedin

2016

Fungal Diversity

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“…CV procedures were also developed to assess consistency between fossil and molecular age estimates (Near and Sanderson 2004;Near et al 2005;Rutschmann et al 2007). They aim to detect point calibrations that poorly predict other calibration dates in the dataset, and are therefore suspected to be erroneous.…”

Section: Fossil Accuracy Assessmentmentioning

confidence: 99%

On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks

Eme

Sharpe

Brown

et al. 2014

Cold Spring Harbor Perspectives in Biology

209

153

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Our understanding of the phylogenetic relationships among eukaryotic lineages has improved dramatically over the few past decades thanks to the development of sophisticated phylogenetic methods and models of evolution, in combination with the increasing availability of sequence data for a variety of eukaryotic lineages. Concurrently, efforts have been made to infer the age of major evolutionary events along the tree of eukaryotes using fossilcalibrated molecular clock-based methods. Here, we review the progress and pitfalls in estimating the age of the last eukaryotic common ancestor (LECA) and major lineages. After reviewing previous attempts to date deep eukaryote divergences, we present the results of a Bayesian relaxed-molecular clock analysis of a large dataset (159 proteins, 85 taxa) using 19 fossil calibrations. We show that for major eukaryote groups estimated dates of divergence, as well as their credible intervals, are heavily influenced by the relaxed molecular clock models and methods used, and by the nature and treatment of fossil calibrations. Whereas the estimated age of LECA varied widely, ranging from 1007 (943-1102) Ma to 1898 (1655 -2094) Ma, all analyses suggested that the eukaryotic supergroups subsequently diverged rapidly (i.e., within 300 Ma of LECA). The extreme variability of these and previously published analyses preclude definitive conclusions regarding the age of major eukaryote clades at this time. As more reliable fossil data on eukaryotes from the Proterozoic become available and improvements are made in relaxed molecular clock modeling, we may be able to date the age of extant eukaryotes more precisely.

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“…These methodological advances facilitate comprehensive quantification of uncertainty in molecular dating, whose sources include analysis of molecular sequence data (e.g., inter-partition conflict) and the use of fossil taxa as calibration points. Sources of uncertainty engendered by fossil calibrators include estimating the age of each fossil, the accurate assignment of fossils in the phylogeny, the use of appropriate prior distributions for fossil calibrators, and potential conflict between multiple calibration points [14][15][16]. Consequently, even under relaxed clock methods, molecular dates often have very large variance.…”

Section: Introductionmentioning

confidence: 99%

Cross-bracing uncalibrated nodes in molecular dating improves congruence of fossil and molecular age estimates

Sharma

Wheeler

2014

Front Zool

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Introduction: The practice of molecular dating is an essential tool for hypothesis testing in evolutionary biology. Vagaries of fossilization and taphonomic bias commonly engender high uncertainty in molecular dating in taxonomic groups wherein few fossils can be unambiguously assigned to phylogenetic nodes. A recent and novel implementation in molecular dating, "cross-bracing", exploits gene duplications by formally linking calibrated node dates throughout the paralogous subtrees through hierarchical Bayesian models. An unexplored refinement of this method is cross-bracing nodes with unknown dates, in addition to calibrated nodes, such that all nodes representing the same cladogenetic events have linked priors. We applied such a refinement to molecular dating in chelicerates, one of the earliest groups of arthropods present in the fossil record, but whose molecular dating has been greatly inconsistent in the literature. We inferred divergence times using hemocyanin paralogs isolated from de novo assembled transcriptomic libraries, and multiple fossil calibrations. Results: We show that extending cross-bracing to uncalibrated nodes greatly reduced variance in estimates of divergence times throughout the phylogeny, particularly for estimated diversification ages of spiders and scorpions, whereas cross-bracing calibrated nodes alone did not affect age estimation for uncalibrated, derived clades. Comparing ages inferred with extended cross-bracing to the fossil record, we observe smaller gaps between diversification and the first appearance of crown group fossils than have previously been inferred, particularly for spiders. Our dating indicates that scorpions have a Silurian origin, but diversification of extant lineages occurred near the Triassic-Jurassic boundary, falsifying previous inference of Permian diversification age based on extant distribution alone. Conclusion: The significant reduction of variance in divergence time estimates upon extending cross-bracing to uncalibrated nodes makes this approach greatly suited for evolutionary inference in groups with poor fossil records, with particular reference to terrestrial arthropods.

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Assessing Calibration Uncertainty in Molecular Dating: The Assignment of Fossils to Alternative Calibration Points

Cited by 128 publications

References 113 publications

Phylogeny, taxonomy and diversification events in the Caliciaceae

Phylogeny, taxonomy and diversification events in the Caliciaceae

On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks

Cross-bracing uncalibrated nodes in molecular dating improves congruence of fossil and molecular age estimates

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