Best Practices for Justifying Fossil Calibrations

By James, F., Parham, Philip, J. C, Donoghue, Christopher, J., Bell, Tyler and 46 more. Systematic Biology, 2011

685 citations recorded by the source corpus.

Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule, with replacement rates established (calibrated) using paleontological age estimates from textbooks (e.g., Dodson 1960). Since that time, the amount of molecular sequence data has increased dramatically, affording ever-greater opportunities to apply molecular divergence approaches to fundamental problems in evolutionary biology. To capitalize on these opportunities, increasingly sophisticated divergence dating methods have been, and continue to be, developed. In contrast, comparatively, little attention has been devoted to critically assessing the paleontological and associated geological data used in divergence dating analyses. The lack of rigorous protocols for assigning calibrations based on fossils raises serious questions about the credibility of divergence dating results (e.g., Shaul and Graur 2002; Brochu et al. 2004; Graur and Martin 2004; Hedges and Kumar 2004; Reisz and Muller 2004a, 2004b; Theodor 2004; van Tuinen and Hadly 2004a, 2004b; van Tuinen et al. 2004; Benton and Donoghue 2007; Donoghue and Benton 2007; Parham and Irmis 2008; Ksepka 2009; Benton et al. 2009; Heads 2011). The assertion that incorrect calibrations will negatively influence divergence dating studies is not controversial. Attempts to identify incorrect calibrations through the use of a posteriori methods are available (e.g., Near and Sanderson 2004; Near et al. 2005; Rutschmann et al. 2007; Marshall 2008; Pyron 2010; Dornburg et al. 2011). We do not deny that a posteriori methods are a useful means of evaluating calibrations, but there can be no substitute for a priori assessment of the veracity of paleontological data. Incorrect calibrations, those based upon fossils that are phylogenetically misplaced or assigned incorrect ages, clearly introduce error into an analysis. Consequently, thorough and explicit justification of both phylogenetic and chronologic age assessments is necessary for all fossils used for calibration. Such explicit justifications will help to ensure that divergence dating studies are based on the best available data. Unfortunately, the majority of previously published calibrations lack explicit explanations and justifications of the age and phylogenetic position of the key fossils. In the absence of explicit justifications, it is difficult to distinguish between correct and incorrect calibrations, and it becomes difficult to reevaluate previous claims in light of new data. Paleontology is a dynamic science, with new data and perspectives constantly emerging as a result of new discoveries (see Kimura 2010 for a recent case where the age of the earliest known record of a clade was more than doubled). Calibrations based upon the best available evidence at a given time can become inappropriate as the discovery of new specimens, new phylogenetic analyses, and ongoing stratigraphic and geochronologic revisions refine our understanding of the fossil record. Our primary goals in this paper are to establish the best practices for justifying fossils used for the temporal calibration of molecular phylogenies. Our examples derive mainly, but not exclusively, from the vertebrate fossil record. We hope that our recommendations will lead to more credible calibrations and, as a result, more reliable divergence dates throughout the tree of life. A secondary goal is to help the community (researchers, editors, and reviewers) who might be unfamiliar with fossils to understand and overcome the challenges associated with using paleontological data. In order to accomplish these goals, we present a specimen-based protocol for selecting and documenting relevant fossils and discuss future directions for evaluating and utilizing phylogenetic and temporal data from the fossil record. We likewise encourage biologists relying on nonfossil calibrations for molecular divergence estimates (e.g., ages of island or mountain range formations, continental drift, and biomarkers) to develop their own set of rigorous guidelines so that their calibrations may also be evaluated in a systematic way.

Subfields: Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/33d698b335a28feef60fac64c32561aecd33ad2d

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Citations in the corpus

The emerging field of geogenomics: Constraining geological problems with genetic data (2014, background): “It is the responsibility of the researcher to fully report uncertainty associated with time estimates (Bromham and Penny, 2003; Graur and Martin, 2004; Parham, 2012).”
A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera (2012, background): “DOI:10.1093/sysbio/sys058 Advance Access publication on June 20, 2012 A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera FREDRIK RONQUIST1,∗, SERAINA KLOPFSTEIN1, LARS VILHELMSEN2, SUSANNE SCHULMEISTER3, DEBRA L. MURRAY4, AND ALEXANDR P.…”
Evolutionary History of the Hymenoptera. (2017, methodology): “Divergence timeswere calibrated using 14 fossils (Data S1F), selected following best-practice recommendations [39] and representing extant lineages distributed across the entire Hymenoptera Tree of Life.”
Evolutionary origin of species diversity on the Qinghai–Tibet Plateau (2021, background): “…2021 www.jse.ac.cn 1146 Mao et al. length of the phylogeny is accurate and available fossils are correctly extracted and applied to fossil calibration (e.g., Parham et al., 2012; Wang & Mao, 2016), the age estimates from molecular dating may become more reliable than before in the future.”
The timescale of early land plant evolution (2018, positive): “To achieve this, we constructed 37 fossil calibrations with minimum and soft maximum constraints, following best practice (37).”
Constraints on the timescale of animal evolutionary history (2015, methodology): “This contribution represents one of a series, with calibration dates assessed and presented according to the principles enunciated by Parham et al. (2012).”
The peril of dating beetles (2017, methodology): “© 2016 The Royal Entomological Society, Systematic Entomology, 42, 1–10 FC, fossil calibration number; CR, Parham et al. (2012) criteria; CR1, single/multiple operational taxonomic units (OTUs) with museum numbers; CR2, apomorphy-based or phylogenetic analysis; CR3, agreement of morphology and…”
A multigene phylogeny and timeline for Trichoptera (Insecta) (2020, background): “(2014) confined their fossil calibration points according to Parham et al. (2012). No Trichoptera were included as calibrations, and the closest fossil calibration points in their study were within Lepidoptera.”
The fossilized birth–death process for coherent calibration of divergence-time estimates (2013, background): “This factor underscores the importance of carefully curated and analyzed paleontological collections, thus motivating collaboration with experts on extinct organisms and critical assessment of fossil specimens (66).”
Morphology should not be forgotten in the era of genomics—a phylogenetic perspective (2015, neutral): “ Tip dating addresses on the one side the aspect of phylogenetic uncertainty of 233 fossils (see also Parham et al., 2012), but also the concern that the date estimates are more 234 accurate when fossils appear in a specific phylogenetic position, and not…”
A Divergence Dating Analysis of Turtles Using Fossil Calibrations: An Example of Best Practices (2013, methodology): “Using current molecular hypotheses (e.g., Spinks et al., 2004), it is possible to investigate whether known morphological characters diagnose clades recovered by molecular phylogenetic analyses, thereby reconciling the morphological and molecular hypotheses as suggested by Parham et al. (2012).”