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113 results for “Fossil calibration”
Data from: A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa
1.) Applying phylogeny-based analyses of trait evolution and diversification in the fossil record generally involves transforming an unscaled cladogram into a phylogeny scaled to geologic time. Current methods produce single time-scaled phylogenies with artificial zero-length branches and no indication of the uncertainty in the temporal relationships. 2.) Here I present a stochastic algorithm for time-scaling phylogenies of fossil taxa by randomly sampling node ages from a constrained distribution, with the ultimate goal of producing large samples of time-scaled phylogenies for a given dataset as the basis for phylogeny-based analyses. I describe how this stochastic approach can be extended to consider potential ancestral relationships and resolve polytomies. 3) The stochastic selection of node ages in this algorithm is weighted by the probability density of the total inferable unobserved evolutionary history at single divergence events in a tree, a distribution dependent on rates of branching, extinction and sampling in the fossil record. 4) The combined time-scaling method must be calibrated with explicit estimates of three rates: branching, extinction and sampling, and thus is named the cal3 time-scaling method, included in the R library paleotree. I test the time-scaling capabilities of the cal3 and older time-scaling methods in simulations. cal3 produces samples of time-scaled trees that better bracket the uncertainty in the true node ages than existing time-scaling methods. This is true even in simulations under a 'terminal-taxon' model of differentiation that violates many of the assumptions of the cal3 method. 5) The cal3 method provides a new approach for time-scaling paleontological cladograms, calibrated to estimated sampling and diversification rates, allowing for better estimates of uncertainty in the phylogenetic time-scaling. The cal3 method is robust to relaxation of at least some model assumptions. Additional work is needed to analyze the impact of time-scaling approaches on macroevolutionary analyses and to integrate time-scaling with phylogenetic inference.
Data from: Accounting for uncertainty in the evolutionary timescale of green plants through clock-partitioning and fossil calibration strategies
Establishing an accurate evolutionary timescale for green plants (Viridiplantae) is essential to understanding their interaction and coevolution with the Earth's climate and the many organisms that rely on green plants. Despite being the focus of numerous studies, the timing of the origin of green plants and the divergence of major clades within this group remain highly controversial. Here, we infer the evolutionary timescale of green plants by analysing 81 protein-coding genes from 99 chloroplast genomes, using a core set of 21 fossil calibrations. We test the sensitivity of our divergence-time estimates to various components of Bayesian molecular dating, including the tree topology, clock models, clock-partitioning schemes, rate priors, and fossil calibrations. We find that the choice of clock model affects date estimation and that the independent-rates model provides a better fit to the data than the autocorrelated-rates model. Varying the rate prior and tree topology had little impact on age estimates, with far greater differences observed among calibration choices and clock-partitioning schemes. Our analyses yield date estimates ranging from the Paleoproterozoic to Mesoproterozoic for crown-group green plants, and from the Ediacaran to Middle Ordovician for crown-group land plants. We present divergence-time estimates of the major groups of green plants that take into account various sources of uncertainty. Our proposed timeline lays the foundation for further investigations into how green plants shaped the global climate and ecosystems, and how embryophytes became dominant in terrestrial environments.
Data from: Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)
Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using 'early but risky' fossil constraints in addition to 'safe but late' constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown-group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical re-assessment of their phylogenetic position.
FIGURES 19–21 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURES 19–21. Three phylogenetic trees for Nymphalidae: Satyrinae. See text for explanation.
Supplementary material 7 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figue S4
Supplementary material 6 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S3
Supplementary material 12 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S9
Supplementary material 13 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S10
Supplementary material 11 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S8
Supplementary material 10 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S7
Supplementary material 1 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Initial pool of 169 mitochondrial genomes
Figure 1 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure 1 Representative phylogenetic inferences of cockroaches based on various data and methods. McKittrick (1964) and McKittrick and Mackerras (1965): female and male genitalia, proventriculus and oviposition behaviour; discussion. Roth (1970): oothecal rotation; discussion. Klass and Meier (2006): male genitalia, accompanied by ethology etc.; parsimony. Wang et al. (2017): gene fragments (three mitochondrial and two nuclear), incorporating the data from Djernæs et al. (2015) and others; maximum likelihood. Bourguignon et al. (2018): mitogenome; maximum likelihood and Bayesian. Evangelista et al. (2019): transcriptome; maximum likelihood. Taxa are shown in currently recognized rank instead of original designation. Branches in orange, Blaberoidea; in green, Corydioidea; in purple, Blattoidea. Asterisk, paraphyly.
Figure 3 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure 3 Time trees of Dictyoptera estimated by MCMCTREE. Two-calibration result (middle) is regarded as the formal result of this study. Calibrated nodes are coloured, with vertical bars denoting bounds. Calibrations: Qilianiblatta namurensis (green), Valditermes brenanae (red), Piniblattella yixianensis (blue). Abbreviations: A[naplectidae], Dictyop[tera], L[amproblattidae], T[ryonicidae], Xyloph[agodea]. For detailed phylogenies showing species, see Suppl. material 11–13.
Supplementary material 5 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S2
Figure 2 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure 2 Bayesian phylogeny of Dictyoptera inferred from ten protein-coding genes of 85 mitogenomes, excluding the third base of codon. Posterior probabilities are shown in percentage otherwise are 100%. Clades of superfamilies or higher rank are numbered, as indicated by black background in the key. Species of major taxonomic identities (all are clades) are coloured, as indicated in the key. Subfamilies of Blattidae and Blaberidae are labeled; asterisked ones are not monophyletic. For comparison with trial analyses, see Suppl. material 6–10.
Supplementary material 3 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Table S2
Supplementary material 2 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Table S1
Supplementary material 4 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S1
Supplementary material 9 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure S6
Figure 4 from: Li X-R (2022) Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations. Deutsche Entomologische Zeitschrift 69(1): 1-18. https://doi.org/10.3897/dez.69.68373
Figure 4 Comparison among the ages estimated in various studies. The fossils are: Valditermes brenanae Jarzembowski, 1981; Piniblattella yixianensisGao et al., 2018; Nodosigalea burmanica Li & Huang, 2018; Cretaperiplaneta kaonashi Qiu et al., 2020; Stegoblatta irmgardgroehni Anisyutkin & Gröhn, 2012. Abbreviation: ALTB, Anaplectidae + Lamproblattidae + Tryonicidae + Blattidae.
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