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53 results for “molecular clock”
Validating a molecular clock for nudibranchs: No fossils to the rescue
<p>Time-calibrated phylogenies are typically reconstructed with fossil information but for soft-bodied marine invertebrates that lack hard parts, a fossil record is lacking. In these cases, biogeographic calibrations or rates of divergence for related taxa are often used. Although nudibranch phylogenies have advanced with the input of molecular data, no study has derived a divergence rate for this diverse group of invertebrates. Here, we use an updated closure date for the Isthmus of Panama (2.8 ma) to derive the first divergence rates for chromodorid nudibranchs using multi-gene data from a geminate pair with broad phylogeographic sampling. Examining the species <em>Chromolaichma sedna </em>(Marcus & Marcus, 1967), we uncover deep divergences among eastern Pacific and western Atlantic clades and we erect a new species designation for the latter (<em>Chromolaichma hemera</em> sp. nov.). Next, we discover extensive phylogeographic structure within <em>C. hemera</em> sp. nov. <em>sensu lato</em>, thereby refuting the hypothesis of a recent introduction. Lastly, we derive divergence rates for mitochondrial and nuclear loci that exceed known rates for other gastropods and we highlight significant rate heterogeneity both among markers and taxa. Together, these findings improve understanding of nudibranch systematics and provide rates useful to apply to divergence scenarios in this diverse group.</p>
Fig. 2 in Divergence time estimation in Cichorieae (Asteraceae) using a fossil-calibrated relaxed molecular clock
Fig. 2 Chronogram of Cichorieae produced by the program BEAST based on ITS1 and ITS2 sequences (unconstrained topology; maximum clade credibility tree with mean node heights obtained by stem group node calibration). Posterior probabilities of nodes are shown
Data from: Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini)
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Data from: The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?
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Data from: Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations.
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Data from: Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans.
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Validating a molecular clock for nudibranchs: No fossils to the rescue
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Data from: Major radiations in the evolution of caviid rodents: reconciling fossils, ghost lineages, and relaxed molecular clocks
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Data from: A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models
Background: Molecular clock methodologies allow for the estimation of divergence times across a variety of organisms; this can be particularly useful for groups lacking robust fossil histories, such as microbial eukaryotes with few distinguishing morphological traits. Here we have used a Bayesian molecular clock method under three distinct clock models to estimate divergence times within oomycetes, a group of fungal-like eukaryotes that are ubiquitous in the environment and include a number of devastating pathogenic species. The earliest fossil evidence for oomycetes comes from the Lower Devonian (~400 Ma), however the taxonomic affinities of these fossils are unclear. Results: Complete genome sequences were used to identify orthologous proteins among oomycetes, diatoms, and a brown alga, with a focus on conserved regulators of gene expression such as DNA and histone modifiers and transcription factors. Our molecular clock estimates place the origin of oomycetes by at least the mid-Paleozoic (~430-400 Ma), with the divergence between two major lineages, the peronosporaleans and saprolegnialeans, in the early Mesozoic (~225-190 Ma). Divergence times estimated under the three clock models were similar, although only the strict and random local clock models produced reliable estimates for most parameters. Conclusions: Our molecular timescale suggests that modern pathogenic oomycetes diverged well after the origin of their respective hosts, indicating that environmental conditions or perhaps horizontal gene transfer events, rather than host availability, may have driven lineage diversification. Our findings also suggest that the last common ancestor of oomycetes possessed a full complement of eukaryotic regulatory proteins, including those involved in histone modification, RNA interference, and tRNA and rRNA methylation; interestingly no match to canonical DNA methyltransferases could be identified in the oomycete genomes studied here.
Data from: Distinguishing between convergent evolution and violation of the molecular clock for three taxa
We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of lineages after lineage-splitting but also allows for taxa to converge, i.e. become more similar over time. By examining the 3-taxon case in some detail we illustrate that phylogeneticists have been ``spoiled'' in the sense of not having to think about the structural parameters in their models by virtue of the strong assumption that evolution is tree-like. We show that there are not always good statistical reasons to prefer the usual class of tree-like models over more general convergence-divergence models. Specifically we show many 3-taxon data sets can be equally well explained by supposing violation of the molecular clock due to change in the rate of evolution along different edges, or by keeping the assumption of a constant rate of evolution but instead assuming that evolution is not a purely divergent process. Given the abundance of evidence that evolution is not strictly tree-like, our discussion is an illustration that as phylogeneticists we need to think clearly about the structural form of the models we use. For cases with four taxa we show that there will be far greater ability to distinguish models with convergence from non-clock-like tree models.
Data from: The local-clock permutation test: a simple test to compare rates of molecular evolution on phylogenetic trees
Rates of molecular evolution vary substantially between lineages, and a growing research effort is directed at uncovering the causes and consequences of this variation. Comparing local-clocks (rates of molecular evolution estimated from sets of branches of a phylogenetic tree) is a common tool in this research effort. Here, I show that a commonly used test (the Likelihood Ratio Test, LRT) will not be statistically valid for comparing local-clocks in most cases. Instead, I propose the local-clock permutation test (LCPT), a simple test which can be used to test the significance of differences between local-clocks. The LCPT could also be used to test for differences between any parameter that can be assigned to individual branches on a phylogenetic tree. Using simulated data, I show that the LCPT has good power to detect differences between local-clocks.
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.
Data from: Tips and nodes are complimentary not competing approaches to the calibration of molecular clocks
Molecular clock methodology provides the best means of establishing evolutionary timescales, the accuracy and precision of which remain reliant on calibration, traditionally based on fossil constraints on clade (node) ages. Tip calibration has been developed to obviate undesirable aspects of node calibration, including the need for maximum age constraints that are invariably very difficult to justify. Instead, tip calibration incorporates fossil species as dated tips alongside living relatives, potentially improving the accuracy and precision of divergence time estimates. We demonstrate that tip calibration yields node calibrations that violate fossil evidence, contributing to unjustifiably young and ancient age estimates, less precise and (presumably) accurate than conventional node calibration. However, we go on to show that node and tip calibrations are complementary, producing meaningful age estimates, with node minima enforcing realistic ages and fossil tips interacting with node calibrations to objectively define maximum age constraints on clade ages. Together, tip and node calibrations may yield evolutionary timescales that are better justified, more precise and accurate than either calibration strategy can achieve alone.
FIGURE 2 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 2 Total-evidence dated Bayesian tree. Numbers in nodes are posterior probabilities. Red taxa denote the stem group. Red stars show different possible positions of the Early Cretaceous Australian pan- chelid turtles described by Smith (2010) (see Discussion). Concepts and bars in blue are taken from Vlachos et al. (2018). Abbreviations: A, Acanthochelys; BGBU, Beginning of Gondwana breakup; BODP, Beginning of the opening of the Drake Passage; C, Chelus; Ch, Chelodina; Che, Chelidae; Che. +SAec, Chelidae + South American extinct chelids; E, Erymnochelys; EECO, Early Eocene Climatic Optimum; El, Elseya; Elu, Elusor; Em, Emydura; EODP, End of the opening of the Drake Passage; F, Flavemys; H, Hydromedusa; M, Mesoclemmys; My, Myuchelys; Mya, Million years ago; DownloadedOlig., from Brill Oligocene.com; 10/07 OTS/, 2022 → 07:36:56PM via free access
FIGURE 1 Maximum Parsimony phylogenetic analyses. A in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 1 Maximum Parsimony phylogenetic analyses. A: Morphological phylogeny. B: Molecular phylogeny. C: Total-evidence phylogeny. Bootstrap supports are coded in grayscale. Australasian species are shown in red; South American species are shown in green. Abbreviations: A, Acanthochelys; B, Bonapartemys; Ch, Chelodina; El, Elseya; H, Hydromedusa; L, Lomalatachelys; M, Mesoclemmys; Me, Mendozachelys; My, Myuchelys; Pa, Palaeophrynops; Ph, Phrynops; Pl, Platemys; Pr, Prochelidella; Ps, Pseudemydura; Ri, Rionegrochelys; Y, Yaminuechelys. †, extinct taxa.
Data from: Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution
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Data from: Tips and nodes are complimentary not competing approaches to the calibration of molecular clocks
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Data from: A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models
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Data from: Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution
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Data from: The local-clock permutation test: a simple test to compare rates of molecular evolution on phylogenetic trees
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