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53 results for “molecular clock”
Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression
<p>Molecular sequence data from rapidly evolving organisms are often sampled at different points in time. Sampling times can then be used for molecular clock calibration. The root-to-tip (RTT) regression is an essential tool to assess the degree to which the data behave in a clock-like fashion. Here, we introduce Clockor2, a client-side web application for conducting RTT regression. Clockor2 uniquely allows users to quickly fit local and global molecular clocks, thus handling the increasing complexity of genomic datasets that sample beyond the assumption homogeneous host populations. Clockor2 is efficient, handling trees of up to the order of 10^4 tips, with significant speed increases compared to other RTT regression applications. Although clockor2 is written as a web application, all data processing happens on the client-side, meaning that data never leaves the user's computer. Clockor2 is freely available at https://clockor2.github.io/</p>
Linked collectors and determiners for: Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea).
Natural history specimen data linked to collectors and determiners held within, "Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/6c479acc-8b18-4f0b-a6e5-85bcd6d7b6b7">https://bionomia.net/dataset/6c479acc-8b18-4f0b-a6e5-85bcd6d7b6b7</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/6c479acc-8b18-4f0b-a6e5-85bcd6d7b6b7">https://gbif.org/dataset/6c479acc-8b18-4f0b-a6e5-85bcd6d7b6b7</a>. Formatted as a Frictionless Data package.
FIGURE 2 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 2 Opening of Tasman Sea; Pal., Paleocene; P, Pliocene; Pe, Pelomedusa; Pel, Pelusios; Pelt, Peltocephalus; (cont.) Ph, Phrynops; Pl, Platemys; Ple, Pleurodira; Po, Podocnemis; Ps, Pseudemydura; Q, Quaternary; R, Rheodytes; Rh, Rhinemys. *, constrained nodes based on the TE MP topology; †, extinct taxa; ↑, origin of total groups Pan-Chelidae and Pan-Pelomedusioides. Downloaded from Brill.com10/07/2022 07:36:56PM via free access
FIGURE 3 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 3 Comparison of the three dating analyses performed in this study (simplified trees). Node number as in table 2. Abbreviations of analyses as in table 1. Abbreviations of geological events as in fig. 2. Abbrevia- tions of genera as in figs. 1 and 2. * constrained nodes based on the MP topologies; ↑, origin of total groups Pan-Chelidae and Pan- Pelomedusioides.
FIGURE 4 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 4 Comparison of dates produced by the three analyses of this study and four previous molecular clock studies. Abbreviations: Dea (2011), Dornburg et al. (2011); Jea (2013), Joyce et al. (2013); Pea (2017), Pereira et al. (2017); TS-M TD, This study morphological tip-dating; TS- ND, This study node-dating; TS-TE TD, This study total-evidence tip- dating; R&DF (2016), Rodrigues & Diniz-Filho (2016). Node numbers as in table 2.
Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression
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Two notorious nodes: A critical examination of relaxed molecular clock age estimates of the bilaterian animals and placental mammals
<p><span>The popularity of relaxed clock Bayesian inference of clade origin timings has generated several recent publications with focal results considerably older than the fossils of the clades in question. Here we critically examine two such clades: the animals (with focus on the bilaterians); and the mammals (with focus on the placentals). Each example displays a set of characteristic pathologies which, although much commented on, are rarely corrected for. We conclude that in neither case does the molecular clock analysis provide any evidence for an origin of the clade deeper than what is suggested by the fossil record. In addition, both these clades have other features (including, in the case of the placental mammals, proximity to a large mass extinction) that allow us to generate precise expectations of the timings of their origins. Thus, in these instances the fossil record can provide a powerful test of molecular clock methodology, and why it goes astray; and we have every reason to think these problems are general. </span></p>
Quantum coherent spin-electric control in a molecular nanomagnet at clock transitions. Open data set
<p>Data supporting the related publication.</p>
Two notorious nodes: A critical examination of relaxed molecular clock age estimates of the bilaterian animals and placental mammals
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Data from: The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?
The use of nucleotide and amino acid sequences allows improved understanding of the timing of evolutionary events of life on earth. Molecular estimates of divergence times are, however, controversial and are generally much more ancient than suggested by the fossil record. The limited number of genes and species explored and pervasive variations in evolutionary rates are the most likely sources of such discrepancies. Here we compared concatenated amino acid sequences of 129 proteins from 36 eukaryotes to determine the divergence times of several major clades, including animals, fungi, plants, and various protists. Due to significant variations in their evolutionary rates, and to handle the uncertainty of the fossil record, we used a Bayesian relaxed molecular clock simultaneously calibrated by six paleontological constraints. We show that, according to 95% credibility intervals, the eukaryotic kingdoms diversified 950–1,259 million years ago (Mya), animals diverged from choanoflagellates 761–957 Mya, and the debated age of the split between protostomes and deuterostomes occurred 642–761 Mya. The divergence times appeared to be robust with respect to prior assumptions and paleontological calibrations. Interestingly, these relaxed clock time estimates are much more recent than those obtained under the assumption of a global molecular clock, yet bilaterian diversification appears to be ≈100 million years more ancient than the Cambrian boundary.
Data from: Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini)
Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1α intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from (1) an extrapolated EF-1α exon clock derived from COI-calibrated analysis within the largest New Zealand subclade, (2) post-hoc scaling of the tribe-level chronogram using results from subclade analyses, and (3) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non-Australasian genera belonging to two distal clades. Within Australia, we show that Cicadettini is more widely distributed than any other cicada tribe, diverse in temperate, arid and monsoonal habitats, and nearly absent from rainforests. We comment on the taxonomic implications of our findings for thirteen cicada genera.
Data from: Major radiations in the evolution of caviid rodents: reconciling fossils, ghost lineages, and relaxed molecular clocks
BACKGROUND: Caviidae is a diverse group of caviomorph rodents that is broadly distributed in South America and is divided into three highly divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant and diverse since the late Miocene. Caviids belongs to Cavioidea sensu stricto (Cavioidea s.s.) that also includes a diverse assemblage of extinct taxa recorded from the late Oligocene to the middle Miocene of South America ("eocardiids"). RESULTS: A phylogenetic analysis combining morphological and molecular data is presented here, evaluating the time of diversification of selected nodes based on the calibration of phylogenetic trees with fossil taxa and the use of relaxed molecular clocks. This analysis reveals three major phases of diversification in the evolutionary history of Cavioidea s.s. The first two phases involve two successive radiations of extinct lineages that occurred during the late Oligocene and the early Miocene. The third phase consists of the diversification of Caviidae. The initial split of caviids is dated as middle Miocene by the fossil record. This date falls within the 95% higher probability distribution estimated by the relaxed Bayesian molecular clock, although the mean age estimate ages are 3.5 to 7 Myr older. The initial split of caviids is followed by an obscure period of poor fossil record (refered here as the Mayoan gap) and then by the appearance of highly differentiated modern lineages of caviids, which evidentially occurred at the late Miocene as indicated by both the fossil record and molecular clock estimates. CONCLUSIONS: The integrated approach used here allowed us identifying the agreements and discrepancies of the fossil record and molecular clock estimates on the timing of the major events in cavioid evolution, revealing evolutionary patterns that would not have been possible to gather using only molecular or paleontological data alone.
Data from: Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations.
Reconstructing the chronology of mammalian evolution is a debated issue between molecule- and fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated whether molecular and paleontological estimates of mammalian divergence dates may be reconciled by the local molecular clocks approach, allowing local constancy of substitution rates with variations at larger phylogenetic scales. To handle the difficulty of choosing among all possible rate assignments for various lineages, local molecular clocks were based on the results of branch-length and two-cluster tests. Extensive lineage-specific variation of evolutionary rates was detected, even among rodents. Cross-calibrations indicated some incompatibilities between divergence dates based on different paleontological references. To decrease the impact of a single calibration point, estimates derived from independent calibrations displaying only slight reciprocal incompatibility were averaged. The divergence dates inferred for the split between mice and rats (approximately 13-19 Myr) was younger than previously published molecular estimates. The most recent common ancestors of rodents, primates and rodents, boreoeutherians, and placentals were estimated to be, respectively, approximately 60, 70, 75, and 78 Myr old. Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents.
FIGURES 3–4 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURES 3–4. Wing venation of (A) Pareronia Bingham, 1907 (Pieridae), and (B) Hasora Moore, 1881 (Hesperiidae). See text for explanation.
FIGURE 22 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURE 22. Fossils marked on phylogenetic tree of "redefined" butterflies (Heikkilä et al. 2011), with family trees according to Simonsen et al. (2011, Papilionidae), Warren et al. (2009, Hesperiidae), Wahlberg et al. (2014, Pieridae), Wahlberg et al. (2005, Lycaenidae), and Espeland et al. (2015, Riodinidae).
FIGURE 2 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURE 2. Apomorphies, their placement on a tree, and the assignment of calibration points. See text for explanation.
FIGURES 11–13 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURES 11–13. Ƒanessa pluto Heer, 1849. Figures copied from (1875), Plate II, figures 1, 17 and 7, respectively. (A), copied by Scudder from original description by Heer; (B) and (C), figures sent to Scudder by Mr. Brunner de Wattenwyl, made after the same object. Note differences in wing shape and other details. Figs 14–16. Thaites ruminiana Scudder, 1875. Figures copied from Scudder (1875), Plate III, figures 9, 1 and 3, respectively. (A), underside of fossil; (B), reconstruction of venation; (C), reconstruction of markings. In (A) two separate subcostal veins have been drawn in the forewing, an impossible configuration in Lepidoptera, and apparently a mistake, corrected in (B) and (C). Fig. 17. Cyllo sepulta Boisduval, 1841, wing venation after Scudder (1875). Fig. 18. Butterfly fossil recorded by Wangrin (1939), but shown to be a fraud by Ansorge (2015). Photo kindly provided by J. Ansorge, Horst, Germany (see text for explanation).
FIGURE 23 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURE 23. Distribution of land, epicontinental seas (flooded continental areas) and oceans during the middle Paleocene (Thanetian Stage) at 60 Mya. From Smith, A.G., Smith, D.G. & Funnell, B.M. (1994); with permission of Cambridge University Press and University of East Anglia.
FIGURE 1 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURE 1. Localities of fossil butterflies plotted ion a modern map. See Table 1 for further, complementary information.
FIGURE 5 in Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)
FIGURE 5. Ƒanessa amerindica Miller & Brown, 1989, holotype, collections of Invertebrate Paleontology, University of Florida. Photo by Roger Portell. Fig. 6. Pseudoneorina coulleti Nel & Descimon, 1984. France, Dép. Alpes-de-Haute- Provence, Dauphin, specimen in coll. M. Henrotay; photo by courtesy of M. Henrotay. Fig. 7. Archaeolycorea ferreirai Martins-Neto, 1989. Fig. 4A of original description. Fig. 8. Oligodonta florissantensis Brown, 1976, holotype, collections of Invertebrate Paleontology, University of Florida. Photo by courtesy of Akito Kawahara. Fig. 9. Neorinella garciae Martins- Neto, Kucera-Santos, de Moraes Vieira & de Campos Fragoso, 1993. Fig. 3A of original description. Fig. 10. Protocoeliades kristenseni de Jong, 2016, holotype, Zoologisk Museum, Copenhagen, Denmark. Photo by Department of Paleobiology, National Museum of Natural History, Washington DC, USA.
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