scholarly journals Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds

2007 ◽  
Vol 3 (3) ◽  
pp. 275-279 ◽  
Author(s):  
Kate L Sanders ◽  
Michael S.Y Lee
Keyword(s):  
Molecular Clock ◽  
Cross Validation ◽  
Molecular Dating ◽  
Limiting Factor ◽  
Bayesian Analyses ◽  
Clock Analysis ◽  
Bayesian Relaxed Clock ◽  
Posterior Estimate ◽  
Relaxed Clock

A limiting factor in many molecular dating studies is shortage of reliable calibrations. Current methods for choosing calibrations (e.g. cross-validation) treat them as either correct or incorrect, whereas calibrations probably lie on a continuum from highly accurate to very poor. Bayesian relaxed clock analysis permits inclusion of numerous candidate calibrations as priors: provided most calibrations are reliable, the model appropriate and the data informative, the accuracy of each calibration prior can be evaluated. If a calibration is accurate, then the analysis will support the prior so that the posterior estimate reflects the prior; if a calibration is poor, the posterior will be forced away from the prior. We use this approach to test two fossil dates recently proposed as standard calibrations within vertebrates. The proposed bird–crocodile calibration (approx. 247 Myr ago) appears to be accurate, but the proposed bird–lizard calibration (approx. 255 Myr ago) is substantially too recent.

scholarly journals Phylogenetic revision of Backhousieae (Myrtaceae): Neogene divergence, a revised circumscription of Backhousia and two new species

2012 ◽  
Vol 25 (6) ◽  
pp. 404 ◽  
Author(s):  
Mark G. Harrington ◽  
Betsy R. Jackes ◽  
Matthew D. Barrett ◽  
Lyn A. Craven ◽  
Russell L. Barrett
Keyword(s):  
New Species ◽  
New South ◽  
Phylogenetic Analyses ◽  
Internal Transcribed Spacers ◽  
Molecular Dating ◽  
Undescribed Species ◽  
South Wales ◽  
Bayesian Relaxed Clock ◽  
Phylogenetic Revision ◽  
Relaxed Clock

Backhousieae is a small tribe of Myrtaceae composed of two genera (Backhousia and Choricarpia) endemic to Australia. Phylogenetic analyses (parsimony, maximum likelihood and Bayesian) were performed on a combined chloroplast (matK, trnH–psbA, trnC–psbM, trnL–F, rps16) and nuclear (internal transcribed spacers) dataset for all nine species of Backhousia, two species of Choricarpia and two undescribed species. Backhousieae is monophyletic; however, Choricarpia is embedded within Backhousia. In all analyses there were four strongly supported clades containing two to four taxa, with no support for relationships among clades, and the relationships of B. bancroftii and B. citriodora remain unresolved. Bayesian relaxed-clock molecular dating indicated that the Backhousieae has been potentially present in rainforest across Australia for more than 50 million years. The current distribution of Backhousia is inferred to be largely due to the contraction of Australian rainforest in the Neogene. New combinations in Backhousia are made for the two species of Choricarpia, and B. gundarara and B. tetraptera are described as new species. B. gundarara is known only from the Kimberley region of Western Australia, widely disjunct from the remaining Backhousia in eastern Queensland and New South Wales, and appears to be a lineage isolated by increasing aridity during the Miocene.

scholarly journals Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Science ◽  
2021 ◽  
pp. eabh2644 ◽  
Author(s):  
Nuno R. Faria ◽  
Thomas A. Mellan ◽  
Charles Whittaker ◽  
Ingra M. Claro ◽  
Darlan da S. Candido ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Genome Sequencing ◽  
Immune Evasion ◽  
Molecular Clock ◽  
Spike Protein ◽  
Dynamical Model ◽  
Mortality Data ◽  
Clock Analysis ◽  
Protection Against Infection ◽  
Molecular Clock Analysis

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

scholarly journals Simulation and Sensitivity Analysis and Cross-Validation, Demonstrating the Utility of Genteract GxE Discovery methods

2020 ◽  
Author(s):  
Brody Holohan ◽  
Raphael Laderman
Keyword(s):  
Complex Traits ◽  
Statistical Power ◽  
Cross Validation ◽  
Environmental Changes ◽  
Disease Incidence ◽  
Limiting Factor ◽  
Individual Response ◽  
Analytical Technique ◽  
Gene Environment ◽  
Study Results

AbstractGene-environment interactions are at the heart of why many complex traits are not fully heritable, and why prediction of disease incidence and individual response to environmental changes based on genetics has been underwhelming in utility. Understanding these interactions is the primary limiting factor for the application of personalized medicine, but current methods are not well suited for dealing with complex traits that pose both a dimensionality and sparse data problem to unsupervised analysis methods. Genteract has developed a proprietary analytical technique that allows for detection and interpretation of GxEs regarding specific pairs of a single phenotype with a single environmental factor; these methods allow us to develop a platform that can be used to predict how individuals will respond to changes in their environment based on their genetics. To validate the methods we performed two types of testing: cross-validation against a dataset of clinical study results, and application of the methods in a simulated dataset. These tests enable a greater understanding of the methods’ utility, statistical power and predictive capabilities.

scholarly journals Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates

2009 ◽  
Vol 5 (6) ◽  
pp. 812-816 ◽  
Author(s):  
Davin H. E. Setiamarga ◽  
Masaki Miya ◽  
Yusuke Yamanoue ◽  
Yoichiro Azuma ◽  
Jun G. Inoue ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Molecular Clock ◽  
Divergence Time ◽  
Evolutionary Rates ◽  
Implicit Assumption ◽  
Molecular Evolutionary Rates ◽  
Clock Analysis ◽  
The Japanese Archipelago ◽  
Two Populations ◽  
Rates Of Molecular Evolution

The southern and northern Japanese populations of the medaka fish provide useful tools to gain insights into the comparative genomics and speciation of vertebrates, because they can breed to produce healthy and fertile offspring despite their highly divergent genetic backgrounds compared with those of human–chimpanzee. Comparative genomics analysis has suggested that such large genetic differences between the two populations are caused by higher molecular evolutionary rates among the medakas than those of the hominids. The argument, however, was based on the assumption that the two Japanese populations diverged approximately at the same time (4.0–4.7 Myr ago) as the human–chimpanzee lineage (5.0–6.0 Myr ago). This can be misleading, because the divergence time of the two populations was calculated based on estimated, extremely higher molecular evolutionary rates of other fishes with an implicit assumption of a global molecular clock. Here we show that our estimate, based on a Bayesian relaxed molecular-clock analysis of whole mitogenome sequences from 72 ray-finned fishes (including 14 medakas), is about four times older than that of the previous study (18 Myr). This remarkably older estimate can be reconciled with the vicariant events of the Japanese archipelago, and the resulting rates of molecular evolution are almost identical between the medaka and hominid lineages. Our results further highlight the fact that reproductive isolation may not evolve despite a long period of geographical isolation.

scholarly journals Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting

2013 ◽  
Vol 280 (1770) ◽  
pp. 20131733 ◽  
Author(s):  
Matt Friedman ◽  
Benjamin P. Keck ◽  
Alex Dornburg ◽  
Ron I. Eytan ◽  
Christopher H. Martin ◽  
...  
Keyword(s):  
Evolutionary Developmental Biology ◽  
Molecular Clocks ◽  
Distributional Pattern ◽  
Cichlid Species ◽  
Biogeographic Patterns ◽  
Cichlid Fishes ◽  
Clock Analysis ◽  
Model Clade ◽  
Relaxed Molecular Clock ◽  
Relaxed Clock

Cichlid fishes are a key model system in the study of adaptive radiation, speciation and evolutionary developmental biology. More than 1600 cichlid species inhabit freshwater and marginal marine environments across several southern landmasses. This distributional pattern, combined with parallels between cichlid phylogeny and sequences of Mesozoic continental rifting, has led to the widely accepted hypothesis that cichlids are an ancient group whose major biogeographic patterns arose from Gondwanan vicariance. Although the Early Cretaceous ( ca 135 Ma) divergence of living cichlids demanded by the vicariance model now represents a key calibration for teleost molecular clocks, this putative split pre-dates the oldest cichlid fossils by nearly 90 Myr. Here, we provide independent palaeontological and relaxed-molecular-clock estimates for the time of cichlid origin that collectively reject the antiquity of the group required by the Gondwanan vicariance scenario. The distribution of cichlid fossil horizons, the age of stratigraphically consistent outgroup lineages to cichlids and relaxed-clock analysis of a DNA sequence dataset consisting of 10 nuclear genes all deliver overlapping estimates for crown cichlid origin centred on the Palaeocene ( ca 65–57 Ma), substantially post-dating the tectonic fragmentation of Gondwana. Our results provide a revised macroevolutionary time scale for cichlids, imply a role for dispersal in generating the observed geographical distribution of this important model clade and add to a growing debate that questions the dominance of the vicariance paradigm of historical biogeography.

scholarly journals Complete Genomic Sequence of Human Coronavirus OC43: Molecular Clock Analysis Suggests a Relatively Recent Zoonotic Coronavirus Transmission Event

2005 ◽  
Vol 79 (3) ◽  
pp. 1595-1604 ◽  
Author(s):  
Leen Vijgen ◽  
Els Keyaerts ◽  
Elien Moës ◽  
Inge Thoelen ◽  
Elke Wollants ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Complete Genome ◽  
Recent Common Ancestor ◽  
Human Coronavirus ◽  
Transmission Event ◽  
Most Recent Common Ancestor ◽  
A Genome ◽  
Clock Analysis ◽  
Group 2 ◽  
Molecular Clock Analysis

ABSTRACT Coronaviruses are enveloped, positive-stranded RNA viruses with a genome of approximately 30 kb. Based on genetic similarities, coronaviruses are classified into three groups. Two group 2 coronaviruses, human coronavirus OC43 (HCoV-OC43) and bovine coronavirus (BCoV), show remarkable antigenic and genetic similarities. In this study, we report the first complete genome sequence (30,738 nucleotides) of the prototype HCoV-OC43 strain (ATCC VR759). Complete genome and open reading frame (ORF) analyses were performed in comparison to the BCoV genome. In the region between the spike and membrane protein genes, a 290-nucleotide deletion is present, corresponding to the absence of BCoV ORFs ns4.9 and ns4.8. Nucleotide and amino acid similarity percentages were determined for the major HCoV-OC43 ORFs and for those of other group 2 coronaviruses. The highest degree of similarity is demonstrated between HCoV-OC43 and BCoV in all ORFs with the exception of the E gene. Molecular clock analysis of the spike gene sequences of BCoV and HCoV-OC43 suggests a relatively recent zoonotic transmission event and dates their most recent common ancestor to around 1890. An evolutionary rate in the order of 4 × 10−4 nucleotide changes per site per year was estimated. This is the first animal-human zoonotic pair of coronaviruses that can be analyzed in order to gain insights into the processes of adaptation of a nonhuman coronavirus to a human host, which is important for understanding the interspecies transmission events that led to the origin of the severe acute respiratory syndrome outbreak.

scholarly journals Evaluating the Impact of Purifying Selection on Species-level Molecular Dating

2019 ◽  
Author(s):  
Chong He ◽  
Dan Liang ◽  
Peng Zhang
Keyword(s):  
Molecular Clock ◽  
Neutral Theory ◽  
Purifying Selection ◽  
Selective Constraint ◽  
Species Level ◽  
Molecular Dating ◽  
Substitution Saturation ◽  
Time Estimates ◽  
Branch Lengths ◽  
The Impact

AbstractThe neutral theory of molecular evolution suggests that the constancy of the molecular clock relies on the neutral condition. Thus, purifying selection, the most common type of natural selection, could influence the constancy of the molecular clock, and the use of genes/sites under purifying selection may produce less reliable molecular dating results. However, in current practices of species-level molecular dating, some researchers prefer to select slowly evolving genes/sites to avoid the potential impact of substitution saturation. These genes/sites are generally under a strong influence of purifying selection. Here, from the data of 23 published mammal genomes, we constructed datasets under various selective constraints. We compared the differences in branch lengths and time estimates among these datasets to investigate the impact of purifying selection on species-level molecular dating. We found that as the selective constraint increases, terminal branches are extended, which introduces biases into the result of species-level molecular dating. This result suggests that in species-level molecular dating, the impact of purifying selection should be taken into consideration, and researchers should be more cautious with the use of genes/sites under purifying selection.

scholarly journals RelTime relaxes the strict molecular clock throughout the phylogeny

2017 ◽  
Author(s):  
Fabia U. Battistuzzi ◽  
Qiqing Tao ◽  
Lance Jones ◽  
Koichiro Tamura ◽  
Sudhir Kumar
Keyword(s):  
Molecular Phylogeny ◽  
Molecular Clock ◽  
Evolutionary Rates ◽  
Molecular Dating ◽  
Divergence Times ◽  
Similar Time ◽  
Time Estimates ◽  
Theoretical Analyses ◽  
Strict Molecular Clock ◽  
Median Rate

AbstractThe RelTime method estimates divergence times when evolutionary rates vary among lineages. Theoretical analyses show that RelTime relaxes the strict molecular clock throughout a molecular phylogeny, and it performs well in the analysis of empirical and computer simulated datasets in which evolutionary rates are variable. Lozano-Fernandez et al. (2017) found that the application of RelTime to one metazoan dataset (Erwin et al. 2011) produced equal rates for several ancient lineages, which led them to speculate that RelTime imposes a strict molecular clock for deep animal divergences. RelTime does not impose a strict molecular clock. The pattern observed by Lozano-Fernandez et al. (2017) was a result of the use of an option to assign the same rate to lineages in RelTime when the rates are not statistically significantly different. The median rate difference was 5% for many deep metazoan lineages for Erwin et al. (2011) dataset, so the rate equality was not rejected. In fact, RelTime analysis with and without the option to test rate differences produced very similar time estimates. We found that the Bayesian time estimates vary widely depending on the root priors assigned, and that the use of less restrictive priors produce Bayesian divergence times that are concordant with those from RelTime for Erwin et al. (2011) dataset. Therefore, it is prudent to discuss Bayesian estimates obtained under a range of priors in any discourse about molecular dating, including method comparisons.

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