scholarly journals Biogeographic calibrations for the molecular clock

2015 ◽  
Vol 11 (9) ◽  
pp. 20150194 ◽  
Author(s):  
Simon Y. W. Ho ◽  
K. Jun Tong ◽  
Charles S. P. Foster ◽  
Andrew M. Ritchie ◽  
Nathan Lo ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Temporal Information ◽  
Rate Variation ◽  
Molecular Clocks ◽  
Climatic Data ◽  
Absolute Time ◽  
Biological Studies ◽  
Clock Models

Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses.

The molecular clock and evolutionary timescales

2018 ◽  
Vol 46 (5) ◽  
pp. 1183-1190 ◽  
Author(s):  
Arong Luo ◽  
Simon Y. W. Ho
Keyword(s):  
Molecular Clock ◽  
Statistical Models ◽  
Evolutionary Rate ◽  
Genomic Data ◽  
Genetic Distances ◽  
Genetic Change ◽  
Amino Acid Sequences ◽  
Rate Variation ◽  
Molecular Clocks ◽  
History Of

The molecular clock provides a valuable means of estimating evolutionary timescales from genetic and biochemical data. Proposed in the early 1960s, it was first applied to amino acid sequences and immunological measures of genetic distances between species. The molecular clock has undergone considerable development over the years, and it retains profound relevance in the genomic era. In this mini-review, we describe the history of the molecular clock, its impact on evolutionary theory, the challenges brought by evidence of evolutionary rate variation among species, and the statistical models that have been developed to account for these heterogeneous rates of genetic change. We explain how the molecular clock can be used to infer rates and timescales of evolution, and we list some of the key findings that have been obtained when molecular clocks have been applied to genomic data. Despite the numerous challenges that it has faced over the decades, the molecular clock continues to offer the most effective method of resolving the details of the evolutionary timescale of the Tree of Life.

scholarly journals Divergence dating using mixed effects clock modelling: An application to HIV-1

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
Magda Bletsa ◽  
Marc A Suchard ◽  
Xiang Ji ◽  
Sophie Gryseels ◽  
Bram Vrancken ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Mixed Effects ◽  
Recent Common Ancestor ◽  
Rate Variation ◽  
Clock Model ◽  
Data Set ◽  
Genome Data ◽  
Most Recent Common Ancestor ◽  
Clock Models ◽  
Hiv 1

Abstract The need to estimate divergence times in evolutionary histories in the presence of various sources of substitution rate variation has stimulated a rich development of relaxed molecular clock models. Viral evolutionary studies frequently adopt an uncorrelated clock model as a generic relaxed molecular clock process, but this may impose considerable estimation bias if discrete rate variation exists among clades or lineages. For HIV-1 group M, rate variation among subtypes has been shown to result in inconsistencies in time to the most recent common ancestor estimation. Although this calls into question the adequacy of available molecular dating methods, no solution to this problem has been offered so far. Here, we investigate the use of mixed effects molecular clock models, which combine both fixed and random effects in the evolutionary rate, to estimate divergence times. Using simulation, we demonstrate that this model outperforms existing molecular clock models in a Bayesian framework for estimating time-measured phylogenies in the presence of mixed sources of rate variation, while also maintaining good performance in simpler scenarios. By analysing a comprehensive HIV-1 group M complete genome data set we confirm considerable rate variation among subtypes that is not adequately modelled by uncorrelated relaxed clock models. The mixed effects clock model can accommodate this rate variation and results in a time to the most recent common ancestor of HIV-1 group M of 1920 (1915–25), which is only slightly earlier than the uncorrelated relaxed clock estimate for the same data set. The use of complete genome data appears to have a more profound impact than the molecular clock model because it reduces the credible intervals by 50 per cent relative to similar estimates based on short envelope gene sequences.

Central and Peripheral Clock Control of Circadian Feeding Rhythms

2021 ◽  
pp. 074873042110458
Author(s):  
Carson V. Fulgham ◽  
Austin P. Dreyer ◽  
Anita Nasseri ◽  
Asia N. Miller ◽  
Jacob Love ◽  
...  
Keyword(s):  
Locomotor Activity ◽  
Circadian Clock ◽  
Feeding Behavior ◽  
Molecular Clock ◽  
Fat Body ◽  
Molecular Clocks ◽  
Central Brain ◽  
Feeding Rhythms ◽  
Free Running ◽  
The Brain

Many behaviors exhibit ~24-h oscillations under control of an endogenous circadian timing system that tracks time of day via a molecular circadian clock. In the fruit fly, Drosophila melanogaster, most circadian research has focused on the generation of locomotor activity rhythms, but a fundamental question is how the circadian clock orchestrates multiple distinct behavioral outputs. Here, we have investigated the cells and circuits mediating circadian control of feeding behavior. Using an array of genetic tools, we show that, as is the case for locomotor activity rhythms, the presence of feeding rhythms requires molecular clock function in the ventrolateral clock neurons of the central brain. We further demonstrate that the speed of molecular clock oscillations in these neurons dictates the free-running period length of feeding rhythms. In contrast to the effects observed with central clock cell manipulations, we show that genetic abrogation of the molecular clock in the fat body, a peripheral metabolic tissue, is without effect on feeding behavior. Interestingly, we find that molecular clocks in the brain and fat body of control flies gradually grow out of phase with one another under free-running conditions, likely due to a long endogenous period of the fat body clock. Under these conditions, the period of feeding rhythms tracks with molecular oscillations in central brain clock cells, consistent with a primary role of the brain clock in dictating the timing of feeding behavior. Finally, despite a lack of effect of fat body selective manipulations, we find that flies with simultaneous disruption of molecular clocks in multiple peripheral tissues (but with intact central clocks) exhibit decreased feeding rhythm strength and reduced overall food intake. We conclude that both central and peripheral clocks contribute to the regulation of feeding rhythms, with a particularly dominant, pacemaker role for specific populations of central brain clock cells.

Understanding Molecular Clocks and Time Trees

2021 ◽  
pp. 326-337
Author(s):  
Andrew V. Z. Brower ◽  
Randall T. Schuh
Keyword(s):  
Amino Acid ◽  
Molecular Clock ◽  
Significant Error ◽  
Evolutionary Tree ◽  
Molecular Clocks ◽  
Amino Acid Substitutions ◽  
Absolute Minimum ◽  
Short Time ◽  
Over Time ◽  
Age Estimates

This chapter examines molecular clocks and time trees. Although laden with numerous process assumptions that may or may not be true (or knowable), the idea is appealingly straightforward: if amino acid substitutions in proteins occurred at a relatively steady pace that were more or less constant both over time and along each of the branches of a diverging evolutionary tree, then the number of substitutions would be directly related to the time since the taxa in question diverged from one another. However, evidence does not support a universal molecular clock. Evidence might or might not support “local” clocklike evolution among closely related taxa over relatively short time spans. Although absolute minimum ages for clades may be inferred from fossils, from biogeographical patterns, or extrapolated from secondary calibrations, such age estimates are subject to potentially significant error due to vagaries of geological dating as well as ambiguities of fossil identity. The test of a time tree hypothesis is to discover new fossil evidence that corroborates or falsifies it.

scholarly journals Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations

2015 ◽  
Vol 32 (11) ◽  
pp. 2986-2995 ◽  
Author(s):  
David A. Duchêne ◽  
Sebastian Duchêne ◽  
Edward C. Holmes ◽  
Simon Y.W. Ho
Keyword(s):  
Molecular Clock ◽  
Clock Models ◽  
Predictive Simulations

scholarly journals The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates

2018 ◽  
Author(s):  
Brice A. J. Sarver ◽  
Matthew W. Pennell ◽  
Joseph W. Brown ◽  
Sara Keeble ◽  
Kayla M. Hardwick ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Substitution Rate ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Parameter Estimates ◽  
Molecular Clocks ◽  
Estimation Of Parameters ◽  
Rate Heterogeneity ◽  
Diversification Rates ◽  
The Impact

AbstractComparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. However, the effect that the selection of these priors has on the inference of comparative parameters has not been thoroughly investigated. Such uncertainty may systematically bias phylogenetic reconstruction and, subsequently, parameter estimation. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we use BEAST to simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation rates and extinction rates) from these trees. When substitution rate heterogeneity is large, parameter estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.

scholarly journals Clock gene expression in gravid uterus and extra-embryonic tissues during late gestation in the mouse

2010 ◽  
Vol 22 (5) ◽  
pp. 743 ◽  
Author(s):  
Christine K. Ratajczak ◽  
Erik D. Herzog ◽  
Louis J. Muglia
Keyword(s):  
Molecular Clock ◽  
Clock Genes ◽  
Circadian Rhythmicity ◽  
Late Gestation ◽  
Gravid Uterus ◽  
Fetal Membranes ◽  
Molecular Clocks ◽  
Potential Contribution ◽  
Rhythmic Expression ◽  
Clock Gene Expression

Evidence in humans and rodents suggests the importance of circadian rhythmicity in parturition. A molecular clock underlies the generation of circadian rhythmicity. While this molecular clock has been identified in numerous tissues, the expression and regulation of clock genes in tissues relevant to parturition is largely undefined. Here, the expression and regulation of the clock genes Bmal1, Clock, cryptochrome (Cry1/2) and period (Per1/2) was examined in the murine gravid uterus, placenta and fetal membranes during late gestation. All clock genes examined were expressed in the tissues of interest throughout the last third of gestation. Upregulation of a subset of these clock genes was observed in each of these tissues in the final two days of gestation. Oscillating expression of mRNA for a subset of the examined clock genes was detected in the gravid uterus, placenta and fetal membranes. Furthermore, bioluminescence recording on explants from gravid Per2::luciferase mice indicated rhythmic expression of PER2 protein in these tissues. These data demonstrate expression and rhythmicity of clock genes in tissues relevant to parturition indicating a potential contribution of peripheral molecular clocks to this process.

scholarly journals The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

2008 ◽  
Vol 363 (1496) ◽  
pp. 1435-1443 ◽  
Author(s):  
Kevin J Peterson ◽  
James A Cotton ◽  
James G Gehling ◽  
Davide Pisani
Keyword(s):  
Molecular Clock ◽  
Cambrian Explosion ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Historical Records ◽  
Calibration Point ◽  
Geological Time ◽  
Fossil Records

Unravelling the timing of the metazoan radiation is crucial for elucidating the macroevolutionary processes associated with the Cambrian explosion. Because estimates of metazoan divergence times derived from molecular clocks range from quite shallow (Ediacaran) to very deep (Mesoproterozoic), it has been difficult to ascertain whether there is concordance or quite dramatic discordance between the genetic and geological fossil records. Here, we show using a range of molecular clock methods that the major pulse of metazoan divergence times was during the Ediacaran, which is consistent with a synoptic reading of the Ediacaran macrobiota. These estimates are robust to changes in priors, and are returned with or without the inclusion of a palaeontologically derived maximal calibration point. Therefore, the two historical records of life both suggest that although the cradle of Metazoa lies in the Cryogenian, and despite the explosion of ecology that occurs in the Cambrian, it is the emergence of bilaterian taxa in the Ediacaran that sets the tempo and mode of macroevolution for the remainder of geological time.

Sign in / Sign up

Export Citation Format

Share Document