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.

scholarly journals Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i884-i894
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Sequence Divergence ◽  
Molecular Dating ◽  
Divergence Times ◽  
Time Reversibility ◽  
Sequence Alignments ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Substitution Process ◽  
The Impact

Abstract Motivation As the number and diversity of species and genes grow in contemporary datasets, two common assumptions made in all molecular dating methods, namely the time-reversibility and stationarity of the substitution process, become untenable. No software tools for molecular dating allow researchers to relax these two assumptions in their data analyses. Frequently the same General Time Reversible (GTR) model across lineages along with a gamma (+Γ) distributed rates across sites is used in relaxed clock analyses, which assumes time-reversibility and stationarity of the substitution process. Many reports have quantified the impact of violations of these underlying assumptions on molecular phylogeny, but none have systematically analyzed their impact on divergence time estimates. Results We quantified the bias on time estimates that resulted from using the GTR + Γ model for the analysis of computer-simulated nucleotide sequence alignments that were evolved with non-stationary (NS) and non-reversible (NR) substitution models. We tested Bayesian and RelTime approaches that do not require a molecular clock for estimating divergence times. Divergence times obtained using a GTR + Γ model differed only slightly (∼3% on average) from the expected times for NR datasets, but the difference was larger for NS datasets (∼10% on average). The use of only a few calibrations reduced these biases considerably (∼5%). Confidence and credibility intervals from GTR + Γ analysis usually contained correct times. Therefore, the bias introduced by the use of the GTR + Γ model to analyze datasets, in which the time-reversibility and stationarity assumptions are violated, is likely not large and can be reduced by applying multiple calibrations. Availability and implementation All datasets are deposited in Figshare: https://doi.org/10.6084/m9.figshare.12594638.

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 The evolution of methods for establishing evolutionary timescales

2016 ◽  
Vol 371 (1699) ◽  
pp. 20160020 ◽  
Author(s):  
Philip C. J. Donoghue ◽  
Ziheng Yang
Keyword(s):  
Fossil Record ◽  
Environmental Influence ◽  
Molecular Dating ◽  
Divergence Times ◽  
Fossil Species ◽  
Time Estimates ◽  
Fossil Evidence ◽  
Probability Densities ◽  
History Of ◽  
Lineage Divergence

The fossil record is well known to be incomplete. Read literally, it provides a distorted view of the history of species divergence and extinction, because different species have different propensities to fossilize, the amount of rock fluctuates over geological timescales, as does the nature of the environments that it preserves. Even so, patterns in the fossil evidence allow us to assess the incompleteness of the fossil record. While the molecular clock can be used to extend the time estimates from fossil species to lineages not represented in the fossil record, fossils are the only source of information concerning absolute (geological) times in molecular dating analysis. We review different ways of incorporating fossil evidence in modern clock dating analyses, including node-calibrations where lineage divergence times are constrained using probability densities and tip-calibrations where fossil species at the tips of the tree are assigned dates from dated rock strata. While node-calibrations are often constructed by a crude assessment of the fossil evidence and thus involves arbitrariness, tip-calibrations may be too sensitive to the prior on divergence times or the branching process and influenced unduly affected by well-known problems of morphological character evolution, such as environmental influence on morphological phenotypes, correlation among traits, and convergent evolution in disparate species. We discuss the utility of time information from fossils in phylogeny estimation and the search for ancestors in the fossil record. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

scholarly journals A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times

2002 ◽  
Vol 18 (1) ◽  
pp. 115-123 ◽  
Author(s):  
T.-K. Seo ◽  
J. L. Thorne ◽  
M. Hasegawa ◽  
H. Kishino
Keyword(s):  
Molecular Clock ◽  
Sampling Design ◽  
Evolutionary Rates ◽  
Divergence Times

scholarly journals Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated

2020 ◽  
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Sequence Divergence ◽  
Molecular Dating ◽  
Divergence Times ◽  
Time Reversibility ◽  
Sequence Alignments ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Substitution Process ◽  
The Impact

AbstractMotivationAs the number and diversity of species and genes grow in contemporary datasets, two common assumptions made in all molecular dating methods, namely the time-reversibility and stationarity of the substitution process, become untenable. No software tools for molecular dating allow researchers to relax these two assumptions in their data analyses. Frequently the same General Time Reversible (GTR) model across lineages along with a gamma (+Γ) distributed rates across sites is used in relaxed clock analyses, which assumes time-reversibility and stationarity of the substitution process. Many reports have quantified the impact of violations of these underlying assumptions on molecular phylogeny, but none have systematically analyzed their impact on divergence time estimates.ResultsWe quantified the bias on time estimates that resulted from using the GTR+Γ model for the analysis of computer-simulated nucleotide sequence alignments that were evolved with non-stationary (NS) and non-reversible (NR) substitution models. We tested Bayesian and RelTime approaches that do not require a molecular clock for estimating divergence times. Divergence times obtained using a GTR+Γ model differed only slightly (∼3% on average) from the expected times for NR datasets, but the difference was larger for NS datasets (∼10% on average). The use of only a few calibrations reduced these biases considerably (∼5%). Confidence and credibility intervals from GTR+Γ analysis usually contained correct times. Therefore, the bias introduced by the use of the GTR+Γ model to analyze datasets, in which the time-reversibility and stationarity assumptions are violated, is likely not large and can be reduced by applying multiple calibrations.AvailabilityAll datasets are deposited in Figshare: https://doi.org/10.6084/[email protected]

Molecular phylogenetics of circumglobal Euphausia species (Euphausiacea: Crustacea)

2000 ◽  
Vol 57 (S3) ◽  
pp. 51-58 ◽  
Author(s):  
Simon N Jarman ◽  
Nicholas G Elliott ◽  
Stephen Nicol ◽  
Andrew McMinn
Keyword(s):  
Genetic Differentiation ◽  
Molecular Clock ◽  
Molecular Phylogenetics ◽  
Divergence Time ◽  
Divergence Times ◽  
Antarctic Species ◽  
Time Estimates ◽  
Antarctic Convergence ◽  
History Of ◽  
The Antarctic

The speciation history of members of the krill genus Euphausia with continuous circumglobal distributions was investigated by phylogenetic and molecular clock analyses of their mitochondrial DNA. Molecular clock estimates for divergence times of Antarctic and sub-Antarctic species of Euphausia of ~15 million years ago were fairly close to the time of formation of the Antarctic Convergence, consistent with their vicariant speciation. However, the confidence limits quantified for these time estimates were large at ~11 million and ~25 million years. A divergence time of between ~10 million years for Euphausia triacantha and Euphausia longirostris suggested that migration across oceanographic fronts like the Antarctic Convergence may also lead to speciation in krill. Genetic differentiation between Euphausia vallentini and Euphausia lucens was found to be relatively minor and occurred between 0.76 million and 1.65 million years ago. These species have overlapping ranges, suggesting that there is potential for sympatric genetic differentiation in krill.

Molecular Phylogeny and Biogeography of the Tasmanian and New Zealand Mudfishes (Salmoniformes : Galaxiidae)

1997 ◽  
Vol 45 (1) ◽  
pp. 39 ◽  
Author(s):  
J. M. Waters ◽  
R. W. G. White
Keyword(s):  
New Zealand ◽  
Molecular Phylogeny ◽  
Molecular Clock ◽  
Convergent Evolution ◽  
Sequence Data ◽  
Mitochondrial Genes ◽  
Divergence Times ◽  
Marine Dispersal ◽  
Close Phylogenetic Relationship ◽  
Phylogenetic Affinities

The phylogenetic affinities of the diadromous Tasmanian mudfish, Galaxias cleaveri, have long been problematic. Some systematists have suggested that this species is closely related to the morphologically similar but non-diadromous New Zealand mudfish genus, Neochanna, while others argued that the similarities represent convergent evolution. Most recently, the Tasmanian mudfish was allocated to Neochanna on morphological grounds. The current paper presents sequence data from two mitochondrial genes that support this decision, revealing a close phylogenetic relationship between Tasmanian and New Zealand mudfish. Molecular clock calibrations are used to examine hypotheses of mudfish evolution and biogeography. Estimated divergence times are consistent with the suggestion that Neochanna burrowsius and N. apoda were separated by the uplift of New Zealand’s southern Alps about five million years ago. In addition, the divergence of the Tasmanian and New Zealand mudfish appears to postdate the rifting of Gondwana and is best explained by marine dispersal during the Pliocene.

Molecular phylogeny and biogeography of the Tasmanian and New Zealand mudfishes (Salmoniformes : Galaxiidae)

1997 ◽  
Vol 45 (6) ◽  
pp. 671
Author(s):  
J. M. Waters ◽  
R. W. G. White
Keyword(s):  
New Zealand ◽  
Molecular Phylogeny ◽  
Molecular Clock ◽  
Convergent Evolution ◽  
Sequence Data ◽  
Mitochondrial Genes ◽  
Divergence Times ◽  
Marine Dispersal ◽  
Close Phylogenetic Relationship ◽  
Phylogenetic Affinities

The phylogenetic affinities of the diadromous Tasmanian mudfish, Galaxias cleaveri, have long been problematic. Some systematists have suggested that this species is closely related to the morphologically similar but non-diadromous New Zealand mudfish genus, Neochanna, while others argued that the similarities represent convergent evolution. Most recently, the Tasmanian mudfish was allocated to Neochanna on morphological grounds. The current paper presents sequence data from two mitochondrial genes that support this decision, revealing a close phylogenetic relationship between Tasmanian and New Zealand mudfish. Molecular clock calibrations are used to examine hypotheses of mudfish evolution and biogeography. Estimated divergence times are consistent with the suggestion that Neochanna burrowsius and N. apoda were separated by the uplift of New Zealand’s southern Alps about five million years ago. In addition, the divergence of the Tasmanian and New Zealand mudfish appears to postdate the rifting of Gondwana and is best explained by marine dispersal during the Pliocene.

Estimating divergence times of notothenioid fishes using a fossil-calibrated molecular clock

2004 ◽  
Vol 16 (1) ◽  
pp. 37-44 ◽  
Author(s):  
THOMAS J. NEAR
Keyword(s):  
Maximum Likelihood ◽  
Molecular Clock ◽  
Nucleotide Substitution ◽  
Divergence Time ◽  
Divergence Times ◽  
Substitution Rates ◽  
Cold Adapted ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Nucleotide Substitution Rates

Hypotheses concerning the diversification of notothenioid fishes have relied extensively on estimates of divergence times using molecular clock methods. The timing of diversification of the cold adapted antifreeze glycoprotein (AFGP)-bearing Antarctic notothenioid clade in the middle to late Miocene has been correlated with the onset of polar climatic conditions along the Antarctic Continental Shelf. Critical examination of the previous molecular clock analyses of notothenioids reveals several problems associated with heterogeneity of nucleotide substitution rates among lineages, the application of potentially inappropriate nucleotide substitution rates, and the lack of confidence intervals for divergence time estimates. In this study, the notothenioid partial gene mtDNA 12S-16S rRNA (PG-rRNA) molecular clock was reanalysed using a tree-based maximum likelihood strategy that attempts to account for rate heterogeneity of nucleotide substitution rates among lineages using the penalized likelihood method, and bootstrap resampling to estimate confidence intervals of divergence time estimates. The molecular clock was calibrated using the notothenioid fossil Proeleginops grandeastmanorum. Divergence time estimates for all nodes in the PG-rRNA maximum likelihood tree were substantially older than previous estimates. In particular, the estimated age of the AFGP-bearing Antarctic notothenioid clade predates the onset of extensive sea ice and development of polar conditions by at least 10 million years. Despite caveats involving the fossil calibration and limitations of the PG-rRNA dataset, these divergence time estimates provide initial observations for the development of a novel model of the diversification of cold adapted Antarctic notothenioid fishes.

scholarly journals Reliable confidence intervals for RelTime estimates of evolutionary divergence times

2019 ◽  
Author(s):  
Qiqing Tao ◽  
Koichiro Tamura ◽  
Beatriz Mello ◽  
Sudhir Kumar
Keyword(s):  
Confidence Intervals ◽  
Divergence Time ◽  
Simulated Data ◽  
Molecular Dating ◽  
Divergence Times ◽  
Rate Variation ◽  
Evolutionary Divergence ◽  
Posterior Density ◽  
Divergence Time Estimates ◽  
Highest Posterior Density

AbstractConfidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated with clock calibrations. Reliable tests of biological hypotheses demand reliable CIs. However, current non-Bayesian methods may produce unreliable CIs because they do not incorporate rate variation among lineages and interactions among clock calibrations properly. Here, we present a new analytical method to calculate CIs of divergence times estimated using the RelTime method, along with an approach to utilize multiple calibration uncertainty densities in these analyses. Empirical data analyses showed that the new methods produce CIs that overlap with Bayesian highest posterior density (HPD) intervals. In the analysis of computer-simulated data, we found that RelTime CIs show excellent average coverage probabilities, i.e., the true time is contained within the CIs with a 95% probability. These developments will encourage broader use of computationally-efficient RelTime approach in molecular dating analyses and biological hypothesis testing.

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