Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times

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.

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Reliable confidence intervals for RelTime estimates of evolutionary divergence times

10.1101/677286 ◽

2019 ◽

Cited By ~ 1

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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60 million years of co-divergence in the fig–wasp symbiosis

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2005.3249 ◽

2005 ◽

Vol 272 (1581) ◽

pp. 2593-2599 ◽

Cited By ~ 152

Author(s):

Nina Rønsted ◽

George D Weiblen ◽

James M Cook ◽

Nicolas Salamin ◽

Carlos A Machado ◽

...

Keyword(s):

Phylogenetic Trees ◽

Time Frame ◽

Molecular Dating ◽

Fig Wasp ◽

Geological Time ◽

Molecular Phylogenetic ◽

Pollinator Specialization ◽

Phylogenetic Hypotheses ◽

Fossil Data ◽

Plant Pollinator

Figs ( Ficus ; ca 750 species) and fig wasps (Agaoninae) are obligate mutualists: all figs are pollinated by agaonines that feed exclusively on figs. This extraordinary symbiosis is the most extreme example of specialization in a plant–pollinator interaction and has fuelled much speculation about co-divergence. The hypothesis that pollinator specialization led to the parallel diversification of fig and pollinator lineages (co-divergence) has so far not been tested due to the lack of robust and comprehensive phylogenetic hypotheses for both partners. We produced and combined the most comprehensive molecular phylogenetic trees to date with fossil data to generate independent age estimates for fig and pollinator lineages, using both non-parametric rate smoothing and penalized likelihood dating methods. Molecular dating of ten pairs of interacting lineages provides an unparalleled example of plant–insect co-divergence over a geological time frame spanning at least 60 million years.

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RelTime relaxes the strict molecular clock throughout the phylogeny

10.1101/220194 ◽

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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The reanalysis of biogeography of the Asian tree frog,Rhacophorus(Anura: Rhacophoridae): geographic shifts and climatic change influenced the dispersal process and diversification

PeerJ ◽

10.7717/peerj.3995 ◽

2017 ◽

Vol 5 ◽

pp. e3995 ◽

Cited By ~ 5

Author(s):

Tao Pan ◽

Yanan Zhang ◽

Hui Wang ◽

Jun Wu ◽

Xing Kang ◽

...

Keyword(s):

Climate Change ◽

Tibetan Plateau ◽

Southeast Asia ◽

Molecular Dating ◽

Divergence Times ◽

The Tibetan Plateau ◽

Tree Frog ◽

Ancestral Area ◽

Distinct Lineage ◽

Asian Monsoons

Rapid uplifts of the Tibetan Plateau and climate change in Asia are thought to have profoundly modulated the diversification of most of the species distributed throughout Asia. The ranoid tree frog genusRhacophorus, the largest genus in the Rhacophoridae, is widely distributed in Asia and especially speciose in the areas south and east of the Tibetan Plateau. Here, we infer phylogenetic relationships among species and estimate divergence times, asking whether the spatiotemporal characteristics of diversification withinRhacophoruswere related to rapid uplifts of the Tibetan Plateau and concomitant climate change. Phylogenetic analysis recovered distinct lineage structures inRhacophorus, which indicated a clear distribution pattern from Southeast Asia toward East Asia and India. Molecular dating suggests that the first split within the genus date back to the Middle Oligocene (approx. 30 Ma). TheRhacophoruslineage through time (LTT) showed that there were periods of increased speciation rate: 14–12 Ma and 10–4 Ma. In addition, ancestral area reconstructions supported Southeast Asia as the ancestral area ofRhacophorus. According to the results of molecular dating, ancestral area reconstructions and LTT we think the geographic shifts, the staged rapid rises of the Tibetan Plateau with parallel climatic changes and reinforcement of the Asian monsoons (15 Ma, 8 Ma and 4–3 Ma), possibly prompted a burst of diversification inRhacophorus.

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Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times

Molecular Biology and Evolution ◽

10.1093/molbev/msz236 ◽

2019 ◽

Vol 37 (1) ◽

pp. 280-290 ◽

Cited By ~ 3

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

Abstract Confidence 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 dating analyses. Empirical data analyses showed that the new methods produce CIs that overlap with Bayesian highest posterior density intervals. In the analysis of computer-simulated data, we found that RelTime CIs show excellent average coverage probabilities, that is, the actual time is contained within the CIs with a 94% probability. These developments will encourage broader use of computationally efficient RelTime approaches in molecular dating analyses and biological hypothesis testing.

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Population genetic structure of the endangered yellow spotted mountain newt (Neurergus derjugini: Amphibia, Caudata) inferred from mitochondrial DNA sequences

Herpetological Journal ◽

10.33256/hj29.1.3747 ◽

2019 ◽

pp. 37-47 ◽

Cited By ~ 1

Author(s):

Tayebe Salehi

Keyword(s):

Dna Sequences ◽

Phylogenetic Trees ◽

Transition Period ◽

Isolation By Distance ◽

Haplotype Diversity ◽

Haplotype Network ◽

Molecular Dating ◽

Middle Pleistocene ◽

Restricted Gene Flow ◽

Historical Factors

The yellow spotted mountain newt (Neurergus derjugini) is a critically endangered species restricted to fragmented habitats in highland streams of the middle Zagros Mountain in Iran and Iraq. We examined the species phylogeography by investigating sequences of a mitochondrial fragment of the ND2 gene for 77 individuals from 15 locations throughout the species known distribution. We found relatively high haplotype diversity (0.82 ± 0.025) but low nucleotide diversity (0.0038 ± 0.00022) across all populations. Phylogenetic trees supported monophyly, and the segregation of haplotypes was concordant with the haplotype network. We found a significant correlation between geographical and genetic distances among populations (r = 0.54, P ˂ 0.01), suggesting restricted gene flow. Molecular dating suggested that haplogroups diverged during the early or middle Pleistocene. Bayesian skyline plot provided evidence for an expansion of populations during the Pleistocene-Holocene transition period. Taken together, isolation by distance due to low dispersal capability, habitat fragmentation, and historical factors have shaped the current population structure of N. derjugini.

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The evolution of methods for establishing evolutionary timescales

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2016.0020 ◽

2016 ◽

Vol 371 (1699) ◽

pp. 20160020 ◽

Cited By ~ 41

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’.

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Annonaceae substitution rates: a codon model perspective

Revista Brasileira de Fruticultura ◽

10.1590/s0100-29452014000500013 ◽

2014 ◽

Vol 36 (spe1) ◽

pp. 108-117 ◽

Cited By ~ 1

Author(s):

Lars Willem Chatrou ◽

Michael David Pirie ◽

Robin Van Velzen ◽

Freek Theodoor Bakker

Keyword(s):

Dna Sequences ◽

Phylogenetic Trees ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sequence Divergence ◽

High Ratio ◽

Molecular Dating ◽

Codon Model ◽

Synonymous Substitutions ◽

Branch Lengths

The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.

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

10.1101/2020.07.09.195487 ◽

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]

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