The Molecular Clock and Evolutionary Rates Across the Tree of Life

2020 ◽  
pp. 3-23
Author(s):  
Simon Y. W. Ho
Keyword(s):  
Molecular Clock ◽  
Tree Of Life ◽  
Evolutionary Rates

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 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.

It's a protist-eat-protist world: recalcitrance, predation, and evolution in the Tonian–Cryogenian ocean

2018 ◽  
Vol 2 (2) ◽  
pp. 173-180 ◽  
Author(s):  
Phoebe A. Cohen ◽  
Leigh Anne Riedman
Keyword(s):  
Molecular Clock ◽  
Fossil Record ◽  
Critical Role ◽  
Indirect Evidence ◽  
Tree Of Life ◽  
Current Understanding ◽  
Evolutionary Transitions ◽  
Ecological Interaction ◽  
Fossil Evidence ◽  
Multiple Metrics

Predation, and how organisms respond to it, is an important ecological interaction across the tree of life. Much of our understanding of predation focuses on modern metazoa. However, predation is equally important in single-celled eukaryotes (commonly referred to as protists). In the fossil record, we see evidence of protists preying on other protists beginning in the Tonian Period (1000–720 Ma). In addition, the first evidence of eukaryotic biomineralization and the appearance of multiple unmineralized but recalcitrant forms are also seen in the Tonian and Cryogenian (720–635 Ma), potentially indirect evidence of predation. This fossil evidence, coupled with molecular clock analyses, is coincident with multiple metrics that show an increase in the diversity of eukaryotic clades and fossil assemblages. Predation, thus, may have played a critical role in the diversification of eukaryotes and the evolution of protistan armor in the Neoproterozoic Era. Here, we review the current understanding of predation in the Tonian and Cryogenian oceans as viewed through the fossil record, and discuss how the rise of eukaryotic predation upon other eukaryotes (eukaryovory) may have played a role in major evolutionary transitions including the origins of biomineralization.

Origins and evolution of AIDS viruses: estimating the time-scale

2000 ◽  
Vol 28 (2) ◽  
pp. 275-282 ◽  
Author(s):  
P. M. Sharp ◽  
E. Bailes ◽  
F. Gao ◽  
B. E. Beer ◽  
V. M. Hirsch ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Host Species ◽  
Time Scale ◽  
Evolutionary Tree ◽  
Evolutionary Rates ◽  
Sooty Mangabey ◽  
Dependent Manner ◽  
Primate Lentiviruses ◽  
Stark Contrast ◽  
Hiv 1

The primate lentiviruses comprise SIV strains from various host species, as well as two viruses, HIV-1 and HIV-2, that cause AIDS in humans. The origins of HIV-1 and HIV-2 have been traced to cross-species transmissions from chimpanzees and sooty mangabey monkeys respectively. Two approaches have been taken to estimate the time-scale of the evolution of these viruses. Certain groups of SIV strains appear to have evolved in a host-dependent manner, implying a time-scale of many thousands or even millions of years. In stark contrast, molecular clock calculations have previously been used to estimate a time-scale of only tens or hundreds of years. Those calculations largely ignored heterogeneity of evolutionary rates across different sites within sequences. In fact, the distribution of rates at different sites seems extremely skewed in HIV-1, and so the time-depth of the primate lentivirus evolutionary tree may have been underestimated by at least a factor of ten. However, these date estimates still seem to be far too recent to be consistent with host-dependent evolution.

scholarly journals A new method for detecting autocorrelation of evolutionary rates in large phylogenies

2018 ◽  
Author(s):  
Qiqing Tao ◽  
Koichiro Tamura ◽  
Fabia Battistuzzi ◽  
Sudhir Kumar
Keyword(s):  
Sequence Data ◽  
Tree Of Life ◽  
Evolutionary Rates ◽  
New Method ◽  
Sequence Evolution ◽  
Computationally Efficient ◽  
Evolutionary Patterns ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Evolution Of Mammals

AbstractNew species arise from pre-existing species and inherit similar genomes and environments. This predicts greater similarity of mutation rates and the tempo of molecular evolution between direct ancestors and descendants, resulting in autocorrelation of evolutionary rates within lineages in the tree of life. Surprisingly, molecular sequence data have not confirmed this expectation, possibly because available methods lack power to detect autocorrelated rates. Here we present a machine learning method to detect the presence evolutionary rate autocorrelation in large phylogenies. The new method is computationally efficient and performs better than the available state-of-the-art methods. Application of the new method reveals extensive rate autocorrelation in DNA and amino acid sequence evolution of mammals, birds, insects, metazoans, plants, fungi, and prokaryotes. Therefore, rate autocorrelation is a common phenomenon throughout the tree of life. These findings suggest concordance between molecular and non-molecular evolutionary patterns and will foster unbiased and precise dating of the tree of life.

scholarly journals Phylogeographic analysis reveals an ancient East African origin of the human herpes simplexvirus 2 dispersal out-of-Africa.

2022 ◽  
Author(s):  
Jennifer L. Havens ◽  
Sebastien Calvignac-Spencer ◽  
Kevin Merkel ◽  
Sonia Burrel ◽  
David Boutolleau ◽  
...  
Keyword(s):  
East Africa ◽  
Molecular Clock ◽  
Central Africa ◽  
Human Migration ◽  
Evolutionary Rates ◽  
Human Herpes ◽  
Phylogeographic Analysis ◽  
West And Central Africa ◽  
Out Of Africa ◽  
Competing Hypotheses

Human herpes simplex virus 2 (HSV-2) is a globally ubiquitous, slow evolving DNA virus. HSV-2 genomic diversity can be divided into two main groups: an African lineage and worldwide lineage. Competing hypotheses have been put forth to explain the history of HSV-2. HSV-2 may have originated in Africa and then followed the first wave of human migration out of Africa between 50-100 kya. Alternatively, HSV-2 may have migrated out of Africa via the trans-Atlantic slave trade within the last 150-500 years. The lack of HSV-2 genomes from West and Central Africa, combined with a lack of molecular clock signal in HSV-2 has precluded robust testing of these competing hypotheses. Here, we expand the geographic sampling of HSV-2 genomes in order to resolve the geography and timing of divergence events within HSV-2. We analyze 65 newly sequenced HSV-2 genomes collected from primarily West and Central Africa along with 330 previously published genomes sampled over a 47-year period. Evolutionary simulations confirm that the molecular clock in HSV-2 is too slow to be detected using available data. However, phylogeographic analysis indicates that all biologically plausible evolutionary rates would place the ancestor of the worldwide lineage in East Africa, arguing against the trans-Atlantic slave trade as the source of worldwide diversity. The best supported evolutionary rates between 4.2x10-8 and 5.6x10-8 substitutions/site/year suggest a most recent common ancestor for HSV-2 around 90-120 kya and initial dispersal around 21.9-29.3 kya. These dates suggest HSV-2 left Africa during subsequent waves of human migration out of East Africa.

scholarly journals A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies

2019 ◽  
Vol 36 (4) ◽  
pp. 811-824 ◽  
Author(s):  
Qiqing Tao ◽  
Koichiro Tamura ◽  
Fabia U. Battistuzzi ◽  
Sudhir Kumar
Keyword(s):  
Machine Learning ◽  
Sequence Data ◽  
Tree Of Life ◽  
Evolutionary Rates ◽  
Sequence Evolution ◽  
Machine Learning Method ◽  
Learning Method ◽  
Evolutionary Patterns ◽  
Molecular Sequence Data ◽  
Molecular Sequence

Abstract New species arise from pre-existing species and inherit similar genomes and environments. This predicts greater similarity of the tempo of molecular evolution between direct ancestors and descendants, resulting in autocorrelation of evolutionary rates in the tree of life. Surprisingly, molecular sequence data have not confirmed this expectation, possibly because available methods lack the power to detect autocorrelated rates. Here, we present a machine learning method, CorrTest, to detect the presence of rate autocorrelation in large phylogenies. CorrTest is computationally efficient and performs better than the available state-of-the-art method. Application of CorrTest reveals extensive rate autocorrelation in DNA and amino acid sequence evolution of mammals, birds, insects, metazoans, plants, fungi, parasitic protozoans, and prokaryotes. Therefore, rate autocorrelation is a common phenomenon throughout the tree of life. These findings suggest concordance between molecular and nonmolecular evolutionary patterns, and they will foster unbiased and precise dating of the tree of life.

scholarly journals Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies

2020 ◽  
Vol 38 (1) ◽  
pp. 307-317
Author(s):  
Xavier Didelot ◽  
Igor Siveroni ◽  
Erik M Volz
Keyword(s):  
Molecular Clock ◽  
Real Data ◽  
Evolutionary Rates ◽  
Data Sets ◽  
Clock Rate ◽  
Clock Model ◽  
Genomic Epidemiology ◽  
Molecular Clock Model ◽  
Clock Models ◽  
Relaxed Clock

Abstract Phylogenetic dating is one of the most powerful and commonly used methods of drawing epidemiological interpretations from pathogen genomic data. Building such trees requires considering a molecular clock model which represents the rate at which substitutions accumulate on genomes. When the molecular clock rate is constant throughout the tree then the clock is said to be strict, but this is often not an acceptable assumption. Alternatively, relaxed clock models consider variations in the clock rate, often based on a distribution of rates for each branch. However, we show here that the distributions of rates across branches in commonly used relaxed clock models are incompatible with the biological expectation that the sum of the numbers of substitutions on two neighboring branches should be distributed as the substitution number on a single branch of equivalent length. We call this expectation the additivity property. We further show how assumptions of commonly used relaxed clock models can lead to estimates of evolutionary rates and dates with low precision and biased confidence intervals. We therefore propose a new additive relaxed clock model where the additivity property is satisfied. We illustrate the use of our new additive relaxed clock model on a range of simulated and real data sets, and we show that using this new model leads to more accurate estimates of mean evolutionary rates and ancestral dates.

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