scholarly journals An examination of phylogenetic models of substitution rate variation among lineages

2009 ◽  
Vol 5 (3) ◽  
pp. 421-424 ◽  
Author(s):  
Simon Y.W. Ho
Keyword(s):  
Significant Variation ◽  
Divergence Times ◽  
Rate Variation ◽  
Rate Heterogeneity ◽  
Phylogenetic Methods ◽  
Molecular Evolutionary Rates ◽  
Clock Models ◽  
Substitution Rate Variation ◽  
Relaxed Molecular Clock ◽  
Phylogenetic Models

Molecular evolutionary rates can show significant variation among lineages, complicating the task of estimating substitution rates and divergence times using phylogenetic methods. Accordingly, relaxed molecular clock models have been developed to accommodate such rate heterogeneity, but these often make the assumption of rate autocorrelation among lineages. In this paper, I examine the validity of this assumption.

scholarly journals Nucleotide substitutions during speciation may explain substitution rate variation

2020 ◽  
Author(s):  
Thijs Janzen ◽  
Folmer Bokma ◽  
Rampal S. Etienne
Keyword(s):  
Molecular Clock ◽  
Molecular Mechanisms ◽  
Phylogenetic Reconstruction ◽  
Mutation Rates ◽  
Rate Variation ◽  
Nucleotide Substitutions ◽  
Strict Molecular Clock ◽  
Substitution Rate Variation ◽  
Relaxed Molecular Clock ◽  
Evolutionary Lineages

ABSTRACTAlthough molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which, however, is just a statistical distribution of mutation rates without any underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life.

scholarly journals Substitution Rate Variation in a Robust Procellariiform Seabird Phylogeny is not Solely Explained by Body Mass, Flight Efficiency, Population Size or Life History Traits

2021 ◽  
Author(s):  
Andrea Estandia ◽  
R. Terry Chesser ◽  
Helen F. James ◽  
Max A. Levy ◽  
Joan Ferrer Obiol ◽  
...  
Keyword(s):  
Life History ◽  
Population Size ◽  
Body Mass ◽  
Substitution Rate ◽  
Life History Traits ◽  
Nuclear Dna ◽  
Major Influence ◽  
Rate Variation ◽  
Rate Heterogeneity ◽  
Substitution Rate Variation

Substitution rate variation among branches can lead to inaccurate reconstructions of evolutionary relationships and obscure the true phylogeny of affected clades. Body mass is often assumed to have a major influence on substitution rate, though other factors such as population size, life history traits, and flight demands are also thought to have an influence. Birds of the order Procellariiformes-which encompasses petrels, storm-petrels and albatrosses-show a striking 900-fold difference in body mass between the smallest and largest members, divergent life history traits, and substantial heterogeneity in mitochondrial substitution rates. Here, we used genome-scale nuclear DNA sequence data from 4365 ultraconserved element loci (UCEs) in 51 procellariiform species to examine whether phylogenetic reconstruction using genome-wide datasets is robust to the presence of rate heterogeneity, and to identify predictors of substitution rate variation. Our results provide a backbone phylogeny for procellariiform seabirds and resolve several controversies about the evolutionary history of the order, demonstrating that albatrosses are basal, storm-petrels are paraphyletic and diving petrels nestled within the Procellariidae. We find evidence of rate variation; however, all phylogenetic analyses using both concatenation and multispecies coalescent approaches recovered the same branching topology, including analyses implementing different clock models, and analyses of the most and least clock-like loci. Overall, we find that rate heterogeneity is little impacted by body mass, population size, age at first breeding, and longevity but moderately correlated with hand-wing index, a proxy for wing shape and flight efficiency. Given our results and the context of the broader literature perhaps it is time that we begin to question the prevailing paradigm that one or a few traits largely explain rate variation and accept instead that substitution rate may be the product of weak interactions among many, potentially taxon-specific, variables.

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.

scholarly journals Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles

2010 ◽  
Vol 277 (1700) ◽  
pp. 3587-3592 ◽  
Author(s):  
Soo Hyung Eo ◽  
J. Andrew DeWoody
Keyword(s):  
Species Richness ◽  
Nuclear Data ◽  
Synonymous Substitution ◽  
Evolutionary Rates ◽  
Rate Variation ◽  
Substitution Rates ◽  
Diversification Rates ◽  
Extinction Process ◽  
Molecular Evolutionary Rates ◽  
Speciation Rates

Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation–extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO 3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.

Viral Substitution Rate Variation Can Arise from the Interplay between Within-Host and Epidemiological Dynamics

2013 ◽  
Vol 182 (4) ◽  
pp. 494-513 ◽  
Author(s):  
Stacy O. Scholle ◽  
Rolf J. F. Ypma ◽  
Alun L. Lloyd ◽  
Katia Koelle
Keyword(s):  
Substitution Rate ◽  
Rate Variation ◽  
Substitution Rate Variation

scholarly journals Large Evolutionary Rate Heterogeneity among and within HIV-1 Subtypes and CRFs

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1689
Author(s):  
Arshan Nasir ◽  
Mira Dimitrijevic ◽  
Ethan Romero-Severson ◽  
Thomas Leitner
Keyword(s):  
Evolutionary Rate ◽  
Virus Genome ◽  
Rate Variation ◽  
Human Populations ◽  
Host Immune System ◽  
Virus Spread ◽  
Rate Heterogeneity ◽  
Hiv 1 ◽  
Subtype 3 ◽  
Diverse Virus

HIV-1 is a fast-evolving, genetically diverse virus presently classified into several groups and subtypes. The virus evolves rapidly because of an error-prone polymerase, high rates of recombination, and selection in response to the host immune system and clinical management of the infection. The rate of evolution is also influenced by the rate of virus spread in a population and nature of the outbreak, among other factors. HIV-1 evolution is thus driven by a range of complex genetic, social, and epidemiological factors that complicates disease management and prevention. Here, we quantify the evolutionary (substitution) rate heterogeneity among major HIV-1 subtypes and recombinants by analyzing the largest collection of HIV-1 genetic data spanning the widest possible geographical (100 countries) and temporal (1981–2019) spread. We show that HIV-1 substitution rates vary substantially, sometimes by several folds, both across the virus genome and between major subtypes and recombinants, but also within a subtype. Across subtypes, rates ranged 3.5-fold from 1.34 × 10−3 to 4.72 × 10−3 in env and 2.3-fold from 0.95 × 10−3 to 2.18 × 10−3 substitutions site−1 year−1 in pol. Within the subtype, 3-fold rate variation was observed in env in different human populations. It is possible that HIV-1 lineages in different parts of the world are operating under different selection pressures leading to substantial rate heterogeneity within and between subtypes. We further highlight how such rate heterogeneity can complicate HIV-1 phylodynamic studies, specifically, inferences on epidemiological linkage of transmission clusters based on genetic distance or phylogenetic data, and can mislead estimates about the timing of HIV-1 lineages.

scholarly journals Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times

2019 ◽  
Vol 37 (1) ◽  
pp. 280-290 ◽  
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.

scholarly journals Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae

2009 ◽  
Vol 9 (1) ◽  
pp. 260 ◽  
Author(s):  
Daniel B Sloan ◽  
Bengt Oxelman ◽  
Anja Rautenberg ◽  
Douglas R Taylor
Keyword(s):  
Phylogenetic Analysis ◽  
Substitution Rate ◽  
Rate Variation ◽  
Substitution Rate Variation

scholarly journals Grouping substitution types into different relaxed molecular clocks

2016 ◽  
Vol 371 (1699) ◽  
pp. 20150141 ◽  
Author(s):  
Hui-Jie Lee ◽  
Hirohisa Kishino ◽  
Nicolas Rodrigue ◽  
Jeffrey L. Thorne
Keyword(s):  
Divergence Time ◽  
Time Estimation ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Nucleotide Substitutions ◽  
Change Over Time ◽  
Divergence Time Estimation ◽  
Group Change ◽  
Relaxed Molecular Clock ◽  
Over Time

Different types of nucleotide substitutions experience different patterns of rate change over time. We propose clustering context-dependent (or context-independent) nucleotide substitution types according to how their rates change and then using the grouping for divergence time estimation. With our models, relative rates among types that are in the same group are fixed, whereas absolute rates of the types within a group change over time according to a shared relaxed molecular clock. We illustrate our procedure by analysing a 0.15 Mb intergenic region to infer divergence times relating eight primates. The different groupings of substitution types that we explore have little effect on the posterior means of divergence times, but the widths of the credibility intervals decrease as the number of groups increases. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

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