scholarly journals The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis

2019 ◽  
Vol 15 ◽  
pp. 117693431985598 ◽  
Author(s):  
Beatriz Mello ◽  
Carlos G Schrago
Keyword(s):  
Substitution Rate ◽  
Relative Rate ◽  
Gene Tree ◽  
Great Apes ◽  
Rate Variation ◽  
Evolutionary Trend ◽  
Branch Lengths ◽  
Alternative Scenarios ◽  
Genomic Regions ◽  
Substitution Rate Variation

The recent surge of genomic data has prompted the investigation of substitution rate variation across the genome, as well as among lineages. Evolutionary trees inferred from distinct genomic regions may display branch lengths that differ between loci by simple proportionality constants, indicating that rate variation follows a pacemaker model, which may be attributed to lineage effects. Analyses of genes from diverse biological clades produced contrasting results, supporting either this model or alternative scenarios where multiple pacemakers exist. So far, an evaluation of the pacemaker hypothesis for all great apes has never been carried out. In this work, we tested whether the evolutionary rates of hominids conform to pacemakers, which were inferred accounting for gene tree/species tree discordance. For higher precision, substitution rates in branches were estimated with a calibration-free approach, the relative rate framework. A predominant evolutionary trend in great apes was evidenced by the recovery of a large pacemaker, encompassing most hominid genomic regions. In addition, the majority of genes followed a pace of evolution that was closely related to the strict molecular clock. However, slight rate decreases were recovered in the internal branches leading to humans, corroborating the hominoid slowdown hypothesis. Our findings suggest that in great apes, life history traits were the major drivers of substitution rate variation across the genome.

scholarly journals Gene tree discordance causes apparent substitution rate variation

2015 ◽  
Author(s):  
Fabio K. Mendes ◽  
Matthew W. Hahn
Keyword(s):  
Substitution Rate ◽  
Incomplete Lineage Sorting ◽  
False Positive Rate ◽  
Gene Tree ◽  
Species Tree ◽  
Rate Variation ◽  
Species Trees ◽  
Lineage Sorting ◽  
Gene Tree Discordance ◽  
Substitution Rate Variation

Substitution rates are known to be variable among genes, chromosomes, species, and lineages due to multifarious biological processes. Here we consider another source of substitution rate variation due to a technical bias associated with gene tree discordance, which has been found to be rampant in genome-wide datasets, often due to incomplete lineage sorting (ILS). This apparent substitution rate variation is caused when substitutions that occur on discordant gene trees are analyzed in the context of a single, fixed species tree. Such substitutions have to be resolved by proposing multiple substitutions on the species tree, and we therefore refer to this phenomenon as "SPILS" (Substitutions Produced by Incomplete Lineage Sorting). We use simulations to demonstrate that SPILS has a larger effect with increasing levels of ILS, and on trees with larger numbers of taxa. Specific branches of the species trees are consistently, but erroneously, inferred to be longer or shorter, and we show that these branches can be predicted based on discordant tree topologies. Moreover, we observe that fixing a species tree topology when performing tests of positive selection increases the false positive rate, particularly for genes whose discordant topologies are most affected by SPILS. Finally, we use data from multipleDrosophilaspecies to show that SPILS can be detected in nature. While the effects of SPILS are modest per gene, it has the potential to affect substitution rate variation whenever high levels of ILS are present, particularly in rapid radiations. The problems outlined here have implications for character mapping of any type of trait, and for any biological process that causes discordance. We discuss possible solutions to these problems, and areas in which they are likely to have caused faulty inferences of convergence and accelerated evolution.

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

Molecular evolution and phylogeny of the atpB-rbcL spacer of chloroplast DNA in the true mosses

Genome ◽  
2000 ◽  
Vol 43 (3) ◽  
pp. 417-426 ◽  
Author(s):  
Tzen-Yuh Chiang ◽  
Barbara A Schaal
Keyword(s):  
Molecular Evolution ◽  
Chloroplast Dna ◽  
Molecular Clock ◽  
Evolutionary Rate ◽  
Relative Rate ◽  
Gene Tree ◽  
Rbcl Gene ◽  
Evolutionary Trend ◽  
Nucleotide Substitutions ◽  
Spacer Length

The nucleotide variation of a noncoding region between the atpB and rbcL genes of the chloroplast genome was used to estimate the phylogeny of 11 species of true mosses (subclass Bryidae). The A+T rich (82.6%) spacer sequence is conserved with 48% of bases showing no variation between the ingroup and outgroup. Rooted at liverworts, Marchantia and Bazzania, the monophyly of true mosses was supported cladistically and statistically. A nonparametric Wilcoxon Signed-Ranks test Ts statistic for testing the taxonomic congruence showed no significant differences between gene trees and organism trees as well as between parsimony trees and neighbor-joining trees. The reconstructed phylogeny based on the atpB-rbcL spacer sequences indicated the validity of the division of acrocarpous and pleurocarpous mosses. The size of the chloroplast spacer in mosses fits into an evolutionary trend of increasing spacer length from liverworts through ferns to seed plants. According to the relative rate tests, the hypothesis of a molecular clock was supported in all species except for Thuidium, which evolved relatively fast. The evolutionary rate of the chloroplast DNA spacer in mosses was estimated to be (1.12 ± 0.019) × 10-10 nucleotides per site per year, which is close to the nonsynonymous substitution rates of the rbcL gene in the vascular plants. The constrained molecular evolution (total nucleotide substitutions, K approximately 0.0248) of the chloroplast DNA spacer is consistent with the slow evolution in morphological traits of mosses. Based on the calibrated evolutionary rate, the time of the divergence of true mosses was estimated to have been as early as 220 million years ago.Key words: atpB-rbcL noncoding spacer, chloroplast DNA, gene tree, molecular evolution, molecular clock, mosses, phylogeny.

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 Compensatory Evolution in RNA Secondary Structures Increases Substitution Rate Variation among Sites

2008 ◽  
Vol 25 (8) ◽  
pp. 1778-1787 ◽  
Author(s):  
J. L. Knies ◽  
K. K. Dang ◽  
T. J. Vision ◽  
N. G. Hoffman ◽  
R. Swanstrom ◽  
...  
Keyword(s):  
Substitution Rate ◽  
Secondary Structures ◽  
Rate Variation ◽  
Rna Secondary Structures ◽  
Compensatory Evolution ◽  
Substitution Rate Variation

scholarly journals Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees

2018 ◽  
Author(s):  
Zhirui Hu ◽  
Timothy B. Sackton ◽  
Scott V. Edwards ◽  
Jun S. Liu
Keyword(s):  
Substitution Rate ◽  
Phylogenetic Trees ◽  
Rate Variation ◽  
Strong Indicator ◽  
Convergent Rate ◽  
Conserved Noncoding Elements ◽  
Bayesian Relaxed Clock ◽  
Genomic Regions ◽  
Clock Models ◽  
Better Than

AbstractConservation of DNA sequence over evolutionary time is a strong indicator of function, and gain or loss of sequence conservation can be used to infer changes in function across a phylogeny. Changes in evolutionary rates on particular lineages in a phylogeny can indicate shared functional shifts, and thus can be used to detect genomic correlates of phenotypic convergence. However, existing methods do not allow easy detection of patterns of rate variation, which causes challenges for detecting convergent rate shifts or other complex evolutionary scenarios. Here we introduce PhyloAcc, a new Bayesian method to model substitution rate changes in conserved elements across a phylogeny. The method assumes several categories of substitution rate for each branch on the phylogenetic tree, estimates substitution rates per category, and detects changes of substitution rate as the posterior probability of a category switch. Simulations show that PhyloAcc can detect genomic regions with rate shifts in multiple target species better than previous methods and has a higher accuracy of reconstructing complex patterns of substitution rate changes than prevalent Bayesian relaxed clock models. We demonstrate the utility of PhyloAcc in two classic examples of convergent phenotypes: loss of flight in birds and the transition to marine life in mammals. In each case, our approach reveals numerous examples of conserved non-exonic elements with accelerations specific to the phenotypically convergent lineages. Our method is widely applicable to any set of conserved elements where multiple rate changes are expected on a phylogeny.

scholarly journals An improved method for fitting gamma distribution to substitution rate variation among sites

2018 ◽  
Author(s):  
Xuhua Xia
Keyword(s):  
Gamma Distribution ◽  
Substitution Rate ◽  
Shape Parameter ◽  
Pairwise Comparison ◽  
Simultaneous Estimation ◽  
Rate Variation ◽  
Simple Method ◽  
Site Specific ◽  
Specific Number ◽  
Substitution Rate Variation

AbstractGamma distribution has been used to fit substitution rate variation over site. One simple method to estimate the shape parameter of the gamma distribution is to 1) reconstruct a phylogenetic tree and the ancestral states of internal nodes, 2) perform pairwise comparison between nodes on each side of each branch to count the number of “observed” substitutions for each site, and apply correction of multiple hits to derive the estimated number of substitutions for each site, and 3) fit the site-specific substitution data to gamma distribution to obtain the shape parameter α This method is fast but its accuracy depends much on the accuracy of the estimated site-specific number of substitutions. The existing method has three shortcomings. First, it uses Poisson correction which is inadequate for almost any nucleotide sequences. Second, it does independent estimation for the number of substitutions at each site without making use of information at all sites. Third, the program implementing the method has never been made publically available. I have implemented in DAMBE software a new method based on the F84 substitution model with simultaneous estimation that uses information from all sites in estimating the number of substitutions at each site. DAMBE is freely available at available athttp://dambe.bio.uottawa.ca

scholarly journals Substitution rate variation in closely related rodent species

Heredity ◽  
1997 ◽  
Vol 78 (1) ◽  
pp. 21-31 ◽  
Author(s):  
Dan Fieldhouse ◽  
Fariborz Yazdani ◽  
G Brian Golding
Keyword(s):  
Substitution Rate ◽  
Rodent Species ◽  
Rate Variation ◽  
Substitution Rate Variation
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