scholarly journals Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

2012 ◽  
Vol 29 (9) ◽  
pp. 2157-2167 ◽  
Author(s):  
Guy Baele ◽  
Philippe Lemey ◽  
Trevor Bedford ◽  
Andrew Rambaut ◽  
Marc A. Suchard ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Model Comparison ◽  
Clock Model ◽  
Molecular Clock Model

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.

scholarly journals Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary

2017 ◽  
Vol 114 (35) ◽  
pp. E7282-E7290 ◽  
Author(s):  
Liang Liu ◽  
Jin Zhang ◽  
Frank E. Rheindt ◽  
Fumin Lei ◽  
Yanhua Qu ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Mass Extinction ◽  
Sensitivity Analyses ◽  
Divergence Times ◽  
Delayed Response ◽  
Clock Model ◽  
Molecular Clock Model ◽  
Shift Analysis ◽  
Continuous Radiation ◽  
Genome Scale

The timing of the diversification of placental mammals relative to the Cretaceous–Paleogene (KPg) boundary mass extinction remains highly controversial. In particular, there have been seemingly irreconcilable differences in the dating of the early placental radiation not only between fossil-based and molecular datasets but also among molecular datasets. To help resolve this discrepancy, we performed genome-scale analyses using 4,388 loci from 90 taxa, including representatives of all extant placental orders and transcriptome data from flying lemurs (Dermoptera) and pangolins (Pholidota). Depending on the gene partitioning scheme, molecular clock model, and genic deviation from molecular clock assumptions, extensive sensitivity analyses recovered widely varying diversification scenarios for placental mammals from a given gene set, ranging from a deep Cretaceous origin and diversification to a scenario spanning the KPg boundary, suggesting that the use of suboptimal molecular clock markers and methodologies is a major cause of controversies regarding placental diversification timing. We demonstrate that reconciliation between molecular and paleontological estimates of placental divergence times can be achieved using the appropriate clock model and gene partitioning scheme while accounting for the degree to which individual genes violate molecular clock assumptions. A birth-death-shift analysis suggests that placental mammals underwent a continuous radiation across the KPg boundary without apparent interruption by the mass extinction, paralleling a genus-level radiation of multituberculates and ecomorphological diversification of both multituberculates and therians. These findings suggest that the KPg catastrophe evidently played a limited role in placental diversification, which, instead, was likely a delayed response to the slightly earlier radiation of angiosperms.

The Tempo and Mode of Evolution of Acoustic Communication Signals of Felids

1998 ◽  
Vol 2 (2) ◽  
pp. 233-248 ◽  
Author(s):  
Gustav Peters ◽  
Barbara A. Tonkin-Leyhausen
Keyword(s):  
Molecular Phylogeny ◽  
Molecular Clock ◽  
Acoustic Communication ◽  
Time Scale ◽  
Evolutionary Process ◽  
Time Frame ◽  
Evolutionary Change ◽  
Clock Model ◽  
Communication Signals ◽  
Molecular Clock Model

Based on the molecular clock model of evolution, molecular phylogenies represent reconstructions of the evolutionary process with a time scale. From these, inferences can be drawn about the evolution of other characters, including behaviour patterns. Mapping particular vocalization types in the Felidae (cats) on a published molecular phylogeny of this mammal family reveals that the distribution of these behavioural characters is fully congruent with it. Thence a time frame for the evolution of these vocalizations can be inferred, indicating large differences in their evolutionary age. Phylogenetic stasis for several million years in particular vocalization types refutes the hypothesis that behavioural characters are generally more susceptible to evolutionary change than morphological ones.

scholarly journals Great ape mutation spectra vary across the phylogeny and the genome due to distinct mutational processes that evolve at different rates

2019 ◽  
Author(s):  
Michael E. Goldberg ◽  
Kelley Harris
Keyword(s):  
Replication Timing ◽  
Mutation Rates ◽  
Great Ape ◽  
Mutational Signatures ◽  
Clock Model ◽  
Cis Acting ◽  
Molecular Clock Model ◽  
Species Specific ◽  
Mutation Spectra ◽  
Mutational Processes

ABSTRACTRecent studies of hominoid variation have shown that mutation rates and spectra can evolve rapidly, contradicting the fixed molecular clock model. The relative mutation rates of three-base-pair motifs differ significantly among great ape species, suggesting the action of unknown modifiers of DNA replication fidelity. To illuminate the footprints of these hypothetical mutators, we measured mutation spectra of several functional compartments (such as late-replicating regions) that are likely targeted by localized mutational processes. Using genetic diversity from 88 great apes, we find that compartment-specific mutational signatures appear largely conserved between species. These signatures layer with species-specific signatures to create rich mutational portraits: for example, late-replicating regions in gorillas contain an identifiable mixture of a replication timing signature and a gorilla-specific signature. Our results suggest that cis-acting mutational modifiers are highly conserved between species and transacting modifiers are driving rapid mutation spectrum evolution.

Australasian orchid diversification in time and space: molecular phylogenetic insights from the beard orchids (Calochilus, Diurideae)

2018 ◽  
Author(s):  
Katharina Nargar ◽  
Sarah Molina ◽  
Natascha Wagner ◽  
Lars Nauheimer ◽  
Claire Micheneau ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Divergence Time ◽  
Clock Model ◽  
Infrageneric Classification ◽  
Ancestral Area ◽  
Molecular Clock Model ◽  
Molecular Phylogenetic ◽  
Spatio Temporal ◽  
Vegetative Characters ◽  
Relaxed Molecular Clock

Phylogenetic relationships in Calochilus (~30 species) were inferred based on a supermatrix of 81 loci including 22 species. To examine the spatio-temporal evolution of Calochilus, divergence-time estimations were conducted within a Bayesian framework using an uncorrelated relaxed molecular-clock model, followed by maximum-likelihood ancestral-range reconstructions comparing four biogeographic models. To trace the evolution of key floral and vegetative characters, maximum-likelihood ancestral-character reconstructions were carried out. The stem age of Calochilus was dated to ~12.0 million years ago in the mid-Miocene. Divergence of Calochilus into a tropical and a temperate clade was inferred to have occurred ~7.6 million years ago in the late Miocene. Northern Australia was reconstructed as the ancestral area of the tropical clade and the Euronotian region for the temperate clade. Range expansions from Australia to other Australasian regions, such as New Zealand and New Guinea, were inferred to have occurred only in recent geological times, commencing in the Pleistocene. The infrageneric classification for Calochilus was revised, erecting two subgenera, subgenus Calochilus and subgenus Tropichilus subgen. nov. Section Calochilus Szlach. was recircumscribed, and sect. Abrochilus sect. nov., and section Placochilus sect. nov. were erected. Identification keys to subgenera and sections and a taxonomic synopsis of the genus are provided.

scholarly journals Frequent branch-specific changes of protein substitution rates in closely related lineages

2020 ◽  
Author(s):  
Neel Prabh ◽  
Diethard Tautz
Keyword(s):  
General Pattern ◽  
Sequence Information ◽  
Sequence Evolution ◽  
Clock Model ◽  
Sequence Comparisons ◽  
Protein Coding ◽  
Molecular Clock Model ◽  
Constant Rate ◽  
History Of ◽  
The Individual

AbstractSince its inception, the investigation of protein divergence has revolved around a more or less constant rate of sequence information decay that led to the formation of the molecular clock model for sequence evolution. We use here the classical approach of amino acid sequence comparisons to examine the overall divergence of proteins and the possibility of lineage-specific acceleration. By generating and analysing a high-confidence dataset of 13,160 syntenic orthologs from four ape species, including humans, we found that only less than 1% of the ortholog families are entirely in line with the clock model in each of their branches. The most common departure from the expected decay rate involves higher than expected substitutions on just one or two branches of the individual families. However, when taken as aggregate, even a small set of families conform well with the clock assumptions. We identified ADCYAP1 as the most divergent human protein-coding gene with 10% human-specific substitutions. Such lineage-specific highly accelerated genes were not limited to humans but appear as a general pattern that accompanies the formation of species. Our analysis uncovers a much more dynamic history of substitution rate changes in most protein families than usually assumed. Such fluctuations can result in bursts of rapid acceleration followed by periods of strong conservation that effectively cancel each other. Although this gives an impression of a long-term constant rate, the actual history of protein sequence evolution appears to be more complicated.

scholarly journals Divergence dating using mixed effects clock modelling: An application to HIV-1

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
Magda Bletsa ◽  
Marc A Suchard ◽  
Xiang Ji ◽  
Sophie Gryseels ◽  
Bram Vrancken ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Mixed Effects ◽  
Recent Common Ancestor ◽  
Rate Variation ◽  
Clock Model ◽  
Data Set ◽  
Genome Data ◽  
Most Recent Common Ancestor ◽  
Clock Models ◽  
Hiv 1

Abstract The need to estimate divergence times in evolutionary histories in the presence of various sources of substitution rate variation has stimulated a rich development of relaxed molecular clock models. Viral evolutionary studies frequently adopt an uncorrelated clock model as a generic relaxed molecular clock process, but this may impose considerable estimation bias if discrete rate variation exists among clades or lineages. For HIV-1 group M, rate variation among subtypes has been shown to result in inconsistencies in time to the most recent common ancestor estimation. Although this calls into question the adequacy of available molecular dating methods, no solution to this problem has been offered so far. Here, we investigate the use of mixed effects molecular clock models, which combine both fixed and random effects in the evolutionary rate, to estimate divergence times. Using simulation, we demonstrate that this model outperforms existing molecular clock models in a Bayesian framework for estimating time-measured phylogenies in the presence of mixed sources of rate variation, while also maintaining good performance in simpler scenarios. By analysing a comprehensive HIV-1 group M complete genome data set we confirm considerable rate variation among subtypes that is not adequately modelled by uncorrelated relaxed clock models. The mixed effects clock model can accommodate this rate variation and results in a time to the most recent common ancestor of HIV-1 group M of 1920 (1915–25), which is only slightly earlier than the uncorrelated relaxed clock estimate for the same data set. The use of complete genome data appears to have a more profound impact than the molecular clock model because it reduces the credible intervals by 50 per cent relative to similar estimates based on short envelope gene sequences.

scholarly journals Inferring Evolutionary Timescales without Independent Timing Information: An Assessment of “Universal” Insect Rates to Calibrate a Collembola (Hexapoda) Molecular Clock

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1172
Author(s):  
Aron D. Katz
Keyword(s):  
Molecular Clock ◽  
Average Rate ◽  
Careful Consideration ◽  
Cryptic Diversity ◽  
Timing Information ◽  
Molecular Clock Model ◽  
Nucleotide Substitution Rates ◽  
Taxonomic Groups ◽  
Relaxed Molecular Clock ◽  
Rates Of Molecular Evolution

Previous estimates of nucleotide substitution rates are routinely applied as secondary or “universal” molecular clock calibrations for estimating evolutionary timescales in groups that lack independent timing information. A major limitation of this approach is that rates can vary considerably among taxonomic groups, but the assumption of rate constancy is rarely evaluated prior to using secondary rate calibrations. Here I evaluate whether an insect mitochondrial DNA clock is appropriate for estimating timescales in Collembola—a group of insect-like arthropods characterized by high levels of cryptic diversity. Relative rates of substitution in cytochrome oxidase subunit 1 (COI) were inferred via Bayesian analysis across a topologically constrained Hexapod phylogeny using a relaxed molecular clock model. Rates for Collembola did not differ significantly from the average rate or from the rates estimated for most other groups (25 of 30), suggesting that (1) their apparent cryptic diversity cannot be explained by accelerated rates of molecular evolution and (2) clocks calibrated using “universal” insect rates may be appropriate for estimating evolutionary timescales in this group. However, of the 31 groups investigated, 10 had rates that deviated significantly from the average (6 higher, 4 lower), underscoring the need for caution and careful consideration when applying secondary insect rate calibrations. Lastly, this study exemplifies a relatively simple approach for evaluating rate constancy within a taxonomic group to determine whether the use of secondary rates are appropriate for molecular clock calibrations.

Identifying suboptimalities with factorial model comparison

2018 ◽  
Vol 41 ◽  
Author(s):  
Wei Ji Ma
Keyword(s):  
Experimental Design ◽  
Model Comparison ◽  
Process Models ◽  
Multiple Forms ◽  
Factorial Experimental Design ◽  
Factorial Model ◽  
Multiple Components ◽  
The Many

AbstractGiven the many types of suboptimality in perception, I ask how one should test for multiple forms of suboptimality at the same time – or, more generally, how one should compare process models that can differ in any or all of the multiple components. In analogy to factorial experimental design, I advocate for factorial model comparison.

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