scholarly journals Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates

2014 ◽  
Vol 281 (1786) ◽  
pp. 20140732 ◽  
Author(s):  
Sebastián Duchêne ◽  
Edward C. Holmes ◽  
Simon Y. W. Ho
Keyword(s):  
Time Scales ◽  
Evolutionary Dynamics ◽  
Nucleotide Substitution ◽  
Viral Evolution ◽  
Negative Relationship ◽  
Purifying Selection ◽  
Time Dependent ◽  
Rate Variation ◽  
Nucleotide Substitution Rate ◽  
Evolutionary Time

Time-scales of viral evolution and emergence have been studied widely, but are often poorly understood. Molecular analyses of viral evolutionary time-scales generally rely on estimates of rates of nucleotide substitution, which vary by several orders of magnitude depending on the timeframe of measurement. We analysed data from all major groups of viruses and found a strong negative relationship between estimates of nucleotide substitution rate and evolutionary timescale. Strikingly, this relationship was upheld both within and among diverse groups of viruses. A detailed case study of primate lentiviruses revealed that the combined effects of sequence saturation and purifying selection can explain this time-dependent pattern of rate variation. Therefore, our analyses show that studies of evolutionary time-scales in viruses require a reconsideration of substitution rates as a dynamic, rather than as a static, feature of molecular evolution. Improved modelling of viral evolutionary rates has the potential to change our understanding of virus origins.

scholarly journals Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates

2019 ◽  
Vol 36 (8) ◽  
pp. 1793-1803 ◽  
Author(s):  
Jade Vincent Membrebe ◽  
Marc A Suchard ◽  
Andrew Rambaut ◽  
Guy Baele ◽  
Philippe Lemey
Keyword(s):  
Time Scales ◽  
Molecular Clock ◽  
Evolutionary History ◽  
Foamy Virus ◽  
Time Dependent ◽  
Rate Variation ◽  
Endogenous Virus ◽  
Widespread Application ◽  
Divergence Time Estimates ◽  
Codon Substitution

AbstractMany factors complicate the estimation of time scales for phylogenetic histories, requiring increasingly complex evolutionary models and inference procedures. The widespread application of molecular clock dating has led to the insight that evolutionary rate estimates may vary with the time frame of measurement. This is particularly well established for rapidly evolving viruses that can accumulate sequence divergence over years or even months. However, this rapid evolution stands at odds with a relatively high degree of conservation of viruses or endogenous virus elements over much longer time scales. Building on recent insights into time-dependent evolutionary rates, we develop a formal and flexible Bayesian statistical inference approach that accommodates rate variation through time. We evaluate the novel molecular clock model on a foamy virus cospeciation history and a lentivirus evolutionary history and compare the performance to other molecular clock models. For both virus examples, we estimate a similarly strong time-dependent effect that implies rates varying over four orders of magnitude. The application of an analogous codon substitution model does not implicate long-term purifying selection as the cause of this effect. However, selection does appear to affect divergence time estimates for the less deep evolutionary history of the Ebolavirus genus. Finally, we explore the application of our approach on woolly mammoth ancient DNA data, which shows a much weaker, but still important, time-dependent rate effect that has a noticeable impact on node age estimates. Future developments aimed at incorporating more complex evolutionary processes will further add to the broad applicability of our approach.

The predator-dependent replicator dynamics

2021 ◽  
Author(s):  
Ian Magalhaes Braga ◽  
Lucas Wardil
Keyword(s):  
Time Scales ◽  
Evolutionary Dynamics ◽  
Replicator Dynamics ◽  
Capture Rate ◽  
Evolutionary Game ◽  
Ecological Interactions ◽  
Evolutionary Time ◽  
Predator Prey ◽  
Environmental Interactions ◽  
Selection Of

Abstract Ecological interactions are central to understanding evolution. For example, Darwin noticed that the beautiful colours of the male peacock increase the chance of successful mating. However, the colours can be a threat because of the increased probability of being caught by predators. Eco-evolutionary dynamics takes into account environmental interactions to model the process of evolution. The selection of prey types in the presence of predators may be subjected to pressure on both reproduction and survival. Here, we analyze the evolutionary game dynamics of two types of prey in the presence of predators. We call this model \textit{the predator-dependent replicator dynamics}. If the evolutionary time scales are different, the number of predators can be assumed constant, and the traditional replicator dynamics is recovered. However, if the time scales are the same, we end up with sixteen possible dynamics: the combinations of four reproduction’s games with four predation’s games. We analyze the dynamics and calculate conditions for the coexistence of prey and predator. The main result is that predators can change the equilibrium of the traditional replicator dynamics. For example, the presence of predators can induce polymorphism in prey if one type of prey is more attractive than the other, with the prey ending with a lower capture rate in this new equilibrium. Lastly, we provide two illustrations of the dynamics, which can be seen as rapid feedback responses in a predator-prey evolutionary arm’s race.

scholarly journals Different Within-Host Viral Evolution Dynamics in Severely Immunosuppressed Cases with Persistent SARS-CoV-2

Biomedicines ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 808
Author(s):  
Laura Pérez-Lago ◽  
Teresa Aldámiz-Echevarría ◽  
Rita García-Martínez ◽  
Leire Pérez-Latorre ◽  
Marta Herranz ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Evolutionary Dynamics ◽  
Viral Evolution ◽  
Special Focus ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
New Variant ◽  
History Of ◽  
Evolution Dynamics ◽  
The Uk

A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.7, has recently been reported in the UK, causing global alarm. Most likely, the new variant emerged in a persistently infected patient, justifying a special focus on these cases. Our aim in this study was to explore certain clinical profiles involving severe immunosuppression that may help explain the prolonged persistence of viable viruses. We present three severely immunosuppressed cases (A, B, and C) with a history of lymphoma and prolonged SARS-CoV-2 shedding (2, 4, and 6 months), two of whom finally died. Whole-genome sequencing of 9 and 10 specimens from Cases A and B revealed extensive within-patient acquisition of diversity, 12 and 28 new single nucleotide polymorphisms, respectively, which suggests ongoing SARS-CoV-2 replication. This diversity was not observed for Case C after analysing 5 sequential nasopharyngeal specimens and one plasma specimen, and was only observed in one bronchoaspirate specimen, although viral viability was still considered based on constant low Ct values throughout the disease and recovery of the virus in cell cultures. The acquired viral diversity in Cases A and B followed different dynamics. For Case A, new single nucleotide polymorphisms were quickly fixed (13–15 days) after emerging as minority variants, while for Case B, higher diversity was observed at a slower emergence: fixation pace (1–2 months). Slower SARS-CoV-2 evolutionary pace was observed for Case A following the administration of hyperimmune plasma. This work adds knowledge on SARS-CoV-2 prolonged shedding in severely immunocompromised patients and demonstrates viral viability, noteworthy acquired intra-patient diversity, and different SARS-CoV-2 evolutionary dynamics in persistent cases.

Milankovitch cycles and their effects on species in ecological and evolutionary time

Paleobiology ◽  
1990 ◽  
Vol 16 (1) ◽  
pp. 11-21 ◽  
Author(s):  
K. D. Bennett
Keyword(s):  
Time Scales ◽  
Climatic Changes ◽  
Milankovitch Cycles ◽  
Mass Extinctions ◽  
Geological Time ◽  
Evolutionary Time ◽  
Abiotic Environment ◽  
Earth History ◽  
Microevolutionary Change ◽  
Second Tier

The Quaternary ice ages were paced by astronomical cycles with periodicities of 20–100 k.y. (Milankovitch cycles). These cycles have been present throughout earth history. The Quaternary fossil record, marine and terrestrial, near to and remote from centers of glaciation, shows that communities of plants and animals are temporary, lasting only a few thousand years at the most. Response of populations to the climatic changes of Quaternary Milankovitch cycles can be taken as typical of the way populations have behaved throughout earth history. Milankovitch cycles thus force an instability of climate and other aspects of the biotic and abiotic environment on time scales much less than typical species durations (1–30 m.y.). Any microevolutionary change that accumulates on a time scale of thousands of years is likely to be lost as communities are reorganized following climatic changes. A four-tier hierarchy of time scales for evolutionary processes can be constructed as follows: ecological time (thousands of years), Milankovitch cycles (20–100 k.y.), geological time (millions of years), mass extinctions (approximately 26 m.y.). “Ecological time” and “geological time” are defined temporally as the intervals between events of the second and fourth tiers, respectively. Gould's (1985) “paradox of the first tier” can be resolved, at least in part, through the undoing of Darwinian natural selection at the first tier by Milankovitch cycles at the second tier.

scholarly journals Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

2019 ◽  
Author(s):  
Kathryn E. Holt ◽  
Florent Lassalle ◽  
Kelly L. Wyres ◽  
Ryan Wick ◽  
Rafal J. Mostowy
Keyword(s):  
Evolutionary Dynamics ◽  
Bacterial Species ◽  
Purifying Selection ◽  
Evolutionary Forces ◽  
Polysaccharide Synthesis ◽  
Surface Polysaccharides ◽  
Surface Polysaccharide ◽  
Selective Preservation ◽  
Multiple Species

Bacterial capsules and lipopolysaccharides are diverse surface polysaccharides (SPs) that serve as the frontline for interactions with the outside world. While SPs can evolve rapidly, their diversity and evolutionary dynamics across different taxonomic scales has not been investigated in detail. Here, we focused on the bacterial order Enterobacteriales (including the medically-relevant Enterobacteriaceae), to carry out comparative genomics of two SP locus synthesis regions, cps and kps, using 27,334 genomes from 45 genera. We identified high-quality cps loci in 22 genera and kps in 11 genera, around 4% of which were detected in multiple species. We found SP loci to be highly dynamic genetic entities: their evolution was driven by high rates of horizontal gene transfer (HGT), both of whole loci and component genes, and relaxed purifying selection, yielding large repertoires of SP diversity. In spite of that, we found the presence of (near-)identical locus structures in distant taxonomic backgrounds that could not be explained by recent exchange, pointing to long-term selective preservation of locus structures in some populations. Our results reveal differences in evolutionary dynamics driving SP diversity within different bacterial species, with lineages of Escherichia coli, Enterobacter hormachei and Klebsiella aerogenes most likely to share SP loci via recent exchange; and lineages of Salmonella enterica, Citrobacter sakazakii and Serratia marcescens most likely to share SP loci via other mechanisms such as long-term preservation. Overall, the evolution of SP loci in Enterobacteriales is driven by a range of evolutionary forces and their dynamics and relative importance varies between different species.

scholarly journals The life cycle of Drosophila orphan genes

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Nicola Palmieri ◽  
Carolin Kosiol ◽  
Christian Schlötterer
Keyword(s):  
Life Cycle ◽  
Time Scales ◽  
High Rate ◽  
Sequence Evolution ◽  
Functional Requirements ◽  
Evolutionary Time ◽  
Orphan Genes ◽  
Functional Conservation ◽  
Close Relatives ◽  
Obscura Group

Orphans are genes restricted to a single phylogenetic lineage and emerge at high rates. While this predicts an accumulation of genes, the gene number has remained remarkably constant through evolution. This paradox has not yet been resolved. Because orphan genes have been mainly analyzed over long evolutionary time scales, orphan loss has remained unexplored. Here we study the patterns of orphan turnover among close relatives in the Drosophila obscura group. We show that orphans are not only emerging at a high rate, but that they are also rapidly lost. Interestingly, recently emerged orphans are more likely to be lost than older ones. Furthermore, highly expressed orphans with a strong male-bias are more likely to be retained. Since both lost and retained orphans show similar evolutionary signatures of functional conservation, we propose that orphan loss is not driven by high rates of sequence evolution, but reflects lineage-specific functional requirements.

scholarly journals Extinction in complex communities as driven by adaptive dynamics

2021 ◽  
Author(s):  
Vu Nguyen ◽  
Dervis Vural
Keyword(s):  
Time Scales ◽  
Computer Simulations ◽  
Analytical Solutions ◽  
Adaptive Dynamics ◽  
Mathematical Framework ◽  
Evolutionary Time ◽  
Community Interactions ◽  
Fitness Functions ◽  
Evolutionary Changes

In a complex community, species continuously adapt to each other. On rare occasions, the adaptation of a species can lead to the extinction of others, and even its own. ``Adaptive dynamics'' is the standard mathematical framework to describe evolutionary changes in community interactions, and in particular, predict adaptation driven extinction. Unfortunately, most authors implement the equations of adaptive dynamics through computer simulations, that require assuming a large number of questionable parameters and fitness functions. In this study we present analytical solutions to adaptive dynamics equations, thereby clarifying how outcomes depend on any computational input. We develop general formulas that predict equilibrium abundances over evolutionary time scales. Additionally, we predict which species will go extinct next, and when this will happen.

scholarly journals Divergent and convergent evolution of housekeeping genes in human–pig lineage

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4840 ◽  
Author(s):  
Kai Wei ◽  
Tingting Zhang ◽  
Lei Ma
Keyword(s):  
Active Sites ◽  
Evolutionary Dynamics ◽  
Purifying Selection ◽  
Housekeeping Genes ◽  
Neutral Evolution ◽  
Structure Evolution ◽  
Tissue Cell ◽  
Sequencing Data ◽  
Cellular Functions ◽  
Species Specific

Housekeeping genes are ubiquitously expressed and maintain basic cellular functions across tissue/cell type conditions. The present study aimed to develop a set of pig housekeeping genes and compare the structure, evolution and function of housekeeping genes in the human–pig lineage. By using RNA sequencing data, we identified 3,136 pig housekeeping genes. Compared with human housekeeping genes, we found that pig housekeeping genes were longer and subjected to slightly weaker purifying selection pressure and faster neutral evolution. Common housekeeping genes, shared by the two species, achieve stronger purifying selection than species-specific genes. However, pig- and human-specific housekeeping genes have similar functions. Some species-specific housekeeping genes have evolved independently to form similar protein active sites or structure, such as the classical catalytic serine–histidine–aspartate triad, implying that they have converged for maintaining the basic cellular function, which allows them to adapt to the environment. Human and pig housekeeping genes have varied structures and gene lists, but they have converged to maintain basic cellular functions essential for the existence of a cell, regardless of its specific role in the species. The results of our study shed light on the evolutionary dynamics of housekeeping genes.

scholarly journals The Red Queen model of recombination hot-spot evolution: a theoretical investigation

2017 ◽  
Vol 372 (1736) ◽  
pp. 20160463 ◽  
Author(s):  
Thibault Latrille ◽  
Laurent Duret ◽  
Nicolas Lartillot
Keyword(s):  
Gene Conversion ◽  
Recombination Rate ◽  
Evolutionary Dynamics ◽  
Genetic Model ◽  
Hot Spot ◽  
Rate Variation ◽  
Red Queen ◽  
Biased Gene Conversion ◽  
Red Queen Model ◽  
The Red Queen

In humans and many other species, recombination events cluster in narrow and short-lived hot spots distributed across the genome, whose location is determined by the Zn-finger protein PRDM9. To explain these fast evolutionary dynamics, an intra-genomic Red Queen model has been proposed, based on the interplay between two antagonistic forces: biased gene conversion, mediated by double-strand breaks, resulting in hot-spot extinction, followed by positive selection favouring new PRDM9 alleles recognizing new sequence motifs. Thus far, however, this Red Queen model has not been formalized as a quantitative population-genetic model, fully accounting for the intricate interplay between biased gene conversion, mutation, selection, demography and genetic diversity at the PRDM9 locus. Here, we explore the population genetics of the Red Queen model of recombination. A Wright–Fisher simulator was implemented, allowing exploration of the behaviour of the model (mean equilibrium recombination rate, diversity at the PRDM9 locus or turnover rate) as a function of the parameters (effective population size, mutation and erosion rates). In a second step, analytical results based on self-consistent mean-field approximations were derived, reproducing the scaling relations observed in the simulations. Empirical fit of the model to current data from the mouse suggests both a high mutation rate at PRDM9 and strong biased gene conversion on its targets. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.

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