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Name Location Contact Info. Lorem Ipsum Lorem ipsum dolor sit amet. Search: gmail. Add Get Contact Info. We set the standard for finding emails Trusted by over 6. We had no where to begin. Scouring the web at all hours of the night wasn't gonna cut it. RocketReach has given us a great place to start. Our workflow has solid direction now - we have a process in place the begins with RocketReach and ends with huge contact lists for our sales team.. We can divert our attention to actually going after the customer now!

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The most frustrating part was how time consuming this all was. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates , which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination.

This variation was negatively associated with sampling time, with this relationship best described by an exponential decay curve. To avoid potential estimation biases, such time-dependency should be considered when inferring evolutionary time-scales in bacteria. Evolutionary rescue of a parasite population by mutation rate evolution.

The risk of antibiotic resistance evolution in parasites is a major problem for public health. Identifying factors which promote antibiotic resistance evolution is thus a priority in evolutionary medicine. The rate at which new mutations enter the parasite population is one important predictor; however, mutation rate is not necessarily a fixed quantity, as is often assumed, but can itself evolve. Here we explore the possible impacts of mutation rate evolution on the fate of a disease circulating in a host population, which is being treated with drugs, the use of which varies over time.

Using an evolutionary rescue framework, we find that mutation rate evolution provides a dramatic increase in the probability that a parasite population survives treatment in only a limited region, while providing little or no advantage in other regions. Both epidemiological features, such as the virulence of infection, and population genetic parameters, such as recombination rate , play important roles in determining the probability of evolutionary rescue and whether mutation rate evolution enhances the probability of evolutionary rescue or not.

While efforts to curtail mutation rate evolution in parasites may be worthwhile under some circumstances, our results suggest that this need not always be the case. All rights reserved. Estimating evolutionary rates in giant viruses using ancient genomes. Abstract Pithovirus sibericum is a giant Kpb double-stranded DNA virus discovered in a purportedly 30,year-old permafrost sample.

A closely related virus, Pithovirus massiliensis, was recently isolated from a sewer in southern France. An initial comparison of these two virus genomes assumed that P. If correct, this would make pithoviruses among the fastest-evolving DNA viruses, with rates close to those seen in some RNA viruses. To help determine whether this unusually high rate is accurate we utilized the well-known negative association between evolutionary rate and genome size in DNA microbes.

Hence, we estimate that Pithovirus has evolved at least an order of magnitude more slowly than previously suggested. We then used our new rate estimates to infer a time-scale for Pithovirus evolution. Strikingly, this suggests that these viruses could have diverged at least hundreds of thousands of years ago, and hence have evolved over longer time-scales than previously suggested. We propose that the evolutionary rate and time-scale of pithovirus evolution should be reconsidered in the light of these observations and that future estimates of the rate of giant virus evolution should be carefully examined in the context of their biological plausibility.

Does sex speed up evolutionary rate and increase biodiversity? Most empirical and theoretical studies have shown that sex increases the rate of evolution, although evidence of sex constraining genomic and epigenetic variation and slowing down evolution also exists.

Faster rates with sex have been attributed to new gene combinations, removal of deleterious mutations, and adaptation to heterogeneous environments. Slower rates with sex have been attributed to removal of major genetic rearrangements, the cost of finding a mate, vulnerability to predation, and exposure to sexually transmitted diseases. Whether sex speeds or slows evolution, the connection between reproductive mode, the evolutionary rate , and species diversity remains largely unexplored.

Here we present a spatially explicit model of ecological and evolutionary dynamics based on DNA sequence change to study the connection between mutation, speciation, and the resulting biodiversity in sexual and asexual populations. We show that faster speciation can decrease the abundance of newly formed species and thus decrease long-term biodiversity.

In this way, sex can reduce diversity relative to asexual populations, because it leads to a higher rate of production of new species, but with lower abundances. Our results show that reproductive mode and the mechanisms underlying it can alter the link between mutation, evolutionary rate , speciation and biodiversity and we suggest that a high rate of evolution may not be required to yield high biodiversity. Quantifying rates of evolutionary adaptation in response to ocean acidification.

The global acidification of the earth's oceans is predicted to impact biodiversity via physiological effects impacting growth, survival, reproduction, and immunology, leading to changes in species abundances and global distributions. However, the degree to which these changes will play out critically depends on the evolutionary rate at which populations will respond to natural selection imposed by ocean acidification, which remains largely unquantified.

Here we measure the potential for an evolutionary response to ocean acidification in larval development rate in two coastal invertebrates using a full-factorial breeding design. We show that the sea urchin species Strongylocentrotus franciscanus has vastly greater levels of phenotypic and genetic variation for larval size in future CO 2 conditions compared to the mussel species Mytilus trossulus.

Using these measures we demonstrate that S. Our comparisons suggest that information on genetic variation, phenotypic variation, and key demographic parameters, may lend valuable insight into relative evolutionary potentials across a large number of species. We extend the original method for more general use in several key ways: i we increase the support for nucleotide data with additional models, ii we allow for datasets of arbitrary size, iii we support analysis of site-partitioned datasets to correct for the presence of recombination breakpoints, iv we produce rate estimates at all sites rather than at just a subset of sites, and v we implemented LEISR as MPI-enabled to support rapid, high-throughput analysis.

Historian: accurate reconstruction of ancestral sequences and evolutionary rates. Reconstruction of ancestral sequence histories, and estimation of parameters like indel rates , are improved by using explicit evolutionary models and summing over uncertain alignments. The previous best tool for this purpose according to simulation benchmarks was ProtPal, but this tool was too slow for practical use.

Historian combines an efficient reimplementation of the ProtPal algorithm with performance-improving heuristics from other alignment tools. Simulation results on fidelity of rate estimation via ancestral reconstruction, along with evaluations on the structurally informed alignment dataset BAliBase 3.

Published by Oxford University Press. For Permissions, please e-mail: journals. Burning phylogenies: fire, molecular evolutionary rates , and diversification. Mediterranean-type ecosystems are among the most remarkable plant biodiversity "hot spots" on the earth, and fire has traditionally been invoked as one of the evolutionary forces explaining this exceptional diversity.

In these ecosystems, adult plants of some species are able to survive after fire resprouters , whereas in other species fire kills the adults and populations are only maintained by an effective post-fire recruitment seeders. Seeders tend to have shorter generation times than resprouters, particularly under short fire return intervals, thus potentially increasing their molecular evolutionary rates and, ultimately, their diversification.

We explored whether seeder lineages actually have higher rates of molecular evolution and diversification than resprouters. Molecular evolutionary rates in different DNA regions were compared in 45 phylogenetically paired congeneric taxa from fire-prone Mediterranean-type ecosystems with contrasting seeder and resprouter life histories. Differential diversification was analyzed with both topological and chronological approaches in five genera Banksia, Daviesia, Lachnaea, Leucadendron, and Thamnochortus from two fire-prone regions Australia and South Africa.

We found that seeders had neither higher molecular rates nor higher diversification than resprouters. Such lack of differences in molecular rates between seeders and resprouters-which did not agree with theoretical predictions-may occur if 1 the timing of the switch from seeding to resprouting or vice versa occurs near the branch tip, so that most of the branch length evolves under the opposite life-history form; 2 resprouters suffer more somatic mutations and therefore counterbalancing the replication-induced mutations of seeders; and 3 the rate of mutations is not related to shorter generation times because plants do not undergo determinate germ-line replication.

The absence of differential diversification is to be expected if seeders and resprouters. Variances of evolutionary rates among lineages in some proteins are larger than those expected from simple Poisson processes. This phenomenon is called overdispersion of the molecular clock. In this paper, we investigated effects of changing population size on the evolutionary rate by computer simulations assuming the nearly neutral mutation model.

The overdispersion results mainly because the average fitnesses of only a portion of populations go down when the population size is reduced and only in these populations subsequent advantageous substitutions occur after the population size becomes large. Since the fitness reduction after the bottleneck is stochastic, acceleration of the evolutionary rate does not necessarily occur uniformly among loci.

From these results, we argue that the nearly neutral mutation model is a candidate mechanism to explain the overdispersed molecular clock. Gene family size conservation is a good indicator of evolutionary rates. The evolution of duplicate genes has been a topic of broad interest. Here, we propose that the conservation of gene family size is a good indicator of the rate of sequence evolution and some other biological properties.

By comparing the human-chimpanzee-macaque orthologous gene families with and without family size conservation, we demonstrate that genes with family size conservation evolve more slowly than those without family size conservation. Our results further demonstrate that both family expansion and contraction events may accelerate gene evolution, resulting in elevated evolutionary rates in the genes without family size conservation.

In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation. Interestingly, the median evolutionary rate of singletons falls in between those of the above two types of duplicate gene families. Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration. Such a trend accords well with our observations of evolutionary rates.

Our results thus point to the importance of family size conservation in the evolution of duplicate genes. Impact of extracellularity on the evolutionary rate of mammalian proteins. It is of fundamental importance to understand the determinants of the rate of protein evolution. Eukaryotic extracellular proteins are known to evolve faster than intracellular proteins.

Although this rate difference appears to be due to the lower essentiality of extracellular proteins than intracellular proteins in yeast, we here show that, in mammals, the impact of extracellularity is independent from the impact of gene essentiality. Our partial correlation analysis indicated that the impact of extracellularity on mammalian protein evolutionary rate is also independent from those of tissue-specificity, expression level, gene compactness, and the number of protein-protein interactions and, surprisingly, is the strongest among all the factors we examined.

Similar results were also found from principal component regression analysis. Our findings suggest that different rules govern the pace of protein sequence evolution in mammals and yeasts. Diversity-dependent evolutionary rates in early Palaeozoic zooplankton. The extent to which biological diversity affects rates of diversification is central to understanding macroevolutionary dynamics, yet no consensus has emerged on the importance of diversity-dependence of evolutionary rates.

Here, we analyse the species-level fossil record of early Palaeozoic graptoloids, documented with high temporal resolution, to test directly whether rates of diversification were influenced by levels of standing diversity within this major clade of marine zooplankton.

To circumvent the statistical regression-to-the-mean artefact, whereby higher- and lower-than-average values of diversity tend to be followed by negative and positive diversification rates , we construct a non-parametric, empirically scaled, diversity-independent null model by randomizing the observed diversification rates with respect to time. Diversity-dependence persists throughout the Ordovician and Silurian, despite a major increase in the strength and frequency of extinction and speciation pulses in the Silurian.

By contrast to some previous work, we find that diversity-dependence affects rates of speciation and extinction nearly equally on average, although subtle differences emerge when we compare the Ordovician and Silurian. Looking for the optimal rate of recombination for evolutionary dynamics. We consider many-site mutation-recombination models of evolution with selection. We are looking for situations where the recombination increases the mean fitness of the population, and there is an optimal recombination rate.

We found two fitness landscapes supporting such nonmonotonic behavior of the mean fitness versus the recombination rate. The first case is related to the evolution near the error threshold on a neutral-network-like fitness landscape, for moderate genome lengths and large population. The more realistic case is the second one, in which we consider the evolutionary dynamics of a finite population on a rugged fitness landscape the smooth fitness landscape plus some random contributions to the fitness.

We also give the solution to the horizontal gene transfer model in the case of asymmetric mutations. To obtain nonmonotonic behavior for both mutation and recombination, we need a specially designed ideal fitness landscape. Accelerating the Rate of Astronomical Discovery. Special Session 5 on Accelerating the Rate of Astronomical Discovery addressed a range of potential limits to progress - paradigmatic, technological, organisational, and political - examining each issue both from modern and historical perspectives, and drawing lessons to guide future progress.

A number of issues were identified which potentially regulate the flow of discoveries, such as the balance between large strongly-focussed projects and instruments, designed to answer the most fundamental questions confronting us, and the need to maintain a creative environment with room for unorthodox thinkers and bold, high risk, projects.

Also important is the need to maintain historical and cultural perspectives, and the need to engage the minds of the most brilliant young people on the planet, regardless of their background, ethnicity, gender, or geography.

An evolutionary reduction principle for mutation rates at multiple Loci. A model of mutation rate evolution for multiple loci under arbitrary selection is analyzed. Results are obtained using techniques from Karlin Evolutionary Biology, vol. A multivariate form of the reduction principle is found: reduction results at individual loci combine topologically to produce a surface of mutation rate alterations that are neutral for a new modifier allele.

New mutation rates survive if and only if they fall below this surface-a generalization of the hyperplane found by Zhivotovsky et al. USA 91, , for a multilocus recombination modifier. Increases in mutation rates at some loci may evolve if compensated for by decreases at other loci.

The strength of selection on the modifier scales in proportion to the number of germline cell divisions, and increases with the number of loci affected. Loci that do not make a difference to marginal fitnesses at equilibrium are not subject to the reduction principle, and under fine tuning of mutation rates would be expected to have higher mutation rates than loci in mutation-selection balance.

Other results include the nonexistence of 'viability analogous, Hardy-Weinberg' modifier polymorphisms under multiplicative mutation, and the sufficiency of average transmission rates to encapsulate the effect of modifier polymorphisms on the transmission of loci under selection. A conjecture is offered regarding situations, like recombination in the presence of mutation, that exhibit departures from the reduction principle. Constraints for tractability are: tight linkage of all loci, initial fixation at the modifier locus, and mutation distributions comprising transition probabilities of reversible Markov chains.

The rates of evolution of the proteins of any organism vary across orders of magnitude. A primary factor influencing rates of protein evolution is expression. A strong negative correlation between expression levels and evolutionary rates the so-called E—R anticorrelation has been observed in virtually all studied organisms.

This effect is currently attributed to the abundance-dependent fitness costs of misfolding and unspecific protein—protein interactions, among other factors. Secreted proteins are folded in the endoplasmic reticulum, a compartment where chaperones, folding catalysts, and stringent quality control mechanisms promote their correct folding and may reduce the fitness costs of misfolding.

In addition, confinement of secreted proteins to the extracellular space may reduce misinteractions and their deleterious effects. We hypothesize that each of these factors the secretory pathway quality control and extracellular location may reduce the strength of the E—R anticorrelation. Indeed, here we show that among human proteins that are secreted to the extracellular space, rates of evolution do not correlate with protein abundances. This trend is robust to controlling for several potentially confounding factors and is also observed when analyzing protein abundance data for 6 human tissues.

In addition, analysis of mRNA abundance data for 32 human tissues shows that the E—R correlation is always less negative, and sometimes nonsignificant, in secreted proteins. Similar observations were made in Caenorhabditis elegans and in Escherichia coli, and to a lesser extent in Drosophila melanogaster, Saccharomyces cerevisiae and Arabidopsis thaliana. Our observations contribute to understand the causes of the E—R anticorrelation. A strong negative correlation between expression levels and evolutionary rates the so-called E-R anticorrelation has been observed in virtually all studied organisms.

This effect is currently attributed to the abundance-dependent fitness costs of misfolding and unspecific protein-protein interactions, among other factors. We hypothesize that each of these factors the secretory pathway quality control and extracellular location may reduce the strength of the E-R anticorrelation.

In addition, analysis of mRNA abundance data for 32 human tissues shows that the E-R correlation is always less negative, and sometimes nonsignificant, in secreted proteins. Our observations contribute to understand the causes of the E-R anticorrelation. For permissions, please e-mail: journals.

Abstract The accumulation of genome-scale molecular data sets for nonmodel taxa brings us ever closer to resolving the tree of life of all living organisms. However, despite the depth of data available, a number of studies that each used thousands of genes have reported conflicting results.

The focus of phylogenomic projects must thus shift to more careful experimental design. Even though we still have a limited understanding of what are the best predictors of the phylogenetic informativeness of a gene, there is wide agreement that one key factor is its evolutionary rate ; but there is no consensus as to whether the rates derived as optimal in various analytical, empirical, and simulation approaches have any general applicability. We here use simulations to infer optimal rates in a set of realistic phylogenetic scenarios with varying tree sizes, numbers of terminals, and tree shapes.

Furthermore, we study the relationship between the optimal rate and rate variation among sites and among lineages. Finally, we examine how well the predictions made by a range of experimental design methods correlate with the observed performance in our simulations. We find that the optimal level of divergence is surprisingly robust to differences in taxon sampling and even to among-site and among-lineage rate variation as often encountered in empirical data sets.

Focusing on correct recovery either of the most basal node in the phylogeny or of the entire topology, the optimal rate is about 0. Multiple comparisons among genomes can clarify their evolution, speciation, and functional innovations.

To date, the genome sequences of eight grasses representing the most economically important Poaceae grass clades have been published, and their genomic-level comparison is an essential foundation for evolutionary , functional, and translational research. Using a formal and conservative approach, we aligned these genomes. We reconstructed ancestral genome contents for major evolutionary nodes, potentially contributing to understanding the divergence and speciation of grasses.

Adjusted dating to reflect both updated fossil evidence and lineage-specific evolutionary rates suggested that maize subgenome divergence and maize-sorghum divergence were virtually simultaneous, a coincidence that would be explained if polyploidization directly contributed to speciation.

This work lays a solid foundation for Poaceae translational genomics. Published by Elsevier Inc. Controlling laser driven protons acceleration using a deformable mirror at a high repetition rate. Noaman-ul-Haq, M. We present results from a proof-of-principle experiment to optimize laser driven protons acceleration by directly feeding back its spectral information to a deformable mirror DM controlled by evolutionary algorithms EAs.

Moreover, due to spatio-temporal development of the sheath field, modulations in the spectrum are also observed. These results are helpful to develop high repetition rate optimization techniques required for laser-driven ion accelerators.

Island colonisation and the evolutionary rates of body size in insular neonate snakes. Island colonisation by animal populations is often associated with dramatic shifts in body size. However, little is known about the rates at which these evolutionary shifts occur, under what precise selective pressures and the putative role played by adaptive plasticity on driving such changes.

Isolation time played a significant role in the evolution of body size in island Tiger snake populations, where adaptive phenotypic plasticity followed by genetic assimilation fine-tuned neonate body and head size hence swallowing performance to prey size.

Regression line equations were used to calculate body size values to match prey size in four recently isolated populations of Tiger snakes. Rates of evolution in body mass and snout-vent length, calculated for seven island snake populations, were significantly correlated with isolation time. Finally, rates of evolution in body mass per generation were significantly correlated with levels of plasticity in head growth rates.

This study shows that body size evolution occurs at a faster pace in recently isolated populations and suggests that the level of adaptive plasticity for swallowing abilities may correlate with rates of body mass evolution. The population persistence of schizophrenia despite associated reductions in fitness and fecundity suggests that the genetic basis of schizophrenia has a complex evolutionary history. A recent meta-analysis of schizophrenia genome-wide association studies offers novel opportunities for assessment of the evolutionary trajectories of schizophrenia-associated loci.

In this study, we hypothesize that components of the genetic architecture of schizophrenia are attributable to human lineage-specific evolution. Our results suggest that schizophrenia-associated loci enrich in genes near previously identified human accelerated regions HARs. Specifically, we find that genes near HARs conserved in nonhuman primates pHARs are enriched for schizophrenia-associated loci, and that pHAR-associated schizophrenia genes are under stronger selective pressure than other schizophrenia genes and other pHAR-associated genes.

We further evaluate pHAR-associated schizophrenia genes in regulatory network contexts to investigate associated molecular functions and mechanisms. We find that pHAR-associated schizophrenia genes significantly enrich in a GABA-related coexpression module that was previously found to be differentially regulated in schizophrenia affected individuals versus healthy controls.

In another two independent networks constructed from gene expression profiles from prefrontal cortex samples, we find that pHAR-associated schizophrenia genes are located in more central positions and their average path lengths to the other nodes are significantly shorter than those of other schizophrenia genes.

Together, our results suggest that HARs are associated with potentially important functional roles in the genetic architecture of schizophrenia. Evolutionary rescue from extinction is contingent on a lower rate of environmental change. The extinction rate of populations is predicted to rise under increasing rates of environmental change. If a population experiencing increasingly stressful conditions lacks appropriate phenotypic plasticity or access to more suitable habitats, then genetic change may be the only way to avoid extinction.

Evolutionary rescue from extinction occurs when natural selection enriches a population for more stress-tolerant genetic variants. Some experimental studies have shown that lower rates of environmental change lead to more adapted populations or fewer extinctions.

However, there has been little focus on the genetic changes that underlie evolutionary rescue. Here we demonstrate that some evolutionary trajectories are contingent on a lower rate of environmental change.

We allowed hundreds of populations of Escherichia coli to evolve under variable rates of increase in concentration of the antibiotic rifampicin. We then genetically engineered all combinations of mutations from isolates evolved under lower rates of environmental change.

By assessing fitness of these engineered strains across a range of drug concentrations, we show that certain genotypes are evolutionarily inaccessible under rapid environmental change. Rapidly deteriorating environments not only limit mutational opportunities by lowering population size, but they can also eliminate sets of mutations as evolutionary options.

As anthropogenic activities are leading to environmental change at unprecedented rapidity, it is critical to understand how the rate of environmental change affects both demographic and genetic underpinnings of evolutionary rescue.

A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Changes in protein function can lead to changes in the selection acting on specific residues. This can often be detected as evolutionary rate changes at the sites in question. A maximum-likelihood method for detecting evolutionary rate shifts at specific protein positions is presented. The method determines significance values of the rate differences to give a sound statistical foundation for the conclusions drawn from the analyses.

A statistical test for detecting slowly evolving sites is also described. The methods are applied to a set of Myc proteins for the identification of both conserved sites and those with changing evolutionary rates. Those positions with conserved and changing rates are related to the structures and functions of their proteins.

The results are compared with an earlier Bayesian method, thereby highlighting the advantages of the new likelihood ratio tests. Genome-wide investigation reveals high evolutionary rates in annual model plants. Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood.

To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape Vitis vinifera and popular Populus trichocarpa for perennials.

The significant heterogeneity in evolutionary rate between annuals and perennials was consistently found both in nonsynonymous sites and synonymous sites. While a linear correlation of evolutionary rates in orthologous genes between species was observed in nonsynonymous sites, the correlation was weak or invisible in synonymous sites. This tendency was clearer in nuclear genes than in chloroplast genes, in which the overall evolutionary rate was small. The slope of the regression line was consistently lower than unity, further confirming the higher evolutionary rate in annuals at the genomic level.

The higher evolutionary rate in annuals than in perennials appears to be a universal phenomenon both in nuclear and chloroplast genomes in the four dicot model plants we investigated. Therefore, such heterogeneity in evolutionary rate should result from factors that have genome-wide influence, most likely those. Selective modes determine evolutionary rates , gene compactness and expression patterns in Brassica. It has been well documented that most nuclear protein-coding genes in organisms can be classified into two categories: positively selected genes PSGs and negatively selected genes NSGs.

The characteristics and evolutionary fates of different types of genes, however, have been poorly understood. In this study, the rates of nonsynonymous substitution K a and the rates of synonymous substitution K s were investigated by comparing the orthologs between the two sequenced Brassica species, Brassica rapa and Brassica oleracea, and the evolutionary rates , gene structures, expression patterns, and codon bias were compared between PSGs and NSGs.

The resulting data show that PSGs have higher protein evolutionary rates , lower synonymous substitution rates , shorter gene length, fewer exons, higher functional specificity, lower expression level, higher tissue-specific expression and stronger codon bias than NSGs. Although the quantities and values are different, the relative features of PSGs and NSGs have been largely verified in the model species Arabidopsis.

High mutation rates limit evolutionary adaptation in Escherichia coli. Mutation is fundamental to evolution, because it generates the genetic variation on which selection can act. In nature, genetic changes often increase the mutation rate in systems that range from viruses and bacteria to human tumors. Such an increase promotes the accumulation of frequent deleterious or neutral alleles, but it can also increase the chances that a population acquires rare beneficial alleles.

To do so, we evolved multiple replicate populations of asexual E. We measured the ability of evolved populations to grow in their original environment and in more than 90 novel chemical environments. In addition, we subjected the populations to whole genome population sequencing. Although populations with higher mutation rates accumulated greater genetic diversity, this diversity conveyed benefits only for modestly increased mutation rates , where populations adapted faster and also thrived better than their ancestors in some novel environments.

In contrast, some populations at the highest mutation rates showed reduced adaptation during evolution, and failed to thrive in all of the 90 alternative environments. In addition, they experienced a dramatic decrease in mutation rate. Our work demonstrates that the mutation rate changes the global balance between deleterious and beneficial mutational effects on fitness. In contrast to most theoretical models, our experiments suggest that this tipping point already occurs at the modest mutation rates that are found in the wild.

Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles. 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 CO3. 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. Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns. Transcriptomics in non-model plant systems has recently reached a point where the examination of nuclear genome-wide patterns in understudied groups is an achievable reality.

Here, we utilize transcriptome data in the first genome-wide comparative study of molecular evolutionary rate in ferns. Using expressed sequence data for loci, we perform pairwise comparisons of molecular evolutionary rate among 12 species spanning the three largest clades in the family and ask whether previously documented heterogeneity in plastid substitution rates is reflected in their nuclear genomes.

We then inquire whether variation in evolutionary rate is being shaped by genes belonging to specific functional categories and test for differential patterns of selection. We demonstrate that the faster rates characteristic of the vittarioid ferns are likely not driven by positive selection, nor are they unique to any particular type of nucleotide substitution. Our results reinforce recently reviewed mechanisms hypothesized to shape molecular evolutionary rates in vittarioid ferns and provide novel insight into substitution rate variation both within and among fern nuclear genomes.

Reduced evolutionary rate in reemerged Ebola virus transmission chains. On 29 June , Liberia's respite from Ebola virus disease EVD was interrupted for the second time by a renewed outbreak "flare-up" of seven confirmed cases. We demonstrate that, similar to the March flare-up associated with sexual transmission, this new flare-up was a reemergence of a Liberian transmission chain originating from a persistently infected source rather than a reintroduction from a reservoir or a neighboring country with active transmission.

Although distinct, Ebola virus EBOV genomes from both flare-ups exhibit significantly low genetic divergence, indicating a reduced rate of EBOV evolution during persistent infection. Using this rate of change as a signature, we identified two additional EVD clusters that possibly arose from persistently infected sources. These findings highlight the risk of EVD flare-ups even after an outbreak is declared over.

Blackley, David J. Sequence diversity and molecular evolutionary rates between buffalo and cattle. Identification of genes of importance regarding production traits in buffalo is impaired by a paucity of genomic resources. Choice to fill this gap is to exploit data available for cow.

The cross-species application of comparative genomics tools is potential gear to investigate the buffalo genome. However, this is dependent on nucleotide sequences similarity. In this study, gene diversity between buffalo and cattle was determined using 86 gene orthologues. There were significantly higher non-synonymous substitutions both in cattle and buffalo; however, there was similar difference in terms of dN- dS 4. Higher rate of non-synonymous substitutions at similar level in buffalo and cattle indicated a similar positive selection pressure.

Results for relative rate test were assessed with the chi-squared test. There was no significance difference on unique mutations between cattle and buffalo lineages at synonymous sites. However, there was a significance difference on unique mutations for non-synonymous sites, indicating ongoing mutagenic process that generates substitutional mutation at approximately the same rate at silent sites.

Moreover, despite of common ancestry, our results indicate a different divergent time among genes of cattle and buffalo. This is the first demonstration that variable rates of molecular evolution may be present within the family Bovidae.

Evolutionary rate of a gene affected by chromosomal position. Genes evolve at different rates depending on the strength of selective pressure to maintain their function. Chromosomal position can also have an influence [1] [2]. The pseudoautosomal region PAR of mammalian sex chromosomes is a small region of sequence identity that is the site of an obligatory pairing and recombination event between the X and Y chromosomes during male meiosis [3] [4] [5] [6].

During female meiosis, X chromosomes can pair and recombine along their entire length. Recombination in the PAR is therefore approximately 10 times greater in male meiosis compared with female meiosis [4] [5] [6]. In humans [7] [9], the rat, and the wild mouse species Mus spretus, the gene is entirely X-unique. Here, we report that the rate of sequence divergence of the 3' end of the Fxy gene is much higher estimated at fold higher for synonymous sites when pseudoautosomal present on both the X and Y chromosomes than when X-unique.

Thus, chromosomal position can directly affect the rate of evolution of a gene. This finding also provides support for the suggestion that regions of the genome with a high recombination frequency, such as the PAR, may have an intrinsically elevated rate of sequence divergence. Assessing fluctuating evolutionary pressure in yeast and mammal evolutionary rate covariation using bioinformatics of meiotic protein genetic sequences.

The evolutionary rate co-variation in meiotic proteins has been reported for yeast and mammal using phylogenic branch lengths which assess retention, duplication and mutation. The bioinformatics of the corresponding DNA sequences could be classified as a diagram of fractal dimension and Shannon entropy. Results from biomedical gene research provide examples on the diagram methodology. The identification of adaptive selection using entropy marker and functional-structural diversity using fractal dimension would support a regression analysis where the coefficient of determination would serve as evolutionary pathway marker for DNA sequences and be an important component in the astrobiology community.

Regression with high R-sq values or a triangular-like cluster pattern for concordant pairs in co-variation among the studied species could serve as evidences for the possible location of common ancestors in the entropy-fractal dimension diagram, consistent with an example of the human-chimp common ancestor study using the FOXP2 regulated genes reported in human fetal brain study. The Deinococcus radiodurans R1 Rad-A could be viewed as an outlier in the RAD50 diagram and also in the free energy versus fractal dimension regression Cook's distance, consistent with a non-Earth source for this radiation resistant bacterium.

Convergent and divergent fluctuating evolutionary. Reconciling extreme branch length differences: decoupling time and rate through the evolutionary history of filmy ferns. The rate of molecular evolution is not constant across the Tree of Life. Characterizing rate discrepancies and evaluating the relative roles of time and rate along branches through the past are both critical to a full understanding of evolutionary history.

In this study, we explore the interactions of time and rate in filmy ferns Hymenophyllaceae , a lineage with extreme branch length differences between the two major clades. We test for the presence of significant rate discrepancies within and between these clades, and we separate time and rate across the filmy fern phylogeny to simultaneously yield an evolutionary time scale of filmy fern diversification and reconstructions of ancestral rates of molecular evolution.

Our results indicate that the branch length disparity observed between the major lineages of filmy ferns is indeed due to a significant difference in molecular evolutionary rate. The estimation of divergence times reveals that the timing of crown group diversification was not concurrent for the two lineages, and the reconstruction of ancestral rates of molecular evolution points to a substantial rate deceleration in one of the clades. Further analysis suggests that this may be due to a genome-wide deceleration in the rate of nucleotide substitution.

Evolutionary rates for multivariate traits: the role of selection and genetic variation. A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are, in part, due to genetic architecture. We find some evidence that sexually selected traits exhibit faster rates of evolution compared with life-history or morphological traits.

This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G, we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates. DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood.

The study of discrete characters is crucial for the understanding of evolutionary processes. Even though great advances have been made in the analysis of nucleotide sequences, computer programs for non-DNA discrete characters are often dedicated to specific analyses and lack flexibility.

Discrete characters often have different transition rate matrices, variable rates among sites and sometimes contain unobservable states. To obtain the ability to accurately estimate a variety of discrete characters, programs with sophisticated methodologies and flexible settings are desired. DiscML performs maximum likelihood estimation for evolutionary rates of discrete characters on a provided phylogeny with the options that correct for unobservable data, rate variations, and unknown prior root probabilities from the empirical data.

DiscML was developed as a unified R program for estimating evolutionary rates of discrete characters with no restriction on the number of character states, and with flexibility to use different transition models. Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling. Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts.

Lin et al. Here, we revisit this dataset using a full probabilistic Bayesian phylogenetic framework that adequately accounts for the non-independence of sequence data when estimating evolutionary parameters. Examination of the transmission chain data under a flexible coalescent prior reveals a general inconsistency between the estimated timings and clustering patterns and the known transmission history, highlighting the need to incorporate host transmission information in the analysis.

Using an explicit genealogical transmission chain model, we find strong support for a transmission-associated decrease of the overall evolutionary rate. However, in contrast to the initially reported larger transmission effect on non-synonymous substitution rate , we find a similar decrease in both non-synonymous and synonymous substitution rates that cannot be adequately explained by the colonization-adaptation-transmission model.

More generally, this study illustrates that ignoring phylogenetic relationships can lead to misleading evolutionary estimates. Assessing the determinants of evolutionary rates in the presence of noise. Although protein sequences are known to evolve at vastly different rates , little is known about what determines their rate of evolution. However, a recent study using principal component regression PCR has concluded that evolutionary rates in yeast are primarily governed by a single determinant related to translation frequency.

Here, we demonstrate that noise in biological data can confound PCRs, leading to spurious conclusions. When equalizing noise levels across 7 predictor variables used in previous studies, we find no evidence that protein evolution is dominated by a single determinant. Our results indicate that a variety of factors--including expression level, gene dispensability, and protein-protein interactions--may independently affect evolutionary rates in yeast.

More accurate measurements or more sophisticated statistical techniques will be required to determine which one, if any, of these factors dominates protein evolution. Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes.

Changes in transcriptional orientation "CTOs" occur frequently in prokaryotic genomes. Such changes usually result from genomic inversions, which may cause a conflict between the directions of replication and transcription and an increase in mutation rate. However, CTOs do not always lead to the replication-transcription confrontation.

The currently existing CTOs may indicate relaxation of selection pressure. Therefore, it is of interest to investigate whether CTOs have an independent effect on the evolutionary rates of the affected genes, and whether these genes are subject to any type of selection pressure in prokaryotes. Three closely related enterbacteria, Escherichia coli, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium, were selected for comparisons of synonymous dS and nonsynonymous dN substitution rate between the genes that have experienced changes in transcriptional orientation changed-orientation genes, "COGs" and those that do not same-orientation genes, "SOGs".

Confounding factors in the estimation of evolutionary rates , such as gene essentiality, gene expression level, replication-transcription confrontation, and decreased dS at gene terminals were controlled in the COG-SOG comparisons. Therefore, the increases in evolutionary rates in COGs may be mainly mutation-driven.

Here we show that CTOs can increase the evolutionary rates of the affected genes. This effect is independent of the replication-transcription confrontation, which is suggested to be the major cause. Conclusions Here we show that CTOs can increase the evolutionary rates of the affected genes.

This effect is independent of the replication. Phylogenetic inference artifacts can occur when sequence evolution deviates from assumptions made by the models used to analyze them.

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