That is absurd. Even evolutionists are now agreeing that what they once rejected as impossible, and then grudgingly admitted as rare, now must be treated as a significant mode of the origins of new genes. As Light, Basile and Elofsson write in their 2014 review which I referenced, It has even been proposed that the creation of novel genes, a continuous process where most de novo genes are short-lived, is as frequent as gene duplications. Likewise Neme and Tautz explain, there is now rapidly increasing evidence that de novo evolution of transcripts and genes is not only a theoretical possibility, but might even have been a rather active process throughout evolution. And even Zimmer admitted in the NY Times piece, Far from being a fluke, these studies suggest that de novo genes are abundant. Nick you have an ax to grind that wont let acknowledge the clear evidence ...
TY - JOUR. T1 - Synonymous substitution rates in Drosophila. T2 - Mitochondrial versus nuclear genes. AU - Moriyama, Etsuko N.. AU - Powell, Jeffrey R.. PY - 1997. Y1 - 1997. N2 - Synonymous substitution rates in mitochondrial and nuclear genes of Drosophila were compared. To make accurate comparisons, we considered the following: (1) relative synonymous rates, which do not require divergence time estimates, should be used; (2) methods estimating divergence should take into account base composition; (3) only very closely related species should be used to avoid effects of saturation; (4) the heterogeneity of rates should be examined. We modified the methods estimating synonymous substitution numbers to account for base composition bias. By using these methods, we found that mitochondrial genes have 1.7-3.4 times higher synonymous substitution rates than the fastest nuclear genes or 4.5-9.0 times higher rates than the average nuclear genes. The average rate of synonymous transversions was 2.7 ...
De novo genes are new genes that arise spontaneously from junk DNA [De novo gene birth]. The frequency of de novo gene creation is important for an understanding of evolution. If its a frequent event, then species with a large amount of junk DNA might have a selective advantage over species with less junk DNA, especially in a changing environment.. Last week I read a short Nature article on de novo genes [Levy, 2019] and I think the subject deserves more attention. Most new genes in a species appear to arise by gene duplication and subsequent divergence but de novo genes are genes that are unrelated to genes in any other clade so we can assume that they are created from junk DNA that accidentally becomes associated with a promoter causing the DNA to be transcribed. A new gene is formed if the RNA acquires a function. If the transcript contains an open reading frame then it may be translated to produce a polypeptide and if the polypeptide performs a new function then the resulting de novo gene ...
The distribution of fitness effects (DFE) encompasses the fraction of deleterious, neutral, and beneficial mutations. It conditions the evolutionary trajectory of populations, as well as the rate of adaptive molecular evolution (alpha). Inferring DFE and a from patterns of polymorphism, as given through the site frequency spectrum (SFS) and divergence data, has been a longstanding goal of evolutionary genetics. A widespread assumption shared by previous inference methods is that beneficial mutations only contribute negligibly to the polymorphism data. Hence, a DFE comprising only deleterious mutations tends to be estimated from SFS data, and alpha is then predicted by contrasting the SFS with divergence data from an outgroup. We develop a hierarchical probabilistic framework that extends previous methods to infer DFE and alpha from polymorphism data alone. We use extensive simulations to examine the performance of our method. While an outgroup is still needed to obtain an unfolded SFS, we show ...
Graduate Student (PhD) positions are available in Dr. Eirin-Lopezs Chromatin Structure & Evolution Lab at the Department of Biological Sciences in Florida International University (biology.fiu.edu) starting in Fall 2015.. We are looking for enthusiastic, dynamic and independent students broadly interested in studying the interface between evolution, epigenetics and adaptation. Students would ideally have a B.S. degree in Biology or related discipline (academic training in biology, statistics, genetics and evolution) and must be proficient in English (both spoken and written). Candidates with additional knowledge on computer science and/or bioinformatics are encouraged to apply. Our research addresses the study of chromatin and epigenetics from different perspectives, most notably evolution, development and adaptation. To this end we use marine invertebrates as model systems in the lab, as well as a wide range of eukaryote groups in molecular evolutionary analyses. Our current projects combine ...
The recombinational environment is predicted to influence patterns of protein sequence evolution through the effects of Hill-Robertson interference among linked sites subject to selection. In freely recombining regions of the genome, selection should more effectively incorporate new beneficial mutations, and eliminate deleterious ones, than in regions with low rates of genetic recombination. We examined the effects of recombinational environment on patterns of evolution using a genome-wide comparison of Drosophila melanogaster and D. yakuba. In regions of the genome with no crossing over, we find elevated divergence at nonsynonymous sites and in long introns, a virtual absence of codon usage bias, and an increase in gene length. However, we find little evidence for differences in patterns of evolution between regions with high, intermediate, and low crossover frequencies. In addition, genes on the fourth chromosome exhibit more extreme deviations from regions with crossing over than do other, no
Bgee allows to automatically compare gene expression patterns between species, by referencing expression data on anatomical ontologies, and designing homology relationships between them.
Genotyping and sequencing of a number of eukaryotic genomes provide us with an opportunity to study the temporal and functional character of evolutionary changes in metazoans. Here we provide a framework for identifying changes in evolutionary constraints on mutated positions in the human genome. Due to lack of SNP data, in the current analysis we captured only higher order patterns at the level of functional categories. But upon availability of resequencing data, using BaseDiver it is possible to achieve higher resolution. In this work we restricted the use of BaseDiver to coding regions only, where most of the base positions are under selection and the effects of hitchhiking are small, it can be used to identify changes in constraints in non-coding regions as well.. Recently outliers of evolutionary patterns like ultra-conserved elements in higher eukaryotes and highly accelerated regions in humans have been identified [4, 7]; here we attempt to capture the comprehensive spectrum of evolution ...
Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood and has been attributed to host genetics, host immune responses, co-infection, viral genetics, and adaptation. Here, we develop a new relaxed-clock phylogenetic method to estimate absolute rates of synonymous and nonsynonymous substitution through time. We identify an unexpected association between the synonymous substitution rate of HIV and disease progression parameters. Since immune activation is the major determinant of HIV disease progression, we propose that this process can also determine viral generation times, by creating favourable conditions for HIV replication. These conclusions may apply more generally to HIV evolution, since we also observed an overall low synonymous substitution rate for HIV-2, which is known to be less pathogenic than HIV-1 and capable of tempering the detrimental effects of
Abstract: Using genomic information from mosquito, red flour beetle, honeybee, mouse, and sea anemone, we have studied the molecular evolution of 91 Drosophila genes involved in eye primordium determination, retinal differentiation, and phototransduction. Our results show that the majority of these gene sequences predate the diversification of endopterygote insects. However, all three functional groups contain a conspicuous fraction of evolutionarily younger genes, which originated by tandem duplication in the lineage leading to Drosophila, whereas gene duplications are rare in other insect lineages. We conclude that the retention of duplicated genes spiked during the early diversification of the higher Diptera possibly due to an extended period of exceptional population size reduction. Genetic data suggest that gene duplication played an important role in the evolution of visual performance in the fast flying higher Diptera by spatial or intracellular subfunctionalization. Developmental gene ...
Once they had finished their analysis, Bill Martins team was left with just 355 genes from the original 11,000, and they argue that these 355 definitely belonged to LUCA and can tell us something about how LUCA lived.. Such a small number of genes, of course, would not support life as we know it, and critics immediately latched onto this apparent gene shortage, pointing out that essential components capable of nucleotide and amino acid biosynthesis, for example, were missing. We didnt even have a complete ribosome, admits Martin.. However, their methodology required that they omit all genes that have undergone LGT, so had a ribosomal protein undergone LGT, it wouldnt be included in the list of LUCAs genes. They also speculated that LUCA could have gotten by using molecules in the environment to fill the functions of lacking genes, for example molecules that can synthesize amino acids. After all, says Martin, biochemistry at this early stage in lifes evolution was still primitive and all ...
Biological systems are resistant to perturbations caused by the environment and by the intrinsic noise of the system. Robustness to mutations is a particular aspect of robustness in which the phenotype is resistant to genotypic variation. Mutational robustness has been linked to the ability of the system to generate heritable genetic variation (a property known as evolvability). It is known that greater robustness leads to increased evolvability. Therefore, mechanisms that increase mutational robustness fuel evolvability. Two such mechanisms, molecular chaperones and gene duplication, have been credited with enormous importance in generating functional diversity through the increase of systems robustness to mutational insults. However, the way in which such mechanisms regulate robustness remains largely uncharacterized. In this review, I provide evidence in support of the role of molecular chaperones and gene duplication in innovation. Specifically, I present evidence that these mechanisms ...
Molecular evolution is not based on scientific authority. . . . There are assertions that such evolution occurred, but absolutely none are supported by pertinent experiments or calculations. Since no one knows molecular evolution by direct experience, and since there is no authority on which to base claims of knowledge, it can truly be said that . . . the assertion of Darwinian molecular evolution is merely bluster. - quote by Michael Behe on YourDictionary.
One of the most intriguing puzzles in biology is the degree to which evolution is repeatable. The repeatability of evolution, or parallel evolution, has been studied in a variety of model systems, but has rarely been investigated with clinically relevant viruses. To investigate parallel evolution of HIV-1, we passaged two replicate HIV-1 populations for almost one year in each of two human T-cell lines. For each of the four evolution lines, we determined the genetic composition of the viral population at nine time points by deep sequencing the entire genome. Mutations that were carried by the majority of the viral population accumulated continuously over one year in each evolution line. Many majority mutations appeared in more than one evolution line, i.e. our experiments showed an extreme degree of parallel evolution. In one of the evolution lines, 62% of the majority mutations also occur in another line. The parallelism impairs our ability to reconstruct the evolutionary history by ...
Gene duplication and loss are predicted to be at least of the order of the substitution rate and are key contributors to the development of novel gene function and overall genome evolution. Although it has been established that proteins evolve more rapidly after gene duplication, we were interested in testing to what extent this reflects causation or association. Therefore, we investigated the rate of evolution prior to gene duplication in chordates. Two patterns emerged; firstly, branches, which are both preceded by a duplication and followed by a duplication, display an elevated rate of amino acid replacement. This is reflected in the ratio of nonsynonymous to synonymous substitution (mean nonsynonymous to synonymous nucleotide substitution rate ratio [Ka:Ks]) of 0.44 compared with branches preceded by and followed by a speciation (mean Ka:Ks of 0.23). The observed patterns suggest that there can be simultaneous alteration in the selection pressures on both gene duplication and amino acid ...
How does nature make new things that have new functions? How does it make something simple into something more complex? Evolution.. In nature, evolution is manifested in the progression of changes in the genetic composition of all organisms over generations as they adapt to altered living conditions. Researchers have been studying natures process of change for more than a century in a desire to understand it and, in the lab, control or direct evolution at the molecular level at an unprecedented rate.. Molecular evolution (the process of evolution at the DNA, RNA, and protein level) emerged as a field in the 1960s, so its inevitable that the field itself has also evolved.. Over the past 30 years or so, scientists have figured out how to use some of the mechanisms that biology uses for evolution - extracting the tools for evolving molecules out of biological systems and putting them into the hands of laboratory investigators, says M.G. Finn, professor and chair in the School of Chemistry and ...
If you have a question about this talk, please contact Xin Wang.. Differences in the gene regulatory network are hypothesized to contribute significantly to phenotypic divergence between and within species. Non-coding sequences with bursts of lineage-specific changes are promising candidates, because clusters of nearby substitutions are a hallmark of selection potentially modify evolutionarily conserved regulatory elements. Performing a comprehensive, genome-wide analysis, we find that genomic loci with high substitution rates in the human-chimp lineage are over-represented near genes that duplicated in the human-chimp ancestor. We also developed a method to screen for nucleotide substitutions predicted to affect transcription factor binding. Rates of binding site divergence are elevated in non-coding sequences near duplicated loci with accelerated substitution rates. Finally, GC-biased gene conversion (gBGC) is a non-adaptive, recombination-associated explanation for accelerated substitution ...
Abstract: A faster rate of adaptive evolution of X-linked genes compared with autosomal genes may be caused by the fixation of new recessive or partially recessive advantageous mutations (the Faster-X effect). This effect is expected to be largest for mutations that affect only male fitness and absent for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using genes with different levels of sex-biased expression and by estimating the extent of adaptive evolution of non-synonymous mutations from polymorphism and divergence data. We detected both a Faster-X effect and an effect of male-biased gene expression. There was no evidence for a strong association between the two effects-modest levels of male-biased gene expression increased the rate of adaptive evolution on both the autosomes and the X chromosome, but a Faster-X effect occurred for both unbiased genes and female-biased genes. The rate of genetic recombination did not influence the ...
Page 1 of 5 - Does The E. Coli Long-term Evolution Experiment Evolution - posted in Best all time threads.: The E. Coli long-term evolution experiment is an ongoing study led by Richard Lenski. The study tracks genetic changes in 12 initially nearly identical populations of asexual Escherichia coli bacteria. The experiment started on February 24, 1988 and on February 14, 2010 the populations reached the milestone of 50,000 generations.QUESTIONS:What implications does this study have on the...
Evolution is defined as adapted set of positively favorable changes across successive generations in heritable characteristics of different biological species [1]. It often imposes divergence in the organisms at every evolutionary level, be it genetic or epigenetic [2]. Canalization thus study the genotypic variants contributing to the similar phenotype [3]. Hence irrespective of genotypes, genetic alterations assisting the individuals phenotype solely guides the evolutionary adaptation. In this regard, the molecular clock hypothesis proposed by Zuckerkandl & Pauling [4] seems to be correct. Sarich & Wilson [5,6] also demonstrated the divergence of humans and apes approximately 5 million years ago through the same hypothesis. Evolutionary factors Evolution being highly dimensional phenomenon is almost impossible to explain simply. Even the mathematical analysis fails to correctly track the evolutionary rate in a population [7,8]. While diversions exist for every evolved factor among different ...
The neutral theory of molecular evolution has been instrumental in organizing our thinking about the nature of evolutionary forces shaping variation at the DNA level. More importantly, it has provided empiricists with a strong set of testable predictions and hence, a useful null hypothesis against which to test for the presence of selection. Evidence indicates that the neutral theory cannot explain key features of protein evolution nor patterns of biased codon usage in certain species. Whereas we now have a reasonable model of selection acting on synonymous changes in Drosophila, protein evolution remains poorly understood. Despite limitations in the applicability of the neutral theory, it is likely to remain an integral part of the quest to understand molecular evolution. ...
Transcript of 1963 Macy Conference The Fifth Macy Conference on Genetics, held November 3-6, 1963 at Princeton University, brought together several well-known geneticists of that time period to discuss important issues in population genetics. This conference took place just before the emergence of the field of molecular evolution. Attendees included: Walter Bodmer, James Crow, Everett Dempster, Theodosius Dobzhansky, L.C. Dunn, Barry Falconer, Dick Lewontin, Howard Levene, H.J. Muller, James Neel, Bruce Wallace, and Jack Schull, among others. The format of the conference was short individual presentations followed by an informal free-for-all discussion. Fortunately, a stenographer was present throughout the conference to preserve the interactions of these scientists. We have posted the entire transcript, dividing it up by sessions. Although we have only listed the paper titles, there is extensive discussion and debate among the scientists recorded throughout the transcript. (To get to the Table ...
TheInfoList.com - (Convergent_evolution) CONVERGENT EVOLUTION is the independent evolution of similar features in species of different lineages. CONVERGENT EVOLUTION Convergent evolution creates ANALOGOUS STRUCTURES that have similar form or function but were not present in the last common ancestor of those groups. The cladistic term for the same phenomenon is homoplasy
Is the rate of insertion and deletion mutation male-biased? - Molecular evolutionary analysis of avian and primate sex chromosome sequence. ...
Encontre molecular evolution com ótimos preços e condições na Saraiva. Temos Molecular Systematics and Plant Evolution, Molecular Evolution and Phylogenetics e muito mais.
TY - JOUR. T1 - Adaptive evolution in humans revealed by the negative correlation between the polymorphism and fixation phases of evolution. AU - Gojobori, Jun. AU - Tang, Hua. AU - Akey, Joshua M.. AU - Wu, Chung I.. PY - 2007/3/6. Y1 - 2007/3/6. N2 - The selective forces acting on amino acid substitutions may be different in the two phases of molecular evolution: polymorphism and fixation. Negative selection and genetic drift may dominate the first phase, whereas positive selection may become much more significant in the second phase. However, the conventional dichotomy of synonymous vs. nonsynonymous changes does not offer the resolution needed to study the dynamics of these two phases. Following previously published methods, we separated amino acid changes into 75 elementary types (1-bp substitution between their respective codons). The likelihood of each type of amino acid change becoming polymorphic (PI, which stands for polymorphic index), relative to synonymous changes, can then be ...
Evolution and coexistence in response to a key innovation in a long-term evolution experiment with Escherichia coli Caroline B. Turner, Zachary D. Blount, Daniel H. Mitchell, Richard E. Lenski doi: http://dx.doi.org/10.1101/020958 Evolution of a novel function can greatly alter the effects of an organism on its environment. These environmental changes can, in turn, affect the…
Abstract A protein domain is a well-defined region within a protein that performs a specific function. Thus duplication of a protein domain may enhance the function of the protein. The fact that many extant proteins contain duplicated domains suggests that present-day complex proteins have evolved from simple proteins mainly via domain duplication.
The ratio of non-synonymous to synonymous substitutions, known as the Ka/Ks ratio,is used to estimate both purifying and positive Darwinian selection.A Ka/Ks ratio significantly greater than 1 is indicative of positive selection, whereas values significantly smaller than 1 are indicative of purifying selection.We present an algorithmic web-based tool which calculates the Ka/Ks ratio for each codon site in a codon-based multiple sequence alignment (Doron-Faigenboim et al. 2005;Stern et al.2006).Selecton implements both an empirical Bayesian algorithm (Yang et al.2000)as well as a maximum-likelihood algorithm (Goldman and Yang 1994),which the user may choose (the default algorithm is the Bayesian one).On the one hand,through its user-friendly interface Selecton enables simplicity of use for non-expert users.The minimal input to the server consists of merely a file of homologous DNA coding sequences.On the other hand,Selecton further implements a wide variety of user options which enable maximal ...
We describe a method of designing artificial sequences that resemble naturally occurring sequences in terms of their compatibility with a template structure and its functional constraints. The design procedure is a Monte Carlo simulation of amino acid substitution process. The selective fixation of substitutions is dictated by a simple scoring function derived from the template structure and a multiple alignment of its homologs. Designed sequences represent an enlargement of sequence space around native sequences. We show that the use of designed sequences improves the performance of profile-based homology detection. The difference in position-specific conservation between designed sequences and native sequences is helpful for prediction of functionally important residues. Our sequence selection criteria in evolutionary simulations introduce amino acid substitution rate variation among sites in a natural way, providing a better model to test phylogenetic methods. ...
The rapid accumulation of genome sequences is a major challenge to researchers attempting to extract the maximum functional and evolutionary information from the new genomes. To avoid informational overflow from the constant influx of new genome sequences, a comprehensive evolutionary classification of the genes from all sequenced genomes is required. Such classifications are based on two fundamental notions from evolutionary biology: orthology and paralogy, which describe the two fundamentally different types of homologous relationships between genes [1-4]. Orthologs are homologous genes derived by vertical descent from a single ancestral gene in the last common ancestor of the compared species. Paralogs, in contrast, are homologous genes, which, at some stage of evolution of the respective gene family, have evolved by duplication of an ancestral gene. The notions of orthology and paralogy are intimately linked because, if a duplication (s) occurred after the speciation event that separated the ...
MBLs Workshop on Molecular Evolution is the most prestigious workshop serving the field of evolutionary studies. Founded in 1988, it is the longest-running workshop if its kind, and it has earned worldwide recognition for its rich and intensive learning experience. Students work closely with internationally-recognized scientists, receiving (i) high-level instruction in the principles of molecular evolution and evolutionary genomics, (ii) advanced training in statistical methods best suited to modern datasets, and (iii) hands-on experience with the latest software tools (often from the authors of the programs they are using). The material is delivered via lectures, discussions, and bioinformatic exercises motivated by contemporary topics in molecular evolution. A hallmark of this workshop is the direct interaction between students and field-leading scientists. The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of ...
MBLs Workshop on Molecular Evolution is the most prestigious workshop serving the field of evolutionary studies. Founded in 1988, it is the longest-running workshop if its kind, and it has earned worldwide recognition for its rich and intensive learning experience. Students work closely with internationally-recognized scientists, receiving (i) high-level instruction in the principles of molecular evolution and evolutionary genomics, (ii) advanced training in statistical methods best suited to modern datasets, and (iii) hands-on experience with the latest software tools (often from the authors of the programs they are using). The material is delivered via lectures, discussions, and bioinformatic exercises motivated by contemporary topics in molecular evolution. A hallmark of this workshop is the direct interaction between students and field-leading scientists. The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of ...
Why some individuals develop AIDS rapidly whereas others remain healthy without treatment for many years remains a central question of HIV research. An evolutionary perspective reveals an apparent conflict between two levels of selection on the virus. On the one hand, there is rapid evolution of the virus in the host, and on the other, new observations indicate the existence of virus factors that affect the virulence of infection whose influence persists over years in infected individuals and across transmission events. Here, we review recent evidence that shows that viral genetic factors play a larger role in modulating disease severity than anticipated. We propose conceptual models that reconcile adaptive evolution at both levels of selection. Evolutionary analysis provides new insight into HIV pathogenesis.. ...
Although positive selection has been detected in many genes, its overall contribution to protein evolution is debatable. If the bulk of molecular evolution is neutral, then the ratio of amino-acid (A) to synonymous (S) polymorphism should, on average, equal that of divergence. A comparison of the A/ …
Packing flaws create sticky, interactive proteins that spread in small populations. Over four billion years of evolution, plants and animals grew far more complex than their single-celled ancestors. But a new comparison of proteins shared across species finds that complex organisms, including humans, have accumulated structural weaknesses that may have actually launched the long journey from microbe to man.. The study, published in Nature, suggests that the random introduction of errors into proteins, rather than traditional natural selection, may have boosted the evolution of biological complexity. Flaws in the packing of proteins that make them more unstable in water could have promoted protein interactions and intracellular teamwork, expanding the possibilities of life.. Everybody wants to say that evolution is equivalent to natural selection and that things that are sophisticated and complex have been absolutely selected for, said study co-author Ariel Fernández, PhD, a visiting ...
On the Evolution of Species was published in the year 1859 and it went on to becoming one of the most influential books of the time. The theory came to be widely accepted by the scientific community and overthrew many other popular streams of thought and Philosophy on evolution. Many of these theories had theological bases. The strong scientific backing of Darwins ideas convinced most people about the soundness of his theory. Although as the body of scientific knowledge grew and more and more data on obscure species emerged, the Darwinian thought has been challenged more than once, the theory of evolution remains the single most important thought behind our attempts to explain our evolution on this planet. Today there are groups of scientists who have put Darwin in the perspective of genes, namely have explained or tried to the evolution of species in terms of genetics. This new breed of Darwinism has come to be known as Neo-Darwinism. Richard Dawkins is arguably the most well-known and witty ...
TY - JOUR. T1 - Molecular evolution of a developmental pathway. T2 - Phylogenetic analyses of transforming growth factor-β family ligands, receptors and Smad signal transducers. AU - Newfeld, Stuart. AU - Wisotzkey, Robert G.. AU - Kumar, Sudhir. PY - 1999/6/1. Y1 - 1999/6/1. N2 - Intercellular signaling by transforming growth factor-β (TGF-β) proteins coordinates developmental decisions in many organisms. A receptor complex and Smad signal transducers are required for proper responses to TGF- β signals. We have taken a phylogenetic approach to understanding the developmental evolutionary history of TGF-β signaling pathways. We were interested in detecting evolutionary influences among the physically interacting multigene families encoding TGF-β ligands, receptors, and Smads. Our analyses included new ligands and Smads identified from genomic sequence as well as the newest published family members. From an evolutionary perspective we find that (I) TGF-β pathways do not predate the ...
The significance of N-glycosylation of the TGF-β-type ligands has been studied previously. For example, N-glycosylation of the BMP2 prodomain affects the folding and secretion of ligands, and non-glycosylated BMP2 and BMP6 produced in bacterial cells appear to be less active than the glycosylated ligands (Schmoekel et al., 2004; Saremba et al., 2008; van de Watering et al., 2012; Hang et al., 2014). Addition of an N-glycosylation motif in Nodal changes the stability of ligands, resulting in an increased signaling range (Le Good et al., 2005). These facts suggest that N-glycosylation of ligands may play significant roles in vivo. However, these roles have been largely unexplored because of a lack of in vivo model systems. By employing both in vivo studies and cell-based experiments, we investigated how N-glycosylation modifications of the BMP-type ligands impact developmental processes. The in vivo rescue experiments revealed that these motifs are crucial for fly viability and are required to ...
The global effects of epistasis on protein and RNA function are revealed by an unsupervised model of amino acid co-conservation in evolutionary sequence variation. Many high-throughput experimental technologies have been developed to assess the effects of large numbers of mutations (variation) on phenotypes. However, designing functional assays for these methods is challenging, and systematic testing of all combinations is impossible, so robust methods to predict the effects of genetic variation are needed. Most prediction methods exploit evolutionary sequence conservation but do not consider the interdependencies of residues or bases. We present EVmutation, an unsupervised statistical method for predicting the effects of mutations that explicitly captures residue dependencies between positions. We validate EVmutation by comparing its predictions with outcomes of high-throughput mutagenesis experiments and measurements of human disease mutations and show that it outperforms methods that do not account
In the accompanying paper (Nagy, Szláma, Szarka, Trexler, Bányai, Patthy, Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors) we showed that in the case of UniProtKB/TrEMBL, RefSeq, EnsEMBL and NCBIs GNOMON predicted protein sequences of Metazoan species the contribution of erroneous (incomplete, abnormal, mispredicted) sequences to domain architecture (DA) differences of orthologous proteins might be greater than those of true gene rearrangements. Based on these findings, we suggest that earlier genome-scale studies based on comparison of predicted (frequently mispredicted) protein sequences may have led to some erroneous conclusions about the evolution of novel domain architectures of multidomain proteins. In this manuscript we examine the impact of confusing paralogous and epaktologous multidomain proteins (i.e., those that are related only through the independent acquisition of the same domain types) on conclusions drawn about DA evolution of
When the coding regions of 11 genes from rodents (mouse or rat) and man are compared with those from another mammalian species (usually bovine), it is found that rodents evolve significantly faster than man. The ratio of the number of nucleotide substitutions in the rodent lineage to that in the human lineage since their divergence is 2.0 for synonymous substitutions and 1.3 for nonsynonymous substitutions. Rodents also evolve faster in the 5 and 3 untranslated regions of five different mRNAs; the ratios are 2.6 and 3.1, respectively. The numbers of nucleotide substitutions between members of the beta-globin gene family that were duplicated before the man-mouse split are also higher in mouse than in man. The difference is, again, greater for synonymous substitutions than for nonsynonymous substitutions. This tendency is more consistent with the neutralist view of molecular evolution than with the selectionist view. A simple explanation for the higher rates in rodents is that rodents have ...
Life: The Science of Biology 11th Edition answers to Chapter 23 - Evolution of Genes and Genomes - 23.4 - Molecular Evolution Has Many Practical Applications - 23.4 Recap - Learning Outcomes - Page 504 3 including work step by step written by community members like you. Textbook Authors: Sadava, David E.; Hillis, David M.; Heller, H. Craig; Hacker, Sally D. , ISBN-10: 1-31901-016-4, ISBN-13: 978-1-31901-016-4, Publisher: W. H. Freeman
Key innovations in the history of life are often caused by the acquisition of a qualitatively new trait that is an evolutionary novelty which allows the exploitation of new resources or habitats and thus triggers an adaptive radiation. Such innovations are typically rare and difficult to predict because they result from complex nonadditive (i.e., epistatic) genetic interactions or ecological interactions, within or between species, that develop only over the course of long evolutionary trajectories. Evolution of a new trait can be conceptually divided into three steps: potentiation, actualization, and refinement. First, one or more potentiating events may be necessary to generate a genetic background or environmental conditions that make a new trait accessible to evolution. Genetic potentiation, for example, may involve a period of nonadaptive genetic drift wherein a phenotype stays constant or the accumulation of mutations that are immediately advantageous for reasons unrelated to the new ...
While the theory of descent with modification in the broad sense is supported, the conventional paradigm that the history of life maps as the tree of life-a tree beginning with one universal common ancestor as the trunk and then progressively branching, with modern species at the twig ends-is being re-drawn at both the base of the trunk and the branches. These revisions arise as scientists gain more understanding about the hidden world of microbes (unicellular organisms and viruses).. The great diversity, abundance, and ubiquity of the single-celled organisms (bacteria, archaea, and some protists) has gained widespread recognition in recent years, and considerable progress has been made in incorporating that knowledge into the story of evolution. In contrast, the place of viruses in the story of evolution remains much more speculative.. There are proposals that the tree of life instead of being simple at its base, may be considerably more complex. Sequencing the genomes of specific organisms ...
Author Summary The relationship between morphological and molecular evolution is a central issue to the understanding of eukaryote evolution. In particular, there is much interest in how duplicate genes have contributed to morphological diversification during evolution. As a mechanism of functionalization of duplicate genes, differentiation of both gene expression and protein function are believed to be important. Although it has been reported that both expression and protein divergence tend to increase as a duplication ages, it is unclear whether expression or protein divergence in duplicate genes is greater in those genes that have undergone functionalization compared with those that have not. Here, we studied 492 duplicate gene pairs associated with various degrees of morphological diversification in Arabidopsis thaliana. Using these data, we found that the divergence of both expression and protein sequence were important sources for morphological diversification of duplicate genes. Although both
Proteins often differ in amino-acid sequence across species. This difference has evolved by the accumulation of neutral mutations by random drift, the fixation of adaptive mutations by selection, or a mixture of the two. Here we propose a simple statistical test of the neutral protein evolution hypothesis based on a comparison of the number of amino-acid replacement substitutions to synonymous substitutions in the coding region of a locus. If the observed substitutions are neutral, the ratio of replacement to synonymous fixed differences between species should be the same as the ratio of replacement to synonymous polymorphisms within species. DNA sequence data on the Adh locus (encoding alcohol dehydrogenase, EC 1.1.1.1) in three species in the Drosophila melanogaster species subgroup do not fit this expectation; instead, there are more fixed replacement differences between species than expected. We suggest that these excess replacement substitutions result from adaptive fixation of selectively ...
Gene duplication provide a means to evolve novel biological functions and changes in protein functions may then provide different evolutionary constraints on duplicated genes. Functional divergence of a protein family can occur after major evolutionary events such as gene duplication or speciation. Some of them result in different evolutionary rates at certain amino acid residues, which is termed type I functional divergence [33, 34]. To estimate functional divergence in the vertebrate anoctamin family, we have conducted pair-wise functional divergence analysis between anoctamin paralogous genes using DIVERGE [35]. Table 1 shows the coefficient of functional divergence (θ) of pair-wise comparisons between the members of the anoctamin family. All comparisons showed θ , 0 with p , 0.05, suggesting that a site-specific rate shift after gene duplication is a common phenomenon in the evolution of the anoctamin family. Further analysis was subsequently focused on ano1/ano2, and ano1/ano4. Amino ...
An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. New Archaeal Clusters of Orthologous Genes (arCOGs) were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon) using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for
The known functions of RNA structures have expanded of late, such that RNA is considered a more active player in molecular biology. The presence of RNA secondary structure in a sequence should constrain evolution of its constituent nucleotides because of the requirement to maintain the base-pairing regions in the structure. In a previous work, we found support for this hypothesis in nine molecules from various organisms, the exception being a structure found in a protein-coding region of the HIV-1 genome. In this work, I examine the interaction of constraints imposed by RNA structures and host-induced hypermutation on molecular evolution in HIV-1. I conclude that RNA structures in HIV do evolve via compensatory evolution, but that hypermutation can obscure the expected signal. Since RNAs known roles have increased, so have the methods for identification and prediction of RNA structures in genetic sequence. I use a method adapted for searching in multiple coding regions to identify conserved RNA ...
Any change in the molecular structure is harmful. The origins of the neutral theory of molecular evolution Michael R. Dietrich 1 Journal of the History of Biology volume 27 , pages 21 - 59 ( 1994 ) Cite this article 1983. Hubbells original model has been extensively tested, and maximum likelihood techniques have added a rigorous backbone to the estimation of neutral model parameters. Alternatively, molecular evolution may be mainly driven by natural selection. He is most known as an advocate of the, International Encyclopedia of the Social & Behavioral Sciences. Darwins core insight was that organisms with disadvantageous traits would slowly be weeded out through negative (or purifying) selection, while those with advantageous features would reproduce more often and pass those features on to the next generation (positive selection). Motoo Kimura, as founder of the neutral theory, is uniquely placed to write this book. As such, these models can detect positive selection at individual sites only ...
Adaptive protein evolution at the Adh locus in Drosophila.: Proteins often differ in amino-acid sequence across species. This difference has evolved by the accu
Certain techniques of molecular evolution - the generation and selection of functional molecules using biological mechanisms in the test tube - are well established, but still only used by laboratories expert in the art. Principal examples include directed evolution, SELEX, and yeast, bacterial and phage surface display selection methods. These techniques provide access to peptides and polynucleotides with an enormous range of properties. Many labs at Tech (and everywhere else) often want to gain access to these tools, but make do without them because it is too difficult and time consuming to get started.. The Molecular Evolution Core Facility is housed in two convenient locations for researchers across the biotechnology campus at Georgia Tech. One is an 800-sq.-ft. suite on the second floor of the Krone Engineered Biosystems Building and another is a multi-functional lab on the third floor of the Petit H. Parker Institute of Bioengineering and Bioscience building . The purpose of the facility ...
Ancestral reconstruction (also known as Character Mapping or Character Optimization) is the extrapolation back in time from measured characteristics of individuals (or populations) to their common ancestors. It is an important application of phylogenetics, the reconstruction and study of the evolutionary relationships among individuals, populations or species to their ancestors. In the context of evolutionary biology, ancestral reconstruction can be used to recover different kinds of ancestral character states of organisms that lived millions of years ago. These states include the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the composition of a genome (e.g., gene order), a measurable characteristic of an organism (phenotype), and the geographic range of an ancestral population or species (ancestral range reconstruction). This is desirable because it allows us to examine parts of phylogenetic trees corresponding to the distant past, clarifying the ...
Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of
Gene loss pattern after teleost-specific whole genome duplication. Figure 2. Gene loss pattern after teleost-specific whole genome duplication.. A: Species tree showing major vertebrate groups and their evolutionary relationships.. B: The comparison of genomes between two species with the coloured lines showing corresponding genes between human and medaka (upper circle) and between zebrafish and medaka (lower circle). The structure is quite different between human and medaka, while it is similar between zebrafish and medaka.. C: Gene loss pattern showing the two-phase loss of duplicate genes in teleost fishes. A and C use the same timeline.. The results of this study suggest that approximately 80% of the duplicate genes were lost in the first 60 million years after the whole genome duplication event (Fig. 2C). Considering that the first vertebrates appeared on Earth about 500 million years ago (Fig. 2A), 60 million years is a very short time. Dr Inoue states that it is possible that genome ...
In plants, tandem, segmental and whole-genome duplications are prevalent, resulting in large numbers of duplicate loci. Recent studies suggest that duplicate genes diverge predominantly through the partitioning of expression and that breadth of gene expression is related to the rate of gene duplication and protein sequence evolution. Here, we utilize expressed sequence tag (EST) data to study gene duplication and expression patterns in the monosaccharide transporter (MST) gene family across the land plants. In Arabidopsis, there are 53 MST genes that form seven distinct subfamilies. We created profile hidden Markov models of each subfamily and searched EST databases representing diverse land plant lineages to address the following questions: 1) Are homologs of each Arabidopsis subfamily present in the earliest land plants? 2) Do expression patterns among subfamilies and individual genes within subfamilies differ across lineages? 3) Has gene duplication within each lineage resulted in lineage-specific
The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations. We have isolated homologues to the Arabidopsis APETALA3 (ASAP3/TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL A/B BINDING PROTEIN9 (ASCAB9) photosynthetic structural gene from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. We have compared rates of regulatory and structural gene evolution in the Hawaiian species to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases ...
How does nature make new things that have new functions? How does it make something simple into something more complex? Evolution.. In nature, evolution is manifested in the progression of changes in the genetic composition of all organisms over generations as they adapt to altered living conditions. Researchers have been studying natures process of change for more than a century in a desire to understand it and, in the lab, control or direct evolution at the molecular level at an unprecedented rate.. Molecular evolution (the process of evolution at the DNA, RNA, and protein level) emerged as a field in the 1960s, so its inevitable that the field itself has also evolved.. Over the past 30 years or so, scientists have figured out how to use some of the mechanisms that biology uses for evolution - extracting the tools for evolving molecules out of biological systems and putting them into the hands of laboratory investigators, says M.G. Finn, professor and chair in the School of Chemistry and ...
From millions of real job salary data. Foundation For Applied Molecular Evolution Postdoctoral Associate salary data. Average Foundation For Applied Molecular Evolution Postdoctoral Associate salary is Detailed Foundation For Applied Molecular Evolution Postdoctoral Associate starting salary, median salary, pay scale, bonus data report
Biologists have long noted the tremendous diversity of behaviors, morphological traits and molecules involved in mating and reproduction. In this thesis, I investigate the molecular evolution of reproductive proteins in the vinegar fly Drosophila melanogaster, focusing on a class of ejaculate proteins known as accessory gland proteins (?Acps?). Previous work has documented extensive evidence for rapid, adaptive evolution of some Acps. It is generally thought that male-female interactions, e.g., sexual conflict and cryptic female choice, drive rapid Acp evolution, although evidence specifically favoring this hypothesis in D. melanogaster is limited. Here, I describe biochemical and structural studies on a particularly rapidly evolving Acp, ovulin. I argue that structural features of ovulin may contribute to its ability to tolerate high sequence diversity. I also investigate the molecular evolution of a class of Acps and female reproductive tract proteins that (I argue) are particularly likely to ...
BACKGROUND: Although homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown. Recombination can reduce genome size by enabling the removal of LTR retrotransposons, alter codon usage by GC biased gene conversion, contribute to complex histories of gene duplication and loss through tandem duplication, and enhance purifying selection on genes. Therefore, variation in recombination rate across species may explain some of the variation in genomic architecture as well as rates of molecular evolution. We used phylogenetic comparative methods to investigate the evolution of global meiotic recombination rate in angiosperms and its effects on genome architecture and selection at the molecular level using genetic maps and genome sequences from thirty angiosperm species. RESULTS: Recombination rate is negatively correlated with genome size, which is likely caused by the ...
Molecular evolution is the process of evolution at the scale of DNA, RNA and proteins. Our goal was to study molecular evolution of viruses with special reference to Influenza A Virus. The recent Influenza A/H1N1(2009) outbreak has been the focus of intense research because of its high level of infectivity across the globe. Analysis of nucleotide sequence polymorphism in the genomic segments encoding the two most immunologically important proteins of influenza A, neuraminidase (NA) and hemagglutinin (HA), showed that the H1N1 (2009) has resulted from the spread of an HA segment of recent origin and low diversity through a population of ancient and much more diverse NA segments. We also studied about the selection pattern of CTL epitope and CTL non-epitope regions of different proteins of Influenza and found that natural selection is the main pattern of selection with epitope regions being more conserved than non-epitope regions. This dissertation also focuses on implementation of a methodology to study
Gene family evolution is determined by microevolutionary processes (e.g., point mutations) and macroevolutionary processes (e.g., gene duplication and loss), yet macroevolutionary considerations are rarely incorporated into gene phylogeny reconstruction methods. We present a dynamic program to find the most parsimonious gene family tree with respect to a macroevolutionary optimization criterion, the weighted sum of the number of gene duplications and losses. The existence of a polynomial delay algorithm for duplication/loss phylogeny reconstruction stands in contrast to most formulations of phylogeny reconstruction, which are NP-complete. We next extend this result to obtain a two-phase method for gene tree reconstruction that takes both micro- and macroevolution into account. In the first phase, a gene tree is constructed from sequence data, using any of the previously known algorithms for gene phylogeny construction. In the second phase, the tree is refined by rearranging regions of the tree that do
Models of molecular evolution that incorporate the ratio of nonsynonymous to synonymous polymorphism (dN/dS ratio) as a parameter can be used to identify sites that are under diversifying selection or functional constraint in a sample of gene sequences. However, when there has been recombination in the evolutionary history of the sequences, reconstructing a single phylogenetic tree is not appropriate, and inference based on a single tree can give misleading results. In the presence of high levels of recombination, the identification of sites experiencing diversifying selection can suffer from a false-positive rate as high as 90%. We present a model that uses a population genetics approximation to the coalescent with recombination and use reversible-jump MCMC to perform Bayesian inference on both the dN/dS ratio and the recombination rate, allowing each to vary along the sequence. We demonstrate that the method has the power to detect variation in the dN/dS ratio and the recombination rate and does not
Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields of phylogenetics and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes. Phylogenetics compares and analyzes the sequences of single genes, or a small number of genes, as well as many other types of data. Four major areas fall under phylogenomics: Prediction of gene function Establishment and clarification of evolutionary relationships Gene family evolution Prediction and retracing lateral gene transfer. When Jonathan Eisen originally coined phylogenomics, it applied to prediction of gene function. Before the use of phylogenomic techniques, predicting gene function was done primarily by comparing the gene sequence with the sequences of genes with known functions. When several genes with similar ...
Predicting adaptive trajectories is a major goal of evolutionary biology and useful for practical applications. Systems biology has enabled the development of genome-scale metabolic models. However, analysing these models via flux balance analysis (FBA) cannot predict many evolutionary outcomes including adaptive diversification, whereby an ancestral lineage diverges to fill multiple niches. Here we combine in silico evolution with FBA and apply this modelling framework, evoFBA, to a long-term evolution experiment with Escherichia coli. Simulations predicted the adaptive diversification that occurred in one experimental population and generated hypotheses about the mechanisms that promoted coexistence of the diverged lineages. We experimentally tested and, on balance, verified these mechanisms, showing that diversification involved niche construction and character displacement through differential nutrient uptake and altered metabolic regulation. The evoFBA framework represents a promising new way to
Symposium: Genome Evolution in Microbial Eukaryotes June 2nd, Smithfield Rhode Island To elucidate principles of eukaryotic genome evolution, we must increase studies of microbial eukaryotes. The bulk of eukaryotic diversity is microbial yet our current knowledge of eukaryotic genome evolution comes largely from studies of plants, animals and fungi. Our intention in this one-day symposium is to highlight recent achievements in understanding the diversity of eukaryotic genomes, and to expose relevant researchers to advances in techniques for both data acquisition and data analysis. Speakers and titles appear below. Travel funds are available for undergraduates, graduate students and postdocs. These funds will offset costs of those currently working on molecular evolution/genomics of microbial eukaryotes, and those switching into the field. Students and postdocs are encouraged to bring a poster of their work. For more information, visit: ...
Often after natural selection increases the frequency of beneficial alleles in an evolving species, it then maintains the high frequency of these alleles by rejecting harmful or less beneficial alleles. This transformation of positive selection into purifying selection (35) is more likely to occur at nonsynonymous sites than at synonymous sites, where theory predicts synonymous substitutions steadily accumulate over time. Thus, considering the many millions of years of time involved in the descent of the elephant or tenrec lineage (about 78 Ma) and the human or mouse lineage (about 91 Ma), it is not surprising that ,1.4% of the thousands of genes examined have dN/dS ,1 (Table S4) and that the percentage of such likely positively selected genes is smallest for mouse (0.12%). To increase our chances of detecting gene sets that were likely targets of positive selection, we examined by the functional annotation clustering tool (30) the 5% of RefSeqs (389) with the more elevated dN/dS ratios, these ...
Sex chromosomes have evolved from non-sex-determining chromosomes (autosomes) many times throughout the tree of life. Ever since their discovery, these chromosomes have captivated researchers because of their obvious involvement in fundamental aspects of an organisms life, such as sex determination, sexual reproduction and sexual conflicts. Despite this long-lasting fascination, their biology remains unclear in several central aspects, in particular regarding their almost ubiquitous evolution of recombination cessation and impoverished gene content, and the multifaceted consequences thereof. This lack of detailed knowledge about sex chromosome evolution compromises our understanding of fundamental biological questions (e.g. the evolution of sexual conflicts) as well as more practical ones (e.g. about sex-linked genetic diseases).. Our research focuses mainly on Sylvioidea passerine birds where we have recently detected a new sex chromosome, a neo-sex chromosome, which has been formed by a ...
TY - JOUR. T1 - Molecular evolution of aerobic energy metabolism in primates. AU - Grossman, Lawrence I.. AU - Schmidt, Timothy R.. AU - Wildman, Derek E.. AU - Goodman, Morris. PY - 2001. Y1 - 2001. N2 - As part of our goal to reconstruct human evolution at the DNA level, we have been examining Changes in the biochemical machinery for aerobic energy metabolism. We find that protein subunits of two of the electron transfer complexes, complex III and complex IV, and cytochrome c, the protein carrier that connects them, have all undergone a period of rapid protein evolution in the anthropoid lineage that ultimately led to humans. Indeed, subunit IV of cytochrome c oxidase (COX; complex IV) provides one of the best examples of positively selected changes of any protein studied. The rate of subunit IV evolution accelerated in our catarrhine ancestors in the period between 40 to 18 million years ago and then decelerated in the descendant hominid lineages, a pattern of rate changes indicative of ...
Studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation. In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods.
The powerful pressures of sexual and natural selection associated with species recognition and reproduction are thought to manifest in a faster rate of evolution in sex-biased genes, an effect that has been documented particularly for male-biased genes expressed in the reproductive tract. However, little is known about the rate of evolution for genes involved in sexually dimorphic behaviors, which often form the neurological basis of intrasexual competition and mate choice. We used microarray data, designed to uncover sex-biased expression patterns in embryonic chicken brain, in conjunction with data on the rate of sequence evolution for ,4,000 coding regions aligned between chicken and zebra finch in order to study the role of selection in governing the molecular evolution for sex-biased and unbiased genes. Surprisingly, we found that female-biased genes, defined across a range of cutoff values, show a higher rate of functional evolution than both male-biased and unbiased genes. Autosomal ...
Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 transcripts with evidence of homology to venom proteins were discovered. After identifying more than 3,000 putatively orthologous genes across all six taxa, we used comparative analyses to identify 24 instances of
The resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the tree topology in ...
The growing availability of complete genomic sequences from diverse species has brought about the need to scale up phylogenomic analyses, including the reconstruction of large collections of phylogenetic trees. Here, we present the third version of PhylomeDB (http://phylomeDB.org), a public database for genome-wide collections of gene phylogenies (phylomes). Currently, PhylomeDB is the largest phylogenetic repository and hosts 17 phylomes, comprising 416,093 trees and 165,840 alignments. It is also a major source for phylogeny-based orthology and paralogy predictions, covering about 5 million proteins in 717 fully-sequenced genomes. For each protein-coding gene in a seed genome, the database provides original and processed alignments, phylogenetic trees derived from various methods and phylogeny-based predictions of orthology and paralogy relationships. The new version of phylomeDB has been extended with novel data access and visualization features, including the possibility of programmatic ...
Model violations constitute the major limitation in inferring accurate phylogenies. Characterizing properties of the data that are not being correctly handled by current models is therefore of prime importance. One of the properties of protein evolution is the variation of the relative rate of substitutions across sites and over time, the latter is the phenomenon called heterotachy. Its effect on phylogenetic inference has recently obtained considerable attention, which led to the development of new models of sequence evolution. However, thus far focus has been on the quantitative heterogeneity of the evolutionary process, thereby overlooking more qualitative variations. We studied the importance of variation of the site-specific amino-acid substitution process over time and its possible impact on phylogenetic inference. We used the CAT model to define an infinite mixture of substitution processes characterized by equilibrium frequencies over the twenty amino acids, a useful proxy for qualitatively
It is widely accepted that during vertebrate evolution two whole genome duplication (WGD) events occurred, followed by another in the lineage leading to teleosts (Amores et al., 1998; Dehal and Boore, 2005; Holland et al., 1994; Ohno et al., 1968; Taylor et al., 2003; Wittbrodt and Schartl, 1998). These events coincided with a rapid expansion in organismal complexity particularly in teleosts, a lineage that constitutes half of extant vertebrates. The persistence of many duplicate genes after these WGD events forms the basis of the duplication-degeneration-complementation (DDC) model of gene evolution (Force et al., 1999). The DDC model predicts that at least some aspects of ancestral gene function are sub-partitioned between duplicate genes in a complementary manner, such that each copy remains indispensable. At the same time, redundancy of associated cis-regulatory elements may increase the evolvability of these sequences (Jimenez-Delgado et al., 2009) and their potential to direct novel gene ...
Maternal RNAs play a critical role in early development. Variation in the diversity and levels of maternally derived gene transcripts may be central to the origin of phenotypic novelty -- a longstanding problem in evolution and development. By studying maternal transcriptomes within and between divergent species, a better understanding of the evolutionary forces acting on maternal RNA allocation is possible. We present the first maternal transcriptome of the red flour beetle, Tribolium castaneum. Using a tiled whole-genome microarray, we found that 58.2% of T. castaneum genes are maternally loaded into eggs. Comparison of known Drosophila melanogaster maternal genes to our results showed widespread conservation of maternal expression with T. castaneum. Additionally, we found that many genes previously reported as having sex or tissue specific expression in T. castaneum were also maternally loaded. Identification of such pleiotropy is vital for proper modeling and testing of evolutionary theory using
Background Comparative approaches using protostome and deuterostome data have greatly contributed to understanding gene function and organismal complexity. The family 2 G-protein coupled receptors (GPCRs) are one of the largest and best studied hormone and neuropeptide receptor families. They are suggested to have arisen from a single ancestral gene via duplication events. Despite the recent identification of receptor members in protostome and early deuterostome genomes, relatively little is known about their function or origin during metazoan divergence. In this study a comprehensive description of family 2 GPCR evolution is given based on in silico and expression analyses of the invertebrate receptor genes. Results Family 2 GPCR members were identified in the invertebrate genomes of the nematodes C. elegans and C. briggsae, the arthropods D. melanogaster and A. gambiae (mosquito) and in the tunicate C. intestinalis. This suggests that they are of ancient origin and have evolved through ...
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010). Lecture Goals: The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. Laboratory Goals: Labs will cover basic techniques in molecular ...
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010). Lecture Goals: The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. Laboratory Goals: Labs will cover basic techniques in molecular ...