Trends in evolutionary biology最新文献

{"title":"Evolution of the ferritin family in vertebrates","authors":"Jun Lee, K. Wan, A. Mohd-Adnan, T. Gabaldón","doi":"10.4081/EB.2012.E3","DOIUrl":"https://doi.org/10.4081/EB.2012.E3","url":null,"abstract":"Ferritins are ubiquitous, highly-conserved proteins that constitute one of the most important components of the cellular machinery devoted to the management of iron levels. Various ferritins have been described in vertebrates, though their exact functions and phylogenetic relationships remain to be established. Our attempts to properly annotate two ferritin subunits isolated from the Asian sea bass Lates calcarifer, prompted us to investigate the evolutionary relationships among vertebrate ferritins and their relationships with non-vertebrate homologs. We carried out a detailed screening of mined ferritin sequences by examining the regulatory elements and gene structures. Subsequently, we performed comprehensive phylogenetic analyses involving the various metazoan and vertebrate ferritin chain types, respectively. Our analyses suggest that a single ferritin chain duplicated in the early vertebrates and that the various ferritin chain types in vertebrate and non-vertebrate species evolved independently through lineage-specific duplications. Notably, this includes the mitochondrial ferritin found only in insects and mammals that we show to result from two parallel lineage-specific duplications followed by convergent events of mitochondrial targeting. Regarding the various cytosolic ferritin chains in vertebrates, our results suggest a scenario of a duplication at the base of vertebrates followed by more recent duplications in teleosts and amphibians. This scenario implies that the light chain in mammals is orthologous to the middle chain in teleosts, in contrast to previous claims of a paralogous relationship coupled with differential gene loss. We hypothesise that the extensive differences in sequence and function between these two orthologous chains may have been driven by the adaptation of tetrapods to terrestrial environments, which involved changes in the dynamics of iron uptake and storage. Altogether, our analyses clarify the evolutionary relationships among vertebrate ferritins and pave the way for the interpretation of functional adaptations within an evolutionary framework.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"4 1","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2012-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2012.E3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Convergent evolution: limited forms most beautiful","authors":"D. Liberles","doi":"10.4081/EB.2012.E2","DOIUrl":"https://doi.org/10.4081/EB.2012.E2","url":null,"abstract":"Convergent Evolution: Limited Forms Most Beautiful by George McGhee attempts the first systematic examination of the timely topic of convergent evolution. The author’s expertise and passion really lie in studies of morphology and behavior and these trajectories are the strongest of the work.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"4 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2012.E2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sex and the origin of genetic exchanges","authors":"T. Lodé","doi":"10.4081/EB.2012.E1","DOIUrl":"https://doi.org/10.4081/EB.2012.E1","url":null,"abstract":"Sex refers to any biological process selected for genetic exchange but the reason for why sex is so common in Eukaryotes continues to resist understanding. Bacteria appear to adapt and proliferate despite the fact that they lack genes for sex. To understand why sex has evolved, we must answer two crucial questions: i) what are the key differences between eukaryotes and bacteria and ii) why do some eukaryotes use asexual reproduction. Recently, new ideas about the evolution of sex are being proposed which point out that sex and recombination could be the result of very primitive interactions.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"4 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2012-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2012.E1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Species tree inference in the age of genomics","authors":"Nathan V. Whelan","doi":"10.4081/EB.2011.E5","DOIUrl":"https://doi.org/10.4081/EB.2011.E5","url":null,"abstract":"Species trees are an essential tool in conservation and evolutionary biology. In phylogenomics, not only is data choice ( e.g. using unlinked orthologs rather than paralogs) an important systematic consideration, but the choice of phylogenetic algorithm is also important. Since individual gene phylogenies can differ from the true species phylogeny, new methods have been proposed for species tree estimation using multiple unlinked genes. Improvements in genome sequencing technologies have increased the amount of data available to researchers and this has increased the utility of multi-locus species tree inference methods. The Bayesian methods BEST and *BEAST that incorporate a coalescent model to account for gene tree and species tree conflict offer promising advances in species tree inference directly from DNA sequences. Methods that infer species trees from gene trees rather than directly from sequence data such as STAR, STEAC, NJst and the likelihood method STEM have been recently developed as computationally efficient alternatives. Bayesian concordance analysis, which has been shown to perform well when horizontal gene transfer is the cause of gene tree and species tree conflict, is also discussed. Furthermore, methods for species delimitation including a non-parametric species tree inference method that does not require a priori species assignments can remove subjectivity from species delimitation. Here, I review the assumptions, required inputs, and the performance of these methods under simulation and in recent empirical studies. Researchers in many disciplines should understand the methods available for phylogenomic species tree inference in order to enhance evolutionary and conservation studies.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"3 1","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2011-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2011.E5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chimeras are not everything","authors":"K. Dittmar","doi":"10.4081/EB.2011.E4","DOIUrl":"https://doi.org/10.4081/EB.2011.E4","url":null,"abstract":"The uniting thread of the book is an attempt at an integrated view of the evolution of sensory systems, life, and its consciousness. To accomplish this, the book fuses opinions from different fields of science, and just like the greek mythical fire-breathing chimera, the result is strong, but also impossible. The book starts out with prototypes of life, and their complex beginnings and interactions. Viruses are introduced as harbingers of selves, as regulators of life and creators of novel genetic combinations. This is followed by an argument for the simultaneous nature of growth processes and early life, contrasting it to the galvanism of the primordial soup theory. Bacterial signaling and sensing is treated as the forerunner of community forming and interaction.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"3 1","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2011-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2011.E4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new direction for directed mutation","authors":"Zhongge Zhang, M. Yen, M. Saier","doi":"10.4081/EB.2011.E3","DOIUrl":"https://doi.org/10.4081/EB.2011.E3","url":null,"abstract":"Directed mutation is a controversial process that allows mutations to occur at higher frequencies when they are beneficial. Here we review evidence for transposon-mediated directed mutation. crp deletion mutants (Glp–) of Escherichia coli (E. coli) mutate specifically to glycerol utilization (Glp+) at rates that are enhanced by glycerol or the loss of the glycerol repressor (GlpR), and depressed by glucose or glpR overexpression. Of the four tandem GlpRbinding sites (O1-O4), O4 specifically controls glpFK expression while O1 controls mutation rate. Mutation is due to insertion of the IS5 transposon into a specific site upstream of the glpFK promoter. Mutational control by GlpR is independent of the selection and assay procedures, and IS5 insertion into other gene activation sites is unaffected by the presence of glycerol or the loss of GlpR. The results establish an example of transposon-mediated directed mutation, identify the protein responsible for its regulation, and define essential features of the mechanism involved. We discuss this phenomenon from an evolutionary standpoint and provide examples of analogous switch mechanisms that may or may not be directed.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"3 1","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2011-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2011.E3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An alternative to the RNA World Hypothesis","authors":"B. Francis","doi":"10.4081/EB.2011.E2","DOIUrl":"https://doi.org/10.4081/EB.2011.E2","url":null,"abstract":"The RNA world hypothesis for the origin of life is widely accepted in spite of the complexity of RNA synthesis. An alternative hypothesis is advanced for the origin and evolution of protein and nucleic acid synthesis. At an early stage synthesis of poly-( b -malic acid), the initial evolutionary predecessor of nucleic acids, and polypeptides was coupled. This evolved into a singlet coding system in which glycine and alanine were specified by two derivatives of malic acid with different amide side chains. In stages, the linear polyester backbone evolved into the phosphodiester backbone of RNA and the amide side chains evolved into the purine and pyrimidine bases. The replication process for RNA used aminoacyl-NMP monomers (N= pyrimidine or purine) with a singlet coding system in which the four bases coded for glycine, alanine, valine and aspartic acid. Ribosomal protein synthesis (RPS) evolved from coupled replication by using tRNAs and separating fidelity checking and peptide bond formation functions into small and large ribosomal subunits. Continuity was maintained during the transition to the triplet process by using the same catalysts that aminoacylated NMPs to aminoacylate four different bases at the 3’ ends of the original tRNAs. Four GNC codons used the central base to designate the same four amino acids that were coded in singlet replication. Triplet-coded protein synthesis had the advantage of producing multiple copies of protein from a single copy of RNA, and eventually replaced protein synthesis via singlet-coded replication. Evolution of the simple triplet-coded process into RPS is described.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"3 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2011-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2011.E2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution after gene duplication","authors":"T. Pupko","doi":"10.4081/EB.2011.E1","DOIUrl":"https://doi.org/10.4081/EB.2011.E1","url":null,"abstract":"","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"3 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2011-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2011.E1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Finding the balance between the mathematical and biological optima in multiple sequence alignment","authors":"M. Anisimova, G. Cannarozzi, D. Liberles","doi":"10.4081/EB.2010.E7","DOIUrl":"https://doi.org/10.4081/EB.2010.E7","url":null,"abstract":"Recent advances in evolutionary modelling and alignment methodology enable alignment of sequences with special features and incorporate structural and functional information. However, our reviewing experience and a recent study by Morrison 1 suggest that these newer methods are under-utilized (especially in the communities of molecular systematics and experimental biology), and the resulting alignments are often curated manually. Most often, no clear biological reasoning is invoked during manual alignment; instead only aesthetic qualities are considered, as measured by eye. Such subjectivity is not consistent with core scientific principles. Although we recognize that methodological problems still exist, computerized alignment methods are currently more realistic and can model a variety of evolutionary mechanisms. We also suggest future directions for the further improvement of automatic alignment methods based upon disconnects of existing methods with underlying biological mechanisms. Alignment as a statement of","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"2 1","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2010-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2010.E7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preliminary genetic status of the spotted seal Phoca largha in Liaodong Bay (China) based on microsatellite and mitochondrial DNA analyses","authors":"Xiang Li, Athanasia C. Tzika, Yingying Liu, K. Doninck, Qian Zhu, M. Milinkovitch","doi":"10.4081/EB.2010.E6","DOIUrl":"https://doi.org/10.4081/EB.2010.E6","url":null,"abstract":"The Liaodong Bay spotted seal (Phoca largha) population experienced several drastic declines in the last 80 years. Recent studies are contradictory regarding the level of genetic diversity and population structure of P. largha, possibly because of the use of non-species-specific nuclear markers. Here, we report on i) the first isolation and character­ization of 10 species-specific polymorphic microsatellite loci for the spotted seal, ii) sequences of a 572 bp mtDNA fragment in 25 Liaodong Bay individuals that we analyzed together with all published haplotypes from Liaodong Bay and Japan. Intermediate genetic diversity in microsatellite loci was found in the Liaodong Bay population and the effective popu­lation size estimates were 41.8 to 86.8 individuals. Low mtDNA genetic variability, especially nucleotide diversity, in the Liaodong Bay population was detected, but Bayesian skyline plots did not show any evidence of recent bottleneck. Both F-statistics and the haplotypic network indicate a clear differentiation between the Liaodong Bay and Japanese populations separated by a fixed mutation. Analysis of mtDNA data indicates that Liaodong Bay female seals show fidelity to their breeding site, and breeding time data suggest that this population is reproductively isolated from popu­lations in other breeding areas. The observed low genetic diversity in mtDNA and the intermediate levels of nuclear microsatellite diversity, combined with the potential genetic isolation, suggest that the Liaodong Bay population might be at risk and that further investigation of the population genetics of spotted seals across their whole range is warranted for proper management of the species.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"72 1","pages":"33-38"},"PeriodicalIF":0.0,"publicationDate":"2010-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2010.E6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}