Trends in evolutionary biology最新文献

{"title":"Potential impact of primate‐specific SVA retrotransposons during the evolution of human cognitive function.","authors":"O. Vasieva, S. Cetiner, Abigail L Savage, G. Schumann, V. Bubb, J. Quinn","doi":"10.4081/EB.2017.6514","DOIUrl":"https://doi.org/10.4081/EB.2017.6514","url":null,"abstract":"The SVA family of hominid-specific non-LTR retrotransposon comprises the youngest group of transposable elements in the human genome. The propagation of the most ancient SVA subfamily took place about 13.5 million years ago, and the youngest SVA subfamily appeared in the human genome after the human/chimpanzee divergence. Functional analysis of genes associated with SVA insertions demonstrated their link to multiple ontological categories, with one of the major categories being attributed to brain function. Further analysis of this subset demonstrated that SVA elements expanded their presence in the human genome at different stages of hominoid evolution and were associated with progressively evolving behavioral features that indicate a potential impact of SVA propagation on the cognitive ability of a modern human. Our analysis suggests a potential role of SVAs in the evolution of human central nervous system and especially in the emergence of functional trends relevant to social and parental behavior. Coevolution of behavioral features and reproductive functions are suggested by our analysis and discussed.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2017.6514","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46739746","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":"Male-killing in African butterflies","authors":"S. S. H. Hassan, Eihab Idris","doi":"10.4081/EB.2013.E2","DOIUrl":"https://doi.org/10.4081/EB.2013.E2","url":null,"abstract":"Female-biased sex ratios occur in many insect species as a consequence of infection by maternally-inherited male-killing bacterial endosymbionts. In this paper, we revise the research conducted on the phenomenon of male-killing in African nymphalid butterflies, with special focus on the cases of Danaus chrysippus , Acraea encedon and Acraea encedana . The evolution of male-killing in each case was addressed, together with the phylogeny of male-killers that were identified from this group. Moreover, the potential impacts that male-killers might impose on the evolution of their butterfly hosts were thoroughly investigated. In the end of this review, we present a number of unanswered questions to be targeted by future research work on the male-killing in these butterflies.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"5 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2013-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2013.E2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148556","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":"Recent advances of studies on alternative intron retention","authors":"Lei-lei Zhan","doi":"10.4081/EB.2013.E1","DOIUrl":"https://doi.org/10.4081/EB.2013.E1","url":null,"abstract":"Alternative splicing, allowing multiple mRNAs to be generated from a single gene, is a major source of proteome diversity in eukaryotes. Intron retention (IR), one type of alternative splicing, is the complete retention of an intron in a mature transcript. IR is believed to be associated with failure of the recognition of weak splice sites flanking introns. Mutations in DNA sequences, including point mutations and sequence insertions or deletions, can be at the origin and evolution of IR. The strength of weaker splice sites is the main cause of IR, but some cis -regulatory elements and trans -regulatory factors can also play crucial roles in regulating IR. IR can result in the regulation of gene expression and may contribute to increase protein diversity. IR has been shown to occur in a variety of diseases, and it frequently leads to aberrant splicing.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"5 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2013-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2013.E1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148537","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":"What is Life? How Chemistry Becomes Biology","authors":"N. Lehman","doi":"10.4081/EB.2013.BR1","DOIUrl":"https://doi.org/10.4081/EB.2013.BR1","url":null,"abstract":"","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"5 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2013-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2013.BR1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148916","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":"Codon evolution: Mechanisms and Models","authors":"S. Lindgreen","doi":"10.4081/EB.2012.E8","DOIUrl":"https://doi.org/10.4081/EB.2012.E8","url":null,"abstract":"The unifying principle in almost all of bioinformatics is sequence analysis: no matter if you are predicting the structure of proteins, analyzing the genetic variation in a population, or deciphering the evolutionary history of your favorite gene, your analysis hinges on looking at biological sequences and how they change over time, between species, or from gene to gene. Biological sequence analysis is the cornerstone.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"4 1","pages":"8"},"PeriodicalIF":0.0,"publicationDate":"2012-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2012.E8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148788","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":"CASS: Protein sequence simulation with explicit genotype-phenotype mapping","authors":"Johan A. Grahnen, D. Liberles","doi":"10.4081/EB.2012.E9","DOIUrl":"https://doi.org/10.4081/EB.2012.E9","url":null,"abstract":"CASS (coarse-grained artificial sequence simulator) is a software package for simulating protein sequences with an explicit genotype-to-phenotype mapping that takes protein structure and function into account. It is capable of reproducing many structure-specific properties of protein sequence evolution, most notably spatial and temporal variation in rates, and has been used to investigate several hypotheses about the influence of thermodynamics on molecular evolution. The software is implemented in object-oriented C++, is supported on Linux, and the source code is made freely available under the GPL v3 license at http://www.wyomingbioinformatics.org/Liberle sGroup/CASS/.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"4 1","pages":"9"},"PeriodicalIF":0.0,"publicationDate":"2012-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2012.E9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148855","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: a view from the 21st century","authors":"C. Seoighe","doi":"10.4081/EB.2012.E6","DOIUrl":"https://doi.org/10.4081/EB.2012.E6","url":null,"abstract":"","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"4 1","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2012-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2012.E6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148673","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":"Evolutionary dynamics of simple sequence repeats across long evolutionary time scale in genus Drosophila","authors":"Lothar Wissler, L. Godmann, E. Bornberg-Bauer","doi":"10.4081/EB.2012.E7","DOIUrl":"https://doi.org/10.4081/EB.2012.E7","url":null,"abstract":"Repetitive DNA is among the fastest evolving types of genomic DNA, which includes simple sequence repeats (SSRs), short regions of tandemly repeated one to six nucleotides long motifs. SSRs are found most frequently in noncoding regions. Repeat number variation occurs rapidly and is presumably neutral such that polymorphic SSRs are frequently used as genetic markers to characterize and classify populations. Despite their rapid evolution, recent reports suggested that SSR loci can be retained over hundreds of millions of years. We here investigate the dynamics and genomic features of SSR evolution in syntenic regions conserved across twelve Drosophila species and within a D. melanogaster population dataset. We find that SSR loci decay exponentially with time, the percentage of retained SSRs mostly reflects species relationships and correlates well with the sequence similarity of neighboring genes. About 47% of repeat loci within syntenic regions may share common ancestry due to predicted conservation in at least two species from the Drosophila subgenera Sophophora and Drosophila respectively, i.e. after 80 million years of divergence time. Since loci which are highly polymorphic at the population level also decay faster across species, SSR evolution appears to be a gradual process in which conservation pressure may act at relatively constant rates across time scales. A higher proportion of SSR loci are retained among Drosophila subgenus species considering their evolutionary distance and the expected decay rate estimated across all Drosophila species. This prolonged SSR retention might be caused by a higher SSR mutation rate and a lower nucleotide substitution rate in the Drosophila subgenus compared to Sophophora species. SSRs in exons and on autosomes evolve more slowly than SSRs located outside of exons or on the sex chromosome, respectively, both within and across species. SSR variability and phylogenetic conservation thus varies depending on the genomic location. These findings provide new insights into the dynamics of SSRs at both micro- and macro-evolutionary scales. The development of robust models of SSR long-term evolution will facilitate more in-depth analyses in general and the prediction of neutrally evolving SSRs and SSRs evolving under purifying selection, extending our knowledge of the functional impact of SSRs in genome evolution.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"4 1","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2012-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2012.E7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148733","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":"Proving universal common ancestry with similar sequences.","authors":"Leonardo de Oliveira Martins, David Posada","doi":"10.4081/eb.2012.e5","DOIUrl":"10.4081/eb.2012.e5","url":null,"abstract":"<p><p>Douglas Theobald recently developed an interesting test putatively capable of quantifying the evidence for a Universal Common Ancestry uniting the three domains of life (Eukarya, Archaea and Bacteria) against hypotheses of Independent Origins for some of these domains. We review here his model, in particular in relation to the treatment of Horizontal Gene Transfer (HGT) and to the quality of sequence alignment.</p>","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2012-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694314/pdf/emss-52347.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31545418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of epigenetics in plant adaptation","authors":"A. Robertson, D. Wolf","doi":"10.4081/EB.2012.E4","DOIUrl":"https://doi.org/10.4081/EB.2012.E4","url":null,"abstract":"Recent work in the field of plant epigenetics is adding to a growing understanding of how epigenetic variation can be an important source of phenotypic variation in natural populations. Therefore, it has the potential to play a major role in adaptation to environmental change. Most epigenetic variation is reset between generations, however, in some instances environmentally-induced epigenetic variation can result in heritable phenotypic plasticity that invokes Lamarkian-like inheritance. Epigenetic variation can also be the result of random epimutations that can have both higher mutation and reversal rates than DNA sequence mutations. We discuss several examples documenting epigenetic variation in wild populations. We also discuss laboratory studies that investigate the rate of epimutations and reversals, and how that has been incorporated into evolutionary theory. We suggest that modern evolutionary theory will benefit from the incorporation of epigenetics, but it is not in need of a complete revision, as has been suggested.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"4 1","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2012-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2012.E4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148616","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}