International journal of evolutionary biology最新文献_第2页

DNA methylation, epigenetics, and evolution in vertebrates: facts and challenges. 脊椎动物的DNA甲基化、表观遗传学和进化:事实和挑战。

International journal of evolutionary biology Pub Date : 2014-01-01 Epub Date: 2014-01-16 DOI: 10.1155/2014/475981

Annalisa Varriale

{"title":"DNA methylation, epigenetics, and evolution in vertebrates: facts and challenges.","authors":"Annalisa Varriale","doi":"10.1155/2014/475981","DOIUrl":"https://doi.org/10.1155/2014/475981","url":null,"abstract":"DNA methylation is a key epigenetic modification in the vertebrate genomes known to be involved in biological processes such as regulation of gene expression, DNA structure and control of transposable elements. Despite increasing knowledge about DNA methylation, we still lack a complete understanding of its specific functions and correlation with environment and gene expression in diverse organisms. To understand how global DNA methylation levels changed under environmental influence during vertebrate evolution, we analyzed its distribution pattern along the whole genome in mammals, reptiles and fishes showing that it is correlated with temperature, independently on phylogenetic inheritance. Other studies in mammals and plants have evidenced that environmental stimuli can promote epigenetic changes that, in turn, might generate localized changes in DNA sequence resulting in phenotypic effects. All these observations suggest that environment can affect the epigenome of vertebrates by generating hugely different methylation patterns that could, possibly, reflect in phenotypic differences. We are at the first steps towards the understanding of mechanisms that underlie the role of environment in molding the entire genome over evolutionary times. The next challenge will be to map similarities and differences of DNA methylation in vertebrates and to associate them with environmental adaptation and evolution. ","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2014 ","pages":"475981"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/475981","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32139854","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}

引用次数: 93

A syntenic region conserved from fish to Mammalian x chromosome. 从鱼类到哺乳动物的x染色体保守的同染色体区域。

International journal of evolutionary biology Pub Date : 2014-01-01 Epub Date: 2014-11-18 DOI: 10.1155/2014/873935

Guijun Guan, Meisheng Yi, Tohru Kobayashi, Yunhan Hong, Yoshitaka Nagahama

{"title":"A syntenic region conserved from fish to Mammalian x chromosome.","authors":"Guijun Guan, Meisheng Yi, Tohru Kobayashi, Yunhan Hong, Yoshitaka Nagahama","doi":"10.1155/2014/873935","DOIUrl":"https://doi.org/10.1155/2014/873935","url":null,"abstract":"Sex chromosomes bearing the sex-determining gene initiate development along the male or female pathway, no matter which sex is determined by XY male or ZW female heterogamety. Sex chromosomes originate from ancient autosomes but evolved rapidly after the acquisition of sex-determining factors which are highly divergent between species. In the heterogametic male system (XY system), the X chromosome is relatively evolutionary silent and maintains most of its ancestral genes, in contrast to its Y counterpart that has evolved rapidly and degenerated. Sex in a teleost fish, the Nile tilapia (Oreochromis niloticus), is determined genetically via an XY system, in which an unpaired region is present in the largest chromosome pair. We defined the differences in DNA contents present in this chromosome with a two-color comparative genomic hybridization (CGH) and the random amplified polymorphic DNA (RAPD) approach in XY males. We further identified a syntenic segment within this region that is well conserved in several teleosts. Through comparative genome analysis, this syntenic segment was also shown to be present in mammalian X chromosomes, suggesting a common ancestral origin of vertebrate sex chromosomes. ","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2014 ","pages":"873935"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/873935","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32906574","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}

引用次数: 1

Evolution of the B-Block Binding Subunit of TFIIIC That Binds to the Internal Promoter for RNA Polymerase III. 结合RNA聚合酶III内部启动子的TFIIIC B-Block结合亚基的进化

International journal of evolutionary biology Pub Date : 2014-01-01 Epub Date: 2014-02-12 DOI: 10.1155/2014/609865

Sachiko Matsutani

{"title":"Evolution of the B-Block Binding Subunit of TFIIIC That Binds to the Internal Promoter for RNA Polymerase III.","authors":"Sachiko Matsutani","doi":"10.1155/2014/609865","DOIUrl":"https://doi.org/10.1155/2014/609865","url":null,"abstract":"Eukaryotic RNA polymerase III transcribes tRNA genes, and this requires the transcription factor TFIIIC. Promoters are within genes, with which the B-block binding subunit of TFIIIC associates to initiate transcription. The binding subunits are more than 1000 amino acids in length in various eukaryotic species. There are four regions with conserved sequence similarities in the subunits. The helix-turn-helix motif is included in one of these regions and has been characterized as the B-block_TFIIIC family in the Pfam database. In the NCBI and EMBL translated protein databases, there are archaeal proteins (approximately 100 amino acids in length) referred to as B-block binding subunits. Most of them contain a B-block_TFIIIC motif. DELTA-BLAST searches using these archaeal proteins as queries showed significant multiple blast hits for many eukaryotic B-block binding subunits on the same proteins. This result suggests that eukaryotic B-block binding subunits were constituted by repeating a small unit of B-block_TFIIIC over a long evolutionary period. Bacterial proteins have also been annotated as B-block binding subunits in the databases. Here, some of them were confirmed to have significant similarities to B-block_TFIIIC. These results may imply that part of the RNAP III transcription machinery existed in the common ancestry of prokaryotes and eukaryotes. ","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2014 ","pages":"609865"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/609865","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32223828","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}

引用次数: 4

Diversification in monkeyflowers: an investigation of the effects of elevation and floral color in the genus mimulus. 猕猴桃花的多样性:海拔和花色对猕猴桃属植物的影响。

International journal of evolutionary biology Pub Date : 2014-01-01 Epub Date: 2014-01-05 DOI: 10.1155/2014/382453

Ezgi Ogutcen, Brooklyn Hamper, Jana C Vamosi

{"title":"Diversification in monkeyflowers: an investigation of the effects of elevation and floral color in the genus mimulus.","authors":"Ezgi Ogutcen, Brooklyn Hamper, Jana C Vamosi","doi":"10.1155/2014/382453","DOIUrl":"https://doi.org/10.1155/2014/382453","url":null,"abstract":"The vast diversity of floral colours in many flowering plant families, paired with the observation of preferences among pollinators, suggests that floral colour may be involved in the process of speciation in flowering plants. While transitions in floral colour have been examined in numerous genera, we have very little information on the consequences of floral colour transitions to the evolutionary success of a clade. Overlaid upon these patterns is the possibility that certain floral colours are more prevalent in certain environments, with the causes of differential diversification being more directly determined by geographical distribution. Here we examine transition rates to anthocyanin + carotenoid rich (red/orange/fuschia) flowers and examine whether red/orange flowers are associated with differences in speciation and/or extinction rates in Mimulus. Because it has been suggested that reddish flowers are more prevalent at high elevation, we also examine the macroevolutionary evidence for this association and determine if there is evidence for differential diversification at high elevations. We find that, while red/orange clades have equivalent speciation rates, the trait state of reddish flowers reverts more rapidly to the nonreddish trait state. Moreover, there is evidence for high speciation rates at high elevation and no evidence for transition rates in floral colour to differ depending on elevation. ","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2014 ","pages":"382453"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/382453","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32102235","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}

引用次数: 4

Genetics of Sub-Saharan African Human Population: Implications for HIV/AIDS, Tuberculosis, and Malaria. 撒哈拉以南非洲人口的遗传学：对艾滋病毒/艾滋病、结核病和疟疾的影响》。

International journal of evolutionary biology Pub Date : 2014-01-01 Epub Date: 2014-08-18 DOI: 10.1155/2014/108291

Gerald Mboowa

{"title":"Genetics of Sub-Saharan African Human Population: Implications for HIV/AIDS, Tuberculosis, and Malaria.","authors":"Gerald Mboowa","doi":"10.1155/2014/108291","DOIUrl":"10.1155/2014/108291","url":null,"abstract":"Sub-Saharan Africa has continued leading in prevalence and incidence of major infectious disease killers such as HIV/AIDS, tuberculosis, and malaria. Epidemiological triad of infectious diseases includes susceptible host, pathogen, and environment. It is imperative that all aspects of vertices of the infectious disease triad are analysed to better understand why this is so. Studies done to address this intriguing reality though have mainly addressed pathogen and environmental components of the triad. Africa is the most genetically diverse region of the world as well as being the origin of modern humans. Malaria is relatively an ancient infection in this region as compared to TB and HIV/AIDS; from the evolutionary perspective, we would draw lessons that this ancestrally unique population now under three important infectious diseases both ancient and exotic will be skewed into increased genetic diversity; moreover, other evolutionary forces are also still at play. Host genetic diversity resulting from many years of malaria infection has been well documented in this population; we are yet to account for genetic diversity from the trio of these infections. Effect of host genetics on treatment outcome has been documented. Host genetics of sub-Saharan African population and its implication to infectious diseases are an important aspect that this review seeks to address. ","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2014 ","pages":"108291"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151494/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32652551","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}

引用次数: 0

Mycobacterium tuberculosis H37Rv: In Silico Drug Targets Identification by Metabolic Pathways Analysis. 结核分枝杆菌H37Rv:基于代谢途径分析的药物靶点识别

International journal of evolutionary biology Pub Date : 2014-01-01 Epub Date: 2014-02-25 DOI: 10.1155/2014/284170

Asad Amir, Khyati Rana, Arvind Arya, Neelesh Kapoor, Hirdesh Kumar, Mohd Asif Siddiqui

{"title":"Mycobacterium tuberculosis H37Rv: In Silico Drug Targets Identification by Metabolic Pathways Analysis.","authors":"Asad Amir, Khyati Rana, Arvind Arya, Neelesh Kapoor, Hirdesh Kumar, Mohd Asif Siddiqui","doi":"10.1155/2014/284170","DOIUrl":"https://doi.org/10.1155/2014/284170","url":null,"abstract":"Mycobacterium tuberculosis (Mtb) is a pathogenic bacteria species in the genus Mycobacterium and the causative agent of most cases of tuberculosis. Tuberculosis (TB) is the leading cause of death in the world from a bacterial infectious disease. This antibiotic resistance strain lead to development of the new antibiotics or drug molecules which can kill or suppress the growth of Mycobacterium tuberculosis. We have performed an in silico comparative analysis of metabolic pathways of the host Homo sapiens and the pathogen Mycobacterium tuberculosis (H37Rv). Novel efforts in developing drugs that target the intracellular metabolism of M. tuberculosis often focus on metabolic pathways that are specific to M. tuberculosis. We have identified five unique pathways for Mycobacterium tuberculosis having a number of 60 enzymes, which are nonhomologous to Homo sapiens protein sequences, and among them there were 55 enzymes, which are nonhomologous to Homo sapiens protein sequences. These enzymes were also found to be essential for survival of the Mycobacterium tuberculosis according to the DEG database. Further, the functional analysis using Uniprot showed involvement of all the unique enzymes in the different cellular components. ","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2014 ","pages":"284170"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/284170","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32252890","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}

引用次数: 29

Individual Genetic Contributions to Genital Shape Variation between Drosophila simulans and D. mauritiana. 模拟果蝇和毛里求斯果蝇生殖器形状变异的个体遗传贡献。

International journal of evolutionary biology Pub Date : 2014-01-01 Epub Date: 2014-09-08 DOI: 10.1155/2014/808247

Hélène LeVasseur-Viens, Amanda J Moehring

{"title":"Individual Genetic Contributions to Genital Shape Variation between Drosophila simulans and D. mauritiana.","authors":"Hélène LeVasseur-Viens, Amanda J Moehring","doi":"10.1155/2014/808247","DOIUrl":"https://doi.org/10.1155/2014/808247","url":null,"abstract":"External genitalia are one of the most rapidly evolving morphological features in insects. In the Drosophila melanogaster species subgroup, males possess a nonfertilizing external genital structure, called the posterior lobe, which is highly divergent among even closely related species. A previous study on this subgroup mapped two genomic regions that affect lobe size and four that affect lobe shape differences between D. mauritiana and D. sechellia; none of the regions affected both size and shape. Here, we investigate whether three of these significant regions also affect lobe size and shape differences between the overlapping species pair D. mauritiana and D. simulans. We found that the same three regions of D. mauritiana, previously shown to affect lobe morphology in a D. sechellia genetic background, also affect lobe morphology in a D. simulans genetic background, with one of the regions affecting both size and shape. Two of the regions also affected morphology when introgressed in the reciprocal direction. The overlap of regions affecting genital morphology within related species pairs indicates either that there is a common underlying genetic basis for variation in genital morphology within this species group or that there are multiple adjacent loci with the potential to influence genital morphology. ","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2014 ","pages":"808247"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/808247","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32744289","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}

引用次数: 8

Is the frequency content of the calls in north american treefrogs limited by their larynges? 北美树蛙叫声的频率是否受到喉部的限制?

International journal of evolutionary biology Pub Date : 2014-01-01 Epub Date: 2014-09-23 DOI: 10.1155/2014/198069

Marcos Gridi-Papp

{"title":"Is the frequency content of the calls in north american treefrogs limited by their larynges?","authors":"Marcos Gridi-Papp","doi":"10.1155/2014/198069","DOIUrl":"https://doi.org/10.1155/2014/198069","url":null,"abstract":"A high diversity of mating calls is found among frogs. The calls of most species, however, are simple, in comparison to those of mammals and birds. In order to determine if the mechanics of the larynx could explain the simplicity of treefrog calls, the larynges of euthanized males were activated with airflow. Laryngeal airflow, sound frequency, and sound intensity showed a positive direct relationship with the driving air pressure. While the natural calls of the studied species exhibit minimal frequency modulation, their larynges produced about an octave of frequency modulation in response to varying pulmonary pressure. Natural advertisement calls are produced near the higher extreme of frequency obtained in the laboratory and at a slightly higher intensity (6 dB). Natural calls also exhibit fewer harmonics than artificial ones, because the larynges were activated with the mouth of the animal open. The results revealed that treefrog larynges allow them to produce calls spanning a much greater range of frequencies than observed in nature; therefore, the simplicity of the calls is not due to a limited frequency range of laryngeal output. Low frequencies are produced at low intensities, however, and this could explain why treefrogs concentrate their calling at the high frequencies. ","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2014 ","pages":"198069"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/198069","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32761036","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}

引用次数: 11

A mechanistic explanation linking adaptive mutation, niche change, and fitness advantage for the wrinkly spreader. 一种机制解释，将适应性突变、生态位变化和起皱传播者的适应性优势联系起来。

International journal of evolutionary biology Pub Date : 2014-01-01 Epub Date: 2014-01-16 DOI: 10.1155/2014/675432

Andrew J Spiers

{"title":"A mechanistic explanation linking adaptive mutation, niche change, and fitness advantage for the wrinkly spreader.","authors":"Andrew J Spiers","doi":"10.1155/2014/675432","DOIUrl":"https://doi.org/10.1155/2014/675432","url":null,"abstract":"Experimental evolution studies have investigated adaptive radiation in static liquid microcosms using the environmental bacterium Pseudomonas fluorescens SBW25. In evolving populations a novel adaptive mutant known as the Wrinkly Spreader arises within days having significant fitness advantage over the ancestral strain. A molecular investigation of the Wrinkly Spreader has provided a mechanistic explanation linking mutation with fitness improvement through the production of a cellulose-based biofilm at the air-liquid interface. Colonisation of this niche provides greater access to oxygen, allowing faster growth than that possible for non-biofilm-forming competitors located in the lower anoxic region of the microcosm. Cellulose is probably normally used for attachment to plant and soil aggregate surfaces and to provide protection in dehydrating conditions. However, the evolutionary innovation of the Wrinkly Spreader in static microcosms is the use of cellulose as the matrix of a robust biofilm, and is achieved through mutations that deregulate multiple diguanylate cyclases leading to the over-production of cyclic-di-GMP and the stimulation of cellulose expression. The mechanistic explanation of the Wrinkly Spreader success is an exemplar of the modern evolutionary synthesis, linking molecular biology with evolutionary ecology, and provides an insight into the phenomenal ability of bacteria to adapt to novel environments. ","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2014 ","pages":"675432"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/675432","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32139855","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}

引用次数: 31

Infectious disease, endangerment, and extinction. 传染病、濒危和灭绝。

International journal of evolutionary biology Pub Date : 2013-01-01 Epub Date: 2013-01-16 DOI: 10.1155/2013/571939

Ross D E Macphee, Alex D Greenwood

引用次数: 64