International journal of evolutionary biology最新文献

{"title":"The evolution of sex-related traits and genes 2012.","authors":"Alberto Civetta, José M Eirín-López, Rob Kulathinal, Jeremy L Marshall","doi":"10.1155/2013/590769","DOIUrl":"https://doi.org/10.1155/2013/590769","url":null,"abstract":"The second special issue on the evolution of sex-related traits and genes brings together a wide variety of papers that explore issues dealing with diverse topics such as behavior, organismal defense systems, molecular evolution, speciation, and genomics. This broad diversity reflects the recent expansion of the field of reproductive biology and evolution. The review by R. S. Singh and S. Jagadeeshan provides a historical perspective that describes the breadth of work that has emanated from early protein electrophoresis studies to the genomics-based approaches that are more common today. The authors illustrate how the study of sex- and reproductive-related (SRR) genes has now impacted fields of evolution spanning from selection and speciation to gene birth and evolutionary developmental genetics. \u0000 \u0000A review article and a research article address questions related to mating preferences across two very different systems, Tetrahymena and Drosophila. S. S. Phadke et al. address an interesting question about the evolution of sex: does the evolution of more than one sex necessarily lead to the evolution of mating preferences? Using the ciliate species, Tetrahymena thermophila, which has up to seven “sexes,” they tested the mating frequencies of four of the sexes to determine if they exhibited mating preferences. Their results suggest that mating is random among the four sexes, thus concluding that the evolution of multiple sexes does not necessarily lead to the evolution of mate preferences. They discuss their findings in the context of ciliate evolution as well as the evolution of sex in general. A review by A. J. Moehring and M. Laturney offers a clear insight into our current understanding of the genetic basis and evolution of sexual isolation between species. The review focuses on female mate preference as a premating behavioural barrier and highlights two interesting commonalities across a wide variety of Drosophila species: different genes control conspecific and heterospecific male choice and a preferential location of genes for heterospecific male rejection in areas of low recombination. Another paper in this issue deals with the question of reproductive isolation between species. J. L. Marshall and N. DiRienzo address a central question in evolutionary biology about whether the same genetic and developmental pathways contribute to reproductive isolation at both intraspecific and interspecific levels. The authors characterize a postmating, prezygotic phenotype, the ability of males to induce egglaying in females, between diverging populations, and species of crickets. Using mating assays and RNAi, the authors demonstrate similar decreases in female fecundity and the abundance of a particular female protein within populations as well as between species. While their results are suggestive of a connection between incompatibilities found within species and reproductive isolation between species, the authors also discuss alternative explanations an","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2013 ","pages":"590769"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/590769","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31439290","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":"Pathogen-driven selection in the human genome.","authors":"Rachele Cagliani,&nbsp;Manuela Sironi","doi":"10.1155/2013/204240","DOIUrl":"https://doi.org/10.1155/2013/204240","url":null,"abstract":"<p><p>Infectious diseases and epidemics have always accompanied and characterized human history, representing one of the main causes of death. Even today, despite progress in sanitation and medical research, infections are estimated to account for about 15% of deaths. The hypothesis whereby infectious diseases have been acting as a powerful selective pressure was formulated long ago, but it was not until the availability of large-scale genetic data and the development of novel methods to study molecular evolution that we could assess how pervasively infectious agents have shaped human genetic diversity. Indeed, recent evidences indicated that among the diverse environmental factors that acted as selective pressures during the evolution of our species, pathogen load had the strongest influence. Beside the textbook example of the major histocompatibility complex, selection signatures left by pathogen-exerted pressure can be identified at several human loci, including genes not directly involved in immune response. In the future, high-throughput technologies and the availability of genetic data from different populations are likely to provide novel insights into the evolutionary relationships between the human host and its pathogens. Hopefully, this will help identify the genetic determinants modulating the susceptibility to infectious diseases and will translate into new treatment strategies.</p>","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":" ","pages":"204240"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/204240","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40227437","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":"Undersampling taxa will underestimate molecular divergence dates: an example from the South american lizard clade liolaemini.","authors":"James A Schulte","doi":"10.1155/2013/628467","DOIUrl":"https://doi.org/10.1155/2013/628467","url":null,"abstract":"Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. Here, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini using several alternative subsampling strategies for both time calibrations and taxa numbers. Penalized likelihood (PL) and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa) mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. Using all calibrations and penalized likelihood, clades with very low taxon sampling had node age estimates younger than clades with more complete taxon sampling. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points: (1) whenever possible, authors should strongly consider adding as many taxa as possible, including numerous outgroups, prior to node age estimation to avoid considerable node age underestimation and (2) using more, critically assessed, and accurate fossil calibrations should yield improved divergence time estimates.","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2013 ","pages":"628467"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/628467","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31858330","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":"Modeling extinction risk of endemic birds of mainland china.","authors":"Youhua Chen","doi":"10.1155/2013/639635","DOIUrl":"https://doi.org/10.1155/2013/639635","url":null,"abstract":"<p><p>The extinction risk of endemic birds of mainland China was modeled over evolutionary time. Results showed that extinction risk of endemic birds in mainland China always tended to be similar within subclades over the evolutionary time of species divergence, and the overall evolution of extinction risk of species presented a conservatism pattern, as evidenced by the disparity-through-time plot. A constant-rate evolutionary model was the best one to quantify the evolution of extinction risk of endemic birds of mainland China. Thus, there was no rate shifting pattern for the evolution of extinction risk of Chinese endemic birds over time. In a summary, extinction risk of endemic birds of mainland China is systematically quantified under the evolutionary framework in the present work. </p>","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2013 ","pages":"639635"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/639635","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32055768","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":"Erratum to “Evolution of the FGF Gene Family”","authors":"Silvan Oulion, S. Bertrand, H. Escrivá","doi":"10.1155/2012/789125","DOIUrl":"https://doi.org/10.1155/2012/789125","url":null,"abstract":"The authors would like to make the following correction. In Figure  4 in the original paper shows two blue stars indicating genome duplications in the wrong place of the phylogenetic tree. This figure should be replaced by the following figure. The previous legend of Figure  4 is correct.","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2012 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/789125","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64353159","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":"Analysis of the meiotic segregation in intergeneric hybrids of tilapias.","authors":"Etienne Bezault,&nbsp;Xavier Rognon,&nbsp;Frederic Clota,&nbsp;Karim Gharbi,&nbsp;Jean-Francois Baroiller,&nbsp;Bernard Chevassus","doi":"10.1155/2012/817562","DOIUrl":"https://doi.org/10.1155/2012/817562","url":null,"abstract":"<p><p>Tilapia species exhibit a large ecological diversity and an important propensity to interspecific hybridisation. This has been shown in the wild and used in aquaculture. However, despite its important evolutionary implications, few studies have focused on the analysis of hybrid genomes and their meiotic segregation. Intergeneric hybrids between Oreochromis niloticus and Sarotherodon melanotheron, two species highly differentiated genetically, ecologically, and behaviourally, were produced experimentally. The meiotic segregation of these hybrids was analysed in reciprocal second generation hybrid (F2) and backcross families and compared to the meiosis of both parental species, using a panel of 30 microsatellite markers. Hybrid meioses showed segregation in accordance to Mendelian expectations, independent from sex and the direction of crosses. In addition, we observed a conservation of linkage associations between markers, which suggests a relatively similar genome structure between the two parental species and the apparent lack of postzygotic incompatibility, despite their important divergence. These results provide genomics insights into the relative ease of hybridisation within cichlid species when prezygotic barriers are disrupted. Overall our results support the hypothesis that hybridisation may have played an important role in the evolution and diversification of cichlids.</p>","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2012 ","pages":"817562"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/817562","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9374986","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":"Alternative splicing: a potential source of functional innovation in the eukaryotic genome.","authors":"Lu Chen,&nbsp;Jaime M Tovar-Corona,&nbsp;Araxi O Urrutia","doi":"10.1155/2012/596274","DOIUrl":"https://doi.org/10.1155/2012/596274","url":null,"abstract":"<p><p>Alternative splicing (AS) is a common posttranscriptional process in eukaryotic organisms, by which multiple distinct functional transcripts are produced from a single gene. The release of the human genome draft revealed a much smaller number of genes than anticipated. Because of its potential role in expanding protein diversity, interest in alternative splicing has been increasing over the last decade. Although recent studies have shown that 94% human multiexon genes undergo AS, evolution of AS and thus its potential role in functional innovation in eukaryotic genomes remain largely unexplored. Here we review available evidence regarding the evolution of AS prevalence and functional role. In addition we stress the need to correct for the strong effect of transcript coverage in AS detection and set out a strategy to ultimately elucidate the extent of the role of AS in functional innovation on a genomic scale.</p>","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2012 ","pages":"596274"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/596274","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9375104","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":"Evolution of lysine biosynthesis in the phylum deinococcus-thermus.","authors":"Hiromi Nishida,&nbsp;Makoto Nishiyama","doi":"10.1155/2012/745931","DOIUrl":"https://doi.org/10.1155/2012/745931","url":null,"abstract":"<p><p>Thermus thermophilus biosynthesizes lysine through the α-aminoadipate (AAA) pathway: this observation was the first discovery of lysine biosynthesis through the AAA pathway in archaea and bacteria. Genes homologous to the T. thermophilus lysine biosynthetic genes are widely distributed in bacteria of the Deinococcus-Thermus phylum. Our phylogenetic analyses strongly suggest that a common ancestor of the Deinococcus-Thermus phylum had the ancestral genes for bacterial lysine biosynthesis through the AAA pathway. In addition, our findings suggest that the ancestor lacked genes for lysine biosynthesis through the diaminopimelate (DAP) pathway. Interestingly, Deinococcus proteolyticus does not have the genes for lysine biosynthesis through the AAA pathway but does have the genes for lysine biosynthesis through the DAP pathway. Phylogenetic analyses of D. proteolyticus lysine biosynthetic genes showed that the key gene cluster for the DAP pathway was transferred horizontally from a phylogenetically distant organism.</p>","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2012 ","pages":"745931"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/745931","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9376236","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":"Comparative pathogenomics of bacteria causing infectious diseases in fish.","authors":"Ponnerassery S Sudheesh,&nbsp;Aliya Al-Ghabshi,&nbsp;Nashwa Al-Mazrooei,&nbsp;Saoud Al-Habsi","doi":"10.1155/2012/457264","DOIUrl":"https://doi.org/10.1155/2012/457264","url":null,"abstract":"<p><p>Fish living in the wild as well as reared in the aquaculture facilities are susceptible to infectious diseases caused by a phylogenetically diverse collection of bacterial pathogens. Control and treatment options using vaccines and drugs are either inadequate, inefficient, or impracticable. The classical approach in studying fish bacterial pathogens has been looking at individual or few virulence factors. Recently, genome sequencing of a number of bacterial fish pathogens has tremendously increased our understanding of the biology, host adaptation, and virulence factors of these important pathogens. This paper attempts to compile the scattered literature on genome sequence information of fish pathogenic bacteria published and available to date. The genome sequencing has uncovered several complex adaptive evolutionary strategies mediated by horizontal gene transfer, insertion sequence elements, mutations and prophage sequences operating in fish pathogens, and how their genomes evolved from generalist environmental strains to highly virulent obligatory pathogens. In addition, the comparative genomics has allowed the identification of unique pathogen-specific gene clusters. The paper focuses on the comparative analysis of the virulogenomes of important fish bacterial pathogens, and the genes involved in their evolutionary adaptation to different ecological niches. The paper also proposes some new directions on finding novel vaccine and chemotherapeutic targets in the genomes of bacterial pathogens of fish.</p>","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2012 ","pages":"457264"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/457264","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9432107","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":"Postzygotic Isolation Evolves before Prezygotic Isolation between Fresh and Saltwater Populations of the Rainwater Killifish, Lucania parva.","authors":"Genevieve M Kozak,&nbsp;Arthur B Rudolph,&nbsp;Beatrice L Colon,&nbsp;Rebecca C Fuller","doi":"10.1155/2012/523967","DOIUrl":"https://doi.org/10.1155/2012/523967","url":null,"abstract":"<p><p>Divergent natural selection has the potential to drive the evolution of reproductive isolation. The euryhaline killifish Lucania parva has stable populations in both fresh water and salt water. Lucania parva and its sister species, the freshwater L. goodei, are isolated by both prezygotic and postzygotic barriers. To further test whether adaptation to salinity has led to the evolution of these isolating barriers, we tested for incipient reproductive isolation within L. parva by crossing freshwater and saltwater populations. We found no evidence for prezygotic isolation, but reduced hybrid survival indicated that postzygotic isolation existed between L. parva populations. Therefore, postzygotic isolation evolved before prezygotic isolation in these ecologically divergent populations. Previous work on these species raised eggs with methylene blue, which acts as a fungicide. We found this fungicide distorts the pattern of postzygotic isolation by increasing fresh water survival in L. parva, masking species/population differences, and underestimating hybrid inviability.</p>","PeriodicalId":73449,"journal":{"name":"International journal of evolutionary biology","volume":"2012 ","pages":"523967"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/523967","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9743766","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}