Trends in evolutionary biology最新文献

{"title":"Life from an RNA World: the ancestor within","authors":"N. Lehman","doi":"10.4081/EB.2010.E5","DOIUrl":"https://doi.org/10.4081/EB.2010.E5","url":null,"abstract":"Life from an RNA World: The Ancestor Within is a great place to find all of the arguments for the existence of an “RNA World” neatly compiled in a short and fluid book. I read this pithy work in only a few days while commuting back and forth on public transit. Consequently my first reaction regarding the best audience for the book was that it was for non-scientists, or for those with a basic knowledge of biology but not getting paid to be a scientist. For me it was a smooth, easy read, and I imagine that many of my fellow passengers on the bus or the train saw me nodding my head spontaneously on many occasions.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"2 1","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2010-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2010.E5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148316","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":"Comparative analysis of the mitochondrial genomes in Drosophila virilis species group (Diptera: Drosophilidae)","authors":"B. Andrianov, I. Goryacheva, N. Mugue, S. Sorokina, T. Gorelova, V. Mitrofanov","doi":"10.4081/EB.2010.E4","DOIUrl":"https://doi.org/10.4081/EB.2010.E4","url":null,"abstract":"We present comparative analysis of mitogenomics data of the Drosophila virilis group based on newly obtained complete mt-genome sequence of Drosophila littoralis, previously published mt-genome sequence of D. virilis and fragments of mt-genomes of other Drosophila species belonging to the virilis group. Drosophila of the virilis group shared most recent common ancestry 40 MYA with D. melanogaster. Therefore, presented data help to overview the evolution of the genus. The mt-genome of D. littoralis is a circular molecule of 16,017 bp with a total A+T content of 76.2%. The gene order is consistent with other Drosophila genomes. All tRNAs can be folded in the form of a typical clover-leaf structure except for tRNASer(AGN). In the control region of D. littoralis we found four conserved sequence elements: 275 bp highly conserved sequence element, two thymidylate stretches and a G-island. The most variable genes in Drosophila of the virilis group are nad6, nad3 and nad4L. The most conservative is cox1. We revealed long intergenic sequences’ (TA)n separating atp6 and cox3 genes in the mitochondrial genomes of Drosophila of the virilis group. In other insect species these genes have no or few separating nucleotides. We detected fragments of mitochondrial genes atp6 and cox3 in the nuclear genome of D. virilis. These mitochondrial pseudogenes are marked by site-specific insertions of Tv1 retrotransposon in the (TA)n intergenic spacer sequences.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"2 1","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2010-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2010.E4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148303","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":"Angiosperm polyploids and their road to evolutionary success","authors":"Jeffrey A. Fawcett, Y. Peer","doi":"10.4081/EB.2010.E3","DOIUrl":"https://doi.org/10.4081/EB.2010.E3","url":null,"abstract":"The abundance of polyploidy among flowering plants has long been recognized, and recent studies have uncovered multiple ancient polyploidization events in the evolutionary history of several angiosperm lineages. Once polyploids are formed they must get locally established and then propagate and survive while adapting to different environments and avoiding extinction. This might ultimately lead to their long-term evolutionary success, where their descendant lineages survive for tens of millions of years. Along this road to evolutionary success, polyploids must overcome several obstacles, to which several genetic and ecological factors are likely to contribute. One recurrent observation, based on present-day polyploids, has been the high frequency of polyploids in harsh environments. Also, recent studies proposed that the success of certain ancient polyploids might be linked to periods of climatic change. Although we are still in the early stages of unraveling the factors that resulted in the long-term evolutionary success of ancient polyploids, the advances in genomic sequencing and molecular dating methods promise to enhance our understanding. It, therefore, seems timely to review our current knowledge of what determines the success of polyploids. Here, we discuss especially how harsh conditions or periods of climatic change might affect the rate of formation, establishment, persistence and long-term evolutionary success of polyploids in angiosperms.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"2 1","pages":"16-21"},"PeriodicalIF":0.0,"publicationDate":"2010-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2010.E3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148237","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":"Multiple approaches to study color pattern evolution in butterflies","authors":"A. Monteiro, Kathleen M. Prudic","doi":"10.4081/EB.2010.E2","DOIUrl":"https://doi.org/10.4081/EB.2010.E2","url":null,"abstract":"The myriad colors and patterns on butterfly wings have caught the attention of biologists for well over a century. Today, with the advent of more sophisticated genetic and developmental tools, it is possible to identify and study the evolution of genes, gene networks, and the effect of the environment on the networks underlying wing color patterning. In addition, using molecular phylogenies and the comparative approach, it is possible to infer ancestral wing patterns, direction of evolutionary change, and occurrence of parallelism and convergence. Finally, the driving forces behind wing pattern evolution can be estimated using bioassay studies such as predator‐prey and mate choice experiments. Here we review the different approaches to answer both proximate and ultimate questions about butterfly wing pattern evolution, and we highlight future research directions in a field that has the potential to become truly integrative.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"2 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2010-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2010.E2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148187","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":"PANDITplus: toward better integration of evolutionary view on molecular sequences with supplementary bioinformatics resources","authors":"S. Dimitrieva, M. Anisimova","doi":"10.4081/EB.2010.E1","DOIUrl":"https://doi.org/10.4081/EB.2010.E1","url":null,"abstract":"Recent comparative genomic and other large-scale bioinformatics studies increasingly have been using gene annotations, functional classifications, and complimentary data from the emerging “-omics” disciplines. Indeed, such analyses have better chances to uncover hidden patterns in complex multidimensional and heterogeneous biological systems data. On the other hand, inferences from such studies are extremely sensitive to data samples and quality, and are more difficult to compare or replicate owing to differences in supplementary data sources at times not publicly available. As a contribution toward the unification and integration of good quality data from heterogeneous bioinformatics resources, we present here an integrated data bank PANDITplus. It is built as an extension of PANDIT, the database of PFAM alignments and phylogenetic trees for known protein domains and families spanning lineages from the three domains of life. PANDITplus is a relational database containing information on functional categories, metabolic pathways, protein–protein interactions, disease associations, gene expression, three-dimensional structure, as well as estimates from evolutionary analyses of selective pressures. User-friendly interface enables customized queries and fast data access. We recommend PANDITplus as a common bioinformatics platform for testing evolutionary hypotheses, which go beyond the mere inferences from molecular data by incorporating supplementary gene information. Equally, PANDITplus provides an excellent resource for the development, testing, and comparison of statistical models of substitution and probabilistic dependencies between a molecular sequence and its various attributes. The database may be accessed via http://www.panditplus.org.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"2 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2010-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2010.E1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70147969","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 in action across life at “Evolution Canyons”, Israel","authors":"E. Nevo","doi":"10.4081/EB.2009.E3","DOIUrl":"https://doi.org/10.4081/EB.2009.E3","url":null,"abstract":"The \"Evolution Canyon\" model reveals evolution in action across life at a microscale involving biodiversity divergence, adaptation and incipient sympatric ecological speciation across life. The model highlights diverse taxa species richness, genomics, proteomics and phenomics phenomena by exploring genetic polymorphisms at protein and DNA levels and, recently, genome-wide gene expression and regulation. Genetic diversity and divergence reveal evolutionary dynamics of natural populations exposed to sharp-interslope, ecologically divergent, tropical and temperate microclimates on a xeric, tropical, \"African\" south-facing slope (AS) abutting with a mesic, temperate, \"European\" north-facing slope (ES) separated by 200 meters on average. Four \"Evolution Canyons” (EC) are currently being investigated in Israel in the Carmel, Galilee, Negev, and Golan Mountains (EC I-IV), respectively. We identified 2,500 species in ECI (Carmel) from bacteria to mammals in an area of 7,000 m2. Local biodiversity patterns parallel global patterns. Higher terrestrial species richness was found on the AS. Aquatic species richness prevails on the ES. In 9 out of 14 (64%) model organisms across life, we identified a significantly higher genetic polymorphism on the more stressful AS. Likewise, in some model taxa, we found largely higher levels of mutation rates, gene conversion, recombination, DNA repair, genome size, small sequence repeats (SSRs), single nucleotide polymorphism (SNPs), retrotransposons, transposons, candidate gene diversity, and genome-wide gene expression and regulation on the more stressful AS. Remarkably, interslope incipient sympatric ecological speciation was found across life from bacteria to mammals. The \"Evolution Canyon\" model represents the Israeli ecological analogue of the Galapagos Islands. Micro- climatic selection overrides gene flow and drift, and drives both interslope adaptive divergence and incipient sympatric ecological speciation at a microscale. The EC model could potentially highlight many mysteries of evolutionary biology including the genetic basis of adaptation and speciation, especially now with the rapid high-throughput techniques of whole genome analysis.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"1 1","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2009-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2009.E3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148405","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":"Textbook of Structural Biology by Anders Liljas, Lars Liljas, Jure Piskur, Göran Lindblom, Poul Nissen, and Morten Kjeldgaard","authors":"J. Echave","doi":"10.4081/EB.2009.E2","DOIUrl":"https://doi.org/10.4081/EB.2009.E2","url":null,"abstract":"Textbook of Structural Biology  By Anders Liljas, Lars Liljas, Jure Piskur, Goran Lindblom, Poul Nissen, and Morten Kjeldgaard Publisher: World Scientific Publishing Co. Pte. Ltd. Number of Pages: 572 Publication Year: 2009 ISBN-10: 981-277-208-1 ISBN-13: 978-981-277-208-4 Binding: Paperback","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"1 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2009-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2009.E2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148360","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":"Charles Darwin as a theoretical biologist in the mechanistic tradition","authors":"D. Penny","doi":"10.4081/EB.2009.E1","DOIUrl":"https://doi.org/10.4081/EB.2009.E1","url":null,"abstract":"Charles Darwin has had more impact on biological sciences, and society generally, than any other 19th century biologist. Yet his modus operandi as a scientist is poorly known by evolutionists, and often seriously misinterpreted. Two important aspects of his reasoning discussed here are his hypothetico-deductive approach and his search for mechanisms to explain past events. A wide range of statements from his autobiography and letters show that he worked explicitly in the hypothetico-deductive model. The extracts include strong statements that theories were essential even to know what data to collect; to hold theories only as hypotheses; the necessity to search for data that contradict a cherished theory. He also built on the very mechanistic geological tradition of James Hutton and Charles Lyell, and thus brought into historical biology the search for mechanisms that could be studied in the present to explain events in the past. Taken together, the statements show an excellent scientist working effectively on conceptual issues, whilst searching for mechanisms that could be studied in the present and that would have operated in the past. In retrospect, our understanding has been hampered by forcing overly-simplistic binary choices, such as uniformitarianism and catastrophism. It is important, especially in teaching and interactions with the public, that Darwin’s mode of working is better known, and we need to be more proactive in getting across the message that evolution is good testable science.","PeriodicalId":89866,"journal":{"name":"Trends in evolutionary biology","volume":"1 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2009-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4081/EB.2009.E1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70148277","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}