共查询到20条相似文献,搜索用时 15 毫秒
1.
Background
Intermediate forms in the evolution of new adaptations such as transitions from water to land and the evolution of flight are often poorly understood. Similarly, the evolution of superfast sonic muscles in fishes, often considered the fastest muscles in vertebrates, has been a mystery because slow bladder movement does not generate sound. Slow muscles that stretch the swimbladder and then produce sound during recoil have recently been discovered in ophidiiform fishes. Here we describe the disturbance call (produced when fish are held) and sonic mechanism in an unrelated perciform pearl perch (Glaucosomatidae) that represents an intermediate condition in the evolution of super-fast sonic muscles.Results
The pearl perch disturbance call is a two-part sound produced by a fast sonic muscle that rapidly stretches the bladder and an antagonistic tendon-smooth muscle combination (part 1) causing the tendon and bladder to snap back (part 2) generating a higher-frequency and greater-amplitude pulse. The smooth muscle is confirmed by electron microscopy and protein analysis. To our knowledge smooth muscle attachment to a tendon is unknown in animals.Conclusion
The pearl perch, an advanced perciform teleost unrelated to ophidiiform fishes, uses a slow type mechanism to produce the major portion of the sound pulse during recoil, but the swimbladder is stretched by a fast muscle. Similarities between the two unrelated lineages, suggest independent and convergent evolution of sonic muscles and indicate intermediate forms in the evolution of superfast muscles. 相似文献2.
Background
Protein-coding change is one possible genetic mechanism underlying the evolution of adaptive wing colour pattern variation in Heliconius butterflies. Here we determine whether 38 putative genes within two major Heliconius patterning loci, HmYb and HmB, show evidence of positive selection. Ratios of nonsynonymous to synonymous nucleotide changes (ω) were used to test for selection, as a means of identifying candidate genes within each locus that control wing pattern. 相似文献3.
Background
Proteins show a broad range of evolutionary rates. Understanding the factors that are responsible for the characteristic rate of evolution of a given protein arguably is one of the major goals of evolutionary biology. A long-standing general assumption used to be that the evolution rate is, primarily, determined by the specific functional constraints that affect the given protein. These constrains were traditionally thought to depend both on the specific features of the protein's structure and its biological role. The advent of systems biology brought about new types of data, such as expression level and protein-protein interactions, and unexpectedly, a variety of correlations between protein evolution rate and these variables have been observed. The strongest connections by far were repeatedly seen between protein sequence evolution rate and the expression level of the respective gene. It has been hypothesized that this link is due to the selection for the robustness of the protein structure to mistranslation-induced misfolding that is particularly important for highly expressed proteins and is the dominant determinant of the sequence evolution rate. 相似文献4.
Background
Recent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven exploration of the deepest roots of viruses. Here we briefly review the current views of virus evolution and propose a new, coherent scenario that appears to be best compatible with comparative-genomic data and is naturally linked to models of cellular evolution that, from independent considerations, seem to be the most parsimonious among the existing ones. 相似文献5.
Arnold J Bendich 《Biology direct》2010,5(1):42
Background
Several proposals have been made to explain the rise of multicellular life forms. An internal environment can be created and controlled, germ cells can be protected in novel structures, and increased organismal size allows a "division of labor" among cell types. These proposals describe advantages of multicellular versus unicellular organisms at levels of organization at or above the individual cell. I focus on a subsequent phase of evolution, when multicellular organisms initiated the process of development that later became the more complex embryonic development found in animals and plants. The advantage here is realized at the level of the mitochondrion and chloroplast. 相似文献6.
7.
Background
Co-evolution is the process in which two (or more) sets of orthologs exhibit a similar or correlative pattern of evolution. Co-evolution is a powerful way to learn about the functional interdependencies between sets of genes and cellular functions and to predict physical interactions. More generally, it can be used for answering fundamental questions about the evolution of biological systems. Orthologs that exhibit a strong signal of co-evolution in a certain part of the evolutionary tree may show a mild signal of co-evolution in other branches of the tree. The major reasons for this phenomenon are noise in the biological input, genes that gain or lose functions, and the fact that some measures of co-evolution relate to rare events such as positive selection. Previous publications in the field dealt with the problem of finding sets of genes that co-evolved along an entire underlying phylogenetic tree, without considering the fact that often co-evolution is local.Results
In this work, we describe a new set of biological problems that are related to finding patterns of local co-evolution. We discuss their computational complexity and design algorithms for solving them. These algorithms outperform other bi-clustering methods as they are designed specifically for solving the set of problems mentioned above. We use our approach to trace the co-evolution of fungal, eukaryotic, and mammalian genes at high resolution across the different parts of the corresponding phylogenetic trees. Specifically, we discover regions in the fungi tree that are enriched with positive evolution. We show that metabolic genes exhibit a remarkable level of co-evolution and different patterns of co-evolution in various biological datasets. In addition, we find that protein complexes that are related to gene expression exhibit non-homogenous levels of co-evolution across different parts of the fungi evolutionary line. In the case of mammalian evolution, signaling pathways that are related to neurotransmission exhibit a relatively higher level of co-evolution along the primate subtree.Conclusions
We show that finding local patterns of co-evolution is a computationally challenging task and we offer novel algorithms that allow us to solve this problem, thus opening a new approach for analyzing the evolution of biological systems. 相似文献8.
Background
Many of the mutations accumulated by naturally evolving proteins are neutral in the sense that they do not significantly alter a protein's ability to perform its primary biological function. However, new protein functions evolve when selection begins to favor other, "promiscuous" functions that are incidental to a protein's original biological role. If mutations that are neutral with respect to a protein's primary biological function cause substantial changes in promiscuous functions, these mutations could enable future functional evolution. 相似文献9.
10.
Nitchakarn Noranate Franck Prugnolle Hélène Jouin Adama Tall Laurence Marrama Cheikh Sokhna Marie-Thérèse Ekala Micheline Guillotte Emmanuel Bischoff Christiane Bouchier Jintana Patarapotikul Jun Ohashi Jean-François Trape Christophe Rogier Odile Mercereau-Puijalon 《BMC microbiology》2009,9(1):1-25
Background
Genetic evidence for diversifying selection identified the Merozoite Surface Protein1 block2 (PfMSP1 block2) as a putative target of protective immunity against Plasmodium falciparum. The locus displays three family types and one recombinant type, each with multiple allelic forms differing by single nucleotide polymorphism as well as sequence, copy number and arrangement variation of three amino acid repeats. The family-specific antibody responses observed in endemic settings support immune selection operating at the family level. However, the factors contributing to the large intra-family allelic diversity remain unclear. To address this question, population allelic polymorphism and sequence variant-specific antibody responses were studied in a single Senegalese rural community where malaria transmission is intense and perennial.Results
Family distribution showed no significant temporal fluctuation over the 10 y period surveyed. Sequencing of 358 PCR fragments identified 126 distinct alleles, including numerous novel alleles in each family and multiple novel alleles of recombinant types. The parasite population consisted in a large number of low frequency alleles, alongside one high-frequency and three intermediate frequency alleles. Population diversity tests supported positive selection at the family level, but showed no significant departure from neutrality when considering intra-family allelic sequence diversity and all families combined. Seroprevalence, analysed using biotinylated peptides displaying numerous sequence variants, was moderate and increased with age. Reactivity profiles were individual-specific, mapped to the family-specific flanking regions and to repeat sequences shared by numerous allelic forms within a family type. Seroreactivity to K1-, Mad20- and R033 families correlated with the relative family genotype distribution within the village. Antibody specificity remained unchanged with cumulated exposure to an increasingly large number of alleles.Conclusion
The Pfmsp1 block2 locus presents a very large population sequence diversity. The lack of stable acquisition of novel antibody specificities despite exposure to novel allelic forms is reminiscent of clonal imprinting. The locus appears under antibody-mediated diversifying selection in a variable environment that maintains a balance between the various family types without selecting for sequence variant allelic forms. There is no evidence of positive selection for intra-family sequence diversity, consistent with the observed characteristics of the antibody response. 相似文献11.
Paschall JE Oleksiak MF VanWye JD Roach JL Whitehead JA Wyckoff GJ Kolell KJ Crawford DL 《BMC genomics》2004,5(1):96
Background
While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. 相似文献12.
S. Del Vecchio E. Fantinato J.A.M. Janssen F. Bioret A. Acosta I. Prisco R. Tzonev C. Marcenò J. Rodwell G. Buffa 《应用植被学》2018,21(2):312-321
Question
Coastal environments have often been described as azonal. While this characteristic is clear for the foredune system, it seems less evident for more inland fixed dunes, which host habitats of major conservation concern, whose features seem to be more related to local climatic conditions. We hypothesized that, unlike other coastal habitats, dune perennial grasslands differ floristically and structurally across their European range and that patterns of variation are linked to the corresponding climate.Location
European coasts (Atlantic Ocean, Baltic, Mediterranean, Black Sea).Methods
We used a large data set of phytosociological relevés, representative of coastal grasslands throughout their European range. The role of climatic variables (temperature, precipitation and continentality) in determining the variability in species composition and vegetation structure (by means of life forms) was investigated through CCA, DCA and GLM. The degree of concentration of species occurrences within groups was calculated through the Phi coefficient.Results
Through multivariate analyses we identified seven major types of coastal grassland, corresponding to different geographic areas. The groups significantly differed in their climatic envelope, as well as in their species composition and community structure.Conclusion
Our results confirm the hypothesis that coastal dune perennial grasslands are subjected to local climate, which exerts significant effects on both floristic composition and community structure. As a consequence, coastal grasslands are particularly prone to the effect of possible climate change, which may alter species composition and distribution, and lead to shifts in the distribution of native plant communities.13.
Background
The Thecostraca are arguably the most morphologically and biologically variable group within the Crustacea, including both suspension feeders (Cirripedia: Thoracica and Acrothoracica) and parasitic forms (Cirripedia: Rhizocephala, Ascothoracida and Facetotecta). Similarities between the metamorphosis found in the Facetotecta and Rhizocephala suggests a common evolutionary origin, but until now no comprehensive study has looked at the basic evolution of these thecostracan groups. 相似文献14.
Wanlan Wang Kian-Kai Cheng Lingli Deng Jingjing Xu Guiping Shen Julian L. Griffin Jiyang Dong 《Metabolomics : Official journal of the Metabolomic Society》2017,13(1):10
Introduction
The metabolome of a biological system is affected by multiple factors including factor of interest (e.g. metabolic perturbation due to disease) and unwanted factors or factors which are not primarily the focus of the study (e.g. batch effect, gender, and level of physical activity). Removal of these unwanted data variations is advantageous, as the unwanted variations may complicate biological interpretation of the data.Objectives
We aim to develop a new unwanted variations elimination (UVE) method called clustering-based unwanted residuals elimination (CURE) to reduce metabolic variation caused by unwanted/hidden factors in metabolomic data.Methods
A mean-centered metabolomic dataset can be viewed as a combination of a studied factor matrix and a residual matrix. The CURE method assumes that the residual should be normally distributed if it only contains inter-individual variation. However, if the residual forms multiple clusters in feature subspace of principal components analysis or partial least squares discriminant analysis, the residual may contain variation due to unwanted factors. This unwanted variation is removed by doing K-means data clustering and removal of means for each cluster from the residuals. The process is iterated until the residual no longer forms multiple clusters in feature subspace.Results
Three simulated datasets and a human metabolomic dataset were used to demonstrate the performance of the proposed CURE method. CURE was found able to remove most of the variations caused by unwanted factors, while preserving inter-individual variation between samples.Conclusion
The CURE method can effectively remove unwanted data variation, and can serve as an alternative UVE method for metabolomic data.15.
Background
Alternative splicing (AS) is important for evolution and major biological functions in complex organisms. However, the extent of AS in mammals other than human and mouse is largely unknown, making it difficult to study AS evolution in mammals and its biomedical implications. 相似文献16.
Background
The Eocene, a time of fluctuating environmental change and biome evolution, was generally driven by exceptionally warm temperatures. The Messel (47.8 Ma) and Eckfeld (44.3 Ma) deposits offer a rare opportunity to take a census of two, deep-time ecosystems occurring during a greenhouse system. An understanding of the long-term consequences of extreme warming and cooling events during this interval, particularly on angiosperms and insects that dominate terrestrial biodiversity, can provide insights into the biotic consequences of current global climatic warming.Methodology/Principal Findings
We compare insect-feeding damage within two middle Eocene fossil floras, Messel and Eckfeld, in Germany. From these small lake deposits, we studied 16,082 angiosperm leaves and scored each specimen for the presence or absence of 89 distinctive and diagnosable insect damage types (DTs), each of which was allocated to a major functional feeding group, including four varieties of external foliage feeding, piercing- and-sucking, leaf mining, galling, seed predation, and oviposition. Methods used for treatment of presence–absence data included general linear models and standard univariate, bivariate and multivariate statistical techniques.Conclusions/Significance
Our results show an unexpectedly high diversity and level of insect feeding than comparable, penecontemporaneous floras from North and South America. In addition, we found a higher level of herbivory on evergreen, rather than deciduous taxa at Messel. This pattern is explained by a ca. 2.5-fold increase in atmospheric CO2 that overwhelmed evergreen antiherbivore defenses, subsequently lessened during the more ameliorated levels of Eckfeld times. These patterns reveal important, previously undocumented features of plant-host and insect-herbivore diversification during the European mid Eocene. 相似文献17.
Evolution of mosaic operons by horizontal gene transfer and gene displacement <Emphasis Type="Italic">in situ</Emphasis>
下载免费PDF全文
![点击此处可从《Genome biology》网站下载免费的PDF全文](/ch/ext_images/free.gif)
Background
Shuffling and disruption of operons and horizontal gene transfer are major contributions to the new, dynamic view of prokaryotic evolution. Under the 'selfish operon' hypothesis, operons are viewed as mobile genetic entities that are constantly disseminated via horizontal gene transfer, although their retention could be favored by the advantage of coregulation of functionally linked genes. Here we apply comparative genomics and phylogenetic analysis to examine horizontal transfer of entire operons versus displacement of individual genes within operons by horizontally acquired orthologs and independent assembly of the same or similar operons from genes with different phylogenetic affinities.Results
Since a substantial number of operons have been identified experimentally in only a few model bacteria, evolutionarily conserved gene strings were analyzed as surrogates of operons. The phylogenetic affinities within these predicted operons were assessed first by sequence similarity analysis and then by phylogenetic analysis, including statistical tests of tree topology. Numerous cases of apparent horizontal transfer of entire operons were detected. However, it was shown that apparent horizontal transfer of individual genes or arrays of genes within operons is not uncommon either and results in xenologous gene displacement in situ, that is, displacement of an ancestral gene by a horizontally transferred ortholog from a taxonomically distant organism without change of the local gene organization. On rarer occasions, operons might have evolved via independent assembly, in part from horizontally acquired genes.Conclusions
The discovery of in situ gene displacement shows that combination of rampant horizontal gene transfer with selection for preservation of operon structure provides for events in prokaryotic evolution that, a priori, seem improbable. These findings also emphasize that not all aspects of operon evolution are selfish, with operon integrity maintained by purifying selection at the organism level.18.
19.
Renfree MB Papenfuss AT Deakin JE Lindsay J Heider T Belov K Rens W Waters PD Pharo EA Shaw G Wong ES Lefèvre CM Nicholas KR Kuroki Y Wakefield MJ Zenger KR Wang C Ferguson-Smith M Nicholas FW Hickford D Yu H Short KR Siddle HV Frankenberg SR Chew KY Menzies BR Stringer JM Suzuki S Hore TA Delbridge ML Patel HR Mohammadi A Schneider NY Hu Y O'Hara W Al Nadaf S Wu C Feng ZP Cocks BG Wang J Flicek P Searle SM Fairley S Beal K Herrero J Carone DM Suzuki Y Sugano S Toyoda A Sakaki Y Kondo S 《Genome biology》2011,12(8):R81
20.
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes 总被引:5,自引:0,他引:5
下载免费PDF全文
![点击此处可从《Genome biology》网站下载免费的PDF全文](/ch/ext_images/free.gif)
Koonin EV Fedorova ND Jackson JD Jacobs AR Krylov DM Makarova KS Mazumder R Mekhedov SL Nikolskaya AN Rao BS Rogozin IB Smirnov S Sorokin AV Sverdlov AV Vasudevan S Wolf YI Yin JJ Natale DA 《Genome biology》2004,5(2):R7-28