Is Speciation Accompanied by Rapid Evolution? Insights from Comparing Reproductive and Nonreproductive Transcriptomes in Drosophila

The tempo and mode of evolutionary change during speciation have remained contentious until recently. While much of the evidence claiming speciation is an abrupt and rapid process comes from fossil data, recent molecular phylogenetics show that the background of gradual evolution is often broken by accelerated rates of molecular evolution during speciation. However, what kinds of genes affect or are affected by speciation remains unexplored. Our analysis of 4843 protein-coding genes in five species of the Drosophila melanogaster subgroup shows that while ~70% of genes follow clock-like evolution, between 17–19.67% of loci show signatures of accelerated rates of evolution in recently formed species. These genes show 2-3-fold higher rates of substitution in recently diverged species compared to older species. This fraction of loci affects a diverse range of functions. Only a small proportion of reproductive genes experience speciation-related accelerated changes but many sex-and -reproduction related genes show an interesting pattern of persistent rapid evolution suggesting that sex-and-reproduction related genes are under constant selective pressures. The identification of loci associated with accelerated evolution allows us to address the mechanisms of rapid evolution and speciation, which in our study appears to be a combination of both selection and rapid demographical changes

Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila

<p>Abstract</p> <p>Background</p> <p>Karl Ernst Von Baer noted that species tend to show greater morphological divergence in later stages of development when compared to earlier stages. Darwin originally interpreted these observations via a selectionist framework, suggesting that divergence should be greatest during ontogenic stages in which organisms experienced varying 'conditions of existence' and opportunity for differential selection. Modern hypotheses have focused on the notion that genes and structures involved in early development will be under stronger purifying selection due to the deleterious pleiotropic effects of mutations propagating over the course of ontogeny, also known as the developmental constraint hypothesis.</p> <p>Results</p> <p>Using developmental stage-specific expressed sequence tag (EST) libraries, we tested the 2 hypotheses by comparing the rates of evolution of 7,180 genes obtained from 6 species of the <it>Drosophila melanogaster </it>group with respect to ontogeny, and sex and reproduction-related functions in gonadal tissues. Supporting morphological observations, we found evidence of a pattern of increasing mean evolutionary rate in genes that are expressed in subsequent stages of development. Furthermore, supporting expectations that early expressed genes are constrained in divergence, we found that embryo stage genes are involved in a higher mean number of interactions as compared to later stages. We noted that the accelerated divergence of genes in the adult stage is explained by those expressed specifically in the male gonads, whose divergence is driven by positive selection. In addition, accelerated gonadal gene divergence occurs only in the adult stage, suggesting that the effects of selection are observed primarily at the stages during which they are expected occur. Finally, we also found a significant correlation between temporal specificity of gene expression and evolutionary rate, supporting expectations that genes with ubiquitous expression are under stronger constraint.</p> <p>Conclusion</p> <p>Taken together, these results support both the developmental constraint hypothesis limiting the divergence of early expressed developmentally important genes, leading to a gradient of divergence rates over ontogeny (embryonic < larval/pupal < adult), as well as Darwin's 'selection opportunity' hypothesis leading to increased divergence in adults, particularly in the case of reproductive tissues. We suggest that a constraint early/opportunity late model best explains divergence over ontogeny.</p

Time Dependence of Brans-Dicke Parameter w for an Expanding Universe

We have studied the time dependence of w for an expanding universe in the generalised B-D theory and have obtained its explicit dependence on the nature of matter contained in the universe,in different era.Lastly we discuss how the observed accelerated expansion of the present universe can be accomodated in the formalism.Comment: 10 pages,No figure

Generalization of Linearized Gouy-Chapman-Stern Model of Electric Double Layer for Nanostructured and Porous Electrodes: Deterministic and Stochastic Morphology

We generalize linearized Gouy-Chapman-Stern theory of electric double layer for nanostructured and morphologically disordered electrodes. Equation for capacitance is obtained using linear Gouy-Chapman (GC) or Debye-$\rm{\ddot{u}}$ckel equation for potential near complex electrode/electrolyte interface. The effect of surface morphology of an electrode on electric double layer (EDL) is obtained using "multiple scattering formalism" in surface curvature. The result for capacitance is expressed in terms of the ratio of Gouy screening length and the local principal radii of curvature of surface. We also include a contribution of compact layer, which is significant in overall prediction of capacitance. Our general results are analyzed in details for two special morphologies of electrodes, i.e. "nanoporous membrane" and "forest of nanopillars". Variations of local shapes and global size variations due to residual randomness in morphology are accounted as curvature fluctuations over a reference shape element. Particularly, the theory shows that the presence of geometrical fluctuations in porous systems causes enhanced dependence of capacitance on mean pore sizes and suppresses the magnitude of capacitance. Theory emphasizes a strong influence of overall morphology and its disorder on capacitance. Finally, our predictions are in reasonable agreement with recent experimental measurements on supercapacitive mesoporous systems

Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution

<p>Abstract</p> <p>Background</p> <p>Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs) play a central role. The nematode <it>Caenorhabditis elegans </it>is an established model organism for the study of the roles of TFs in controlling the spatiotemporal pattern of gene expression. Using the fully sequenced genomes of three <it>Caenorhabditid </it>nematode species as well as genome information from additional more distantly related organisms (fruit fly, mouse, and human) we sought to identify orthologous TFs and characterized their patterns of evolution.</p> <p>Results</p> <p>We identified 988 TF genes in <it>C. elegans</it>, and inferred corresponding sets in <it>C. briggsae </it>and <it>C. remanei</it>, containing 995 and 1093 TF genes, respectively. Analysis of the three gene sets revealed 652 3-way reciprocal 'best hit' orthologs (nematode TF set), approximately half of which are zinc finger (ZF-C2H2 and ZF-C4/NHR types) and HOX family members. Examination of the TF genes in <it>C. elegans </it>and <it>C. briggsae </it>identified the presence of significant tandem clustering on chromosome V, the majority of which belong to ZF-C4/NHR family. We also found evidence for lineage-specific duplications and rapid evolution of many of the TF genes in the two species. A search of the TFs conserved among nematodes in <it>Drosophila melanogaster</it>, <it>Mus musculus </it>and <it>Homo sapiens </it>revealed 150 reciprocal orthologs, many of which are associated with important biological processes and human diseases. Finally, a comparison of the sequence, gene interactions and function indicates that nematode TFs conserved across phyla exhibit significantly more interactions and are enriched in genes with annotated mutant phenotypes compared to those that lack orthologs in other species.</p> <p>Conclusion</p> <p>Our study represents the first comprehensive genome-wide analysis of TFs across three nematode species and other organisms. The findings indicate substantial conservation of transcription factors even across distant evolutionary lineages and form the basis for future experiments to examine TF gene function in nematodes and other divergent phyla.</p

Application of Kinematic Wave Equations to Border Irrigation Design

Accuracy of the kinematic wave (KW) approximation was tested on 31 experimental irrigation borders by computing the KW number and its modified version. In a majority of cases. This approximation was found to be sufficiently accurate. A KW model, reported previously, was used to derive dimensionless advance and recession curves for application to border irrigation design. These curves can be developed for a wide range of design variables and parameters for ready practical use. A step by step design procedure, based on this model is presented. Its validity was tested by comparing observed irrigation efficiencies with those computed by the model. A close agreement between computed and observed efficiencies suggests that the KW model is reasonably accurate. Its simplicity and physical basis may justify its large-scale field application

A kinematic model for surface irrigation: Verification by experimental data

An edited version of this paper was published by AGU. Copyright 1983 American Geophysical Union.A kinematic model for surface irrigation is verified by experimental data obtained for 31 borders. These borders are of varied characteristics. Calculated values of advance times, water surface profiles when water reaches the end of the border, and recession times are compared with their observations. The prediction error in most cases remains below 20% for the advance time and below 15% for the recession time. The water surface profiles computed by the model agree with observed profiles reasonably well. For the data analyzed here the kinematic wave model is found to be sufficiently accurate for modeling the entire irrigation cycle except for the vertical recession.This study was supported in part by funds provided by the National Science Foundation under the project Free Boundary Problems in Water Resource Engineering, NSF-ENG-79- 23345

Influence of water deficit on transpiration and radiation use efficiency of chickpea (Cicer arietinum L.)

Information on the relationship between biomass production, radiation use and water use of chickpea (Cicer arietinum L.) is essential to estimate biomass production in different water regimes. Experiments were conducted during three post-rainy seasons on a Vertisol (a typic pallustert) to study the effect of water deficits on radiation use, radiation use efficiency (RUE), transpiration and transpiration efficiency (TE) of chickpea. Different levels of soil water availability were created, either by having irrigated and non-irrigated plots or using a line source. Biomass production was linearly related to both cumulative intercepted solar radiation and transpiration in both well watered and water deficit treatments. Soil water availability did not affect RUE (total dry matter produced per unit of solar radiation interception) when at least 30% of extractable soil water (ESW) was present in the rooting zone, but below 30% ESW, RUE decreased linearly with the decrease in soil water content. RUE was also significantly correlated (R2 = 0.61, P < 0.01) with the ratio of actual to potential transpiration (T/Tp) and it declined curvilinearly with the decrease in T/Tp. TE decreased with the increase in saturation deficit (SD) of air. Normalization of TE with SD gave a conservative value of 4.8 g kPa kg−1. To estimate biomass production of chickpea in different environments, we need to account for the effect of plant water deficits on RUE in a radiation-based model and the effect of SD on TE in a transpiration-based mode

Mapping of the Indian fisheries growth rate and fish consumption through GIS

In the present study, Indian fisheries growth rate and fish consumption have been analyzed through GIS mapping. The analyses were based on the state-level fisheries data of India collected from the secondary sources. Accordingly, the paper contains one thematic map containing two layers. To achieve this, all the data have been brought into a tabular form through Microsoft Excel and then joined to Map Info Professional Version 8.0 GIS software with digitized map oflndia for further analysis to generate thematic maps