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Environmental Selection (environmental + selection)
Selected AbstractsMetagenomic signatures of 86 microbial and viral metagenomesENVIRONMENTAL MICROBIOLOGY, Issue 7 2009Dana Willner Summary Previous studies have shown that dinucleotide abundances capture the majority of variation in genome signatures and are useful for quantifying lateral gene transfer and building molecular phylogenies. Metagenomes contain a mixture of individual genomes, and might be expected to lack compositional signatures. In many metagenomic data sets the majority of sequences have no significant similarities to known sequences and are effectively excluded from subsequent analyses. To circumvent this limitation, di-, tri- and tetranucleotide abundances of 86 microbial and viral metagenomes consisting of short pyrosequencing reads were analysed to provide a method which includes all sequences that can be used in combination with other analysis to increase our knowledge about microbial and viral communities. Both principal component analysis and hierarchical clustering showed definitive groupings of metagenomes drawn from similar environments. Together these analyses showed that dinucleotide composition, as opposed to tri- and tetranucleotides, defines a metagenomic signature which can explain up to 80% of the variance between biomes, which is comparable to that obtained by functional genomics. Metagenomes with anomalous content were also identified using dinucleotide abundances. Subsequent analyses determined that these metagenomes were contaminated with exogenous DNA, suggesting that this approach is a useful metric for quality control. The predictive strength of the dinucleotide composition also opens the possibility of assigning ecological classifications to unknown fragments. Environmental selection may be responsible for this dinucleotide signature through direct selection of specific compositional signals; however, simulations suggest that the environment may select indirectly by promoting the increased abundance of a few dominant taxa. [source] HABITAT-DEPENDENT SONG DIVERGENCE IN THE LITTLE GREENBUL: AN ANALYSIS OF ENVIRONMENTAL SELECTION PRESSURES ON ACOUSTIC SIGNALSEVOLUTION, Issue 9 2002Hans Slabbekoorn Abstract., Bird song is a sexual trait important in mate choice and known to be shaped by environmental selection. Here we investigate the ecological factors shaping song variation across a rainforest gradient in central Africa. We show that the little greenbul (Andropadus virens), previously shown to vary morphologically across the gradient in fitness-related characters, also varies with respect to song characteristics. Acoustic features, including minimum and maximum frequency, and delivery rate of song notes showed significant differences between habitats. In contrast, we found dialectal variation independent of habitat in population-typical songtype sequences. This pattern is consistent with ongoing gene flow across habitats and in line with the view that song variation in the order in which songtypes are produced is not dependent on habitat characteristics in the same way physical song characteristics are. Sound transmission characteristics of the two habitats did not vary significantly, but analyses of ambient noise spectra revealed dramatic and consistent habitat-dependent differences. Matching between low ambient noise levels for low frequencies in the rainforest and lower minimal frequencies in greenbul songs in this habitat suggests that part of the song divergence may be driven by habitat-dependent ambient noise patterns. These results suggest that habitat-dependent selection may act simultaneously on traits of ecological importance and those important in prezygotic isolation, leading to an association between morphological and acoustic divergence. Such an association may promote assortative mating and may be a mechanism driving reproductive divergence across ecological gradients. [source] On mental events, disciplinary boundaries, and reductionism: A reply to PlaudJOURNAL OF CLINICAL PSYCHOLOGY, Issue 9 2001Stephen S. Ilardi Plaud's (2001) radical behavioral manifesto suggests that a psychological science based exclusively upon the study of environment-behavior functional contingencies would yield a discipline unencumbered by mentalism, vaguely delineated disciplinary boundaries, or inappropriate reductionism. In reply, we note that: (a) mental events,e.g., thoughts and feelings,are increasingly accessible to objective investigation, and provide an observable proximal causal mechanism for the environmental selection of behavior; (b) the call for pristine disciplinary boundaries is anachronistic, inasmuch as progress in the natural sciences has engendered disciplinary boundaries that are increasingly porous; (c) cognitive neuroscience facilitates a comprehensive understanding of complex human behavior by mapping out the relationship between such behavior and underlying brain events, thereby engaging in an appropriate form of reductionism (constitutive reductionism) that has become a hallmark of the natural sciences; and (d) ironically, it is radical behaviorism, in its disavowal of the informational level of complexity instantiated in brain events, that engages in inappropriate eliminative reductionism (i.e., reducing neural information to "nothing but" its underlying bring states). © 2001 Jo n Wiley & Sons, Inc. J Clin Psychol 57: 1103,1107, 2001. [source] Divergent character clines across a recent secondary contact zone in a Hispaniolan lizardJOURNAL OF ZOOLOGY, Issue 3 2008M. E. Gifford Abstract Studies of genetic contact zones provide valuable information regarding the processes of population divergence, adaptation and speciation. In this paper, I examine transitions in morphology, mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) haplotypes across a recent secondary contact zone in a Hispaniolan lizard Ameiva chrysolaema. Maximum likelihood cline fitting analyses suggest non-coincidence of cline centers and that the mtDNA cline is significantly displaced to the west of the remaining clines. nDNA and morphological clines are coincident and tend to be associated with the prevailing environmental gradient. The lack of cytonuclear disequilibrium near the center of the contact zone and the non-coincidence of character clines suggest that this zone does not conform to a tension zone model of hybridization; thus, gene flow across the zone does not seem to be impeded. The extremely narrow width of the dorsal scale size cline and the close association of this cline with the steepness of the environmental (precipitation) gradient suggest that this character may be under environmental selection. Taken together, this contact zone appears to be structured by a combination of mtDNA introgression, possibly associated with eastward movement of the zone, and environmental selection on some characters. [source] Copper amendment of agricultural soil selects for bacterial antibiotic resistance in the fieldLETTERS IN APPLIED MICROBIOLOGY, Issue 2 2005J. Berg Abstract Aims:, The objective of this study was to determine whether Cu-amendment of field plots affects the frequency of Cu resistance, and antibiotic resistance patterns in indigenous soil bacteria. Methods and Results:, Soil bacteria were isolated from untreated and Cu-amended field plots. Cu-amendment significantly increased the frequency of Cu-resistant isolates. A panel of isolates were characterized by Gram-reaction, amplified ribosomal DNA restriction analysis and resistance profiling against seven antibiotics. More than 95% of the Cu-resistant isolates were Gram-negative. Cu-resistant Gram-negative isolates had significantly higher incidence of resistance to ampicillin, sulphanilamide and multiple (,3) antibiotics than Cu-sensitive Gram-negative isolates. Furthermore, Cu-resistant Gram-negative isolates from Cu-contaminated plots had significantly higher incidence of resistance to chloramphenicol and multiple (,2) antibiotics than corresponding isolates from control plots. Significance and Impact of the Study:, The results of this field experiment show that introduction of Cu to agricultural soil selects for Cu resistance, but also indirectly selects for antibiotic resistance in the Cu-resistant bacteria. Hence, the widespread accumulation of Cu in agricultural soils worldwide could have a significant effect on the environmental selection of antibiotic resistance. [source] Grapevine biology and adaptation to viticultureAUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH, Issue 2 2000W. JAMES (JIM) HARDIE Abstract This paper provides a context for later papers in these Proceedings on specific aspects of reproductive biology; particularly those aspects that impact on viticulture. In keeping with the concept of ,selfish genes' I posit that grapevine reproductive biology is most usefully introduced in a broad context where particular genotypes within a population are regarded as complex survival machines programmed by their genes to ensure successful cycles of growth and reproductive development. Topics not covered by this symposium such as leaf function, root physiology and nutrition, along with those that are a focus, viz. the physiology of bud fruitfulness, floral anatomy and pericarp development, have all featured in the evolutionary history of Vitis spp. Such adaptive features must be regarded as specialised components of a plant system regulated by a genetic constitution that has successfully evolved over millions of years against unrelenting environmental selection pressures i.e. adaptation by natural selection. Human selection over a subsequent 5000 years or so has added further viticultural refinements to those gene-based adaptive features. 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