Quantitative social dialectology: explaining linguistic variation geographically and socially

In this study we examine linguistic variation and its dependence on both social and geographic factors. We follow dialectometry in applying a quantitative methodology and focusing on dialect distances, and social dialectology in the choice of factors we examine in building a model to predict word pronunciation distances from the standard Dutch language to 424 Dutch dialects. We combine linear mixed-effects regression modeling with generalized additive modeling to predict the pronunciation distance of 559 words. Although geographical position is the dominant predictor, several other factors emerged as significant. The model predicts a greater distance from the standard for smaller communities, for communities with a higher average age, for nouns (as contrasted with verbs and adjectives), for more frequent words, and for words with relatively many vowels. The impact of the demographic variables, however, varied from word to word. For a majority of words, larger, richer and younger communities are moving towards the standard. For a smaller minority of words, larger, richer and younger communities emerge as driving a change away from the standard. Similarly, the strength of the effects of word frequency and word category varied geographically. The peripheral areas of the Netherlands showed a greater distance from the standard for nouns (as opposed to verbs and adjectives) as well as for high-frequency words, compared to the more central areas. Our findings indicate that changes in pronunciation have been spreading (in particular for low-frequency words) from the Hollandic center of economic power to the peripheral areas of the country, meeting resistance that is stronger wherever, for well-documented historical reasons, the political influence of Holland was reduced. Our results are also consistent with the theory of lexical diffusion, in that distances from the Hollandic norm vary systematically and predictably on a word by word basis.     

Sperm mobility: deduction of a model explaining phenotypic variation in roosters (Gallus domesticus)

In previous work, variation in sperm mobility phenotype was attributed to the proportion of ejaculated fowl sperm containing dysfunctional mitochondria. In the present work, latent mitochondrial dysfunction was inferred from patterns of sperm egress from the oviduct's sperm-storage tubules. In addition, experiments were performed to help explain how mitochondrial function could be compromised in viable sperm cells. Confocal microscopy demonstrated that sperm Ca2+ content differed between low and high sperm-mobility phenotypes when sperm were stained with rhod-2 AM, a Ca2+ -specific dye. Fluorescence was associated with the nuclear envelope, a variant of the endoplasmic reticulum, and greater fluorescence was observed in sperm from low sperm-mobility males. Fluorescence was reduced by 50% when motile sperm were rendered immotile by incubation with a Ca2+ chelator. Thus, a relationship was established between a dynamic intracellular Ca2+ pool and sperm motility. Sperm N-methy-D-aspartic acid (NMDA) receptors were inferred by the action of D-homocysteinesulfinic acid, a potent NMDA receptor agonist. Seminal plasma from low sperm mobility males was characterized by an elevated glutamate concentration. Thapsigargin, which inhibits the smooth endoplasmic reticulum Ca2+ pump and thereby promotes Ca2+ efflux, rendered sperm immotile. This effect was blocked by cyclosporin A, which prevents the formation of the mitochondrial permeability transition pore (PTP) in response to elevated mitochondrial Ca2+ content. In summary, we propose that 1) glutamate enables Ca2+ uptake into sperm before ejaculation, 2) excessive Ca2+ uptake triggers formation of the PTP in a subpopulation of sperm, and 3) sperm mobility is decreased in proportion.     

Genetic variation: molecular mechanisms and impact on microbial evolution

On the basis of established knowledge of microbial genetics one can distinguish three major natural strategies in the spontaneous generation of genetic variations in bacteria. These strategies are: (1) small local changes in the nucleotide sequence of the genome, (2) intragenomic reshuffling of segments of genomic sequences and (3) the acquisition of DNA sequences from another organism. The three general strategies differ in the quality of their contribution to microbial evolution. Besides a number of non-genetic factors, various specific gene products are involved in the generation of genetic variation and in the modulation of the frequency of genetic variation. The underlying genes are called evolution genes. They act for the benefit of the biological evolution of populations as opposed to the action of housekeeping genes and accessory genes which are for the benefit of individuals. Examples of evolution genes acting as variation generators are found in the transposition of mobile genetic elements and in so-called site-specific recombination systems. DNA repair systems and restriction-modification systems are examples of modulators of the frequency of genetic variation. The involvement of bacterial viruses and of plasmids in DNA reshuffling and in horizontal gene transfer is a hint for their evolutionary functions. Evolution genes are thought to undergo biological evolution themselves, but natural selection for their functions is indirect, at the level of populations, and is called second-order selection. In spite of an involvement of gene products in the generation of genetic variations, evolution genes do not programmatically direct evolution towards a specific goal. Rather, a steady interplay between natural selection and mixed populations of genetic variants gives microbial evolution its direction.     

Feeding mechanisms in bats: variation within the constraints of flight

By any standard, bats are a successful group of mammals andthe evolution of flight and echolocation were certainly keyinnovations behind their success. That is only part of the story,however. Bats have diversified into trophic niches that rangefrom insectivory to feeding on blood, fruit, or nectar. Whileflight places fundamental constraints on the shape of the postcranialskeleton, skull shape in bats is remarkably diverse. Morphologicalstudies of individual families and sympatric assemblages demonstratethat variation in skull shape is clearly associated with trophicspecialization. Field experiments demonstrate that species-specificbiting behaviors during feeding are common and analyses indicatethat the evolution of cranial morphology and feeding behaviorare correlated. Modeling experiments further suggest that feeding(loading) behaviors and skull shape are functionally linked.If the skulls of bats are under selective pressure for minimalmass because of the energetic demands of flight, then they maybe more "optimized" to meet mechanical demands than are theskulls of other mammals. This would make bats a unique modelsystem for studying the evolution of diversity in skull shapeand its functional implications for the evolution of feedingstrategies in mammals.     

Proximate structural mechanisms for variation in food-chain length

Food-chain length is a central characteristic of ecological communities because of its strong influence on community structure and ecosystem function. While recent studies have started to better clarify the relationship between food-chain length and environmental gradients such as resource availability and ecosystem size, much less progress has been made in isolating the ultimate and proximate mechanisms that determine food-chain length. Progress has been slow, in part, because research has paid little attention to the proximate changes in food web structure that must link variation in food-chain length to the ultimate dynamic mechanism. Here we outline the structural mechanisms that determine variation in food-chain length. We explore the implications of these mechanisms for understanding how changes in food-web structure influence food-chain length using both an intraguild predation community model and data from natural ecosystems. The resulting framework provides the mechanisms for linking ultimate dynamic mechanisms to variation in food-chain length. It also suggests that simple linear food-chain models may make misleading predictions about patterns of variation in food-chain length because they are unable to incorporate important structural mechanisms that alter food-web dynamics and cause non-linear shifts in food-web structure. Intraguild predation models provide a more appropriate theoretical framework for understanding food-chain length in most natural ecosystems because they accommodate all of the proximate structural mechanisms identified here.     

Climatic zonation drives latitudinal variation in speciation mechanisms

Many groups of organisms show greater species richness in the tropics than in the temperate zone, particularly in tropical montane regions. Forty years ago, Janzen suggested that more limited temperature seasonality in the tropics leads to greater climatic zonation and more climatic barriers to organismal dispersal along elevational gradients in the tropics relative to temperate regions. These factors could lead to differences in how species arise in tropical versus temperate regions and possibly contribute to greater tropical diversity. However, no studies have compared the relationships among climate, elevational distribution and speciation in a group inhabiting both tropical and temperate regions. Here, we compare elevational and climatic divergence among 30 sister-species pairs (14 tropical, 16 temperate) within a single family of salamanders (Plethodontidae) that reaches its greatest species richness in montane Mesoamerica. In support of Janzen's hypothesis, we find that sister species are more elevationally and climatically divergent in the tropics than in the temperate zone. This pattern seemingly reflects regional variation in the role of climate in speciation, with niche conservatism predominating in the temperate zone and niche divergence in the tropics. Our study demonstrates how latitudinal differences in elevational climatic zonation may increase opportunities for geographical isolation, speciation and the associated build-up of species diversity in the tropics relative to the temperate zone.     

Pseudomonas siderophores: A mechanism explaining disease-suppressive soils

The membrane-bound hydrogenase ffomPseudomonas pseudoflava GA3 was purified up to a specific activity of 172 μmol H₂ oxidized/min and mg protein and a yield of 31%. The enzyme has a molecular weight of 98,000, consists of two different subunits (65,000 and 30,000), and contains 6 atoms iron and 6 molecules of acid-labile sulfide per molecule of enzyme. The isoelectric point was determined to be 6.5. The enzyme was stable under nitrogen, oxygen, and air atmosphere and unstable under hydrogen. The purified hydrogenase was able to reduce only a few of artificial electron acceptors, i.e., pyocyanine, methylene blue, phenazinemethosulfate, benzylviologen, and dichlorophenolindophenol.     

Maintenance of genetic variation in sexual ornaments: a review of the mechanisms

Female preferences for elaborate male sexual traits have been documented in a number of species in which males contribute only genes to the next generation. In such systems, mate choice has been hypothesised to benefit females genetically. For the genetic benefits to be possible there must be additive genetic variation (V(A)) for sexual ornaments, such that highly ornamented males can pass fitter genes on to the progeny of choosy females. Here, I review the mechanisms that can contribute to the maintenance of this variation. The variation may be limited to sexual ornaments, resulting in Fisherian benefits in terms of the increased reproductive success of male progeny produced by choosy females. Alternatively, ornaments may capture V(A) in other life-history traits. In the latter case, "good genes" benefits may apply in terms of improved performance of the progeny of either sex. Some mechanisms, however, such as negative pleiotropy, sexually antagonistic variation or overdominance, can maintain V(A )in ornaments and other life-history traits with little variation in total fitness, leaving little room for any genetic benefits of mate choice. Distinguishing between these mechanisms has consequences not only for the theory of sexual selection, but also for evolution of sex and for biological conservation. I discuss how the traditional ways of testing for genetic benefits can usefully be supplemented by tests detecting benefits resulting from specific mechanisms maintaining V(A )in sexual ornaments.     

O-antigen structural variation: mechanisms and possible roles in animal/plant-microbe interactions

Current data from bacterial pathogens of animals and from bacterial symbionts of plants support some of the more general proposed functions for lipopolysaccharides (LPS) and underline the importance of LPS structural versatility and adaptability. Most of the structural heterogeneity of LPS molecules is found in the O-antigen polysaccharide. In this review, the role and mechanisms of this striking flexibility in molecular structure of the O-antigen in bacterial pathogens and symbionts are illustrated by some recent findings. The variation in O-antigen that gives rise to an enormous structural diversity of O-antigens lies in the sugar composition and the linkages between monosaccharides. The chemical composition and structure of the O-antigen is strain-specific (interstrain LPS heterogeneity) but can also vary within one bacterial strain (intrastrain LPS heterogeneity). Both LPS heterogeneities can be achieved through variations at different levels. First of all, O-polysaccharides can be modified non-stoichiometrically with sugar moieties, such as glucosyl and fucosyl residues. The addition of non-carbohydrate substituents, i.e. acetyl or methyl groups, to the O-antigen can also occur with regularity, but in most cases these modifications are again non-stoichiometric. Understanding LPS structural variation in bacterial pathogens is important because several studies have indicated that the composition or size of the O-antigen might be a reliable indicator of virulence potential and that these important features often differ within the same bacterial strain. In general, O-antigen modifications seem to play an important role at several (at least two) stages of the infection process, including the colonization (adherence) step and the ability to bypass or overcome host defense mechanisms. There are many reports of modifications of O-antigen in bacterial pathogens, resulting either from altered gene expression, from lysogenic conversion or from lateral gene transfer followed by recombination. In most cases, the mechanisms underlying these changes have not been resolved. However, in recent studies some progress in understanding has been made. Changes in O-antigen structure mediated by lateral gene transfer, O-antigen conversion and phase variation, including fucosylation, glucosylation, acetylation and changes in O-antigen size, will be discussed. In addition to the observed LPS heterogeneity in bacterial pathogens, the structure of LPS is also altered in bacterial symbionts in response to signals from the plant during symbiosis. It appears to be part of a molecular communication between bacterium and host plant. Experiments ex planta suggest that the bacterium in the rhizosphere prepares its LPS for its roles in symbiosis by refining the LPS structure in response to seed and root compounds and the lower pH at the root surface. Moreover, modifications in LPS induced by conditions associated with infection are another indication that specific structures are important. Also during the differentiation from bacterium to bacteroid, the LPS of Rhizobium undergoes changes in the composition of the O-antigen, presumably in response to the change of environment. Recent findings suggest that, during symbiotic bacteroid development, reduced oxygen tension induces structural modifications in LPS that cause a switch from predominantly hydrophilic to predominantly hydrophobic molecular forms. However, the genetic mechanisms by which the LPS epitope changes are regulated remain unclear. Finally, the possible roles of O-antigen variations in symbiosis will be discussed.     

Chromatin diminution is a key process explaining the eukaryotic genome size paradox and some mechanisms of genetic isolation

The functions of redundant (junk, selfish, parasitic, etc.) DNA in eukaryotes can be reliably inferred from chromatin diminution (programmed elimination of up to 94% of the genome from somatic germ cells in Ascaris and Cyclops). These functions should be sought in germ cells, where this DNA is preserved during the entire life time of the species. A possible biological role of redundant DNA as a factor disrupting meiotic chromosome synapsis is suggested. At the same time, chromatin diminution itself can act as a mechanism of postzygotic isolation. All stage of the complex diminution mechanism could not be fixed in the genetic program of the species via gradual accumulation of mutations. The "program" of diminution must have appeared at once and in the completed form.     

Confirmation and explaining how possible

Confirmation in evolutionary biology depends on what biologists take to be the genuine rivals. Investigating what constrains the scope of biological possibility provides part of the story: explaining how possible helps determine what counts as a genuine rival and thus informs confirmation. To clarify the criteria for genuine rivalry I distinguish between global and local constraints on biological possibility, and offer an account of how-possibly explanation. To sharpen the connection between confirmation and explaining how possible I discuss the view that formal inquiry can provide a kind of confirmation-theoretic support for evolutionary models, and offer an example of how-possibly explanation interacting with testing practice.     

Improving yield by exploiting mechanisms underlying natural variation of photosynthesis

Increasing photosynthesis in C3 species has been identified as an approach to increase the yield of crop plants. Most of our knowledge of photosynthetic performance has come from studies in which plants were grown in controlled growth conditions but plants in natural environments have to cope with unpredictable and rapidly changing conditions. Plants adapt to the light environment in which they grow and this is demonstrated by the differences in anatomy and morphology of leaves in sun and shade leaves. Superimposed on this are the dynamic responses of plants to rapid changes in the light environment that occur throughout the day. Application of next generation sequencing (NGS), QTL analysis and innovative phenomic screening can provide information to underpin approaches for breeding of higher yielding crop plants.