Effects of intraspecific larval competition on the development of the African buffalo fly Haematobia thirouxi potans

The effects of larval crowding on development, survival and size of the African buffalo fly, Haematobia thirouxi potans (Bezzi), were examined in small (10 or 20 g) and 1 000 g masses of cattle dung in the laboratory at 25°C. Dung was infested with fly eggs at densities which ranged from 0.05 to 32.0 eggs per g dung; in most cases 90–100% of eggs hatched. The duration of larval developmentin 10 g dung masses was extended by larval crowding at densities above 0.8 eggs per g dung and the development period with 32 eggs per g dung (11 days) was double that observed in uncrowded dung masses. Both size and survival decreased with increasing larval density, but stunting was observed at lower densities than those which reduced survival and so size was the more sensitive index of the adequacy of the larval environment. The effects of larval crowding became evident at lower larval densities in the 1 000 g dung masses than in the 10 g dung masses. There was a minimum size below which third instar larvae failed to pupariate. The probability of survival was related to pupal size and a high proportion of the smaller individuals failed to eclose.

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Effets de la competition intraspécifique sur le développement des larves, la taille des pupes et la survie d'Haematobia thirouxi potans

Résumé Les effets du surpeuplement larvaire sur le développement, la survie et la taille d'Haematobia thirouxi potans, ont été examinés sur de petites quantités de bouse (10 et 20 g) et de plus importantes (1 000 g), au laboratoire à 25°C. Les bouses étaient contaminées avec des oeufs de la mouche à des densités de 0,05 à 32 oeufs par gramme de bouse. Dans la plupart des cas le taux d'éclosion était de 90–100%. La durée du dévelopement larvaire dans 10 g de bouse a été prolongée pour les densités supérieures à 0,8 oeuf per g, et la durée développement pour 32 oeufs per g (11 jours) était le double de celle obtenue grand il n'y avait pas surpeuplement. La taille et la survie diminuent toutes les deux avec la densité larvaire, mais la miniaturisation était observée à des densités où la survie n'était pas modifiée; ainsi la taille est un indice plus sensible de l'adéquation de l'habitat larvaire. Les effets du surpeuplement larvaires deviennent clairs à des densités plus faibles avec 1 000 g de la bouse qu'avec 10 g. Il y a eu une taille minimale endessous de laquelle les larves étaient incapables de former une pupe. La probabilité d'éclosion était liée à la taille de la pupe, et une plus forte proportion de petits individus ne sont pas parvenu à éclore.

     

The importance of clonal growth to the recovery of Gaultheria procumbens L. (Ericaceae) after forest disturbance

We investigated the importance of clonal growth to the recovery of a common eastern North American sub-shrub, Gaultheria procumbens L. (Ericacea), after clearcut logging. Changes in vegetative growth and development of G. procumbens clones and clonal populations were examined in a chronosequence of logged stands representing different stages of successional development after clearcutting (open habitat, young regenerating forest, closed regenerating forest) and in neighboring undisturbed late-successional forests representative of presettlement conditions. We specifically quantified seedling presence and above-ground ramet production, demographic condition (e.g., sexual vs. vegetative stems), belowground rhizome growth and spread, and assessed the degree of intraspecific variation in clonal morphology and biomass allocation in stands differing in their disturbance history and degree of successional development. Recovery in G. procumbens was largely driven by the “release growth” of pre-existing clonal bud-banks in response to canopy removal. Release growth was expressed as greater ramet initiation, rhizome branching and clonal spread. Conversely, we found no evidence of sexual establishment in the species, although production of reproductive biomass (e.g., inflorescence mass, number of flowering shoots) was significant. These findings support a deterministic model of vascular resistance and resilience to catastrophic disturbance, in which recovery of forest plant communities derives from the life-history characteristics of constituent species.     

Non-negative matrix factorization for learning alignment-specific models of protein evolution

Models of protein evolution currently come in two flavors: generalist and specialist. Generalist models (e.g. PAM, JTT, WAG) adopt a one-size-fits-all approach, where a single model is estimated from a number of different protein alignments. Specialist models (e.g. mtREV, rtREV, HIVbetween) can be estimated when a large quantity of data are available for a single organism or gene, and are intended for use on that organism or gene only. Unsurprisingly, specialist models outperform generalist models, but in most instances there simply are not enough data available to estimate them. We propose a method for estimating alignment-specific models of protein evolution in which the complexity of the model is adapted to suit the richness of the data. Our method uses non-negative matrix factorization (NNMF) to learn a set of basis matrices from a general dataset containing a large number of alignments of different proteins, thus capturing the dimensions of important variation. It then learns a set of weights that are specific to the organism or gene of interest and for which only a smaller dataset is available. Thus the alignment-specific model is obtained as a weighted sum of the basis matrices. Having been constrained to vary along only as many dimensions as the data justify, the model has far fewer parameters than would be required to estimate a specialist model. We show that our NNMF procedure produces models that outperform existing methods on all but one of 50 test alignments. The basis matrices we obtain confirm the expectation that amino acid properties tend to be conserved, and allow us to quantify, on specific alignments, how the strength of conservation varies across different properties. We also apply our new models to phylogeny inference and show that the resulting phylogenies are different from, and have improved likelihood over, those inferred under standard models.     

Detecting individual sites subject to episodic diversifying selection

The imprint of natural selection on protein coding genes is often difficult to identify because selection is frequently transient or episodic, i.e. it affects only a subset of lineages. Existing computational techniques, which are designed to identify sites subject to pervasive selection, may fail to recognize sites where selection is episodic: a large proportion of positively selected sites. We present a mixed effects model of evolution (MEME) that is capable of identifying instances of both episodic and pervasive positive selection at the level of an individual site. Using empirical and simulated data, we demonstrate the superior performance of MEME over older models under a broad range of scenarios. We find that episodic selection is widespread and conclude that the number of sites experiencing positive selection may have been vastly underestimated.     

The role of Arabidopsis SCAR genes in ARP2-ARP3-dependent cell morphogenesis

The actin-nucleating ARP2-ARP3 complex controls cell shape in plants in many different cell types. Its activity is controlled by a multimeric complex containing BRK1 (also known as HSPC300), NAP1, SRA1, ABI and SCAR/WAVE. In this study, we focus on the function of the five putative SCAR homologues in Arabidopsis and we provide biochemical evidence that AtSCAR2 can activate the ARP2-ARP3 complex in vitro. Among the single mutants, mutations in only AtSCAR2 result in a subtle or weak phenotype similar to ARP2, ARP3 and other ;distorted' mutants. Double-mutant analysis revealed a redundancy with AtSCAR4. Systematic application of the yeast two-hybrid system and Bimolecular Fluorescence Complementation (BiFC) revealed a complex protein-interaction network between the ARP2-ARP3 complex and its genetically defined regulators. In addition to protein interactions known in other systems, we identified several new interactions, suggesting that SPIKE1 may be an integral component of the SCAR/WAVE complex and that SCAR proteins in plants might act as direct effectors of ROP GTPases.     

Recovery of late-seral vascular plants in a chronosequence of post-clearcut forest stands in coastal Nova Scotia,Canada

We investigated the impacts of clearcutting on the ground vegetation of remnant late-successional coastal Acadian forests in southwestern Nova Scotia. Vegetation was sampled in 750 1-m² quadrats established in 16 stands belonging to different recovery periods since clearcutting (3–54 years) and 9 late-successional forests (100–165 years) with no signs of significant human disturbance. Our objectives were to: i) describe the changes in species richness, diversity, and abundance of ground vegetation after clearcutting; ii) examine the responses of residual species (i.e., late-successional flora) to clearcutting; and iii) determine whether any forest species were restricted to or dependent upon the late-successional stages of stand development for maximal frequency and/or abundance. Although clearcutting had no immediate impact on overall alpha richness or diversity, the richness and diversity of residual plants declined after canopy removal and showed no evidence of recovery over 54 years of secondary succession. Consequently, compositional differences between secondary and late-seral stands persisted for many decades after clearcutting. Several understory herbs (e.g., Coptis trifolia (L.) , Oxalis montana (L.), Monotropa uniflora (L.)) were restricted to or attained their highest frequency and abundance in late-seral forests. These results suggest that the preservation of remnant old stands may be necessary for the maintenance of some residual plants in highly disturbed and fragmented forest landscapes in eastern Canada.     

The <Emphasis Type="Italic">Arabidopsis</Emphasis><Emphasis Type="Italic">KLUNKER</Emphasis> gene controls cell shape changes and encodes the AtSRA1 homolog

The analysis of a group of seven trichome mutants in Arabidopsis, which all show distorted trichomes along with severe actin defects has revealed insight into the role of the actin cytoskeleton in cell shape control. Four of the corresponding genes encode components of a protein complex, the ARP2/3 complex that stimulates the production of fine actin at active growth sites. In this study, we show that another member of the distorted group, KLUNKER (KLK), encodes the AtSRA1 homolog of Arabidopsis and that klk mutants show a similar range of cell shape defects to those of arp2/3 mutants. In animals, SRA1 regulates the activity of the ARP2/3-regulating WAVE-HSPC300 complex in a Rho-dependent manner. Our findings provide evidence that a Rho/ARP2/3 regulation pathway exists in plants.