Risk Assessment of Transgenic Virus-resistant White Clover: Non-target Plant Community Characterisation and Implications for Field Trial Design

One of the most difficult elements of the ecological risk assessment of transgenic plants is investigation of their potential impact on biodiversity in complex non-target communities. This problem is particularly acute for pasture plants, since many have a track record of invasiveness. In this paper we develop an understanding of some aspects of the ecology of Trifolium repens L. (white clover) in montane vegetation communities in southeastern Australia as part of a larger project investigating potential ecological risks associated with commercial release of newly-developed transgenic virus-resistant T. repens cultivars. We use a combination of floristic surveys and biomass sampling to determine the habitat affinity of T. repens, the structure and composition of associated communities, and the scale at which different abiotic and biotic factors correlate with T. repens abundance. We also compare the abundance of native and exotic species within specific morpho-functional groups and use this to determine the relative significance of T. repens as a community constituent, and to identify native species that would be most at risk by expanding populations of T. repens. We found that T. repens comprises a relatively small component of the total community cover and biomass, but is one of the most abundant herbaceous species in mesic Poa – dominated grasslands and Poa-Eucalyptus woodlands in the study area, and that T. repens abundance is correlated at the within-community scale primarily with soil moisture and fertility. At smaller scales T. repens is limited by the hierarchical dominance of native graminoids and we conclude that competition for inter-tussock space in mesic communities is the most likely mechanism by which expanding populations of T. repens would influence populations of associated native species. These results have significant implications for the manner in which future analysis and risk quantification stages of the risk assessment of virus-resistant T.␣repens and other transgenic pasture plants in complex plant communities are performed.     

Describing the organization of dominance relationships by dominance-directed tree method

Methods to describe dominance hierarchies are a key tool in primatology studies. Most current methods are appropriate for analyzing linear and near-linear hierarchies; however, more complex structures are common in primate groups. We propose a method termed "dominance-directed tree." This method is based on graph theory and set theory to analyze dominance relationships in social groups. The method constructs a transitive matrix by imposing transitivity to the dominance matrix and produces a graphical representation of the dominance relationships, which allows an easy visualization of the hierarchical position of the individuals, or subsets of individuals. The method is also able to detect partial and complete hierarchies, and to describe situations in which hierarchical and nonhierarchical principles operate. To illustrate the method, we apply a dominance tree analysis to artificial data and empirical data from a group of Cebus apella.     

Coexistence and divergence of tropical dry forests and savannas in southern Mexico

Aim The purpose of the study was to assess the degree of floristic differentiation between tropical dry forest (TDF) and savanna occurring in a single landscape. This comparison provides information on the responses of vegetation to the prevailing environmental conditions, while it also allows us to make inferences about large‐scale events and processes, both biogeographical and evolutionary. Our approach included three levels of analysis: (1) taxonomic, (2) morphological and (3) vegetational. Location The seasonal dry tropical landscape in the Nizanda region, Oaxaca State, southern Mexico. The landscape comprises a complex vegetation mosaic in which tropical dry forest and savannas are the most conspicuous components. Methods Comparisons between TDF and savanna were based on inventories for these communities produced after 8 years of botanical survey. At the taxonomic level, the relative representation of taxa of different hierarchical levels in each community was examined. Morphological analyses required the classification of species on each of three criteria: (1) growth form, (2) life form and (3) growth habit. Vegetation level analysis was based on the frequencies of taxa in one hundred 100‐m² composition plots with which matrices of binary data were constructed for species, genera and families. These were subjected to classification analysis with Ward's method and using Euclidean distances as the dissimilarity algorithm. Results The combined flora for both communities comprised 600 species, 375 genera and 94 families; between them they shared 31, 40 and 34 taxa, respectively. The corresponding Sørensen similarity values were 10%, 21% and 72%, respectively. Ranking genera and families according to their species richness displayed large differences between savanna and TDF. Large differences between these communities were observed for Acanthaceae, Cactaceae, Euphorbiaceae and Mimosaceae, whereas Fabaceae and Asteraceae had similar high ranks according to the species richness in the two systems. The growth form spectrum diverged between the two communities, with TDF having more trees, shrubs and climbers. Savanna was characterised by forbs and graminoid herbs. Growth habit spectra revealed a clear dominance of herbaceous and suffruticose plants in savanna, and of woody elements and epiphytes in TDF. Regarding Raunkiaer's life forms, savanna had relatively more hemicryptophytes, and TDF more phanerophytes. Classification analyses showed that savanna and TDF forest samples kept their identities, regardless of taxonomic level (species, genera and families) at which the analyses were performed. Main conclusions The TDF and savanna of Nizanda represent two floristic systems with a large degree of differentiation at all taxonomic levels and patterns of morphological attributes. This suggest that the two floristic sets have evolved independently for extended periods of time, despite their close proximity. One important implication of this floristic differentiation is the large joint contribution made by these communities to the regional flora.     

Hormonal correlates of reproductive status in the queenless ponerine ant, Streblognathus peetersi

In colonies of the queenless ant Streblognathus peetersi, dominance interactions produce a reproductive hierarchy in which one individual, the alpha, is capable of producing offspring while her subordinates remain infertile. Based on differences between behaviour and cuticular hydrocarbon profiles, the subordinates can be further divided into high and low ranking workers. Although it had been shown previously that alphas treated with a juvenile hormone analog lose their reproductive status, little was known of the endocrinological basis of dominance in this species. To elucidate the underlying endocrinology of these three ranks, we measured the individual in vitro rate of juvenile hormone (JH) production of excised corpora allata, and the ecdysteroid titer of pooled hemolymph samples. Production of JH was highest in low-ranking workers, intermediate in high rankers, and almost undetectable in alphas. Ecdysteroid titers were low for low rankers, but were more than twice as high for both high rankers and alphas. The results support the hypothesis that JH suppresses ovarian function in these queenless ants, and suggest that ecdysteroids may be responsible for stimulating vitellogenin production. The possible role of these hormones as behavioural modulators is also discussed.     

Goodness-of-fit diagnostics for Bayesian hierarchical models

This article proposes methodology for assessing goodness of fit in Bayesian hierarchical models. The methodology is based on comparing values of pivotal discrepancy measures (PDMs), computed using parameter values drawn from the posterior distribution, to known reference distributions. Because the resulting diagnostics can be calculated from standard output of Markov chain Monte Carlo algorithms, their computational costs are minimal. Several simulation studies are provided, each of which suggests that diagnostics based on PDMs have higher statistical power than comparable posterior-predictive diagnostic checks in detecting model departures. The proposed methodology is illustrated in a clinical application; an application to discrete data is described in supplementary material.     

A simulation study of mutations in the genetic regulatory hierarchy for butterfly eyespot focus determination

The color patterns on the wings of butterflies have been an important model system in evolutionary developmental biology. A recent computational model tested genetic regulatory hierarchies hypothesized to underlie the formation of butterfly eyespot foci [Evans, T.M., Marcus, J.M., 2006. A simulation study of the genetic regulatory hierarchy for butterfly eyespot focus determination. Evol. Dev. 8, 273-283]. The computational model demonstrated that one proposed hierarchy was incapable of reproducing the known patterns of gene expression associated with eyespot focus determination in wild-type butterflies, but that two slightly modified alternative hierarchies were capable of reproducing all of the known gene expressions patterns. Here we extend the computational models previously implemented in Delphi 2.0 to two mutants derived from the squinting bush brown butterfly (Bicyclus anynana). These two mutants, comet and Cyclops, have aberrantly shaped eyespot foci that are produced by different mechanisms. The comet mutation appears to produce a modified interaction between the wing margin and the eyespot focus that results in a series of comet-shaped eyespot foci. The Cyclops mutation causes the failure of wing vein formation between two adjacent wing-cells and the fusion of two adjacent eyespot foci to form a single large elongated focus in their place. The computational approach to modeling pattern formation in these mutants allows us to make predictions about patterns of gene expression, which are largely unstudied in butterfly mutants. It also suggests a critical experiment that will allow us to distinguish between two hypothesized genetic regulatory hierarchies that may underlie all butterfly eyespot foci.     

Forest vegetation across the tropical Pacific: A biogeographically complex region with many analogous environments

The tropical realm of the Pacific contains many islands with closely similar (analogous) environmental settings. Due to the `filter effect' of the ocean, these are occupied by historically different species assemblages. This results in a unique biogeographic complexity not found in any of the continental tropical regions. The paper presents a hierarchical approach to the study of vegetation in analogous environments with data illustrated by a series of diagrams. It begins with differentiating island types and climatic zones. Then it focuses on Pacific-wide biomes, thereafter on island landscape profiles, and finally, on stand-level profiles as a method to compare forest structure and composition among islands in analogous environments at the scale of relevés. The conclusions emphasize the urgent need for intensifying conservation-oriented research and capacity building in all island countries of the Pacific (not only Hawaii) to protect their indigenous biodiversities for sustainable uses and the health of their ecosystems. Attention is also drawn to the scientific advantage of using the Pacific-Asia Biodiversity Transect (PABITRA) Network, since it connects the island areas across biogeographic boundaries in form of an experimental design. This design refers to analogous island environments filled with different sets of biodiversities, which follow a trend of impoverishment with indigenous founder species from west to east.     

Spatial and Temporal Considerations in Restoring Habitat for Wildlife

An accumulated body of theory and empirical evidence suggests that habitat selection by animals is a scale‐dependent, hierarchical process. Hierarchy theory predicts that habitat suitability is influenced by the interaction of factors at multiple spatial scales from the microsite to the landscape and that higher‐order factors impose constraints at lower levels. For instance, large‐scale factors such as landscape context may make a site unsuitable for a species even if the vegetation structure and composition are appropriate. In addition, the spatial arrangement of habitat elements at all scales must be considered when planning restoration efforts. For example, the presence of snags does not ensure that the site will be suitable for snag‐dependent species. The size, age, and spacing of snags and their juxtaposition to other habitat elements must also be considered. Finally, all habitats are dynamic, and therefore the ecological processes that contribute to those dynamics must be maintained or suitable substitutes included in the recovery plan. When considering restoring habitat for wildlife, we recommend that managers: (1) identify the wildlife species they want to target for restoration efforts, (2) consider the size and landscape context of the restoration site and whether it is appropriate for the target species, (3) identify the habitat elements that are necessary for the target species, (4) develop a strategy for restoring those elements and the ecological processes that maintain them, and (5) implement a long‐term monitoring program to gauge the success of the restoration efforts.     

Interspecific interactions among species of the coral genus Porites from Okinawa, Japan

Analysis of field established xenogeneic interactions among five Porites species from Sesoko Island, Okinawa, revealed a transitive type of hierarchy as: P. rus > P. cylindrica > P. lobata > P. australiensis> P. lutea. Out of the 111 interspecific encounters studied, in only 5.4% reciprocal interactions were recorded, and in a single case, the opposite directionality of hierarchy was documented. Allogeneic encounters were also observed. A single major effector mechanism, an overgrowth (together with secondary outcomes such as the formation of small points of rejection, bleaching and pink color formation along a narrow peripheral belt of contacting tissues), was the only response in all 10 xenogeneic and 5 allogeneic combinations. In some massive colonies, a long contacting line of up to 50 cm was established. No sign for allelopathy, stand-off or rejection from a distance (i.e., by sweeper tentacles, sweeper polyps) was observed. Results are discussed with the accumulated data on Porites species from different reefs, worldwide, confirming that this genus is commonly lower in the hierarchy of xenogeneic interactions.