Upward shift of alpine plants increases floristic similarity of mountain summits

Question: Does the upward shift of species and accompanied increase in species richness, induced by climate change, lead to homogenization of Alpine summit vegetation? Location: Bernina region of the Swiss Alps. Methods: Based on a data set from previous literature we expand the analysis from species richness to beta‐diversity and spatial heterogeneity. Species compositions of mountain summits are compared using a two‐component heterogeneity concept including the mean and the variance of Sørensen similarities calculated between the summits. Non‐metric multidimensional scaling is applied to explore developments of single summits in detail. Results: Both heterogeneity components (mean dissimilarity and variance) decrease over time, indicating a trend towards more homogeneous vegetation among Alpine summits. However, the development on single summits is not strictly unidirectional. Conclusions: The upward shift of plant species leads to homogenization of alpine summit regions. Thus, increasing alpha‐diversity is accompanied by decreasing beta‐diversity. Beta‐diversity demands higher recognition by scientists as well as nature conservationists as it detects changes which cannot be described using species richness alone.     

A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium perenne L.) varieties

A sample set of registered perennial ryegrass varieties was used to compare how morphological characterisation and AFLP^® (AFLP^® is a registered trademark of Keygene N.V.) and STS molecular markers described variety relationships. All the varieties were confirmed as morphologically distinct, and both the STS and AFLP markers exposed sufficient genetic diversity to differentiate these registered ryegrass varieties. Distances obtained by each of the approaches were compared, with special attention given to the coincidences and divergences between the methods. When correlations between morphological, AFLP and STS distances were calculated and the corresponding scatter-plots constructed, the variety relationships appeared to be rather inconsistent across the methods, especially between morphology and the molecular markers. However, some consistencies were found for closely related material. An implication could be that these molecular-marker techniques, while not yet suited to certain operations in the traditional registration of new varieties, could be suitable methods for investigating disputable distinctness situations or possible EDV (EDV= essentially derived variety. An EDV is a variety being clearly distinct from, but conforming in the expression of the essential characteristics of, an ’initial variety’ (IV) from which it is found to have been predominantly derived) relationships, subject to establishing standardised protocols and statistical techniques. Some suggestions for such a protocol, including a statistical test for distinctness, are given.     

Reconsidering locomotor habits and life style of the Balearic insular giant rodent Hypnomys Bate, 1918 from the allometry of the limb long bones

The genus Hypnomys Bate, 1918 includes some endemic Neogene chronospecies from Mallorca and Menorca, evolved in insularity conditions from the Lower Pliocene to the human arrival at the archipelago. The study of the allometric proportions (functional length and sagittal diameter) of the limbs’ long bones of Hypnomys eliomyoides Agusti, 1980 (Lower Pleistocene of Menorca), Hypnomys sp. (Pleistocene of Menorca), Hypnomys onicensis (Reumer, 1994) (Upper Pliocene-Lower Pleistocene of Mallorca) and Hypnomys morpheus Bate, 1918 (Upper Pleistocene of Mallorca) only indicates small differences with the garden dormouse (Eliomys quercinus Linnaeus, 1776) and other mainland rodents and insectivores. The study about the locomotion type by means of Similarity Matrix of Bou indicates that 1) Hypnomys spp. presents the greater similarities with the arboreal, jumping and gliding species; 2) the jumping and digging life style of Hypnomys spp. are more developed (25%) than in E. quercinus; 3) the walking locomotion of Hypnomys spp. is only a 7% greater than in E. quercinus; and 4) the degree of similarity with the gliding locomotion of Hypnomys sp. is greater (17%) than in E. quercinus. Some of this data indicates that Hypnomys spp. was better adapted to the arboreal life than E. quercinus, due to the relationship between the jumping and gliding capacities with the arboreal locomotion. The greater similarity of Hypnomys spp. with the walking locomotion does not necessarily involve more terrestrial habits. Our interpretation contrasts with earlier conclusions of Hypnomys life style (Hypnomys cf. onicensis and Hypnomys morpheus) where the terrestrial locomotion was overestimated in front of the arboreal locomotion. The locomotion type of Hypnomys would be related with the presence of important forest masses on the Balearic Islands during the Neogene, a different degree of environmental stress from that of the mainland ecosystems and a probable expansion of the ecological niche occupied by these species.     

Dissimilarity for partially ranked data and its application to cover-abundance data

Cover-abundance estimates are commonly employed in phytosociological investigations to record the performance of species. Because the coded values are on an ordinal scale of measure, various authors have suggested that some transformation is necessary before such values can be used for classification and ordination. However, it is not clear that transformation is a sufficient treatment, and it would seem preferable to use ordinal data directly. In this paper we examine such direct use of partial rankings and show that several dissimilarity measures can be defined for this case without invoking any transformations. They include dissimilarity measures associated with various rank correlation measures and with distances between strings; all the measure are variant forms of Hausdorf's interset distance. Certain other kinds of data, such as those employing dominant and subdominant species and the dry-weight-rank estimation of biomass, are also on an ordinal scale and could be analysed using similar techniques.To illustrate the approach, a string dissimilarity measure is used to analyse a set of data from Slovakian grasslands which appear to reflect a simple gradient. The original data were recorded with 10 classes of performance and are analysed using hierarchical and nondeterministic, overlapping, classifications.     

Anthropogenic disturbances and plant biodiversity in forests of Uttaranchal,central Himalaya

Eight forest types varying in disturbance frequencies were identified along an elevational gradient in Uttaranchal, central Himalaya. Low elevation forests were close to human habitation and had high disturbance frequency, while high elevation forests were situated far from the human habitation and had low disturbance. The dominant tree species at low elevation were Pinus roxburghii and Quercus leucotrichophora, while Q. floribunda and Q. semecarpifolia dominated the high elevation forests. Pyracantha crenulata was the shrub present in all the forests except in Q. semecarpifolia forest and Anaphalis contorta, a herb species, was present in all the forests. Disturbance decreased the dominance of single species and increased the plant biodiversity by mixing species of different successional status. Species richness and diversity for all the vegetation layers were higher in low elevation–high disturbance forests. Mean tree density decreased from high to moderate and increased in low disturbance. The shrub density decreased from high to low disturbance while the reverse occured for herbs. High proportion of early successional species in disturbed forests indicated that disturbance induces succession. The mean number of young individuals increasing from high to low disturbance indicates that disturbance adversely affects regeneration. But, however, the high number of young individuals of Coriaria nepalensis, a small non-leguminous nitrogen fixing tree, in disturbed forests shows that the forest is regenerating. This species could be helpful in the re-establishment of original vegetation through triggering the regeneration of these forests. High elevation–low disturbed forests separated from low elevation–high disturbed forests. Forest type and elevation may have more influence on tree richness while shrub and herb richness may be more sensitive to disturbance and forest types.     

Seedling regeneration,environment and management in a semi‐deciduous African tropical rain forest

Questions: How is seedling regeneration of woody species of semi‐deciduous rain forests affected by (a) historical management for combinations of logging, arboricide treatment or no treatment, (b) forest community type and (c) environmental gradients of topography, light and soil nutrients? Location: Budongo Forest Reserve, Uganda. Methods: Seedling regeneration patterns of trees and shrubs in relation to environmental factors and historical management types were studied using 32 0.5‐ha plots laid out in transects along a topographic gradient. We compared seedling species diversity, composition and distribution patterns along topographic gradients and within types of historical management regimes and forest communities to test whether environmental factors contributed to differences in species composition of seedlings. Results: A total of 85 624 woody seedlings representing 237 species and 46 families were recorded in this rain forest. Cynometra alexandri C.H. Wright and Lasiodiscus mildbraedii Engl. had high seedling densities and were widely distributed throughout the plots. The most species‐rich families were Euphorbiaceae, Fabaceae, Rubiaceae, Meliaceae, Moraceae and Rutaceae. Only total seedling density was significantly different between sites with different historical management, with densities highest in logged, intermediate in logged/arboricided and lowest in the nature reserve. Forest communities differed significantly in terms of seedling diversity and density. Seedling composition differed significantly between transects and forest communities, but not between topographic positions or historical management types. Both Chao‐Jaccard and Chao‐Sørensen abundance‐based similarity estimators were relatively high in the plot, forest community and in terms of historical management levels, corroborating the lack of significant differences in species richness within these groups. The measured environmental variables explained 59.4% of variance in seedling species distributions, with the three most important being soil organic matter, total soil titanium and leaf area index (LAI). Total seedling density was positively correlated with LAI. Differences in diversity of >2.0 cm dbh plants (juveniles and adults) also explained variations in seedling species diversity. Conclusions: The seedling bank is the major route for regeneration in this semi‐deciduous tropical rain forest, with the wide distribution of many species suggesting that these species regenerate continuously. Seedling diversity, density and distribution are largely a function of adult diversity, historical management type and environmental gradients in factors such as soil nutrient content and LAI. The species richness of seedlings was higher in soils both rich in titanium and with low exchangeable cations, as well as in logged areas that were more open and had a low LAI.     

Inference of functional properties from large-scale analysis of enzyme superfamilies

As increasingly large amounts of data from genome and other sequencing projects become available, new approaches are needed to determine the functions of the proteins these genes encode. We show how large-scale computational analysis can help to address this challenge by linking functional information to sequence and structural similarities using protein similarity networks. Network analyses using three functionally diverse enzyme superfamilies illustrate the use of these approaches for facile updating and comparison of available structures for a large superfamily, for creation of functional hypotheses for metagenomic sequences, and to summarize the limits of our functional knowledge about even well studied superfamilies.     

Patterns of floristic diversity in semi-natural coastal vegetation of Lebanon and implications for conservation

The current understanding of the status of the vegetation in Lebanon is largely derived from herbarium data and associated floristic studies produced by early 20th century field botanists. In common with other areas in the Mediterranean, the Lebanese coastline is highly threatened by unregulated development, yet current patterns of species richness along the Lebanese coastal zone are little studied. The objective of this study was to assess the floristic richness of the Lebanese coastal zone and to provide baseline information for conservation planning. For this purpose, permanent sample plots (6m×100m) were established in 26 selected vegetation communities in coastal habitats. Monthly field collections of plant specimens were undertaken between October 1999 and July 2000. A total of 441 species were collected and identified. None of the recorded species are currently considered globally threatened, but two are Lebanese endemics (Matthiola crassifolia Boiss. & Gaill., Origanum ehrenbergii Boiss.). Species richness varied between communities, ranging from six species in a littoral limestone pavement community to 113 in an abandoned terrace community. The similarity between communities, based on Sorensen indices, was low and a large number of species were recorded only once. Cluster analysis showed a grouping of different communities within locations in some instances and the clustering of similar community types regardless of location in others. Species richness in riparian and littoral communities consisted mostly of habitat non-specific species. The low community similarity, patchy species distribution, and predominance of habitat non-specific species all point to the need to complement in situ conservation measures with ex situ conservation.     

Fungal endophyte communities in above- and belowground olive tree organs and the effect of season and geographic location on their structures

Studies comparing fungal endophytes between above- and belowground woody crop organs and the factors that may structure their communities are lacking. Due to its great impact on the Mediterranean Basin, the olive tree was chosen for the isolation of endophytic fungi from roots, leaves and twigs in two seasons in north-eastern Portugal. Nine hundred seventy-six isolates belonging to 38 fungal species were obtained. Phomopsis columnaris, Fusarium oxysporum and Trichoderma gamsii were the most frequently isolated, collectively representing 69% of the isolates. Fungal diversity in the roots was higher than in the aboveground organs and higher in spring than autumn. Endophyte community similarity between the above- and belowground organs and between seasons was low. Species composition also varied spatially, with the fungal composition of the roots varying more among locations than that of the aboveground organs. Our results suggest olive tree endophyte community structure is affected by plant organ, location and season.     

Development of a pharmacophore model for the catecholamine release-inhibitory peptide catestatin: Virtual screening and functional testing identify novel small molecule therapeutics of hypertension

The endogenous catecholamine release-inhibitory peptide catestatin (CST) regulates events leading to hypertension and cardiovascular disease. Earlier we studied the structure of CST by NMR, molecular modeling, and amino acid scanning mutagenesis. That structure has now been exploited for elucidation of interface pharmacophores that mediate binding of CST to its target, with consequent secretory inhibition. Designed pharmacophore models allowed screening of 3D structural domains. Selected compounds were tested on both cultured catecholaminergic cells and an in vivo model of hypertension; in each case, the candidates showed substantial mimicry of native CST actions, with preserved or enhanced potency and specificity. The approach and compounds have thus enabled rational design of novel drug candidates for treatment of hypertension or autonomic dysfunction.