Diversity models applied to a chalk grassland

In a permanent plot experiment started in 1971, the effects of several management regimes on diversity of a Dutch chalk grassland have been investigated and the results have been compared to existing models predicting general trends in diversity. Treatments included grazing, mowing, and leaving untouched; in the mown plots, the effects of fertilizing and sod cutting were also studied. Grazing resulted in the highest diversity, leaving untouched in the lowest (ca. 42 and 15 spp. per m², respectively). Within the mown plots, fertilizing decreased diversity. The effects of sod cutting disappeared after some years. The results conform best with the response surface model of Huston (1979) relating diversity to frequency of population reduction and rate of competitive displacement, but a slight modification of the shape of the surface is suggested.Nomenclature follows van der Meijden et al., 1983.The authors are very grateful to Dr J. Miles (Banchory, U.K.) for stimulating remarks and to Prof. Dr. M. J. A. Werger, Dr R. K. Peet and two reviewers for many valuable comments and suggestions.     

Diversity as a measure of benthic macroinvertebrate community response to water pollution

The assumption that water pollution causes a depression in the diversity of benthic macroinvertebrates as measured by the Shannon index and similar diversity indices is questioned. An interpretation of the community response of benthic macroinvertebrates to pollution in the Millers River, Massachusetts is developed from species presence-absence and abundance data in conjunction with published information on the species' environmental tolerances as compared to chemical water quality data. This interpretation is compared with one derived solely from diversity index values. The interpretations are quite different; the differences may be attributed to other environmental factors such as impoundments and flow reductions which influence the fauna and thus the diversity index value, but which are not related to pollution. In addition, several intrinsic features of the diversity indices increase their bias.Contribution No. 47 of the Massachusetts Cooperative Fishery Unit jointly supported by the U.S. Bureau of Sport Fisheries and Wildlife, the Massachusetts Division of Fisheries and Game, the Massachusetts Division of Marine Fisheries, and the University of Massachusetts.     

Patterns of Rodent Species Diversity and Abundance in a Kenyan Relict Tropical Rainforest

Patterns of rodent species abundance and diversity were examined over a 5 months period in two areas of a Kenyan relict tropical rainforest. The two areas are subjected to different administrations which lead to various levels of anthropogenic disturbance: one can be considered relatively disturbed and one relatively undisturbed. Anthropogenic disturbance causes a reduction in woody stem density between 0 and 1.5 m and reduced understory tree canopy cover. Rodent abundance was estimated using the program CAPTURE and compared with the number of individuals actually captured. Density was estimated with three different methods, two of these utilised a boundary strip to estimate effective size of the area trapped. Density resulted in being relatively high in both areas, so population might have been at a peak. Species richness was higher in the disturbed forest, while species diversity and evenness was higher in the undisturbed forest. We suggest that in the disturbed forest the increase in number of species might be due to sporadical entrance in the forest by non-forest species, while the decrease in diversity might be due to the decrease of lower strata vegetation that occurs in the disturbed forest, hence this factor might affect species equitability. Bibliographic data supports this hypothesis as rodent species diversity and ground vegetation cover have been found to be correlated.     

Application of Diversity Indices to Appraise Plant Availability in the Traditional Medicinal Markets of Johannesburg,South Africa

The lack of scientific rigour in analysing ethnobotanical surveys has prompted researchers to investigate ways of quantitatively describing their data, including the use of ecological diversity indices. There are numerous indices and measures available to describe sample diversity. Twenty-two measures of species richness, diversity and evenness were reviewed using six sets of ethnomedicinal data derived from 50 formal muti shop traders (of different ethnicities) and 100 informal street traders of traditional medicine in Johannesburg, South Africa, and a seventh data set from traders on the western boundary of the Kruger National Park, South Africa. The diversity measures were coupled with species accumulation curves to construct cumulative diversity curves used to determine the minimum viable sample size on which a diversity index should be based, and to better understand the differences in the relative diversities of the samples. Distinct differences in the relative abundance and diversity of plants sold by street traders and shop traders were evident. Species diversity and evenness was found to be higher in shops, thus resulting in a lower dominance in the sale of certain plant species compared to the street traders. A survey of an informal market should include no less than 35 research participants compared to no less than 20 for the muti shops. The use of selected indices of species richness (Margalef's), diversity (Shannon, Simpson's, Fisher's alpha, Hill's numbers) and evenness are recommended as a means of describing patterns exhibited within ethnobotanical data.     

Taxonomy, phylogeny, and distribution of Puccinia graminis, the black stem rust: new insights based on rDNA sequence data

Puccinia graminis (Uredinales) is an economically important and common host-alternating rust species on Berberidaceae/Poaceae (subfamilies Pooideae and Panicoideae) that has been spread globally by human activities from an unknown center of origin. To evaluate the taxonomic implications, phylogenetic relationships, and distribution/spread of this complex species, we sequenced and cladistically analyzed the ITS1, 5.8S, and ITS2 regions from herbarium specimens on various host plants from Iran (17), Europe (1), and North America (4). The ITS region plus the 5.8S gene ranged from 686 to 701 bp, including the flanking partial sequences of the 18S and 28S rDNA. Our phylogenetic analysis included 54 bp of the 18S sequence, the entire ITS1 + 5.8S + ITS2, and 58 bp of the 28S sequence. A second analysis used only the last 42 bp of ITS1, and all the 5.8S and ITS2, to incorporate data from additional sequences downloaded from GenBank. In addition to variation in sequence length, there was variation in sequence content. The analysis does not support classical morphology-based taxonomic concepts of the P. graminis complex. Also, host range, host taxonomy, and geographic origin provide minor information on taxonomic relationships. Puccinia graminis is most probably monophyletic. Coevolutionary aspects can hardly be discussed because of lack of sequence data from alternate host specimens. The occurrence of unrelated fungal taxa on the same host species suggests that, besides coevolution with the host, host jumps and hybridization may have played an important role in the evolution of P. graminis. From rDNA data we conclude that the pathogen was introduced to North America at least twice independently. For a new taxonomic concept, we think the complex has to be split into at least two species. New morphological features and further features other than sequence data, however, must be checked for taxonomic value first and, if necessary, be considered.     

Seasonal patterns in a temperate intertidal fish community on the west coast of South Africa

Synopsis Seasonality was investigated in an intertidal ichthyofaunal community on the west coast of South Africa. Fishes were collected monthly from 12 to 16 intertidal pools between May 1992 and May 1993, using the ichthyocide rotenone. On each occasion sampling effort was divided equally between four biologically determined shore zones, namely the cochlear, lower and upper balanoid and littorina zones. A total of 5 409 fishes belonging to 20 species and five families was collected. All fishes were intertidal residents. No seasonal trend could be found in the total density of fishes during the year, the densities of individual species, species diversity or evenness. Thus species composition remained stable over the year. The proportion of mature individuals of each species decreased in summer as a result of recruitment of juveniles at this time. This almost complete lack of seasonality was attributed to the absence of transient species from this community.     

The Neanderthal taxonomic position: models of intra- and inter-specific craniofacial variation

The Neanderthal taxonomic position is a matter of wide disagreement among paleoanthropologists. Some workers consider this fossil human group to represent a different species, Homo neanderthalensis, while others see it as a subspecies of Homo sapiens. This study developed two models of morphological variation to be applied to a comparison between Neanderthals and modern humans: modern human populations provided a measure of intra-specific variation, while the species and subspecies of Pan provided measures of both intra- and inter-specific morphological differences. Although such an approach has been advocated strongly, it has not been systematically undertaken until recently. The techniques of geometric morphometrics were used to collect data in the form of three-dimensional coordinates of craniofacial landmarks. The data were processed using generalized procrustes analysis, and analyzed by an array of multivariate statistical methods, including principal components analysis, canonical variates analysis and Mahalanobis D(2). The morphological distances between Neanderthals and modern humans, and between Neanderthals and Late Paleolithic/early anatomically modern specimens, are consistently greater than the distances among recent human populations, and greater than the distances between the two chimpanzee species. Furthermore, no strong morphological similarities were found between Neanderthals and Late Paleolithic Europeans. This study does not find evidence for Neanderthal contribution to the evolution of modern Europeans. Results are consistent with the recognition of Neanderthals as a distinct species.     

Sensitivity Profiles of Diversity Indices

The author previously described special sensitivity measures for diversity indices. These measures make possible on analytical treatment of the index sensitivity. In the article a detailed analysis of sensitivity properties of the Hurlbert indices is presented. In the first step the abundances n_k were sequenced in an increasing order. Plotting the sensitivity against n_k or log n_k, essential sensitivity properties can be observed. For example, one can study the sensitivities to changes in the dominant and subdominant abundances, the site of the “nearly neutral” abundance and the site of local sensitivity maxima in the domain of the relatively rare categories. The observations are supported by mathematical reasoning.     

Diversity of properties among catalases

Catalases from 16 different organisms including representatives from all three phylogenetic clades were purified and characterized to provide a comparative picture of their respective properties. Collectively the enzymes presented a diverse range of activities and properties. Specific activities ranged from 20,700 to 273,800 units per milligram of protein and maximal turnover rates ranged from 54,000 to 833,000 per second. The effective concentrations of common catalase inhibitors, cyanide, azide, hydroxylamine, aminotriazole, and mercaptoethanol, varied over a 100- to 1000-fold concentration range, and a broad range of sensitivities to heat inactivation was observed. Michaelis-Menten kinetics were approximately followed only at the low substrate concentrations. At high H(2)O(2) concentrations, inactivation of small-subunit enzymes resulted in lower velocities than what were predicted, whereas large-subunit enzymes had velocities higher than predicted. Kinetic constants such as K(m) and V(max) for catalases must be labeled as "apparent."     

A mechanism of dynamical interactions for two-person social dilemmas

We propose a new mechanism of interactions between game-theoretical agents in which the weights of the connections between interacting individuals are dynamical, payoff-dependent variables. Their evolution depends on the difference between the payoff of the agents from a given type of encounter and their average payoff. The mechanism is studied in the frame of two models: agents distributed on a random graph, and a mean field model. Symmetric and asymmetric connections between the agents are introduced. Long time behavior of both systems is discussed for the Prisoner's Dilemma and the Snow Drift games.     

Differential proteomics reveals novel insights into Nosema–honey bee interactions

Host manipulation is a common strategy by parasites to reduce host defense responses, enhance development, host exploitation, reproduction and, ultimately, transmission success. As these parasitic modifications can reduce host fitness, increased selection pressure may result in reciprocal adaptations of the host. Whereas the majority of studies on host manipulation have explored resistance against parasites (i.e. ability to prevent or limit an infection), data describing tolerance mechanisms (i.e. ability to limit harm of an infection) are scarce. By comparing differential protein abundance, we provide evidence of host-parasite interactions in the midgut proteomes of N. ceranae-infected and uninfected honey bees from both Nosema-tolerant and Nosema-sensitive lineages. We identified 16 proteins out of 661 protein spots that were differentially abundant between experimental groups. In general, infections of Nosema resulted in an up-regulation of the bee's energy metabolism. Additionally, we identified 8 proteins that were differentially abundant between tolerant and sensitive honey bees regardless of the Nosema infection. Those proteins were linked to metabolism, response to oxidative stress and apoptosis. In addition to bee proteins, we also identified 3 Nosema ceranae proteins. Interestingly, abundance of two of these Nosema proteins were significantly higher in infected Nosema-sensitive honeybees relative to the infected Nosema-tolerant lineage. This may provide a novel candidate for studying the molecular interplay between N. ceranae and its honey bee host in more detail.     

马先蒿属花冠形态的多样性与传粉式样的关系

马先蒿属(Pediculais)是有花植物中花冠形态多样化最为集中的属。该属主要的传粉者是熊蜂属(Bormbus)昆虫;在北美,熊蜂和蜂鸟是马先蒿植物一些种类有效的传粉者;也发现壁蜂(Osmia)为其传粉。不同的传粉机制要求某一特定的取食式样储藏和释放花粉。本文讨论了花冠类型的进化趋势与传粉式样和花粉形态的关系。传粉者的选择压力是决定花冠多样化的重要因素之一;花冠类型与传粉者和传粉行为紧密相关。马先蒿植物和传粉者的相互依赖与其花冠类型、功能和物候互相适应,但花冠类型与花粉形态两者之间似乎没有明显的一一对应关系。通过北美、日本和喜马拉雅不同地理分布马先蒿种类的比较研究表明,具有相同花冠类型的种类有着相同的传粉方式,花冠形态与传粉式样存在紧密的协同进化关系。     

Optically active gossypol as a circular dichroism probe of interactions with serum albumins

The (+)-enantiomer of the polyphenolic binaphthyl gossypol, has been shown to be a useful CD probe of interactions with human and bovine serum albumin. (+)-Gossypol binds to albumin with same affinity as recemic (±)-gossypol, as shown by fluorescence quenching, and also displaces bilirubin from its albumin binding site. The CD characteristics of bound gossypol are different in the case of the two proteins.     

Benthic fauna species diversity in six central Florida lakes in summer

The summer macroinvertebrate fauna was studied in six central Florida monomictic lakes during July, 1973. No direct relationships were found between physiochemical conditions and species diversity. Of the 22 species of benthic organisms recorded, only four species were found in all the lakes. Mean species diversity (d) values for the lakes ranged from 0.735 to 1.731.     

Protein-protein interactions as a target for drugs in proteomics

Protein-protein interactions play a central role in numerous processes in the cell and are one of the main fields of functional proteomics. This review highlights the methods of bioinformatics and functional proteomics of protein-protein interaction investigation. The structures and properties of contact surfaces, forces involved in protein-protein interactions, kinetic and thermodynamic parameters of these reactions were considered. The properties of protein contact surfaces depend on their functions. The contact surfaces of permanent complexes resemble domain contacts or the protein core and it is reasonable to consider such complex formation as a continuation of protein folding. Characteristics of contact surfaces of temporary protein complexes share some similarities with active sites of enzymes. The contact surfaces of the temporary protein complexes have unique structure and properties and they are more conservative in comparison with active site of enzymes. So they represent prospective targets for a new generation of drugs. During the last decade, numerous investigations were undertaken to find or design small molecules that block protein dimerization or protein(peptide)-receptor interaction, or, on the contrary, to induce protein dimerization.     

Temporal Patterns of Species Accumulation in a Survey of Lepidoptera in a Beech-Maple Forest

One of the most significant challenges to insect conservation is lack of information concerning species diversity and distribution. Because a complete inventory of all species in an area is virtually impossible, interest has turned to developing statistical techniques to guide sampling design and to estimate total species richness within a site. We used two such techniques, diversity partitioning and non-parametric richness estimation, to determine how variation in sampling effort over time affected species accumulation for a survey of Lepidoptera in an old-growth beech-maple forest. Temporal scaling of sampling effort had significant effects on two measures of species diversity. Increases in species richness were primarily driven by changes in species occurrences with season, while Shannon diversity was largely determined at the scale of individual sampling units (i.e. by spatial effects). Variation in sampling effort affected the values of the two most widely regarded richness estimators (ICE and Chao 2); neither diversity estimator achieved stable values across a range of sampling efforts. Even after 52 trap-nights and accounting for seasonality, rare species (singletons and uniques) remained a significant component of the moth community. To the extent that moth communities in other forest systems are similarly comprised of many rare species, non-parametric richness estimators should be expected to yield variable estimates with increased effort and should only be used to provide a minimum benchmark for predicting the number of species remaining to be sampled. Our results suggest the best strategy for a short-term survey of forest Lepidoptera should emphasize spreading sampling intervals throughout a given year rather than focusing on intensive sampling during a short time period or prolonged sampling over many years.     

Topographic Heterogeneity Plays a Crucial Role for Grasshopper Diversity in a Southern African Megabiodiversity Hotspot

Topographic heterogeneity as a determinant of insect diversity pattern has been little studied. Responses of grasshopper assemblages to three hill sizes were assessed in the arid Succulent Karoo, South Africa. This area is one of the world’s 25 hotspots for conservation priorities. Small hills overall were more speciose than medium or large hills. There were also significantly higher densities of small-sized grasshoppers on small hills than on medium or large ones. The slopes of the three hill sizes did not differ significantly either in their species richness or abundance, and there was no significant difference in species richness between summits only of the three hill sizes. Patterns of grasshopper species dominance were markedly variable among sites, but with clear differences between small and larger hills, associated with vegetation characteristics. Vegetation cover and grass cover was less on the small hills. Grasshopper taxonomic groups varied among the three hill sizes, with small hills being taxonomically more diverse, supporting species from four families and nine subfamilies, while medium and large hills only supported Acrididae. It is concluded that topography has a remarkably strong effect on various aspects of grasshopper spatial heterogeneity and that small hills in particular are a major factor to consider in spatial conservation planning.     

Diversity of protein-protein interactions

In this review, we discuss the structural and functional diversity of protein-protein interactions (PPIs) based primarily on protein families for which three-dimensional structural data are available. PPIs play diverse roles in biology and differ based on the composition, affinity and whether the association is permanent or transient. In vivo, the protomer's localization, concentration and local environment can affect the interaction between protomers and are vital to control the composition and oligomeric state of protein complexes. Since a change in quaternary state is often coupled with biological function or activity, transient PPIs are important biological regulators. Structural characteristics of different types of PPIs are discussed and related to their physiological function, specificity and evolution.