Plant species diversity in abandoned coppice forests in a temperate deciduous forest area of central Japan

We investigated plant species diversity as it related to stand structure and landscape parameters in abandoned coppice forests in a temperate, deciduous forest area of central Japan, where Fagus crenata was originally dominant. The species occurring in the study plots were classified into habitat types based on a statistical analysis of their occurrence bias in particular habitats (e.g., primary forest, coniferous plantation) in the landscape studied. The relationships between stand structure, which reflected the gradient of management, and forest floor plant species diversity (H and J) and richness (number of species per unit area) were not significant. However, these factors did influence the forest floor plant composition of the different types of habitat. According to the multiple regression analysis, species diversity and the richness of forest floor plants was affected by landscape parameters rather than by stand structure. For trees, species richness was mainly affected by the relative dominance of F. crenata, which is one of the stand structure parameters that decreases with intensive management. This is probably because many of the tree species that are characteristic of coppice forests increase after F. crenata have been eliminated by management; these species are not dominant in the original forest, where they are suppressed by F. crenata, the shade-tolerant dominant species. The species diversity (H and J) of trees was positively correlated with some landscape parameters, including the road density around the study plot, which may be associated with the intensity of management activity. The number of disturbance-tolerant species increased with increasing road density. Stand structure mainly affected disturbance-intolerant forest floor plant species and disturbance-tolerant tree species. Thus, the species diversity responses differed between forest floor plants and trees. The impact of forest management on species diversity was more prominent for forest floor plants.     

Species diversities analyzed by density and cover in an early volcanic succession

To evaluate alpha diversities, various variables such as density, cover, volume, and weight have been used. However, density is often a distinct variable from the remaining three. To clarify differences in diversity measured by those two kinds of variables, the data collected in fourteen 2×5 m permanently-marked plots on Mount Usu, Japan, which erupted during 1977 and 1978 in growing seasons from 1983 to 1989 was analyzed, using Shannon's species diversity (H) that is represented as a result of combination of species richness and evenness (J). H and J were evaluated by density (density H and J) and cover (cover H and J). Cover H and J were significantly lower than density H and J, indicating that cover H has different characteristics from density H. Those differences are due to differences in evenness, because species richness is the same. The rank orders of species density are different from those of cover. The predominance of a few perennial herbs greatly decreases cover evenness, while seedling establishment success influences density evenness. Therefore, I propose that, during the early stages of succession on harsh environments such as volcanoes, density diversity represents seedling establishment success rate while cover diversity expresses vegetative reproduction success rate.     

Influence of resource abundance on the structure of the insect community attracted to fermented tree sap

There has been little or no documentation of the insect community attracted to fermented tree sap, despite our familiarity with it. This study describes the influence of resource abundance (exudate quantity) on species richness, insect abundance, and diversity at the patch level in order to elucidate the mechanisms responsible for community structure. Resource abundance was positively correlated with species richness and insect abundance, negatively correlated with the equitability index (J), and not significantly correlated with diversity (Simpsons index of diversity; 1/D). Both correlation analyses and canonical correspondence analysis based on taxonomic categories indicated that responses to resource abundance were much greater in parasitoid wasps (Ichneumonoidea), drosophilid flies (Drosophilidae), and rove beetles (Staphylinidae). Field experiments showed that patches with more of the resource had greater species richness and greater hornet abundance. These results indicate that resource abundance is an important factor that affects community structure at the patch level, although it does not influence diversity directly, due to differences in the response to a resource across subgroups; drosophilid flies, the most abundant group that was heavily dependent on tree sap, make an especially large contribution to the change in J. Various factors influence the variation in the response to resource abundance, including population size, feeding habits, and resource utilization patterns (i.e. whether the species uses patches as habitat).     

Oscillations in density and diversity ofPisidium communities in two biotopes in Southern Poland

Summary From September 1979 to October 1980 in two types of biotopes (in the stream at Kali and in the Biaa Przemsza River near Jaroszowiec, southern Poland)P.amnicum, P.milium, P.subtruncatum, P.nitidum, P.personatum, P.casertanum andP. sp.non det. were found.P.amnicum was accepted as an indicator species for the river community, andP.milium for the stream. The irregular changes of species composition of the sphaeriid community in the stream at Kali are rather accidental and the only temporary occurrence ofP.nitidum, P.personatum andP. sp.non det. in the Biaa Przemsza River might be connected with seasonal migration.The dominance structure of thePisidium community in the stream agrees with the model described by CONNELL (1977) for the communities of large sedentary animals and plants. The dominance relations in the river community are similar to the situation described by CONNELL (1977) as characteristic for small lakes and islands.The density of the Sphaeriidae on the chosen habitat in the Biaa Przemsza River oscillated between 300 and 3.300 ind./m² and it reached almost 130.000 ind./m² in the stream at Kali.The SHANNON-WIENER's diversity index (H) and that of equitability or evenness of species abundances (J) had low values during the whole period of investigation.This study was performed as part of the Problem MRII/15 of the Polish Academy of Sciences.     

Spatial patterns and ecology of benthic communities on a high-latitude South Florida (Broward County,USA) reef system

High-latitude reef communities consisting of typical Caribbean fauna of variable composition and density exist on four parallel ridges at varying depths along the Broward County (Florida, USA) coast. Two of these ridges, at 7–13 and 15–30 m in depth, are drowned early Holocene coral reefs of 5 and 7 ky uncorrected radiocarbon age. In this study, community data were collected on each reef using 50-m, line-intercept transects. Using multivariate non-metric statistics, the data show distinct differences in benthic community structure across several spatial gradients. Diversity indices revealed that while all values were low, species diversity (H) was consistent throughout the county, and species richness (d) and evenness (J) increased along a north-south gradient. Scleractinian coral (27 species) cover was low (<6%) in all areas, and Montastrea cavernosa dominated as the major hermatypic scleractinian. Notably absent was the major Caribbean reef-builder Acropora palmata. A rich alcyonacean fauna was present on all studied reefs, and these were typically the most important faunal group determining community structure. Although during the 2-year period 2000–2002 mean water temperatures never fell below 20 °C, scleractinia were small in size.     

Stand structure and woody species diversity in relation to stand stratification in a subtropical evergreen broadleaf forest, Okinawa Island

Stand structure and woody species diversity in a subtropical evergreen broadleaf forest grown in a silicate habitat, Okinawa Island, have been investigated on the basis of stand stratification. The forest stand consisted of four layers. The floristic composition of the top and the lower three layers was only slightly similar, although approximately one-third of the species were common to them. Mean tree weight decreased from the top toward the bottom layer whereas tree density increased from the top downward. This trend resembled the mean weight–density trajectory of self-thinning plant populations. The relationship between mean tree height and tree density for the upper two layers supported Yamakuras quasi –1/2 power law of tree height. The values of the Shannon–Wiener index, H, and the equitability index, J, tended to increase from the top layer downward except for the bottom layer. The values of H and J were, respectively, 4.83 bit and 0.82 for trees taller than 0.10 m. The lower layers contained many species of smaller height. High species diversity of the forest depended on small trees in the lower layers. Conservation of small trees in the lower layers, especially the bottom layer, is indispensable for sound maintenance of Okinawan evergreen broadleaf forests.     

Hard-coral distribution and cold-water disturbances in South Florida: variation with depth and location

Line transects were used to sample the structure and diversity of the hermatypic coral community (Scleractinia) on four shallow shelf-edge reefs in South Florida (25° 22N to 25° 29N). Low diversities, cover and abundance indicated that this area was a suboptimum habitat for reef-building corals. The lack of acroporids on the shallow fore-reef, the increase in total coral cover with depth and the greater abundance of Montastrea annularis in the deepest zones suggests that cooling of surface water during severe winter cold fronts is a major environmental control on the distribution of hermatypic corals with depth. Such disturbances, occurring more frequently than hurricanes, may preclude the hard-coral community from attaining higher levels of cover and abundance. The shallow zones on the reefs nearest to tidal passes, through which cooled by water enters the reef tract, had the least developed community. In the deeper reef-zones, species richness and abundance increased from north to south over a distance of 13 km.     

Spatial distribution of species diversity indices and their correlation with plot size

In a physiognomically uniform Leucobryo-Pineteum phytocoenose the spatial pattern of point diversity was determined and the effect of quadrat size on the assessment of alpha diversity (in Whittaker's, 1977, sense) was analysed. In both cases the Shannon index of total species diversity and the evenness index were used to measure diversity. A contagious spatial pattern of point diversity and a high variation of point diversity values, as well as a strong non-linear dependence of H and J values on quadrat size, and also a decrease in H and J variation with an increase in quadrat size were found.Nomenclature follows Ehrendorfer (1973). Liste der Gefässpflanzen Mitteleuropas.     

Microbiological synthesis of 5-ethyl- and (E)-5-(2-bromovinyl)-2′-deoxyuridine

Summary The title compounds were prepared by an enzymatic transdeoxyribosylation from 2 dGuo or 2 dThd to the respective heterocyclic bases, 5-ethyluracil and (E)-5-(2-bromovinyl)uracil, using the whole bacterial cells ofEscherichia coli as a biocatalyst.     

Cursorial spiders and succession: age or habitat structure?

Summary The structure of cursorial spider assemblages was examined along a gradient of four temperature successional communities. Species diversity (H), richness (S), and evenness (J) exhibited a dichotomy between herbaceous and woody communities rather than a progressive change with community age: all three parameters were higher in the two younger fields than in the two older woodlands, which is contrary to conventional successional theory. Species importance curves were steeper in the two woody communities. The breadth of the distribution of adult body lengths was greater in the two herbaceous communities. Indices of community similarity revealed neither a successional trend nor the vegetative dichotomy. We suggest the hypothesis that habitat structure is a more important determinant of cursorial spider diversity than successional age per se, and that the switch in dominance from herbaceous to woody vegetation is the critical change. We further suggest that competition for prey is more important to cursorial spiders in early successional (herbaceous) communities, because of a switch in the limiting resource from prey in these communities to the amount of accumulating litter (a spatial resource) in older woody stands. This may explain the greater variation in adult body size of these generalist predators in the two younger communities.     

Snake communities of moist rainforest and derived savanna sites of Nigeria: biodiversity patterns and conservation priorities

The taxonomic composition and the abundance of two communities of snakes were studied in two different areas of southern Nigeria. One community was studied in a derived savanna area (environs of Ejule, 06°54N, 07°23E), and one community was studied in a moist rainforest area (environs of Eket, 04°50N, 07°59E). Both the specific diversity and the mean frequency of observation of snakes were significantly higher in the forest area than in the savanna area, and the dominance index was higher in the savanna than in the forest site. However, most of the species were found in only one of the two areas, depending on their habitat requirements (e.g. Gastropyxis smaragdina, Dispholidus typus, Thelotornis kirtlandii, Dendroaspis jamesoni, Bitis nasicornis, Causus maculatus, etc). The forest community housed a significant number of arboreal and semiaquatic taxa, but in both sites most of the species were terrestrial. The commonest species in the forest area was an oviparous, semiaquatic, batracophagous natricine snake (Afronatrix anoscopus), whereas the commonest species in the savanna area was an oviparous terrestrial lacertophagous psammophine snake (Psammophis phillipsi). Some conservation implications of our biodiversity analyses are presented. It is suggested that the moist rainforest represents a critically endangered habitat, and should deserve special attention by the international scientific community. Oil industry activity is especially dangerous for snake communities, especially in the southernmost regions of Nigeria.     

Candidate gene analysis of anthocyanin pigmentation loci in the<Emphasis Type="Italic"> Solanaceae</Emphasis>

Crop species in the Solanaceae, which includes tomato (Lycopersicon esculentum), potato (Solanum tuberosum), pepper (Capsicum spp.), and eggplant (S. melongena), exhibit natural variation in the types, levels, and tissue-specific expression patterns of anthocyanin pigments. While the identities of the genes underpinning natural variation in anthocyanin traits in these crops are largely unknown, many structural genes and regulators of anthocyanin biosynthesis have been isolated from the solanaceous ornamental species Petunia. To identify candidate genes that may correspond to loci controlling natural variation in the four crops, 13 anthocyanin-related genes were localized on a tomato F₂ genetic map. Gene map positions were then compared to mapped mutants in tomato and through comparative genetic maps to natural variants in potato, eggplant, and pepper. Similar map positions suggest that the tomato mutants anthocyaninless, entirely anthocyaninless, and anthocyanin gainer correspond to flavonoid 35-hydroxylase (f35h), anthocyanidin synthase, and the Petunia Myb domain trancriptional regulatory gene an2, respectively. Similarly potato R, required for the production of red pelargonidin-based pigments, P, required for production of purple delphinidin-based pigments, and I, required for tissue-specific expression in tuber skin, appear to correspond to dihydroflavonol 4-reductase, f35h and an2, respectively. The map location of an2 also overlaps pepper A and eggplant fap10.1, lla10.1, lra10.1, sa10.1, pa10.1 and ca10.1, suggesting that a homologous regulatory locus has been subjected to parallel selection in the domestication of many solanaceous crops. To test the hypothesis that tomato anthocyaninless corresponds to f35h, a portion of the gene was sequenced. A premature stop codon was observed in an anthocyaninless mutant, but not in wild-type.Communicated by H.F. Linskens     

A novel PH-CT-COSY methodology for measuring JPH coupling constants in unlabeled nucleic acids. Application to HIV-2 TAR RNA

A quantitative analysis of J_PH scalar couplings in nucleic acids is difficult due to small couplings to phosphorus, the extreme overlap of the sugar protons and the fast relaxation of the spins involved in the magnetization transfer. Here we present a new methodology that relies on heteronuclear Constant Time Correlation Spectroscopy (CT-COSY). The three vicinal ³J_PH3, ³J_PH5 and ³J_PH5 scalar couplings can be obtained by monitoring the intensity decay of the P_i-H3_{i – 1} peak as a function of the constant time T in a 2D correlation map. The advantage of the new method resides in the possibility of measuring the two ³J_PH5 and ³J_PH5 scalar couplings even in the presence of overlapped H5/H5 resonances, since the quantitative information is extracted from the intensity decay of the P-H3 peak. Moreover, the relaxation of the H3 proton is considerably slower than that of the H5/H5 geminal protons and the commonly populated conformations of the phosphate backbone are associated with large ³J_PH3 couplings and relatively small ³J_{PH5 / H5}. These two facts lead to optimal signal-to-noise ratio for the P-H3 correlation compared to the P-H5/H5 correlation.The heteronuclear CT-COSY experiment is suitable for oligonucleotides in the 10–15 kDa molecular mass range and has been applied to the 30mer HIV-2 TAR RNA. The methodology presented here can be used to measure P-H dipolar couplings (D_PH) as well. We will present qualitative results for the measurement of P-H_base and P-H2 dipolar couplings in the HIV-2 TAR RNA and will discuss the reasons that so far precluded the quantification of the D_PHs for the 30mer RNA.     

Nest site selection and nesting success of five species of passerines in a South American open Prosopis woodland

I analyzed nest site preferences and whether these preferences were linked to nest success of five bird species breeding in an arid area of southern South America. Most nests (90%) were located in three plant species (Geoffroea decorticans, Capparis atamisquea, and Atriplex lampa). Serpophaga griseiceps, Poospiza ornata, and P. torquata nested in plants with size significantly different from randomly selected plants. At the mesohabitat scale (i.e., habitat patch surrounding the nest), four species showed clear differences from random patches within the general habitat, and the remaining species (Saltatricula multicolor) showed a non-significant trend. The daily survival rate of S. griseiceps nests placed in the preferred plant species (i.e., G. decorticans) was lower than those in the other nest-plants. In the other four bird species, nest survival did not differ between preferred and other plants used for nesting. At the scale of microhabitat (i.e., plant size and location of the nest inside the plant), no significant differences were detected between unsuccessful and successful nests. Similarly, unsuccessful nest patches did not differ significantly in habitat features from those that were successful. High nest predation rates found in this habitat (around 85% for the total assemblage) and a relatively high diversity of predators (and of predation tactics) appear to impede the presence of safe sites for nesting (i.e., there are trade-offs between avoidance strategies).     

The sea anemone genus Actinostola Verrill 1883: variability and utility of traditional taxonomic features, and a re-description of Actinostola chilensis McMurrich 1904

Species of the genus Actinostola are known for high variability of features. Anatomy, histology and cnidae of type specimens of five species from South America and Antarctica originally described as members of Actinostola and one species of Stomphia were compared to specimens of Actinostola chilensis collected during this study. None of these traditionally used features clearly distinguish the examined Actinostola species. I therefore propose new distinctive taxonomic features, including in vivo and in situ data. I provide an emended diagnosis of the genus Actinostola and a revised list of its species. I accept the synonymy of A. excelsa, A. pergamentacea and A. intermedia with A. crassicornis, and reject the synonymy of A. chilensis with A. crassicornis and A. intermedia. I re-describe A. chilensis in detail, including in situ information. Specimens of A. chilensis inhabit exposed positions of rocky substrate from 22 m depth down in south Chilean fjords between Puerto Montt (41°3535S, 72°53W) and Puyuhuapi (44°3136S; 72°326W); the most conspicuous features are its relatively large size, bright-orange colour, smooth, tough column and numerous and clearly entacmaeic tentacles.Electronic Supplementary Material  Supplementary material is available in the online version of this article at The publisher regrets that during copy-editing of this article the names of the authors of species were styled incorrectly. Therefore, it was decided to publish this erratum which, due to the nature of the paper, contains the whole original article, but now with the names of species authors styled correctly.The online version of the original article can be found at     

Typhloplanid flatworms (Mesostoma and related genera): Mechanisms of predation and evidence that they structure aquatic invertebrate communities

Mesostoma species and other typhloplanid flatworms are predators found in a wide variety of habitats. Laboratory observations of some Mesostoma spp found in shallow aquatic habitats (referred to as littoral species) have revealed a wide variety of prey killing mechanisms: 1) mucus trapping, 2) sit-and-wait predation, 3) releasing a toxin into the water, and 4) active searching. We review the existing literature on these mechanisms. We also describe for the first time the predatory behavior of a pelagic Mesostoma sp. found in Brazilian lakes.The existing literature is also reviewed to assess the potential impact of Mesostoma species and related genera on the aquatic invertebrate community. Mesostoma has a high potential for population increase and has been found in high densities in some shallow aquatic habitats. Single prey experiments show that a number of Mesostoma species feed heavily on mosquito larvae, some chironomid larvae and some daphnids but considerably less on most copepods and ostracods. Prey preference experiments reflect the same trends. Hence, these predation studies suggest that the flatworms, at high densities, should reduce populations of certain prey speces and, consequently, alter community structure. Field studies support this prediction. Mesostoma species, at high densities, appear to be important predators of mosquito larvae in shallow aquatic habitats even under conditions where high densities of planktivorous fishes had little impact. They also appear to alter zooplankton community structure. However, much of the field evidence is correlational and not experimental. No studies have assessed the impact of pelagic typhloplanids on zooplankton community structure.It is concluded that many more manipulative field experiments are needed to assess the impact of typhloplanids on aquatic invertebrate communities.     

Testing the intermediate disturbance hypothesis on species diversity in herbaceous plant communities along a human trampling gradient using a 4-year experiment in an old-field

The intermediate disturbance hypothesis predicts unimodal relationships between species diversity and disturbance frequency/intensity. To test this hypothesis, species diversity in herbaceous plant communities along a human trampling gradient was investigated by conducting a 4-year experiment in an old-field. In general, species richness (S), the Shannon–Weiner index (H) from plant cover data and species evenness (J) showed negative linear relationships with trampling frequency, in contrast to the prediction of the intermediate disturbance hypothesis. However, the significant relationships between trampling frequency and species diversity were not observed in the fourth year without J, which showed a unimodal relationship. In all experimental years, the number of new species that colonized the plots after 1year was small under frequent trampling, and the number of species lost from the plots was large under infrequent trampling. The relative number and the relative cover of perennial species increased as trampling frequency increased in the first and second years, but this pattern was not observed in the following years because the dominance of perennials further increased at decreasing frequencies of trampling. The similarity in the species composition and the yearly changes in species dominance indicated that trampling at higher frequencies eliminated more trampling-intolerant species only in the early years of the experiment. These results suggest that trampling mediated early changes in species diversity patterns, but competitive interactions were more important in the later experimental years. The time lag in the effects of trampling and competition appears to be attributable to the infrequent occurrence of unimodal patterns of species diversity.     

Sugar conformation of a stereospecific 2′-R or 2′-S deuterium-labeled DNA decamer studied with proton-proton J coupling constants

The sugar conformation of a DNA decamer was studied with proton-proton ³J coupling constants. Two samples, one comprising stereospecifically labeled 2-R-²H for all residues and the other 2-S-²H, were prepared by the method of Kawashima et al. [J. Org. Chem. (1995) 60, 6980–6986; Nucleosides Nucleotides (1995) 14, 333–336], the deuterium labeling being highly stereospecific 99% for all 2-²H, 98% for 2-²H of A, C, and T, and 93% for 2-²H of G). The ³J values of all H1-H2 and H1-H2 pairs, and several H2-H3 and H2-H3 pairs were determined by line fitting of 1D spectra with 0.1–0.2 Hz precision. The observed J coupling constants were explained by the rigid sugar conformation model, and the sugar conformations were found to be between C3-exo and C2-endo with _m values of 26° to 44°, except for the second and 3 terminal residues C2 and C10. For the C2 and C10 residues, the lower fraction of S-type conformation was estimated from J_H1H2 and J_H1H2 values. For C10, the N–S two-site jump model or Gaussian distribution of the torsion angle model could explain the observed J values, and 68% S-type conformation or C1-exo conformation with 27° distribution was obtained, respectively. The differences between these two motional models are discussed based on a simple simulation of J-coupling constants.     

Pressure alters electronic orbital overlap in hydrogen bonds

Pressure-induced changes in ^3h J _NC scalar couplings through hydrogen bonds were investigated in the immunoglobulin binding domain of streptococcal protein G. ¹H, ¹⁵N and ¹³C triple-resonance NMR spectroscopy coupled with the on-line high pressure cell technique was used to monitor ^3h J _NC scalar couplings at 30 and 2000 bar in uniformly labeled ¹⁵N and ¹³C protein isotopes. Both increased and decreased ^3h J _NC scalar couplings were observed at high pressure. No correlation with secondary structure was apparent. The difference in coupling constants as well as pressure-induced chemical shift data suggests a compaction of the helix ends and an increase of the helix pitch at its center in response to pressure. Our data provides the first direct evidence that the electronic orbital overlap in protein backbone hydrogen bonds is altered by pressure.