Scale‐dependent biases in species counts in a grassland

Abstract. Numbers of plant species were recorded in species‐rich meadows in the Bílé Karpaty Mts., SE Czech Republic, with the aim to evaluate the sampling error made by well‐trained observers. Five observers recorded vascular plants in seven plots ranging from 9.8 cm² to 4 m² independently and were not time‐limited. In larger plots a discrepancy of 10–20% was found between individual estimates, in smaller plots discrepancy increased to 33%, on average. The gain in observed species richness by combining records of individual observers (in comparison with the mean numbers estimated by single observers) decreased from the smallest plot (27–82% for two to five observers) to the largest one (13–25%). However, after misidentified and suspicious records were eliminated, the gain was much lower and became scale‐independent; two observers added 12% species, on average, and the increase by combining species lists made by three or more observers was negligible (3% more on average). It is concluded that most discrepancies between individual observers were caused by misidentification of rare seedlings and young plants. We suggest that in species‐rich meadows plants should be recorded by at least three observers together and that they should consult all problematic plant specimens together in the field, to minimize errors.     

Quantifying individual‐ and community‐level effects of competition using experimentally‐determined null species pools

Abstract. The effects of competition on individual fitness and species diversity were investigated in a first‐year old field by comparing the natural community to an experimentally‐determined null community. The species pool for the null community was estimated from low‐density plots, and hypothetical sample plots in the null community were constructed by random sampling from the species pool. Individual plants were larger in low‐density plots than control plots, indicating that competition reduced individual fitness. Competition appeared to reduce diversity in half the plots (i.e. species richness and diversity were lower than in hypothetical null community plots with the same number of individuals), but did not affect diversity in the other plots. However, the reduction in diversity could be explained as an artifact caused by spatial aggregation in control plots. The magnitude of the effects of competition on diversity did not change with plot density, and no species consistently increased or decreased in relative abundance as plot density increased. We conclude that competition had no effect on diversity in this community, despite the strong effect on individual growth.     

MALDI‐TOF‐MS‐based species identification and typing approaches in medical mycology

MALDI‐TOF MS‐based species identification has found its place in many clinical routine diagnostic laboratories over the past years. Several well‐established commercial systems exist and these allow precise analyses not only among bacteria, but also among clinically important yeasts. This methodology shows higher precision than biochemical and microscopic methods at significantly reduced turnaround times. Furthermore, the differentiation of different filamentous fungi including most dermatophytes and zygomycetes has been established. The direct identification of yeasts from blood culture bottles will be possible in a routine fashion with new standardized procedures. In addition to species identification, the MALDI‐TOF MS technology offers several further possibilities, like assays to detect or predict resistance phenotypes in fungi as well as subtyping approaches to detect clinically relevant subgroups. The differences between the commercial systems are discussed with respect to fungi and an overview of their performances provided. Factors influencing outcome of MALDI‐TOF‐based species identification are discussed.     

Multi‐scale responses of plant species diversity in semi‐natural buffer strips to agricultural landscapes

Question: How does agricultural land usage affect plant species diversity in semi‐natural buffer strips at multiple scales? Location: Lepsämä River watershed, Nurmijärvi, Southern Finland. Methods: Species diversity indicators included both richness and evenness. Plant communities in buffer strips were surveyed in 29 sampling sites. Using ArcGIS Desktop 9.0 (ArcInfo) and Fragstats 3.3 for GIS analysis, the landscape composition around each sampling site was characterized by seven parameters in square sectors at five scales: 4, 36, 100, 196, and 324ha. For each scale, Principle Component Analysis was used to examine the importance of each structural metric to diversity indicators using multiple regression and other simple analyses. Results: For all but the smallest scales (4 ha), two structural metrics including the diversity of land cover types and percentage of arable land were positively and negatively correlated with species richness, respectively. Both metrics had the highest correlation coefficients for species richness at the second largest scale (196 ha). The density of arable field edges between the fields was the only metric that correlated with species evenness for all scales, which had highest predictive power at the second smallest scale (36 ha). Conclusions: Species richness and evenness of buffer strips had scale‐dependent relationships to land use in agricultural ecosystems. The results of this study indicated that species richness depends on the pattern of arable land use at large scales, which may relate to the regional species pool. Meanwhile, species evenness depended on the level of field edge density at small scales, which relates to how the nearby farmland was divided by the edges (e.g. many small‐scale fields with high edge density or a few big‐scale fields with low edge density). This implies that it is important to manage the biodiversity of buffer strips within a landscape context at multiple scales.     

Scale‐dependent determinants of plant species richness in a semi‐arid fragmented agro‐ecosystem

Aims: (1) Understanding how the relationship between species richness and its determinants depends on the interaction between scales at which the response and explanatory variables are measured. (2) Quantifying the relative contributions of local, intermediate and large‐scale determinants of species richness in a fragmented agro‐ecosystem. (3) Testing the hypothesis that the relative contribution of these determinants varies with the grain size at which species richness is measured. Location: A fragmented agro‐ecosystem in the Southern Judea Lowland, Israel, within a desert–Mediterranean transition zone. Methods: Plant species richness was estimated using hierarchical nested sampling in 81 plots, positioned in 38 natural vegetation patches within an agricultural matrix (mainly wheat fields) among three land units along a sharp precipitation gradient. Explanatory variables included position along that gradient, patch area, patch isolation, habitat heterogeneity and overall plant density. We used general linear models and hierarchical partitioning of variance to test and quantify the effect of each explanatory variable on species richness at four grain sizes (0.0625, 1, 25 and 225 m²). Results: Species richness was mainly affected by position along a precipitation gradient and overall plant density, and to a lesser extent by habitat heterogeneity. It was also significantly affected by patch area and patch isolation, but only for small grain sizes. The contribution of each explanatory variable to explained variance in species richness varied with grain size, i.e. scale‐dependent. The influence of geographic position and habitat heterogeneity on species richness increased with grain size, while the influence of plant density decreased with grain size. Main conclusions: Species richness is determined by the combined effect of several scale‐dependent determinants. Ability to detect an effect and effect size of each determinant varies with the scale (grain size) at which it is measured. The combination of a multi‐factorial approach and multi‐scale sampling reveals that conclusions drawn from studies that ignore these dimensions are restricted and potentially misleading.     

The effect of the expansion of the clonal grass Calamagrostis epigejos on the species turnover of a semi‐arid grassland

Question: How does the dominance of Calamagrostis epigejos influence species turnover of a grassland? Location: Loess grassland at the foothills of Bükk Mountains, Hungary (47°54’ N., 20°35’ E). Methods: Presence/absence of vascular plants and different performance attributes of C. epigejos were recorded in a plot‐subplot system between 2002 and 2005. Appearance and disappearance rates of grassland species were calculated for pairs of consecutive years. 1. Mean appearance and disappearance rates were compared in grassland plots dominated by C. epigejos and in plots free from this species, based on Monte Carlo randomization. 2. Mean appearance rates were assessed for categories of C. epigejos performance and their confidence intervals were calculated via Monte Carlo randomization. For two performance variables (percentage cover and shoot number) analyses were performed at two spatial scales. Results: 1. C. epigejos.‐dominated plots differed from unaffected ones by significantly lower appearance rates. 2. Change in appearance rates was best explained by differences in percentage cover of C. epigejos. Coarse‐scale C. epigejos performance had a closer correspondence with appearance rate change than fine‐scale performance. Low level C. epigejos performance enhanced appearance rate compared to intact stands, while high level performance decreased it, regardless of the choice of performance measure. Conclusions: C. epigejos lowers species number by hindering reappearance of species of the original grassland. This is best explained by the increased shading effect at the coarse scale. The marked non‐linear initial enhancement in appearance rate, however, can also be taken as an early sign of future species loss.     

Community‐level consequences of species interactions in an annual plant community

Question: How does the intensity of species interactions affect species and functional group composition of an annual plant community? Location: Sede Boqer, Negev Desert, Israel. Methods: The potential for competitive interactions in two annual plant communities (desert and coastal) from semi‐stabilized sand dunes was manipulated by varying seed bank density and therefore the number of potentially interacting individuals. Communities were exposed to three different irrigation regimes, mimicking precipitation at the desert site, the coastal site, and an intermediate precipitation level. Plots were maintained for 3 years, and percentage cover of each species in the plots was recorded at the end of each growing season. We used redundancy analysis to test for effects of initial density, irrigation, and year on the species and functional group composition of the communities. Results: Initial density had significant effects on species composition, and these effects remained significant over 3 years, even as total community percentage cover became more similar among treatments over time. Density effects did not depend on resource availability (irrigation level). Functional group identity or individual plant size did not predict which species would be good competitors, and a species' competitive ability did not predict its abundance in the field. Conclusions: Species interactions strongly affect community composition, and those effects carry over into subsequent years such that competition does not lead to convergence in community structure over time. However, the particular changes in composition observed were not predictable by some of the traits that have been found important in individual‐level experiments. We speculate that the outcome of competition in diverse communities will depend on multiple traits, in contrast to the outcome of individual‐level pairwise experiments. We also speculate that the shift in composition with density could mean that local variation in density may contribute to maintenance of diversity in this system.     

Coarse‐scale plant species richness in relation to environmental heterogeneity

Abstract. We test to what extent mean environmental conditions and environmental heterogeneity are related to species richness in a regular geographical grid system (UTM) of 10 km × 10 km in the NE Iberian Peninsula (i.e. Catalonia, ca. 31 900 km²). Species richness of each UTM quadrat was estimated by compiling a large database (more than a million records) from bibliographic references and atlases. Mean environmental conditions of each quadrat were derived from climatic maps. Environmental heterogeneity was estimated from the diversity of geological substrates and climatic classes in each quadrat. The increase in effective (real) area due to topographic complexity was also considered (derived from the digital elevation model). The statistical analysis was performed by a weighted analysis of deviance assuming a negative binomial error distribution. The results suggest that species richness in the study area is a function of both within‐quadrat heterogeneity (specifically, effective area, heterogeneity of geological substrates, heterogeneity of January temperature) and mean environmental conditions (mean annual temperature, Thornthwaite moisture index and aspect). All these parameters showed a positive relationship with species richness. Quadrat heterogeneity accounted for ca. 2/3 of the explained deviance, suggesting the importance of environmental heterogeneity when using a geographical grid system. The study fits well with earlier results on the importance of climatic parameters on plant species richness and provides one of the few rigorous, quantitative, coarse‐scale studies testing environmental heterogeneity in plant species richness.     

Use of the β‐function to estimate the skewness of species responses

Abstract. Response of a species to an environmental variable may be modeled and predicted using a wide spectrum of different functions. Contrary to other functions (Gaussian, polynomial etc), all parameters of the β‐function are interpretable in ecological terms. However, computational difficulties in the determination of the β‐function parameters initiated controversial debates on the applicability and usefulness of this function in vegetation modelling and gradient analysis. We propose a simple algorithm for fitting the β‐function to observed data. Analytic properties of the algorithm (its ability to recover the known species responses along gradients) are tested using a series of simulated data. In most cases the algorithm correctly estimated parameters of the simulated responses.     

Factors associated with plant species richness in a coastal tall‐grass prairie

Abstract. In this study we examine the factors associated with variations in species richness within a remnant tall‐grass prairie in order to gain insight into the relative importance of controlling variables. The study area was a small, isolated prairie surrounded by wetlands and located within the coastal prairie region, which occurs along the northwestern Gulf of Mexico coastal plain. Samples were taken along three transects that spanned the prairie. Parameters measured included micro‐elevation, soil characteristics, indications of recent disturbance, above‐ground biomass (including litter), light penetration through the plant canopy, and species richness. Species richness was found to correlate with micro‐elevation, certain soil parameters, and light penetration through the canopy, but not with above‐ground biomass. Structural equation analysis was used to assess the direct and indirect effects of micro‐elevation, soil properties, disturbance, and indicators of plant abundance on species richness. The results of this analysis showed that observed variations in species richness were primarily associated with variations in environmental effects (from soil and microtopography) and were largely unrelated to variations in measures of plant abundance (biomass and light penetration). These findings suggest that observed variations in species richness in this system primarily resulted from environmental effects on the species pool. These results fit with a growing body of information that suggests that environmental effects on species richness are of widespread importance.     

Growth releases of three shade‐tolerant species following canopy gap formation in old‐growth forests

Questions: Do the number, duration and magnitude of growth releases following formation of natural, fine‐scale canopy gaps differ among shade‐tolerant Thuja plicata, Tsuga heterophylla and Abies amabilis? What is the relative importance of tree‐level and gap‐level variables in predicting the magnitude and duration of releases? What does this tell us about mechanisms of tree species coexistence in such old‐growth forests? Location: Coastal British Columbia, Canada. Methods: We estimated the timing of formation of 20 gaps using dendroecological techniques and extracted increment cores from all three species growing around or within gaps. Using a species‐ and ecosystem‐specific release‐detection method, we determined the number of trees experiencing a release following gap formation. We quantified the duration and magnitude of individual releases and estimated the influence of tree‐level and gap‐level variables on these release attributes. Results: Eighty‐seven per cent (304 of 348) of all trees experienced a release following gap formation. T. heterophylla and A. amabilis experienced higher magnitude and longer duration releases than T. plicata. The effect of diameter on the duration of releases varied among species, with T. heterophylla and A. amabilis experiencing decreasing, and T. plicata experiencing increasing, duration of releases with increasing diameter. The effect of growth rate prior to a release on the magnitude of releases varied among trees of different diameters, with the slowest growing and smallest individuals of all species experiencing the most intensive releases. Conclusions: Our results provide detailed information on the number, duration and magnitude of growth releases of the above three species following gap formation. Differences in response to canopy gaps suggest differences in how these species ascend to the canopy strata. T. plicata may be less dependent on gaps to reach the canopy. Differing strategies for ascending to the canopy strata may be important in facilitating coexistence of these three species in old‐growth forests of coastal British Columbia.     

Size and heterogeneity rather than landscape context determine plant species richness in semi‐natural grasslands

Question: Is plant diversity in fragmented semi‐natural grasslands related to present and historical landscape context? Location: Southern Sweden. Methods: Plant diversity was described at 30 semi‐natural grassland sites in terms of total and specialist plant species richness at the site and species density at different scales (0.5–10 m²). These measures are commonly used to assess conservation value of semi‐natural grasslands. Landscape context was measured as contemporary connectivity to other semi‐natural grasslands, historical connectivity 50 years ago, amount of linear elements potentially suitable for dispersal (road verges, power line clearings), and amount of forest (inverse of the openness of the landscape). Results: The diversity measures were generally correlated with each other, implying that species richness in a subset of the grassland can predict the total richness. Plant species density at three scales (0.5 m², 10 m² and total) was related to the landscape context using an information theoretic approach. Results showed that total species richness increased with increased size of grasslands, contrary to earlier diversity studies in semi‐natural grasslands. Larger grasslands were more heterogeneous than smaller grasslands, and this is a likely reason for the species‐area relationship. Heterogeneity was also of high importance at the smaller scales (0.5 m², 10 m²). With increased amount of forest, total species richness increased but species density on 10 m² decreased. There was no influence of connectivity in either the contemporary or the historical landscape, contrary to previous studies. Conclusions: Grassland size and heterogeneity are of greater importance for plant diversity in semi‐natural grassland, than grassland connectivity in the landscape.     

The species in primatology

Biologists of the late eighteenth and early nineteenth centuries all bandied about the term “species,” but very rarely actually said what they meant by it. Often, however, one can get inside their thinking by piecing together some of their remarks. One of the most nearly explicit‐appropriately, for the man who wrote a book called The Origin of Species – was Charles Darwin 1 : “Practically, when a naturalist can unite two forms together by others having intermediate characters, he treats the one as a variety of the other… He later translated this into evolutionary terms: “Hereafter, we shall be compelled to acknowledge that the only distinction between species and well‐marked varieties is, that the latter are known, or believed, to be connected at the present day by intermediate gradations, whereas species were formerly thus connected”^1:484‐5