Altitudinal and latitudinal distribution of east Malagasy forest bird communities

Aim To describe variation in forest bird communities with altitude and latitude. Location Eastern Madagascar. Methods Extraction of data from forest bird inventories conducted in eastern Madagascar. Results There is a strong decline in species richness with altitude, above about 1300 m. Below this altitude, species richness is about constant or declines slightly. Seventy-eight percent of species occurring regularly in forest are absent from at least one of low, mid-altitude or high altitude forest. Of eighty-seven species occurring regularly in forest, only four or possibly five have latitudinally limited distributions, over a latitudinal range of over 1200 km. Three or possibly four are limited to the northern two-thirds, and one appears to be at least much more common in the southern half. Main conclusions Eastern Malagasy rain forest birds show previously unanalysed variation in altitudinal distribution. There is much less latitudinal variation. Species currently considered threatened are concentrated in the lowland and high-altitude zones. This may be at least partly due to lack of survey effort giving the impression that these species are rare, but lowland forests at least are under great human pressure. Bird conservation initiatives would probably have most effect if targeted at lowland east Malagasy rain forest.     

Dynamics and spatial organization of plant communities in water-limited systems

A mathematical model for plant communities in water-limited systems is introduced and applied to a mixed woody-herbaceous community. Two feedbacks between biomass and water are found to be of crucial importance for understanding woody-herbaceous interactions: water uptake by plants' roots and increased water infiltration at vegetation patches. The former acts to increase interspecific competition while the latter favors facilitation. The net interspecific interaction is determined by the relative strength of the two feedbacks. The model is used to highlight new mechanisms of plant-interaction change by studying factors that tilt the balance between the two feedbacks. Factors addressed in this study include environmental stresses and patch dynamics of the woody species. The model is further used to study mechanisms of species-diversity change by taking into consideration tradeoffs in species traits and conditions giving rise to irregular patch patterns.     

Niche and metabolic principles explain patterns of diversity and distribution: theory and a case study with soil bacterial communities

The causes of biodiversity patterns are controversial and elusive due to complex environmental variation, covarying changes in communities, and lack of baseline and null theories to differentiate straightforward causes from more complex mechanisms. To address these limitations, we developed general diversity theory integrating metabolic principles with niche-based community assembly. We evaluated this theory by investigating patterns in the diversity and distribution of soil bacteria taxa across four orders of magnitude variation in spatial scale on an Antarctic mountainside in low complexity, highly oligotrophic soils. Our theory predicts that lower temperatures should reduce taxon niche widths along environmental gradients due to decreasing growth rates, and the changing niche widths should lead to contrasting α- and β-diversity patterns. In accord with the predictions, α-diversity, niche widths and occupancies decreased while β-diversity increased with increasing elevation and decreasing temperature. The theory also successfully predicts a hump-shaped relationship between α-diversity and pH and a negative relationship between α-diversity and salinity. Thus, a few simple principles explained systematic microbial diversity variation along multiple gradients. Such general theory can be used to disentangle baseline effects from more complex effects of temperature and other variables on biodiversity patterns in a variety of ecosystems and organisms.     

Sensitivity analysis of Markov models for communities of competing sessile organisms

1. Communities of competing sessile organisms are often modelled using Markov chains. Sensitivity analysis of the stationary distribution of these models tells us how we expect the abundance of each organism to respond to changes in interactions between species. This is important for conservation and management. 2. Markov models for such communities have usually been formulated in discrete time. Each column of the discrete-time transition matrix must sum to 1 (column stochasticity). Sensitivity analysis therefore involves defining a pattern of compensation that maintains column stochasticity as a single transition probability changes. There is little biological theory about the appropriate compensation pattern, but the usual choices involve changing only the elements of a single column of the transition matrix. 3. I argue that if the underlying dynamics occur in continuous time, each transition probability is the net outcome of direct and many indirect interactions. 4. Determining the consequences of changing a single direct interaction will often be of interest. I show how this can be achieved using a continuous-time model. The resulting discrete-time compensation pattern is quite different from those that have been considered elsewhere, with changes occurring in many columns. 5. I also show how to determine which direct interactions are being changed under any discrete-time compensation pattern.     

Co-occurrence patterns of cavity-nesting birds in cottonwood-willow communities

Summary We studied the covariation of six species of cavity-nesting birds to determine the extent to which species' co-occurrence patterns were attributable to interspecific relations. We tested two null hypotheses: (1) inverse relations did not exist among potential competitors for nest trees or nest cavities, and (2) there were no positive relations among potential commensals for nest cavities. Statistical power analyses, and simple, partial, and multiple partial correlation and regression analyses provided little evidence of species-species or higher-order inverse or positive relations. Most of the variation in co-occurrence patterns was associated with stand characteristics. Collectively, an abundance of nest trees and nest cavities, differences among species in acceptable nest-tree and nest-cavity dimensions, and different periods of peak nesting activity appear to be responsible for the lack of negative relations among potential competitors. Positive relations among potential commensals were weak presumably because (1) secondary cavity nesters (SCNs) frequently used cavities that originated from wind-, lightning-, and/or disease-damaged limbs and were thus not dependent completely on primary cavity nesters for cavities, and (2) the lag time for cavity use by SCNs is often two or more seasons. Interspecific relations were apparently not major determinants of community structure during our investigation; assemblages of cavity nesters appeared instead to be influenced more by independent species-specific habitat responses.     

Biodiversity and distribution of epibiontic communities on Caridina ensifera (Crustacea,Decapoda, Atyidae) from Lake Poso: comparison with another ancient lake system of Sulawesi (Indonesia)

Fernandez‐Leborans, G. and von Rintelen, K. 2010. Biodiversity and distribution of epibiontic communities on Caridina ensifera (Crustacea, Decapoda, Atyidae) from Lake Poso: comparison with another ancient lake system of Sulawesi (Indonesia). — Acta Zoologica (Stockholm) 91 : 163–175 The epibiont communities of the shrimp Caridina ensifera, endemic to Lake Poso (Sulawesi, Indonesia), were analysed. Most of the epibiont species were ciliated protozoa belonging to three suctorian genera (Acineta, Podophrya and Spelaeophrya), three peritrich genera (Zoothamnium, Vorticella and Cothurnia), and a haptorid genus (Amphileptus). There was also a rotifer epibiont of the genus Embata. Epibionts were identified to species level. There were 14 to 1114 epibionts per shrimp. The distribution of the epibiont species on the surface of the basibiont was recorded, calculating the number on the different colonized individuals of C. ensifera. The most abundant species, Zoothamnium intermedium and Acineta sulawesiensis, were also the most widely distributed. There was a significant difference between the spatial distributions of the different epibiont species. The analysis of the number of the epibiont species throughout the anteroposterior axis of the shrimp showed a gradient from the anterior to the posterior end of the body. Data from Lake Poso were compared with those of the Malili lake system (Sulawesi), obtained from its endemic shrimp, Caridina lanceolata. Lake Poso had the highest mean diversity, while Lake Mahalona showed the highest maximum diversity. All lakes were correlated with respect to the mean number of epibionts on the anatomical units of the shrimp, which showed a similar general distribution. The distributions of the different epibiont species were compared between the lakes. The possible adaptations of the epibionts as well as the colonization patterns were discussed. From the statistical results and the analysis of the distributions, we propose that in these communities epibiont species have a pattern of colonization in which they follow a behaviour as a whole; each species has a differential distribution, with the species occupying the available substratum with the particular requirements of each functional group, but there is a trend towards maintaining an equilibrium among species and groups, compensating for diversity and number of individuals. In all lakes there was an epibiont distribution model comprising the maintenance of an anteroposterior axis gradient, which was supported by the fluctuation in diversity and number of individuals of the different functional groups of epibiont species. The functional role of the different groups of species seems to tend towards sustainability with little global variation among the lakes.     

Spatial distribution of microbial communities in the cystic fibrosis lung

Cystic fibrosis (CF) is a common fatal genetic disorder with mortality most often resulting from microbial infections of the lungs. Culture-independent studies of CF-associated microbial communities have indicated that microbial diversity in the CF airways is much higher than suggested by culturing alone. However, these studies have relied on indirect methods to sample the CF lung such as expectorated sputum and bronchoalveolar lavage (BAL). Here, we characterize the diversity of microbial communities in tissue sections from anatomically distinct regions of the CF lung using barcoded 16S amplicon pyrosequencing. Microbial communities differed significantly between different areas of the lungs, and few taxa were common to microbial communities in all anatomical regions surveyed. Our results indicate that CF lung infections are not only polymicrobial, but also spatially heterogeneous suggesting that treatment regimes tailored to dominant populations in sputum or BAL samples may be ineffective against infections in some areas of the lung.     

The bacteriophages in human- and animal body-associated microbial communities

Felix d'Herelle first demonstrated, about 90 years ago, the presence of bacteriophages in human and animal body microbiota. Our comprehension of the impact of naturally occurring bacteriophages on symbiotic bacteria, and of their role in general homeostasis of macro-organism, nevertheless remains quite fragmentary. Analysis of data in various human- and animal body-associated microbial systems on phage occurrence, diversity, host specificity and dynamics, as well as host occurrence, specificity and dynamics, suggests that mechanisms which stabilize phage–bacteria coexistence are not identical for either different species or different body sites. Regulation by phage infection instead probably depends on specific physical, chemical and biological conditions, e.g. pH, nutrient densities, host prevalence, relation to mucosa and other surfaces and presence of phage inhibiting substances. In some animal species intestinal bacteriophages thus appear to exert significant selective pressure over at least some resident bacterial populations, resulting in phages playing important roles in the self-regulation of these microbial systems while at the same time contributing to maintenance of bacterial diversity (i.e. 'killing the winner'). Emerging data additionally suggest that bacteriophage particles could play roles in regulating the immune reactions of the macro-organism. Alternatively, for many systems links between phages and community characteristics have not been established.     

Virioplankton and microbial communities in aquatic systems: a seasonal study in two lakes of differing trophy

1. The seasonal and vertical distribution of the abundance of virus‐like particles (VLPs), together with the abundances of other microbial organisms (bacteria, unpigmented and pigmented nanoflagellates and ciliates), were determined in an oligomesotrophic lake (Pavin, France) and in a eutrophic lake (Aydat, France) between March and December 2000. 2. The abundance of the viral plankton and those of other microbial taxa were significantly higher in the more productive system. The same was for the virus‐to‐bacteria quotient (VBQ), which averaged seven in Lake Pavin and nine in Lake Aydat. 3. The abundance of viruses increased during the period of thermal stratification in both lakes, with the highest values being recorded at the end of summer/early autumn in the epi‐ and the metalimnion. The seasonal pattern of abundance of viruses in both lakes in the surface layer was similar, indicating that the dynamics of viruses may be controlled by environmental factors such as light conditions. 4. There was no correlation between the abundance of viruses and protists. We found correlations between viruses and heterotrophic bacteria in the whole water column in Lake Pavin, but only in the dark bottom waters in Lake Aydat. 5. Overall, the empirical findings in this study lead us to speculate that the weaker correlation between bacteria and viruses in Lake Aydat than in Lake Pavin, as well as the higher VBQ in the former, is a consequence of the increasing relative abundance of non‐bacteriophage VLPs along the trophic gradient of aquatic systems.     

On-line gas analysis in animal cell cultivation: I. Control of dissolved oxygen and pH

To monitor gas reaction rates in animal cell culture at constant dissolved oxygen concentration (DO) and constant pH it was necessary to develop improved control methods. Decoupling of both controllrs was obtained by manipulation of molar fractions of oxygen and carbon dioxide in the gas phase. Two pairs of DO and pH controllers were designed and tested both in simulation and exprimental runs. The first controller pair was developed for headspace aeration only, whereas the second controller pair was designed for bubble aeration using a microsparger and flushing the headspace with helium. pH was controlled by a conventional discrete PID controller in its velocity form. For DO control two linear state space feedback controllers with parameter adaptation were established. In these controllers the oxygen uptake rate (OUR) was considered as a disturbance and was not included in the mathematical model. The feedback gain adaptation was based on the difference between the actual molar fraction of oxygen at time step n and the initial molar fraction. This difference is related to OUR and was used to increase or decrease the state feedback controller gain (k and k(1), respectively) in a slow manner. With these controllers it was possible to get an excellent online estimate of OUR. In the case of bubble aeration a simple gas phase mass balance was sufficient, whereas during the headspace aeration a liquid phase balance was required. It has been shown that determination of OUR using gas balance requires a significantly better controller performance compared to just keeping DO and pH within reasonable limits. (c) 1995 John Wiley & Sons, Inc.     

Species abundance distribution and dynamics in two locally coupled communities

This study considered a model for species abundance dynamics in two local community (or islands) connected to a regional metacommunity. The model was analyzed using continuous probabilistic technique that employs Kolmogorov-Fokker-Planck forward equation to derive the probability density of the species abundance in the two local communities. Using this technique, we proposed a classification for the species abundance dynamics in the local communities. This classification was made based on such characteristics as immigration intensity, species representation in the metacommunity and the size of local communities. We further distinguished several different scenarios for species abundance dynamics using different ecological characteristics such as species persistence, extinction and monodominance in one or both local communities. The similarity of the species abundance distributions between the two local communities was studied using the correlation coefficient between species abundances in two local communities. The correlation is a function of migration rates between local communities and between local and metacommunity. Immigration between local communities drives the homogenization of the local communities, while immigration from the metacommunity will differentiate them. This community subdivision model provides useful insights for studying the effect of landscape fragmentation on species diversity.     

Heterogeneous communities with lognormal species abundance distribution: Species-area curves and sustainability

Heterogeneous species abundance models are models in which the dynamics differ between species, described by variation among parameters defining the dynamics. Using a dynamic and heterogeneous species abundance model generating the lognormal species abundance distribution it is first shown that different degrees of heterogeneity may result in equivalent species abundance distributions. An alternative to Preston's canonical lognormal model is defined by assuming that reduction in resources, for example reduction in available area, increases the density regulation of each species. This leads to species-individual curves and species-area curves that are approximately linear in a double logarithmic plot. Preston's canonical parameter gamma varies little along these curves and takes values in the neighborhood of one. Quite remarkably, the curves, which define the sensitivity of the community to area reductions, are independent of the heterogeneity among species for this model. As a consequence, the curves can be estimated from a single sample from the community using the Poisson lognormal distribution. It is shown how to perform sensitivity analysis with respect to over-dispersion in sampling relative to the Poisson distribution as well as sampling intensity, that is, the fraction of the community sampled. The method is exemplified by analyzing three simulated data sets.     

Uncertainty in identifying local extinctions: the distribution of missing data and its effects on biodiversity measures

Identifying local extinctions is integral to estimating species richness and geographic range changes and informing extinction risk assessments. However, the species occurrence records underpinning these estimates are frequently compromised by a lack of recorded species absences making it impossible to distinguish between local extinction and lack of survey effort—for a rigorously compiled database of European and Asian Galliformes, approximately 40% of half-degree cells contain records from before but not after 1980. We investigate the distribution of these cells, finding differences between the Palaearctic (forests, low mean human influence index (HII), outside protected areas (PAs)) and Indo-Malaya (grassland, high mean HII, outside PAs). Such cells also occur more in less peaceful countries. We show that different interpretations of these cells can lead to large over/under-estimations of species richness and extent of occurrences, potentially misleading prioritization and extinction risk assessment schemes. To avoid mistakes, local extinctions inferred from sightings records need to account for the history of survey effort in a locality.     

Geochemical parameters of sedimentation and the distribution of Silurian brachiopod communities in Lithuania

Silurian rocks from borehole cores in the Baltic Basic were analyzed for Si, Al, Ti, Fe, Ca and Mg oxide content and chemical data were related to sedimentary environment, lithology and brachiopod community distribution. Evaluation of these relationships enables precise positioning of closely related communities within Boucot's (1975) brachiopod Benthic Assemblages. Preliminary attempts are made to evaluate climatic change based on Al/Ti oxide ratios.     

乌鲁木齐市小型兽类群落特征与分布格局初步研究

根据2002年7月的调查资料对乌鲁木齐市养禽场鼠类群落进行了研究。结果表明：该地区分布的鼠类可划分为2种群落,(1)褐家鼠 小家鼠群落;(2)小家鼠 灰仓鼠群落。同时对鼠类群落的多样性,均匀度等进行了初步研究。     

Seed size, shape and vertical distribution in the soil: indicators of seed longevity

1. We investigated the vertical distribution of seeds in the soil, using data from nine studies in five European countries. We discovered significant correlations between seed shape and distribution in the soil.
2. The classification of the longevity of seeds of plant species has been improved by the introduction of a 'longevity index', expressing on a continuous scale the most recent information on seed longevity represented as the proportion of non-transient seed bank records in the database of Thompson et al. (1997 ). Remarkably, no difference in seed longevity was found if the index was based on direct observations only when compared with the index based on the complete data set where indirect, 'depth-derived' observations were included.
3. Seed longevity was best estimated using a multiple regression model with an integrated measure of seed size and shape and depth distribution of seeds.
4. The shape of seeds, known to be a consistent character of species, was shown to be constant within species, whereas depth distribution of seeds was highly variable among sites. This is consistent with the variability of seed longevity found in published seed bank data.