Rapid phase-shift reversal on a Jamaican coral reef

Many Caribbean reefs have experienced a phase-shift in community structure, the principle features being a decline in coral cover and an increase in macroalgal biomass. However, one Jamaican reef—Dairy Bull on the north shore near Discovery Bay—is once again dominated by scleractinian corals and several key species have returned. Living coral cover at 6–8 m depth at Dairy Bull has doubled over the past 9 years and is now ~54%. The absolute cover of Acropora cervicornis was <1% in 1995, but increased to ~11% by January 2004. During this time the cover of macroalgae decreased by 90%, from 45 to 6%. We speculate that long-lived colonies of Montastraea annularis may have facilitated the recovery of this reef by providing structural refugia.     

The scale-dependent importance of habitat factors and dispersal limitation in structuring Great Lakes shoreline plant communities

Niche-based and neutral models of community structure posit distinct mechanisms underlying patterns in community structure; correlation between species’ distributions and habitat factors points to niche assembly while spatial pattern independent of habitat suggests neutral assembly via dispersal limitation. The challenge is to disentangle the relative contributions when both processes are operating, and to determine the scales at which each is important. We sampled shoreline plant communities on an island in Lake Michigan, varying the extent and the grain of sampling, and used both distance-based correlation methods and variance partitioning to quantify the proportion of the variation in plant species composition that was attributable to habitat factors and to spatial configuration independent of habitat. Our results were highly scale dependent. We found no distance decay of plant community similarity at the island scale (1−33 km). All of the explained variation (32%) in species composition among samples at this scale was attributed to habitat factors. However, at a site intensively sampled at a smaller scale (5−1,200 m), similarity of species composition did decay with distance. Using a coarse sampling grain (transects), habitat factors explained 40% of the variation, but the purely spatial component explained a comparable 22%. Analyzing plots within transects revealed variation in species composition that was still jointly determined by habitat and spatial factors (18 and 11% of the variance, respectively). For both grain sizes, most of the habitat component was spatially structured, reflecting an abrupt alongshore transition from sandy dunes to cobble beach. Space per se explained more variation in species composition at a second site where the habitat transition was more gradual; here, habitat acted as a less selective filter, allowing the signal of dispersal limitation to be detected more readily. We conclude that both adaptation to specific habitat factors and habitat-independent spatial position indicative of dispersal limitation determine plant species composition in this system. Our results support the prediction that dispersal limitation—a potentially, but not necessarily, neutral driver—is relatively more important at smaller scales.     

Woody species as landscape modulators: their effect on the herbaceous plants in a Mediterranean maquis

“Landscape modulators” are ecosystem engineers that have an impact on community structure by creating patches in the landscape mosaic. Our aim was to study the effect of evergreen-trees, as landscape modulators, on herbaceous plants in a Mediterranean maquis system in northern Israel. We examined the effects of canopy removal and cattle grazing on species richness, plant functional types, and rare plant species in two patch-types: (1) woody—under tree canopy (or the location of a removed canopy); (2) herbaceous—in open areas with no tree canopy. Patch-type and tree removal affected species richness and plant functional types. The extreme negative effect of the woody patch-type on species richness disappeared soon after the removal of the landscape modulator canopy. We conclude that the dominant effect of the evergreen woody landscape modulators can be regulated by canopy removal and grazing for maintaining patch-type and landscape diversities, and consequent high species richness in Mediterranean ecosystems, which is a main goal of global nature conservation policy.     

Abundance, Diversity, and Dynamics of Viruses on Microorganisms in Activated Sludge Processes

We examined the abundance of viruses on microorganisms in activated sludge and the dynamics of their community structure. Direct counting with epifluorescence microscopy and pulsed-field gel electrophoresis (PFGE) were applied to 20 samples from 14 full-scale wastewater treatment plants (wwtps) treating municipal, industrial, or animal wastewater. Furthermore, to observe the dynamics of viral community structure over time, a laboratory-scale sequencing batch reactor was operated for 58 days. The concentrations of virus particles in the wwtps, as quantified by epifluorescence microscopy, ranged from 4.2 × 10⁷ to 3.0 × 10⁹ mL⁻¹. PFGE, improved by the introduction of a higher concentration of Tris–EDTA buffer in the DNA extraction step, was successfully used to profile DNA viruses in the activated sludge. Most of the samples from different wwtps commonly had bands in the 40–70 kb range. In the monitoring of viral DNA size distribution in the laboratory-scale reactor, some bands were observed stably throughout the experimental period, some emerged during the operation, and others disappeared. Rapid emergence and disappearance of two intense bands within 6 days was observed. Our data suggest that viruses—especially those associated with microorganisms—are abundant and show dynamic behavior in activated sludge.     

Some views on the role of noise in “self”-organizing systems

This paper deals with information transfer from the environment and “self”-organization in open, nonlinear systems far from thermodynamic equilibrium — in the presence of either non-stationary phase jitter noise, or amplitude stationary noise. By “self”-organization we mean here the progressive formation within the system of sequential, ordered (coherent) relationships between appropriate dynamical variables-like for example, the phase differences between the oscillating components of the system. We take up (in Section II) the classical Laser as a specific example and examine in detail the influence of phase jitter noise in the mode (phase) locking process. We find—as expected—that phase fluctuations in the cavity cause degradation of the coherent behaviour (i.e. increase the entropy) of the system — which, however, levels off, or saturates with time. Further (in Section III) we examine systems where the number of self-sustained oscillating components may vary with time in such a way that the maximum entropy of the system increases faster than the overall instantaneous entropy. We put forth the hypothesis that in such cases — because of the increase of the redundancy — the system gets organized not just in spite of, but merely because of the presence of Noise. Possible applications in biological systems (especially concerning a model of cerebral organization) are briefly discussed. It is understood here, that the system has to display some preliminary dynamical structure before the organizing procedure takes over. What happens afterwards is the subject of this paper.     

How trophic interaction strength depends on traits

A key problem in community ecology is to understand how individual-level traits give rise to population-level trophic interactions. Here, we propose a synthetic framework based on ecological considerations to address this question systematically. We derive a general functional form for the dependence of trophic interaction coefficients on trophically relevant quantitative traits of consumers and resources. The derived expression encompasses—and thus allows a unified comparison of—several functional forms previously proposed in the literature. Furthermore, we show how a community’s, potentially low-dimens ional, effective trophic niche space is related to its higher-dimensional phenotypic trait space. In this manner, we give ecological meaning to the notion of the “dimensionality of trophic niche space.” Our framework implies a method for directly measuring this dimensionality. We suggest a procedure for estimating the relevant parameters from empirical data and for verifying that such data matches the assumptions underlying our derivation.     

Conservation implications of competition between generalist and specialist rodents in Mediterranean afforested landscape

Density dependent habitat selection at the community level is regarded as a major determinant of biodiversity at the local scale, and data on these processes and how they are affected by human activities is highly applicable to conservation. By studying the competitive relationships between a specialist and a generalist we can acquire valuable insights about how different environmental elements determine species abundance and distribution and consequently biodiversity. Here we describe a study of density dependent processes that determine the community structure of two rodents: a specialist—the broad toothed mouse (Apodemus mystacinus), and a generalist—the common spiny mouse (Acomys cahirinus) in a Mediterranean maqui habitat, and how this structure is impacted by anthropogenic planting of pine stands. We carried out two field experiments: The first, based on open field trapping, looking at how rodent communities change with habitat structure. The second experiment was an enclosure study aimed at validating the habitat preferences and competitive relationship between the specialist and the generalist. We identified asymmetric competition relationships in which the specialist was dominant over the generalist. Competition intensity was lower in maqui with >10% oak cover, although both species abundances were high. Competition was found only during the limiting season (summer). Based on these findings we produced management recommendations to keep indigenous small mammals’ biodiversity high. Density dependent habitat selection processes play a central role in determining biodiversity, and understanding the mechanisms motivating these processes is needed if alterations in biodiversity in response to human disturbance are to be understood.     

Habitat engineering by the invasive zebra mussel <Emphasis Type="Italic">Dreissena polymorpha</Emphasis> (Pallas) in a boreal coastal lagoon: impact on biodiversity

Habitat engineering role of the invasive zebra mussel Dreissena polymorpha (Pallas) was studied in the Curonian lagoon, a shallow water body in the SE Baltic. Impacts of live zebra mussel clumps and its shell deposits on benthic biodiversity were differentiated and referred to unmodified (bare) sediments. Zebra mussel bed was distinguished from other habitat types by higher benthic invertebrate biomass, abundance, and species richness. The impact of live mussels on biodiversity was more pronounced than the effect of shell deposits. The structure of macrofaunal community in the habitats with >10³ g/m² of shell deposits devoid of live mussels was similar to that found within the zebra mussel bed. There was a continuous shift in species composition and abundance along the gradient ‘bare sediments—shell deposits—zebra mussel bed’. The engineering impact of zebra mussel on the benthic community became apparent both in individual patches and landscape-level analyses.     

How well do single samples reflect rotifer species diversity? A test based on interannual variation of rotifer communities in Big Bend National Park (Texas,USA)

Studies of rotifer community composition and dynamics often rely on limited sampling regimes. To determine how well species richness is reflected in these studies, we examined interannual variation of rotifer species richness and monogonont community structure from 10 aquatic systems comprising four habitat types—springs, rock pools (tinajas), former cattle tanks, and artificial ponds—in Big Bend National Park (Texas, USA). Planktonic, littoral, and benthic samples were collected from all sites at about the same date for each of five summers (2001–2005). Our survey yielded 15 monogonont families including 30 genera and 84 species. Two bdelloid taxa also were designated. Species richness varied widely among these four habitats: range, 1–32; mean (±1 SD), 11.2 ± 8.0. Total Species richness in the habitats also varied considerably: springs (54 taxa) > artificial ponds (35 taxa) > tinajas (19 taxa) > cattle tanks (15 taxa). Sessile species comprised ≈13% of the taxa in our samples. Species turnover indices (STI) of these systems indicate low overall relatedness: mean (±1 S.D.) = 85.2 ± 7.1%. The relative frequency of encounter of most taxa in the four systems was low, with 79 taxa (≈92%) having values ≤2.0%. Singleton rates were quite high, ranging from 46.7 to 71.4%, with an overall mean ≈65.1%. Most importantly, we found that both species richness and STI varied considerably among habitat type. Species richness varied by 2–10× between consecutive years and STI ranged from 64 to 89% over the entire study. Our results indicate that rotifer community composition fluctuates greatly over time, and that rotifer community structure may be more labile than is generally believed. Species richness and thus biodiversity may be dramatically underestimated using single sampling or short-term strategies that are often employed in studies of zooplankton community structure. Guest editors: S. S. S. Sarma, R. D. Gulati, R. L. Wallace, S. Nandini, H. J. Dumont & R. Rico-Martínez Advances in Rotifer Research     

Invariance and Meaningfulness in Phenotype spaces

Mathematical spaces are widely used in the sciences for representing quantitative and qualitative relations between objects or individuals. Phenotype spaces—spaces whose elements represent phenotypes—are frequently applied in morphometrics, evolutionary quantitative genetics, and systematics. In many applications, several quantitative measurements are taken as the orthogonal axes of a Euclidean vector space. We show that incommensurable units, geometric dependencies between measurements, and arbitrary spacing of measurements do not warrant a Euclidean geometry for phenotype spaces. Instead, we propose that most phenotype spaces have an affine structure. This has profound consequences for the meaningfulness of biological statements derived from a phenotype space, as they should be invariant relative to the transformations determining the structure of the phenotype space. Meaningful geometric relations in an affine space are incidence, linearity, parallel lines, distances along parallel lines, intermediacy, and ratios of volumes. Biological hypotheses should be phrased and tested in terms of these fundamental geometries, whereas the interpretation of angles and of phenotypic distances in different directions should be avoided. We present meaningful notions of phenotypic variance and other statistics for an affine phenotype space. Furthermore, we connect our findings to standard examples of morphospaces such as Raup’s space of coiled shells and Kendall’s shape space.     

Benthic communities in the Southern Bight of the North Sea and their use in ecological monitoring

Macrobenthic and meiobenthic communities of an area off the Belgian coast of the North Sea were studied from 1970 until 1975 at 74 stations. On the basis of both macro- and meiobenthos, three zones can be distinguished in the area. The coastal zone is characterized by the macrobenthicAbra alba community, corresponding to the meiobenthicMicroarthridion littorale — Halectinosoma herdmani community, and the open sea zone by the macrobenthicVenus gallina community and the meiobenthicLeptastacus laticaudatus — Paramesochra helgolandica community. In between is a transient zone where elements of both other zones mix. The distribution of these zones is governed by the hydrodynamical regime of the region, especially by the residual and tidal current system of the Southern Bight. Within the coastal zone, the composition of the community is influenced by pollution which especially affects the epibenthic detritus-feeders of the meiobenthos. The spatial stability of parameters describing community structure can be used for monitoring changes. Temporal characteristics of these parameters could not be investigated properly, but diversity seems to be much stabler than biomass.     

Regeneration niche differentiates functional strategies of desert woody plant species

Plant communities vary dramatically in the number and relative abundance of species that exhibit facilitative interactions, which contributes substantially to variation in community structure and dynamics. Predicting species’ responses to neighbors based on readily measurable functional traits would provide important insight into the factors that structure plant communities. We measured a suite of functional traits on seedlings of 20 species and mature plants of 54 species of shrubs from three arid biogeographic regions. We hypothesized that species with different regeneration niches—those that require nurse plants for establishment (beneficiaries) versus those that do not (colonizers)—are functionally different. Indeed, seedlings of beneficiary species had lower relative growth rates, larger seeds and final biomass, allocated biomass toward roots and height at a cost to leaf mass fraction, and constructed costly, dense leaf and root tissues relative to colonizers. Likewise at maturity, beneficiaries had larger overall size and denser leaves coupled with greater water use efficiency than colonizers. In contrast to current hypotheses that suggest beneficiaries are less “stress-tolerant” than colonizers, beneficiaries exhibited conservative functional strategies suited to persistently dry, low light conditions beneath canopies, whereas colonizers exhibited opportunistic strategies that may be advantageous in fluctuating, open microenvironments. In addition, the signature of the regeneration niche at maturity indicates that facilitation expands the range of functional diversity within plant communities at all ontogenetic stages. This study demonstrates the utility of specific functional traits for predicting species’ regeneration niches in hot deserts, and provides a framework for studying facilitation in other severe environments.     

Diversity and composition of macrobenthic community associated with sandy shoals of the Louisiana continental shelf

Along the Louisiana, USA continental shelf, sandy shoals are shallow, possibly oxygen-rich “islands” surrounded by deeper muddy deposits prone to hypoxia. Shoals also contain significant quantities of fine sand that may be mined in the future for coastal restoration. The ecological role of shoals remains poorly understood and we hypothesized that shoals provide critical habitat for benthic invertebrates. Using Ship Shoal as a model system, we assessed the diversity and structure of macrobenthic assemblages and how community structure varies with season and environmental parameters. High biomass (averaging 26.7 g m⁻²) and high diversity (161 species) of macrobenthos was found in 2006. Polychaetes (45%—72 species) and crustaceans comprised most of the species (28%—46 species); spionids and amphipods dominated the polychaete and crustacean groups respectively, both in terms of number of species and abundances. Sharp decreases in diversity, abundance and biomass occurred from spring to autumn. Species diversity and total abundance significantly increased with decreasing sediment grain size and increasing bottom water dissolved oxygen. Across seasons, mole crabs Albunea paretii and amphioxus Branchiostoma floridae typified the community and contributed most of the biomass. The polychaetes Nephtys simoni, Neanthes micromma, Dispio uncinata, Mediomastus californiensis and Magelona sp. A, the amphipod Acanthohautorius sp. A and the burrowing shrimp Ogyrides alphaerostris also contributed to variation in community composition. Cluster analyses quantified seasonal variation, mainly based on sharp decreases in abundance, as well as spatial differences in species composition oriented along both east–west and north–south gradients. Variation in benthic assemblages was correlated with water depth and sediment characteristics (mean grain size and percentage of gravel-sized shell debris). We conclude that Ship Shoal is an unrecognized biodiversity hotspot and a hypoxia refuge compared to the immediate surrounding area where the benthic community is affected by seasonal hypoxia events and we discuss how sand-mining may influence this community.     

Observations on the relation between phytoplankton diversity and environmental factors in the Vaal River at Balkfontein,South Africa

The relationship between specific environmental factors as independent variables and temporal changes in phytoplankton community structure in the Vaal River (a turbid system) during 1984 was investigated by employing different diversity indices. Temporal changes in community structure reflected temporal changes in certain environmental factors. Phytoplankton diversity, measured with Shannon-Wie H' and Hurlbert PIE indices, was related firstly to discharge and discharge derived variables (such as SO₄, Si, N and P loading) and secondly to turbidity derived variables (such as euphotic zone depth). Discharge appears to be of prime importance in affecting diversity. Observations were made that shed new light on conditions contributing to the development of an August peak (dominated by Stephanodiscus hantzschii fo. tenuis and Micractinium pusillum) in phytoplankton concentration. Increased environmental stress may reduce the number of sensitive species, thus reducing interspecific competition between tolerant species which could then exploit the — for them — more favourable conditions resulting in an increase in their numbers to peak concentrations.     

Technologic advances in the imaging of ovarian morphology and their roles in ascertaining follicular growth and development in the rhesus monkey

Imaging follicular development has advanced notably from the invasive—laparotomy—to the relatively noninvasive—laparoscopy (making frequent observations over a single cycle possible)—to totally noninvasive approaches such as ultrasonography and magnetic resonance imaging (MRI). Now we can identify the dominant preovulatory follicle (DF) in macaques by day 6 of the menstrual cycle via laparoscopy and by day 6–8 via ultrasonography. MRI scans are remarkably correlated with histologic specimens. We obtained axial, coronal, and sagittal ovarian images with MRI software. Moreover, we are discerning structure/function relationships in ovarian estrogen-receptor systems using X-ray autoradiography and immunocytochemistry. We have localized the estrogen receptor in functional corpus luteum (CL) with ³H-estradiol and in germinal epithelium and granulosa cells with monoclonal antibody to the receptor. We believe that by using a combination of the aforementioned techniques, we will be able to investigate more fully the processes of recruitment and selection of ovarian follicles.     

Temporal niche dynamics, relative abundance and phylogenetic signal of coexisting species

The coexistence of similar species accounts for some 30% of diversity within communities, yet the coexistence and relative abundance of similar species is a continuing ecological conundrum. Using close phylogenetic relatedness as a measure of similarity, we previously demonstrated that neither classic niche theory nor neutral theory can explain the relative abundances of co-occurring pairs of similar tree species in a diverse tropical forest. Here, we show that the stable, focused competition of a temporal niche dynamic fits the distribution of observed fractional abundances (pairwise relative abundances). Previously published, independent evidence of temporal dynamics in this community supports our results; our model identifies additional criteria for field tests of differential sensitivity (DS) temporal dynamics. The success of temporal dynamics at explaining the observed distribution—and the failure of alternative hypotheses to do so—indicates that current diagnostics of community structure and assembly needs general re-examination. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Distance decay of community dynamics in rocky intertidal sessile assemblages evaluated by transition matrix models

It is well known that the similarity in species composition between two communities decays with the geographic distance that separates them. It is thus likely that the similarity in the dynamics of two communities also decays with distance, because the distance–decay relationship is fundamental in nature. However, the distance–decay relationships of community dynamics have not yet been revealed. We used transition matrix models to evaluate distance–decay relationships of seasonal community dynamics (from spring to summer) in rocky intertidal sessile assemblages along the Pacific coast of Japan between 31°N and 43°N. We evaluated the distance–decay relationships of whole-community dynamics and of three dynamics-related components—recruitment, disturbance, and species interaction (competition and facilitation)—for communities separated by distances ranging from several meters to thousands of kilometers. The similarity of the recruitment dynamics among communities declined rapidly with distance within the fine spatial scale, but only moderately within larger scales. The similarity of the disturbance dynamics was independent of distance, and the similarity of species interaction declined slightly with increasing distance. The similarity of whole-community dynamics declined rapidly with distance at a fine spatial scale and moderately at larger scales. The fact that the distance–decay relationship of whole-community dynamics was similar to that of recruitment may suggest that recruitment processes are the most important determinant of spatial variability of community dynamics at our study sites during the study period.     

Human evolution — Where from here?

Thanks to language, mankind is rapidly developing into a eusocial1 animal, within a single world-wide structure. Biological evolution based on random genetic events is no longer a part of the future of the species, and cultural evolution has taken its place. Ease of communication between minds means that distinction between individuals is becoming irrelevant. Future progress in the single world-wide community to which mankind is rapidly developing will rather be a self-guided process — evolution by self-design.      

Theory predicts a rapid transition from niche-structured to neutral biodiversity patterns across a speciation-rate gradient

A central challenge in community ecology is to predict patterns of biodiversity with mechanistic models. The neutral model of biodiversity is a simple model that appears to provide parsimonious and accurate predictions of biodiversity patterns in some ecosystems, even though it ignores processes such as species interactions and niche structure. In a recent paper, we used analytical techniques to reveal why the mean predictions of the neutral model are robust to niche structure in high diversity but not low-diversity ecosystems. In the present paper, we explore this phenomenon further by generating stochastic simulated data from a spatially implicit hybrid niche-neutral model across different speciation rates. We compare the resulting patterns of species richness and abundance with the patterns expected from a pure neutral and a pure niche model. As the speciation rate in the hybrid model increases, we observe a surprisingly rapid transition from an ecosystem in which diversity is almost entirely governed by niche structure to one in which diversity is statistically indistinguishable from that of the neutral model. Because the transition is rapid, one prediction of our abstract model is that high-diversity ecosystems such as tropical forests can be approximated by one simple model—the neutral model—whereas low-diversity ecosystems such as temperate forests can be approximated by another simple model—the niche model. Ecosystems that require the hybrid model are predicted to be rare, occurring only over a narrow range of speciation rates.