The existence and strength of higher order interactions is sensitive to environmental context

One strategy for understanding the dynamics of any complex system, such as a community of competing species, is to study the dynamics of parts of the system in isolation. Ecological communities can be decomposed into single species, and pairs of interacting species. This reductionist strategy assumes that whole-community dynamics are predictable and explainable from knowledge of the dynamics of single species and pairs of species. This assumption will be violated if higher order interactions (HOIs) are strong. Theory predicts that HOIs should be common. But it is difficult to detect HOIs, and to infer their long-term consequences for species coexistence, solely from short-term data. I conducted a protist microcosm experiment to test for HOIs among competing bacterivorous ciliates, and test the sensitivity of HOIs to environmental context. I grew three competing ciliate species in all possible combinations at each of two resource enrichment levels, and used the population dynamic data from the one- and two-species treatments to parameterize a competition model at each enrichment level. I then compared the predictions of the parameterized model to the dynamics of the whole community (three-species treatment). I found that the existence, and thus strength, of HOIs was environment dependent. I found a strong HOI at low enrichment, which enabled the persistence of a species that would otherwise have been competitively excluded. At high enrichment, three-species dynamics could be predicted from a parameterized model of one- and two-species dynamics, provided that the model accounted for nonlinear intraspecific density dependence. The results provide one of the first rigorous demonstrations of the long-term consequences of HOIs for species coexistence, and demonstrate the context dependence of HOIs. HOIs create difficult challenges for predicting and explaining species coexistence in nature.

Decline effects are rare in ecology

The scientific evidence base on any given topic changes over time as more studies are published. Currently, there is widespread concern about non-random, directional changes over time in the scientific evidence base associated with many topics. In particular, if studies finding large effects (e.g., large differences between treatment and control means) tend to get published quickly, while small effects tend to get published slowly, the net result will be a decrease over time in the estimated magnitude of the mean effect size, known as a "decline effect". If decline effects are common, then the published scientific literature will provide a biased and misleading guide to management decisions, and to the allocation of future research effort. We compiled data from 466 meta-analyses in ecology to look for evidence of decline effects. We found that decline effects are rare. Only ~5% of ecological meta-analyses truly exhibit a directional change in mean effect size over time arising for some reason other than random chance, usually but not always in the direction of decline. Most apparent directional changes in mean effect size over time are attributable to regression to the mean, consistent with primary studies being published in random order with respect to the effect sizes they report. Our results are good news: decline effects are the exception to the rule in ecology. Identifying and rectifying rare cases of true decline effects remains an important task, but ecologists should not overgeneralize from anecdotal reports of decline effects.

Experimental evolution of competing bean beetle species reveals long-term reversals of short-term evolution, but no consistent character displacement

Interspecific competition for shared resources should select for evolutionary divergence in resource use between competing species, termed character displacement. Many purported examples of character displacement exist, but few completely rule out alternative explanations. We reared genetically diverse populations of two species of bean beetles, Callosobruchus maculatus and Callosobruchus chinensis, in allopatry and sympatry on a mixture of adzuki beans and lentils, and assayed oviposition preference and other phenotypic traits after four, eight, and twelve generations of (co)evolution. C. maculatus specializes on adzuki beans; the generalist C. chinensis uses both beans. C. chinensis growing in allopatry emerged equally from both bean species. In sympatry, the two species competing strongly and coexisted via strong realized resource partitioning, with C. chinensis emerging almost exclusively from lentils and C. maculatus emerging almost exclusively from adzuki beans. However, oviposition preferences, larval survival traits, and larval development rates in both beetle species did not vary consistently between allopatric versus sympatric treatments. Rather, traits evolved in treatment-independent fashion, with several traits exhibiting reversals in their evolutionary trajectories. For example, C. chinensis initially evolved a slower egg-to-adult development rate on adzuki beans in both allopatry and sympatry, then subsequently evolved back toward the faster ancestral development rate. Lack of character displacement is consistent with a previous similar experiment in bean beetles and may reflect lack of evolutionary trade-offs in resource use. However, evolutionary reversals were unexpected and remain unexplained. Together with other empirical and theoretical work, our results illustrate the stringency of the conditions for character displacement.

The Many Roads to Generality in Ecology

The variety of nature presents a challenge for ecologists. Individual organisms differ from one another in ways both obvious and subtle, even if they’re members of the same species living in the same location. Different populations, species, communities, ecosystems, biomes, habitats, food webs, etc. also differ from another. What, if anything, can be said in general about ecological systems and how they work? If there are generalities in ecology, do they take the form of exceptionless “laws of nature” analogous to the laws of physics? Or do they take some other form? Should ecologists even try to identify ecological generalities? If so, how? The variety of nature is matched by the variety of ecologists’ answers to those questions. I will suggest that all of their answers are right—sometimes. Here I propose a taxonomy of the many different “roads to generality” in ecology: the various different kinds of “generality” that ecologists seek. I argue that each road to generality is valuable in its own way, but that different roads are useful in different contexts and for different purposes. Different roads to generality thus can be complementary to one another, and it would be a mistake for the field of ecology as a whole to focus exclusively on any one of them.

Occasional long distance dispersal increases spatial synchrony of population cycles

Spatially separated populations of the same species often exhibit correlated fluctuations in abundance, a phenomenon known as spatial synchrony. Dispersal can generate spatial synchrony. In nature, most individuals disperse short distances with a minority dispersing long distances. The effect of occasional long distance dispersal on synchrony is untested, and theoretical predictions are contradictory. Occasional long distance dispersal might either increase both overall synchrony and the spatial scale of synchrony, or reduce them. We conducted a protist microcosm experiment to test whether occasional long distance dispersal increases or decreases overall synchrony and the spatial scale of synchrony. We assembled replicate 15-patch ring metapopulations of the protist predator Euplotes patella and its protist prey Tetrahymena pyriformis. All metapopulations experienced the same dispersal rate, but differed in dispersal distance. Some metapopulations experienced strictly short distance (nearest neighbour) dispersal, others experienced a mixture of short- and long distance dispersal. Occasional long distance dispersal increased overall spatial synchrony and the spatial scale of synchrony for both prey and predators, though the effects were not statistically significant for predators. As predicted by theory, dispersal generated spatial synchrony by entraining the phases of the predator-prey cycles in different patches, a phenomenon known as phase locking. Our results are consistent with theoretical models predicting that occasional long distance dispersal increases spatial synchrony. However, our results also illustrate that the spatial scale of synchrony need not match the spatial scale of the processes generating synchrony. Even strictly short distance dispersal maintained high spatial synchrony for many generations at spatial scales much longer than the dispersal distance, thanks to phase locking.

Coevolution of competing Callosobruchus species does not stabilize coexistence

Interspecific resource competition is expected to select for divergence in resource use, weakening interspecific relative to intraspecific competition, thus promoting stable coexistence. More broadly, because interspecific competition reduces fitness, any mechanism of interspecific competition should generate selection favoring traits that weaken interspecific competition. However, species also can adapt to competition by increasing their competitive ability, potentially destabilizing coexistence. We reared two species of bean beetles, the specialist Callosobruchus maculatus and the generalist C. chinensis, in allopatry and sympatry on a mixture of adzuki beans and lentils, and assayed mutual invasibility after four, eight, and twelve generations of evolution. Contrary to the expectation that coevolution of competitors will weaken interspecific competition, the rate of mutual invasibility did not differ between sympatry and allopatry. Rather, the invasion rate of C. chinensis, but not C. maculatus, increased with duration of evolution, as C. chinensis adapted to lentils without experiencing reduced adaptation to adzuki beans, and regardless of the presence or absence of C. maculatus. Our results highlight that evolutionary responses to interspecific competition promote stable coexistence only under specific conditions that can be difficult to produce in practice.

The extended Price equation quantifies species selection on mammalian body size across the Palaeocene/Eocene Thermal Maximum

Species selection, covariation of species' traits with their net diversification rates, is an important component of macroevolution. Most studies have relied on indirect evidence for its operation and have not quantified its strength relative to other macroevolutionary forces. We use an extension of the Price equation to quantify the mechanisms of body size macroevolution in mammals from the latest Palaeocene and earliest Eocene of the Bighorn and Clarks Fork Basins of Wyoming. Dwarfing of mammalian taxa across the Palaeocene/Eocene Thermal Maximum (PETM), an intense, brief warming event that occurred at approximately 56 Ma, has been suggested to reflect anagenetic change and the immigration of small bodied-mammals, but might also be attributable to species selection. Using previously reconstructed ancestor-descendant relationships, we partitioned change in mean mammalian body size into three distinct mechanisms: species selection operating on resident mammals, anagenetic change within resident mammalian lineages and change due to immigrants. The remarkable decrease in mean body size across the warming event occurred through anagenetic change and immigration. Species selection also was strong across the PETM but, intriguingly, favoured larger-bodied species, implying some unknown mechanism(s) by which warming events affect macroevolution.

From Here to Eternity--The Theory and Practice of a Really Long Experiment

In February 1988, Richard Lenski set up 12 replicate populations of a single genotype of Escherichia coli in a simple nutrient medium. He has been following their evolution ever since. Here, Lenski answers provocative questions from Jeremy Fox about his iconic "Long-Term Evolution Experiment" (LTEE). The LTEE is a remarkable case study of the interplay of determinism and chance in evolution—and in the conduct of science.

Richard Lenski has been running his long-term evolution experiment for over 27 years. In this interview, ecologist Jeremy Fox asks him how and why he does it.

Abundance of common species, not species richness, drives delivery of a real-world ecosystem service

Biodiversity-ecosystem functioning experiments have established that species richness and composition are both important determinants of ecosystem function in an experimental context. Determining whether this result holds for real-world ecosystem services has remained elusive, however, largely due to the lack of analytical methods appropriate for large-scale, associational data. Here, we use a novel analytical approach, the Price equation, to partition the contribution to ecosystem services made by species richness, composition and abundance in four large-scale data sets on crop pollination by native bees. We found that abundance fluctuations of dominant species drove ecosystem service delivery, whereas richness changes were relatively unimportant because they primarily involved rare species that contributed little to function. Thus, the mechanism behind our results was the skewed species-abundance distribution. Our finding that a few common species, not species richness, drive ecosystem service delivery could have broad generality given the ubiquity of skewed species-abundance distributions in nature.

Using a "time machine" to test for local adaptation of aquatic microbes to temporal and spatial environmental variation

Local adaptation occurs when different environments are dominated by different specialist genotypes, each of which is relatively fit in its local conditions and relatively unfit under other conditions. Analogously, ecological species sorting occurs when different environments are dominated by different competing species, each of which is relatively fit in its local conditions. The simplest theory predicts that spatial, but not temporal, environmental variation selects for local adaptation (or generates species sorting), but this prediction is difficult to test. Although organisms can be reciprocally transplanted among sites, doing so among times seems implausible. Here, we describe a reciprocal transplant experiment testing for local adaptation or species sorting of lake bacteria in response to both temporal and spatial variation in water chemistry. The experiment used a -80°C freezer as a "time machine." Bacterial isolates and water samples were frozen for later use, allowing transplantation of older isolates "forward in time" and newer isolates "backward in time." Surprisingly, local maladaptation predominated over local adaptation in both space and time. Such local maladaptation may indicate that adaptation, or the analogous species sorting process, fails to keep pace with temporal fluctuations in water chemistry. This hypothesis could be tested with more finely resolved temporal data.

Synchronous dynamics of zooplankton competitors prevail in temperate lake ecosystems

Although competing species are expected to exhibit compensatory dynamics (negative temporal covariation), empirical work has demonstrated that competitive communities often exhibit synchronous dynamics (positive temporal covariation). This has led to the suggestion that environmental forcing dominates species dynamics; however, synchronous and compensatory dynamics may appear at different length scales and/or at different times, making it challenging to identify their relative importance. We compiled 58 long-term datasets of zooplankton abundance in north-temperate and sub-tropical lakes and used wavelet analysis to quantify general patterns in the times and scales at which synchronous/compensatory dynamics dominated zooplankton communities in different regions and across the entire dataset. Synchronous dynamics were far more prevalent at all scales and times and were ubiquitous at the annual scale. Although we found compensatory dynamics in approximately 14% of all combinations of time period/scale/lake, there were no consistent scales or time periods during which compensatory dynamics were apparent across different regions. Our results suggest that the processes driving compensatory dynamics may be local in their extent, while those generating synchronous dynamics operate at much larger scales. This highlights an important gap in our understanding of the interaction between environmental and biotic forces that structure communities.

Imbalance in individual researcher's peer review activities quantified for four British Ecological Society journals, 2003-2010

Researchers contribute to the scientific peer review system by providing reviews, and “withdraw” from it by submitting manuscripts that are subsequently reviewed. So far as we are aware, there has been no quantification of the balance of individual's contributions and withdrawals. We compared the number of reviews provided by individual researchers (i.e., their contribution) to the number required by their submissions (i.e. their withdrawals) in a large and anonymised database provided by the British Ecological Society. The database covered the Journal of Ecology, Journal of Animal Ecology, Journal of Applied Ecology, and Functional Ecology from 2003–2010. The majority of researchers (64%) did not have balanced contributions and withdrawals. Depending on assumptions, 12% to 44% contributed more than twice as much as required; 20% to 52% contributed less than half as much as required. Balance, or lack thereof, varied little in relation to the number of years a researcher had been active (reviewing or submitting). Researchers who contributed less than required did not lack the opportunity to review. Researchers who submitted more were more likely to accept invitations to review. These finding suggest overall that peer review of the four analysed journals is not in crisis, but only due to the favourable balance of over- and under-contributing researchers. These findings are limited to the four journals analysed, and therefore cannot include researcher's other peer review activities, which if included might change the proportions reported. Relatively low effort was required to assemble, check, and analyse the data. Broader analyses of individual researcher's peer review activities would contribute to greater quality, efficiency, and fairness in the peer review system.

Nonlinear effect of dispersal rate on spatial synchrony of predator-prey cycles

Spatially-separated populations often exhibit positively correlated fluctuations in abundance and other population variables, a phenomenon known as spatial synchrony. Generation and maintenance of synchrony requires forces that rapidly restore synchrony in the face of desynchronizing forces such as demographic and environmental stochasticity. One such force is dispersal, which couples local populations together, thereby synchronizing them. Theory predicts that average spatial synchrony can be a nonlinear function of dispersal rate, but the form of the dispersal rate-synchrony relationship has never been quantified for any system. Theory also predicts that in the presence of demographic and environmental stochasticity, realized levels of synchrony can exhibit high variability around the average, so that ecologically-identical metapopulations might exhibit very different levels of synchrony. We quantified the dispersal rate-synchrony relationship using a model system of protist predator-prey cycles in pairs of laboratory microcosms linked by different rates of dispersal. Paired predator-prey cycles initially were anti-synchronous, and were subject to demographic stochasticity and spatially-uncorrelated temperature fluctuations, challenging the ability of dispersal to rapidly synchronize them. Mean synchrony of prey cycles was a nonlinear, saturating function of dispersal rate. Even extremely low rates of dispersal (<0.4% per prey generation) were capable of rapidly bringing initially anti-synchronous cycles into synchrony. Consistent with theory, ecologically-identical replicates exhibited very different levels of prey synchrony, especially at low to intermediate dispersal rates. Our results suggest that even the very low rates of dispersal observed in many natural systems are sufficient to generate and maintain synchrony of cyclic population dynamics, at least when environments are not too spatially heterogeneous.

Biodiversity simultaneously enhances the production and stability of community biomass, but the effects are independent

To predict the ecological consequences of biodiversity loss, researchers have spent much time and effort quantifying how biological variation affects the magnitude and stability of ecological processes that underlie the functioning of ecosystems. Here we add to this work by looking at how biodiversity jointly impacts two aspects of ecosystem functioning at once: (1) the production of biomass at any single point in time (biomass/area or biomass/ volume), and (2) the stability of biomass production through time (the CV of changes in total community biomass through time). While it is often assumed that biodiversity simultaneously enhances both of these aspects of ecosystem functioning, the joint distribution of data describing how species richness regulates productivity and stability has yet to be quantified. Furthermore, analyses have yet to examine how diversity effects on production covary with diversity effects on stability. To overcome these two gaps, we reanalyzed the data from 34 experiments that have manipulated the richness of terrestrial plants or aquatic algae and measured how this aspect of biodiversity affects community biomass at multiple time points. Our reanalysis confirms that biodiversity does indeed simultaneously enhance both the production and stability of biomass in experimental systems, and this is broadly true for terrestrial and aquatic primary producers. However, the strength of diversity effects on biomass production is independent of diversity effects on temporal stability. The independence of effect sizes leads to two important conclusions. First, while it may be generally true that biodiversity enhances both productivity and stability, it is also true that the highest levels of productivity in a diverse community are not associated with the highest levels of stability. Thus, on average, diversity does not maximize the various aspects of ecosystem functioning we might wish to achieve in conservation and management. Second, knowing how biodiversity affects productivity gives no information about how diversity affects stability (or vice versa). Therefore, to predict the ecological changes that occur in ecosystems after extinction, we will need to develop separate mechanistic models for each independent aspect of ecosystem functioning.

When should we expect microbial phenotypic traits to predict microbial abundances?

Species' phenotypic traits may predict their relative abundances. Intuitively, this is because locally abundant species have traits making them well-adapted to local abiotic and biotic conditions, while locally rare species are not as well-adapted. But this intuition may not be valid. If competing species vary in how well-adapted they are to local conditions, why doesn't the best-adapted species simply exclude the others entirely? But conversely, if species exhibit niche differences that allow them to coexist, then by definition there is no single best adapted species. Rather, demographic rates depend on species' relative abundances, so that phenotypic traits conferring high adaptedness do not necessarily confer high abundance. I illustrate these points using a simple theoretical model incorporating adjustable levels of “adaptedness” and “niche differences.” Even very small niche differences can weaken or even reverse the expected correlation between adaptive traits and abundance. Conversely, adaptive traits confer high abundance when niche differences are very strong. Future work should be directed toward understanding the link between phenotypic traits and frequency-dependence of demographic rates.

Phase locking, the Moran effect and distance decay of synchrony: experimental tests in a model system

Spatially separated populations of many species fluctuate synchronously. Synchrony typically decays with increasing interpopulation distance. Spatial synchrony, and its distance decay, might reflect distance decay of environmental synchrony (the Moran effect), and/or short-distance dispersal. However, short-distance dispersal can synchronize entire metapopulations if within-patch dynamics are cyclic, a phenomenon known as phase locking. We manipulated the presence/absence of short-distance dispersal and spatially decaying environmental synchrony and examined their separate and interactive effects on the synchrony of the protist prey species Tetrahymena pyriformis growing in spatial arrays of patches (laboratory microcosms). The protist predator Euplotes patella consumed Tetrahymena and generated predator-prey cycles. Dispersal increased prey synchrony uniformly over both short and long distances, and did so by entraining the phases of the predator-prey cycles. The Moran effect also increased prey synchrony, but only over short distances where environmental synchrony was strongest, and did so by increasing the synchrony of stochastic fluctuations superimposed on the predator-prey cycle. Our results provide the first experimental demonstration of distance decay of synchrony due to distance decay of the Moran effect. Distance decay of the Moran effect likely explains distance decay of synchrony in many natural systems. Our results also provide an experimental demonstration of long-distance phase locking, and explain why cyclic populations provide many of the most dramatic examples of long-distance spatial synchrony in nature.

Coexistence mechanisms and the paradox of the plankton: quantifying selection from noisy data

Many species of phytoplankton typically co-occur within a single lake, as do many zooplankton species (the "paradox of the plankton"). Long-term co-occurrence suggests stable coexistence. Coexistence requires that species be equally "fit" on average. Coexistence mechanisms can equalize species' long-term average fitnesses by reducing fitness differences to low levels at all times, and by causing species' relative fitness to fluctuate over time, thereby reducing differences in time-averaged fitness. We use recently developed time series analysis techniques drawn from population genetics to estimate the strength of net selection (time-averaged selection over a year) and fluctuating selection (an index of the variation in selection throughout the year) in natural plankton communities. Analysis of 99 annual time series of zooplankton species dynamics and 49 algal time series reveals that within-year net selection generally is statistically significant but ecologically weak. Rates of net selection are -10 times faster in laboratory competition experiments than in nature, indicating that natural coexistence mechanisms are strong. Most species experience significant fluctuating selection, indicating that fluctuation-dependent mechanisms may contribute to coexistence. Within-year net selection increases with enrichment, implying that among-year coexistence mechanisms such as trade-offs between competitive ability and resting egg production are especially important at high enrichment. Fluctuating selection also increases with enrichment but is independent of the temporal variance of key abiotic factors, suggesting that fluctuating selection does not emerge solely from variation in abiotic conditions, as hypothesized by Hutchinson. Nor does fluctuating selection vary among lake-years because more variable abiotic conditions comprise stronger perturbations to which species exhibit frequency-dependent responses, since models of this mechanism fail to reproduce observed patterns of fluctuating selection. Instead, fluctuating selection may arise from internally generated fluctuations in relative fitness, as predicted by models of fluctuation-dependent coexistence mechanisms. Our results place novel constraints on hypotheses proposed to explain the paradox of the plankton.

Character convergence under competition for nutritionally essential resources

Resource competition is thought to drive divergence in resource use traits (character displacement) by generating selection favoring individuals able to use resources unavailable to others. However, this picture assumes nutritionally substitutable resources (e.g., different prey species). When species compete for nutritionally essential resources (e.g., different nutrients), theory predicts that selection drives character convergence. We used models of two species competing for two essential resources to address several issues not considered by existing theory. The models incorporated either slow evolutionary change in resource use traits or fast physiological or behavioral change. We report four major results. First, competition always generates character convergence, but differences in resource requirements prevent competitors from evolving identical resource use traits. Second, character convergence promotes coexistence. Competing species always attain resource use traits that allow coexistence, and adaptive trait change stabilizes the ecological equilibrium. In contrast, adaptation in allopatry never preadapts species to coexist in sympatry. Third, feedbacks between ecological dynamics and trait dynamics lead to surprising dynamical trajectories such as transient divergence in resource use traits followed by subsequent convergence. Fourth, under sufficiently slow trait change, ecological dynamics often drive one of the competitors to near extinction, which would prevent realization of long-term character convergence in practice.

‘Partitagin’ a hemorrhagic metalloprotease from Hippasa partita spider venom: Role in tissue necrosis

The poisonous bite by Hippasa partita, a funnel web spider from the Indian subcontinent has been demonstrated to give rise to severe dermo- and myonecrosis. In this work a hemorrhagic metalloprotease, Partitagin was purified from H. partita venom by successive chromatography on Sephadex G-100, DEAE Sephadex A-50 and Biosep DEAE columns. SDS-PAGE, reversed phase HPLC on a C(4) column, N-terminal amino acid sequencing and MALDI-TOF mass spectrometry confirmed the homogeneity. Partitagin was assayed using fat free casein as substrate. EDTA, 1,10-phenanthroline and cyanide, inactivated it irreversibly while, EGTA, PMSF, leupeptin, pepstatin and aprotinin did not inhibit. The presence of Zn(+2) was confirmed by atomic absorption spectrometry. Partitagin caused hemorrhage when tested in a mouse model. Light microscopy of skin tissue sections at the site of injection revealed extensive damage of extracellular matrix (ECM) in which the basement membrane surrounding blood vessels and capillaries showing signs of extensive destruction and also loss of vessel wall integrity. Similar intense damage was also noticed in the ECM of muscle tissue sections but with no damage caused to myocytes. Partitagin showed specificity of action on the components of ECM and degraded collagen type-IV and fibronectin but not collagen type-I. Partitagin was devoid of edema, myotoxicity and lethality. This is the first report on the isolation and characterization of a toxin from spider venom in the Indian subcontinent.

Environmental fluctuations can stabilize food web dynamics by increasing synchrony

Natural food webs are species-rich, but classical theory suggests that they should be unstable and extinction-prone. Asynchronous fluctuations in the densities of competing consumers can stabilize food web dynamics in constant environments. However, environmental fluctuations often synchronize dynamics in nature. Using the same 'diamond-shape' food web model first used to demonstrate the stabilizing effects of asynchrony in constant environments, we show that weak-to-moderate environmentally induced fluctuations in consumer mortality rates stabilize food webs while disrupting asynchrony. Synchrony actually promotes stability because: (i) synchronous declines in consumer density reduce the maximum abundance of top predators and (ii) resource competition quickly converts synchronous increases in consumer density into synchronous declines. These results are robust to details of food web topology and the implementation of environmental fluctuations. The fluctuation strengths that enhance stability are within the range experienced naturally by many species, suggesting that stabilization via environmental fluctuations is a realistic possibility.

Use of SILAC for exploring sheddase and matrix degradation of fibroblasts in culture by the PIII SVMP atrolysin A: Identification of two novel substrates with functional relevance

Snake venom metalloproteinases (SVMPs) in Viperid venoms primarily function to give rise to local and systemic hemorrhage following snake envenomation. Years of research on these toxins, both in vitro and in vivo, indicate that they function by disrupting capillary basement membranes, stromal matrix and cell-cell and cell-matrix contacts to allow escape of capillary contents under pressure. However, most of these studies used either defined substrates in vitro or were limited by relevant antibodies for detection of sites of action in vivo. In this investigation we use stable isotope-labeled amino acids in culture (SILAC) to determine novel proteolytic activities for exogenously added atrolysin A, a hemorrhagic PIII SVMP isolated from Crotalus atrox venom. When comparing the solubilized products of SILAC-labeled cultured human fibroblasts treated with atrolysin A to that of untreated fibroblasts using LC/MS/MS, several proteins were identified as being released into the culture media specifically due to atrolysin A proteolytic activity. These included collagen VI, fibronectin, fibulin 2 and annexin V. Of particular interest was the observation of collagen VI and annexin V in that the release of these substrates could play a role in altering hemostasis and promote hemorrhage caused by the more typical actions of atrolysin A. In summary, this study demonstrates the utility of SILAC for exploring sheddase activity with cells in culture and suggests the presence of two novel substrates for SVMPs that may play a pathological role in altering host hemostasis during envenomation.

Testing the mechanisms by which source-sink dynamics alter competitive outcomes in a model system

Dispersal among sites can affect within-site competitive outcomes via source-sink dynamics. Source-sink dynamics are thought to affect competitive outcomes primarily via spatial subsidies: by redistributing individuals from sources to sinks, source-sink dynamics can alter competitive outcomes in both sources and sinks. However, dispersal also can affect competitive outcomes via demography modification, which occurs when dispersal alters the parameters governing species' per capita demographic rates. For instance, dispersal of exploitative competitors might cause extinction of some of the resources for which competition occurs, thereby altering the competition coefficients. I used protist microcosms as a model system to test whether spatial subsidies alone could explain the effects of source-sink dynamics on competitive outcomes. I examined the long-term outcome of exploitative competition among three bacterivorous ciliate protists in microcosms of high enrichment (sources) and low enrichment (sinks) in both the presence and the absence of dispersal. Dispersal altered competitive outcomes. Fitting mathematical models to the population dynamics revealed that spatial subsidies were insufficient to account for the effects of dispersal. Fitting alternative models strongly suggested that demography modification was an important determinant of competitive outcomes. These results provide the first evidence that dispersal does not simply redistribute competitors but can alter their per capita demographic rates.

USING THE PRICE EQUATION TO PARTITION THE EFFECTS OF BIODIVERSITY LOSS ON ECOSYSTEM FUNCTION

Species loss can impact ecosystem functioning, but no general framework for analyzing these impacts exists. Here I derive a general partitioning of the effects of species loss on any ecosystem function comprising the summed contributions of individual species (e.g., primary productivity). The approach partitions the difference in ecosystem function between two sites (a "pre-loss" site, and a "post-loss" site comprising a strict subset of the species at the pre-loss site) into additive components attributable to different effects. The approach does not assume a particular experimental design or require monoculture data, making it more general than previous approaches. Using the Price Equation from evolutionary biology, I show that three distinct effects cause ecosystem function to vary between sites: the "species richness effect" (SRE; random loss of species richness), the "species composition effect" (SCE; nonrandom loss of high- or low-functioning species), and the "context dependence effect" (CDE; post-loss changes in the functioning of the remaining species). The SRE reduces ecosystem function without altering mean function per species. The SCE is analogous to natural selection in evolution. Nonrandom loss of, for example, high-functioning species will reduce mean function per species, and thus total function, just as selection against large individuals in an evolving population reduces mean body size in the next generation. The CDE is analogous to imperfect transmission in evolution. For instance, any factor (e.g., an environmental change) causing offspring to attain smaller body sizes than their parents (imperfect transmission) will reduce the mean body size in the next generation. Analogously, any factor causing the species remaining at the post-loss site to make smaller functional contributions than at the pre-loss site will reduce mean function per species, and thus total function. I use published data to illustrate how this new partition generalizes previous approaches, facilitates comparative analyses, and generates new empirical insights. In particular, the SCE often is less important than other effects.

Natterins, a new class of proteins with kininogenase activity characterized from Thalassophryne nattereri fish venom

A novel family of proteins with kininogenase activity and unique primary structure was characterized using combined pharmacological, proteomic and transcriptomic approaches of Thalassophryne nattereri fish venom. The major venom components were isolated and submitted to bioassays corresponding to its main effects: nociception and edema. These activities were mostly located in one fraction (MS3), which was further fractionated. The isolated protein, named natterin, was able to induce edema, nociception and cleave human kininogen and kininogen-derived synthetic peptides, releasing kallidin (Lys-bradykinin). The enzymatic digestion was inhibited by kallikrein inhibitors as Trasylol and TKI. Natterin N-terminal peptide showed no similarity with already known proteins present in databanks. Primary structure of natterin was obtained by a transcriptomic approach using a representative cDNA library constructed from T. nattereri venom glands. Several expressed sequence tags (ESTs) were obtained and processed by bioinformatics revealing a major group (18%) of related sequences unknown to gene or protein sequence databases. This group included sequences showing the N-terminus of isolated natterin and was named Natterin family. Analysis of this family allowed us to identify five related sequences, which we called natterin 1-4 and P. Natterin 1 and 2 sequences include the N-terminus of the isolated natterin. Furthermore, internal peptides of natterin 1-3 were found in major spots of whole venom submitted to mass spectrometry/2DGE. Similarly to the ESTs, the complete sequences of natterins did not show any significant similarity with already described tissue kallikreins, kininogenases or any proteinase, all being entirely new. These data present a new task for the knowledge of the action of kininogenases and may help in understanding the mechanisms of T. nattereri fish envenoming, which is an important medical problem in North and Northeast of Brazil.

Structure-based analysis of inhibitor binding to Ht-d

A theoretical study was performed on the structure of both the native and inhibited metalloproteinase Ht-d (E.C. 3.4.24.42) solved at 2.0 A resolution. The energy maps calculated by program GRID clearly showed the extended binding site of Ht-d and allowed localization and characterization of the pockets S1-S3 and S1'-S3'. The GRID energy contour maps point out the particular shape of the S1' pocket in agreement with experimental density maps and inhibited Ht-d structures. Based on the high degree of sequence homology of the Ht-d active site to that of mammalian metalloproteinases, the characterization of active site pockets was extended to neutrophil collagenase, fibroblast collagenase, stromelysin 1 and 2. Thirty residues of the Ht-d propeptide were modeled and optimized with reference to the Ht-d structure, giving insight to the mechanism of natural inhibition in metalloproteinase proenzymes. Kinetic measurements of Ht-d inhibition by a series of synthetic peptides show, in agreement with our Ht-d propeptide model, the crucial role of cysteine and adjacent residues in the specificity of Ht-d propeptide. This study suggests the structural link between Ht-d and mammalian metalloproteinases, contributing to the understanding of the mechanism of natural and synthetic inhibitor binding to metalloproteinases. Therefore, Ht-d is a good model system for the design of novel inhibitors against these enzymes with enhanced potency and specificity.