Hierarchical analysis of species distributions and abundance across environmental gradients

Abiotic and biotic processes operate at multiple spatial and temporal scales to shape many ecological processes, including species distributions and demography. Current debate about the relative roles of niche-based and stochastic processes in shaping species distributions and community composition reflects, in part, the challenge of understanding how these processes interact across scales. Traditional statistical models that ignore autocorrelation and spatial hierarchies can result in misidentification of important ecological covariates. Here, we demonstrate the utility of a hierarchical modeling framework for testing hypotheses about the importance of abiotic factors at different spatial scales and local spatial autocorrelation for shaping species distributions and abundances. For the two orchid species studied, understory light availability and soil moisture helped to explain patterns of presence and abundance at a microsite scale (<4 m2), while soil organic content was important at a population scale (<400 m2). The inclusion of spatial autocorrelation is shown to alter the magnitude and certainty of estimated relationships between abundance and abiotic variables, and we suggest that such analysis be used more often to explore the relationships between species life histories and distributions. The hierarchical modeling framework is shown to have great potential for elucidating ecological relationships involving abiotic and biotic processes simultaneously at multiple scales.     

Modelling the impact of flooding stress on the growth performance of woody species using fuzzy logic

Among the driving processes responsible for riparian forest dynamics the species-specific impact of flooding on the development of woody plants plays a key role—particularly for lowland rivers. Only a few of the forest succession models currently in use incorporate the flooding stress response of trees. This situation is mainly due to the incomplete investigation of the flooding tolerance processes and the related abiotic and biotic factors. In an attempt to use the wide-ranging but still rather vague knowledge available on flooding stress, the research presented in this paper proposes an approach to model tree response to flooding using the fuzzy set theory. The model is illustrated for the case of central European species. Flooding stress response to the abiotic factors of duration, depth and frequency of flooding differs according to five flooding tolerance classes and is expressed by means of a growth factor that limits optimal tree growth. We show that existing fuzzy set theory is able to generate and calibrate a flood stress response model which in turn can be incorporated into more complex forest succession models adapted to riparian areas.     

Non-consumptive effects of predator presence on copepod reproduction: insights from a mesocosm experiment

Reproduction in planktonic animals depends on numerous biotic and abiotic factors. One of them is predation pressure, which can have both direct consumptive effects on population density and sex ratio, and non-consumptive effects, for example on mating and migration behaviour. In copepods, predator vulnerability depends on their sex, motility pattern and mating behaviour. Therefore, copepods can be affected at multiple stages during the mating process. We investigated the reproductive dynamics of the estuarine copepod Eurytemora affinis in the presence and absence of its predator the mysid Neomysis integer in a mesocosm experiment. We found that the proportion of ovigerous females decreased in the presence of predators. This shift was not caused by differential predation as the absolute number of females was unaffected by mysid presence. Presence of predators reduced the ratio of males to non-ovigerous females, but not by predation of males. Our combined results suggest that the shift from ovigerous to non-ovigerous females under the presence of predators was caused by either actively delayed egg production or by shedding of egg sacs. Nauplii production was initially suppressed in the predation treatment, but increased towards the end of the experiment. The proportion of fertilized females was similar in both treatments, but constantly fell behind model predictions using a random mating model. Our results highlight the importance of non-consumptive effects of predators on copepod reproduction and hence on population dynamics.     

Abiotic constraints eclipse biotic resistance in determining invasibility along experimental vernal pool gradients.

Effective management of invasive species requires that we understand the mechanisms determining community invasibility. Successful invaders must tolerate abiotic conditions and overcome resistance from native species in invaded habitats. Biotic resistance to invasions may reflect the diversity, abundance, or identity of species in a community. Few studies, however, have examined the relative importance of abiotic and biotic factors determining community invasibility. In a greenhouse experiment, we simulated the abiotic and biotic gradients typically found in vernal pools to better understand their impacts on invasibility. Specifically, we invaded plant communities differing in richness, identity, and abundance of native plants (the "plant neighborhood") and depth of inundation to measure their effects on growth, reproduction, and survival of five exotic plant species. Inundation reduced growth, reproduction, and survival of the five exotic species more than did plant neighborhood. Inundation reduced survival of three species and growth and reproduction of all five species. Neighboring plants reduced growth and reproduction of three species but generally did not affect survival. Brassica rapa, Centaurea solstitialis, and Vicia villosa all suffered high mortality due to inundation but were generally unaffected by neighboring plants. In contrast, Hordeum marinum and Lolium multiflorum, whose survival was unaffected by inundation, were more impacted by neighboring plants. However, the four measures describing plant neighborhood differed in their effects. Neighbor abundance impacted growth and reproduction more than did neighbor richness or identity, with growth and reproduction generally decreasing with increasing density and mass of neighbors. Collectively, these results suggest that abiotic constraints play the dominant role in determining invasibility along vernal pool and similar gradients. By reducing survival, abiotic constraints allow only species with the appropriate morphological and physiological traits to invade. In contrast, biotic resistance reduces invasibility only in more benign environments and is best predicted by the abundance, rather than diversity, of neighbors. These results suggest that stressful environments are not likely to be invaded by most exotic species. However, species, such as H. marinum, that are able to invade these habitats require careful management, especially since these environments often harbor rare species and communities.     

Invasion, Disturbance, and Competition: Modeling the Fate of Coastal Plant Populations

Abstract:  Wetland habitats are besieged by biotic and abiotic disturbances such as invasive species, hurricanes, habitat fragmentation, and salinization. Predicting how these factors will alter local population dynamics and community structure is a monumental challenge. By examining ecologically similar congeners, such as Iris hexagona and I. pseudacorus (which reproduce clonally and sexually and tolerate a wide range of environmental conditions), one can identify life-history traits that are most influential to population growth and viability. We combined empirical data and stage-structured matrix models to investigate the demographic responses of native ( I. hexagona ) and invasive ( I. pseudacorus ) plant populations to hurricanes and salinity stress in freshwater and brackish wetlands. In our models I. hexagona and I. pseudacorus responded differently to salinity stress, and species coexistence was rare. In 82% of computer simulations of freshwater marsh, invasive iris populations excluded the native species within 50 years, whereas native populations excluded the invasive species in 99% of the simulations in brackish marsh. The occurrence of hurricanes allowed the species to coexist, and species persistence was determined by the length of time it took the ecosystem to recover. Rapid recovery (2 years) favored the invasive species, whereas gradual recovery (30 years) favored the native species. Little is known about the effects of hurricanes on competitive interactions between native and invasive plant species in marsh ecosystems. Our models contribute new insight into the relationship between environmental disturbance and invasion and demonstrate how influential abiotic factors such as climate change will be in determining interspecific interactions.     

Native ecotypic variation and the role of host identity in the spread of an invasive herbivore, Cactoblastis cactorum

Environmental niche models (ENMs) have gained enormous popularity as tools to investigate potential changes in species distributions resulting from climate change and species introductions. Despite recognition that species interactions can influence the dynamics of invasion spread, most implementations of ENMs focus on abiotic factors as the sole predictors of potential range limits. Implicit in this approach is the assumption that biotic interactions are relatively unimportant, either because of scaling issues, or because fundamental and realized niches are equivalent in a species' native range. When species are introduced into exotic landscapes, changes in biotic interactions relative to the native range can lead to occupation of different regions of niche space and apparent shifts in physiological tolerances. We use an escaped biological control organism, Cactoblastis cactorum (Berg.), to assess the role of the environmental envelope as compared with patterns of host-herbivore associations based on collections made in the native range. Because all nonnative populations are derived from a single C. cactorum ecotype, we hypothesize that biotic interactions associated with this ecotype are driving the species' invasion dynamics. Environmental niche models constructed from known native populations perform poorly in predicting nonnative distributions of this species, except where there is an overlap in niche space. In contrast, genetic isolation in the native range is concordant with the observed pattern of host use, and strong host association has been noted in nonnative landscapes. Our results support the hypothesis that the apparent shift in niche space from the native to the exotic ranges results from a shift in biotic interactions, and demonstrate the importance of considering biotic interactions in assessing the risk of future spread for species whose native range is highly constrained by biotic interactions.     

Photosynthate partitioning by phytoplankton in a New Zealand coastal upwelling system

A stimulation model of copepod population dynamics (development rate, fecundity, and mortality) was used to compute the predatory consumption necessary to control population growth in three dominant copepod species (Pseudocalanus sp., Paracalanus parvus, and Calanus finmarchicus) on Georges Bank, given observed seasonal cycles of copepod and predator populations. The model also calculated secondary production of each species. Copepod development rate and fecundity were functions of temperature while mortality was a function of predator abundance and consumption rate. Daily inputs of temperature and predator abundance (chaetognaths, ctenophores, and Centropages spp.) were derived from equations fit to field data. Model runs were made with various consumption rates until the model output matched observed copepod seasonal cycles. Computed consumption rates were low compared with published values from field and laboratory studies indicating that, even at conservative estimates of consumption, predators are able to control these copepod populations. Combined annual secondary production by the small copepod species, Pseudocalanus sp. and P. parvus, was nearly twice that of the larger C. finmarchicus with P. parvus having the highest total annual production.     

Long-term dynamics of biotic and abiotic resistance to exotic species invasion in restored vernal pool plant communities

Invasion of native ecosystems by exotic species can seriously threaten native biodiversity, alter ecosystem function, and inhibit conservation. Moreover, restoration of native plant communities is often impeded by competition from exotic species. Exotic species invasion may be limited by unfavorable abiotic conditions and by competition with native species, but the relative importance of biotic and abiotic factors remains controversial and may vary during the invasion process. We used a long-term experiment involving restored vernal pool plant communities to characterize the temporal dynamics of exotic species invasion, and to evaluate the relative support for biotic and abiotic factors affecting invasion resistance. Experimental pools (n=256) were divided among controls and several seeding treatments. In most treatments, native vernal pool species were initially more abundant than exotic species, and pools that initially received more native seeds exhibited lower frequencies of exotic species over time. However, even densely seeded pools were eventually dominated by exotic species, following extreme climatic events that reduced both native and exotic plant densities across the study site. By the sixth year of the experiment, most pools supported more exotics than native vernal pool species, regardless of seeding treatment or pool depth. Although deeper pools were less invaded by exotic species, two exotics (Hordeum marinum and Lolium multiflorum) were able to colonize deeper pools as soon as the cover of native species was reduced by climatic extremes. Based on an information-theoretic analysis, the best model of invasion resistance included a nonlinear effect of seeding treatment and both linear and nonlinear effects of pool depth. Pool depth received more support as a predictor of invasion resistance, but seeding intensity was also strongly supported in multivariate models of invasion, and was the best predictor of resistance to invasion by H. marinum and L. multilorum. We conclude that extreme climatic events can facilitate exotic species invasions by both reducing abiotic constraints and weakening biotic resistance to invasion.     

Allee effect limits colonization success of sexually reproducing zooplankton

Understanding the dynamics of populations at low density and the role of Allee effects is a priority due to concern about the decline of rare species and interest in colonization/invasion dynamics. Despite well-developed theory and observational support, experimental examinations of the Allee effect in natural systems are rare, partly because of logistical difficulties associated with experiments at low population density. We took advantage of fish introduction and removal in alpine lakes to experimentally test for the Allee effect at the whole-ecosystem scale. The large copepod Hesperodiaptomus shoshone is often extirpated from the water column by fish and sometimes fails to recover following fish disappearance, despite the presence of a long-lived egg bank. Population growth rate of this dioecious species may be limited by mate encounter rate, such that below some critical density a colonizing population will fail to establish. We conducted a multi-lake experiment in which H. shoshone was stocked at densities that bracketed our hypothesized critical density of 0.5-5 copoepods/m3. Successful recovery by the copepod was observed only in the lake with the highest initial density (3 copepods/m3). Copepods stocked into small cages at 3000 copepods/m3 survived and reproduced at rates comparable to natural populations, confirming that the lakes were suitable habitat for this species. In support of mate limitation as the mechanism underlying recovery failure, we found a significant positive relationship between mating success and density across experimental and natural H. shoshone populations. Furthermore, a mesocosm experiment provided evidence of increased per capita population growth rate with increasing population density in another diaptomid species, Skistodiaptomus pallidus. Together, these lines of evidence support the importance of the Allee effect to population recovery of H. shoshone in the Sierra Nevada, and to diaptomid copepods in general.     

Effects of Changes in Biodiversity on Ecosystem Function in Tropical Forests

Changing land use in the tropics has resulted in vast areas of damaged and degraded lands where biodiversity has been reduced. The majority of research on biodiversity has been focused on population and community dynamics and has rarely considered the ecosystem processes that are intimately related. We present a framework for examining the effects of changes in biodiversity on ecosystem function in natural, managed, and damaged tropical forests. Using a whole-ecosystem approach, the framework identifies key nutrient and energy cycling processes and critical junctures or pathways, termed interfaces, where resources are concentrated and transferred between the biotic and abiotic components of the ecosystem. Processes occurring at these interfaces, and the organisms or attributes participating in these processes, exert a strong influence on ecosystem structure. We use examples from Puerto Rico, Southern China, Dominica, and Nicaragua to illustrate how the functional diversity framework can be applied to critically examine the effects of changes in biodiversity on ecosystem function, and the relative success or failure of rehabilitation strategies. The few available data suggest that functional diversity, and not just species richness, is important in maintaining the integrity of nutrient and energy fluxes. High species richness, however, may increase ecosystem resiliency following disturbance by increasing the number of alternative pathways for the flow of resources. We suggest ways in which the framework of functional diversity can be used to design research to examine the effects of changes in biodiversity on ecosystem processes and in the design and evaluation of ecosystem management and land rehabilitation projects in the tropics.     

Recruitment limitation in Dungeness crab populations is driven by variation in atmospheric forcing

Ecologists have long debated the relative importance of biotic interactions vs. abiotic forces on the population dynamics of both marine and terrestrial organisms. Investigation of stock size in Dungeness crab (Cancer magister) is a classic example of this debate. We first tested the hypothesis that adult population size was set by larval success. We found that during a five-year sampling period, adult crab population size from Oregon through central California, USA, as measured by the commercial catch, varied directly with the number of terminal-stage larvae (megalopae) returning to Coos Bay, Oregon, four years earlier; adult population size was largely determined (> 90% of the variation) by success during the larval stage. We then tested whether biotic interactions or abiotic forces caused the variation in larval success. Most of the variation (> 90%) in the number of returning megalopae is explained by the timing of the spring transition, a seasonal shift in atmospheric forcing that drives ocean currents along the west coast of the United States. Early spring transitions lead to larger numbers of returning Dungeness megalopae, while in four other crab taxa, species with very different life history characteristics, early-spring transitions lead to lower numbers of returning megalopae. During the past roughly 30 years, the size of the commercial catch of Dungeness crab is significantly and negatively correlated with the date of the spring transition throughout the California Current system. Long-term variation in the date of the spring transition may explain a major crash in the Dungeness crab fishery in central California, which began in the late 1950s. The data suggest that Dungeness crab population size is determined by variation in larval success and that a significant portion of this variation is due to the timing of the spring transition, a large-scale climatic forcer.     

汞的环境光化学

作为一种全球污染物,汞在水体、底泥、土壤、大气等介质中以各种不同形态存在.各种汞形态具有不同的理化特性及毒性.汞形态的转化对于汞的迁移、毒性、食物链富集放大效应等具有重要影响.光照在汞的形态转化中起着重要作用,主要涉及光氧化、光还原、甲基汞的光降解以及无机汞的光化学甲基化等四个方面.本文对不同环境介质中汞的光化学转化过...     

Population structure of two deep-sea hydrothermal vent gastropods from the Juan de Fuca Ridge, NE Pacific

The gastropods Lepetodrilus fucensis and Depressigyra globulus are abundant faunal components of animal communities at deep-sea hydrothermal vents along the Juan de Fuca Ridge in the NE Pacific. The population structure and recruitment pattern of both species were studied using modal decomposition of length–frequency distributions. Gastropod populations were collected from Axial Volcano and Endeavour Segment in 2002 and 2003. Polymodal size–frequency distributions, particularly at Axial Volcano vent sites, suggest a discontinuous recruitment pattern for D. globulus. In contrast, there were no distinct peaks visible in the distributions of L. fucensis, suggesting a continuous recruitment pattern for this species. For both species, distributions were positively skewed towards the smaller length–classes, implying post-settlement mortality is high. However, variations in growth, due to short- and long-term variability in environmental conditions in the hydrothermal vent habitat, as well as biological interactions, may also be influencing the distribution and abundance of subsequent life-history stages. Using maximum shell lengths from populations of known ages, the growth rate of L. fucensis was estimated as 9.6 μm day⁻¹, indicating adulthood would be reached in ∼1 year. Our results suggest that, despite occupying the same habitat, abundance and population structure are regulated by different biotic and abiotic processes in L. fucensis and D. globulus.     

Can ocean acidification affect population dynamics of the barnacle Semibalanus balanoides at its southern range edge?

The global ocean and atmosphere are warming. There is increasing evidence suggesting that, in addition to other environmental factors, climate change is affecting species distributions and local population dynamics. Additionally, as a consequence of the growing levels of atmospheric carbon dioxide (CO2), the oceans are taking up increasing amounts of this CO2, causing ocean pH to decrease (ocean acidification). The relative impacts of ocean acidification on population dynamics have yet to be investigated, despite many studies indicating that there will be at least a sublethal impact on many marine organisms, particularly key calcifying organisms. Using empirical data, we forced a barnacle (Semibalanus balanoides) population model to investigate the relative influence of sea surface temperature (SST) and ocean acidification on a population nearing the southern limit of its geographic distribution. Hindcast models were compared to observational data from Cellar Beach (southwestern United Kingdom). Results indicate that a declining pH trend (-0.0017 unit/yr), indicative of ocean acidification over the past 50 years, does not cause an observable impact on the population abundance relative to changes caused by fluctuations in temperature. Below the critical temperature (here T(crit) = 13.1 degrees C), pH has a more significant affect on population dynamics at this southern range edge. However, above this value, SST has the overriding influence. At lower SST, a decrease in pH (according to the National Bureau of Standards, pHNBs) from 8.2 to 7.8 can significantly decrease the population abundance. The lethal impacts of ocean acidification observed in experiments on early life stages reduce cumulative survival by approximately 25%, which again will significantly alter the population level at this southern limit. Furthermore, forecast predictions from this model suggest that combined acidification and warming cause this local population to die out 10 years earlier than would occur if there was only global warming and no concomitant decrease in pH.     

Influence of increased cod abundance and temperature on recruitment of northern shrimp (Pandalus borealis)

Despite an increase in northern shrimp (Pandalus borealis) female biomass in the past years, the recruitment of the offshore population north and northeast of Iceland has remained very low. In this study, the influence of abiotic and biotic factors was studied in relation to shrimp recruitment. Two factors, cod (Gadus morhua) abundance and summer sea surface temperature (SST), were found to have a negative effect on offshore shrimp recruitment, explaining 71 % of the observed variation. Both cod abundance and temperature on the offshore shrimp grounds have increased in the past years, while recruitment has decreased and been at historically low levels since 2005. No significant relationship was found between recruitment and spawning biomass, indicating that recruitment variability is mainly driven by other factors. Cod abundance and summer SST are likely to affect different life stages of shrimp, as SST influences shrimp during its planktonic phase while cod abundance influences the demersal stage.     

Influence of corallivory, competition, and habitat structure on coral community shifts

The species composition of coral communities has shifted in many areas worldwide through the relative loss of important ecosystem engineers such as highly branched corals, which are integral in maintaining reef biodiversity. We assessed the degree to which the performance of recently recruited branching corals was influenced by corallivory, competition, sedimentation, and the interactions between these factors. We also explored whether the species-specific influence of these biotic and abiotic constraints helps to explain recent shifts in the coral community in lagoons of Moorea, French Polynesia. Population surveys revealed evidence of a community shift away from a historically acroporid-dominated community to a pocilloporid- and poritid-dominated community, but also showed that the distribution and abundance of coral taxa varied predictably with location in the lagoon. At the microhabitat scale, branching corals grew mainly on dead or partially dead massive Porites ("bommies"), promontories with enhanced current velocities and reduced sedimentation. A demographic study revealed that growth and survival of juvenile Pocillopora verrucosa and Acropora retusa, the two most common branching species of each taxon, were affected by predation and competition with vermetid gastropods. By 24 months of age, 20-60% of juvenile corals suffered partial predation by corallivorous fishes, and injured corals experienced reduced growth and survival. A field experiment confirmed that partial predation by corallivorous fishes is an important, but habitat-modulated, constraint for branching corals. Competition with vermetid gastropods reduced growth of both branching species but unexpectedly also provided an associational defense against corallivory. Overall, the impact of abiotic constraints was habitat-specific and similar for Acropora and Pocillopora, but biotic interactions, especially corallivory, had a greater negative effect on Acropora than Pocillopora, which may explain the local shift in coral community composition.     

Modelling with uncertainty: Introducing a probabilistic framework to predict animal population dynamics

Predictive population models designed to assist managers and policy makers require an explicit treatment of inherent uncertainty and variability. These are particular concerns when modelling non-native and reintroduced species, when data have been collected within one geographical or ecological context but predictions are required for another, or when extending models to predict the consequences of environmental change (e.g., climate or land-use). We present an aspatial, probabilistic framework of hierarchical process models for predicting population growth even when data are sparse or of poor quality. Insight into the factors affecting population dynamics in real landscapes can be provided and Kullback–Leibler distances are used to compare the relative output of models. This flexible yet robust framework gives easily interpretable results, allowing managers as well as modellers to invalidate anomalous models and apply others to real-life scenarios.We illustrate the framework’s power with a meta-analysis of European wild boar (Sus scrofa) data. We test hypotheses about the effect of geographic region, hunting and mast years on wild boar population growth, to build models of wild boar dynamics for the UK. The framework quantifies the importance of hunting pressure as a driver of population growth, and confirms that reproductive success is greatly decreased in poor mast years, suggesting that the key to predicting wild boar dynamics is to ascertain local hunting pressure and to better understand changing food availability. Geography had no significant effect, indicating that it is not a good proxy for modelling the impact of change in climate or land-use on wild boar populations at the European scale. We use the framework to predict population abundance 9 years after an isolated population of wild boar established in the UK; in a comparison with the only field data and two independent modelling exercises, our framework provides the most robust and informative results.     

Effects of an Invasive Plant on Population Dynamics in Toads

When populations decline in response to unfavorable environmental change, the dynamics of their population growth shift. In populations that normally exhibit high levels of variation in recruitment and abundance, as do many amphibians, declines may be difficult to identify from natural fluctuations in abundance. However, the onset of declines may be evident from changes in population growth rate in sufficiently long time series of population data. With data from 23 years of study of a population of Fowler's toad (Anaxyrus [ = Bufo] fowleri) at Long Point, Ontario (1989–2011), we sought to identify such a shift in dynamics. We tested for trends in abundance to detect a change point in population dynamics and then tested among competing population models to identify associated intrinsic and extrinsic factors. The most informative models of population growth included terms for toad abundance and the extent of an invasive marsh plant, the common reed (Phragmites australis), throughout the toads’ marshland breeding areas. Our results showed density‐dependent growth in the toad population from 1989 through 2002. After 2002, however, we found progressive population decline in the toads associated with the spread of common reeds and consequent loss of toad breeding habitat. This resulted in reduced recruitment and population growth despite the lack of significant loss of adult habitat. Our results underscore the value of using long‐term time series to identify shifts in population dynamics coincident with the advent of population decline. Efectos de una Planta Invasora sobre las Dinámica Poblacional de Sapos     

Small-scale grassland assembly patterns differ above and below the soil surface

The existence of deterministic assembly rules for plant communities remains an important and unresolved topic in ecology. Most studies examining community assembly have sampled aboveground species diversity and composition. However, plants also coexist belowground, and many coexistence theories invoke belowground competition as an explanation for aboveground patterns. We used next-generation sequencing that enables the identification of roots and rhizomes from mixed-species samples to measure coexisting species at small scales in temperate grasslands. We used comparable data from above (conventional methods) and below (molecular techniques) the soil surface (0.1 x 0.1 x 0.1 m volume). To detect evidence for nonrandom patterns in the direction of biotic or abiotic assembly processes, we used three assembly rules tests (richness variance, guild proportionality, and species co-occurrence indices) as well as pairwise association tests. We found support for biotic assembly rules aboveground, with lower variance in species richness than expected and more negative species associations. Belowground plant communities were structured more by abiotic processes, with greater variability in richness and guild proportionality than expected. Belowground assembly is largely driven by abiotic processes, with little evidence for competition-driven assembly, and this has implications for plant coexistence theories that are based on competition for soil resources.