Hierarchical Bayesian models in ecology: Reconstructing species interaction networks from non-homogeneous species abundance data

The relationships among organisms and their surroundings can be of immense complexity. To describe and understand an ecosystem as a tangled bank, multiple ways of interaction and their effects have to be considered, such as predation, competition, mutualism and facilitation. Understanding the resulting interaction networks is a challenge in changing environments, e.g. to predict knock-on effects of invasive species and to understand how climate change impacts biodiversity. The elucidation of complex ecological systems with their interactions will benefit enormously from the development of new machine learning tools that aim to infer the structure of interaction networks from field data. In the present study, we propose a novel Bayesian regression and multiple changepoint model (BRAM) for reconstructing species interaction networks from observed species distributions. The model has been devised to allow robust inference in the presence of spatial autocorrelation and distributional heterogeneity. We have evaluated the model on simulated data that combines a trophic niche model with a stochastic population model on a 2-dimensional lattice, and we have compared the performance of our model with L1-penalized sparse regression (LASSO) and non-linear Bayesian networks with the BDe scoring scheme. In addition, we have applied our method to plant ground coverage data from the western shore of the Outer Hebrides with the objective to infer the ecological interactions. (C) 2012 Elsevier B.V. All rights reserved.

Defining the Impact of Non-Native Species

Non-native species cause changes in the ecosystems to which they are introduced. These changes, or some of them, are usually termed impacts; they can be manifold and potentially damaging to ecosystems and biodiversity. However, the impacts of most non-native species are poorly understood, and a synthesis of available information is being hindered because authors often do not clearly define impact. We argue that explicitly defining the impact of non-native species will promote progress toward a better understanding of the implications of changes to biodiversity and ecosystems caused by non-native species; help disentangle which aspects of scientific debates about non-native species are due to disparate definitions and which represent true scientific discord; and improve communication between scientists from different research disciplines and between scientists, managers, and policy makers. For these reasons and based on examples from the literature, we devised seven key questions that fall into 4 categories: directionality, classification and measurement, ecological or socio-economic changes, and scale. These questions should help in formulating clear and practical definitions of impact to suit specific scientific, stakeholder, or legislative contexts.

Parasites that change predator or prey behaviour can have keystone effects on community composition

Parasites play pivotal roles in structuring communities, often via indirect interactions with non-host species. These effects can be density-mediated (through mortality) or trait-mediated (behavioural, physiological and developmental), and may be crucial to population interactions, including biological invasions. For instance, parasitism can alter intraguild predation (IGP) between native and invasive crustaceans, reversing invasion outcomes. Here, we use mathematical models to examine how parasite-induced trait changes influence the population dynamics of hosts that interact via IGP. We show that trait-mediated indirect interactions impart keystone effects, promoting or inhibiting host coexistence. Parasites can thus have strong ecological impacts, even if they have negligible virulence, underscoring the need to consider trait-mediated effects when predicting effects of parasites on community structure in general and biological invasions in particular.

Non-indigenous marine macroalgae in native communities: a case study in the British Isles

It has traditionally been considered that areas with high natural species richness are likely to be more resistant to non-indigenous species than those with lower numbers of species. However, this theory has been the subject of a debate over the last decade, since some studies have shown the opposite trend. In the present study, a macroalgal survey was carried out at 24 localities in Northern Ireland and southern England, using a quadrat approach in the lower littoral. The two opposing hypotheses were tested (negative versus positive relationship between native and non-indigenous species richness) in this marine environment. The effect of the presence of 'impacts', potential sources of disturbance and species introduction (e.g. marina, harbour or aquaculture), was also tested. A positive relationship was found between the number of non-indigenous species and the native species richness at the three different scales tested (quadrats, sites and localities). At no scale did a richer native assemblage appear to restrict the establishment of introduced species. The analyses revealed greater species richness and different community composition, as well as more non-indigenous species, in southern England relative to Northern Ireland. The presence of the considered impacts had an effect on the community composition and species richness in southern England but not in Northern Ireland. Such impacts had no effect on the non-indigenous species richness in either area.

The importance of stakeholder engagement in invasive species management: A cross-jurisdictional perspective in Ireland

The management of invasive non-native species is a frequent cause of conflict in the field of biodiversity conservation because perceptions of their costs and benefits differ among stakeholder groups. A lack of cohesion between scientific researchers, the commercial sector and policy makers lies at the root of a widespread failure to develop and implement sustainable management practices for invasive species. The crisis of this situation is intensified by drivers stemming from international conventions and directives to address invasive species issues. There are further direct conflicts between legislative instruments promoting biodiversity conservation on the one hand while liberalizing trade at the national, European and global level on the other. The island of Ireland provides graphic illustration of the importance of cross-jurisdictional approaches to biological invasions. Using primarily Irish examples in this review, we emphasize the importance of approaching risk assessment, risk reduction and control or eradication policies from a cost-efficient, highly flexible perspective, incorporating linkages between environmental, economic and social objectives. The need for consolidated policies between Northern Ireland and the Republic of Ireland is particularly acute, though few model cross-border mechanisms for such consolidation are available. The importance of engaging affected stakeholders through positive interactions is discussed with regard to reducing the currently fragmented nature of invasive species management between the two jurisdictions.

Do non-native invasive fish support elevated lamprey populations?

Summary
1: Managing populations of predators and their prey to achieve conservation or resource management goals is usually technically challenging and frequently socially controversial. This is true even in the simplest ecosystems but can be made much worse when predator–prey relationships are in?uenced by complex interactions, such as biological invasions, population trends or animal movements.
2: Lough Neagh in Northern Ireland is a European stronghold for pollan Coregonus autumnalis, a coregonine ?sh and for river lampreyLampetra ?uviatilis, which feeds parasitically as an adult. Both species are of high conservation importance. Lampreys are known to consume pollan but detailed knowledge of their interactions is scant. While pollan is well known to be a landlocked species in Ireland, the life cycle of normally anadromous river lamprey in Lough Neagh has been unclear. The Lough is also a highly perturbed ecosystem, supporting several invasive, non-native ?sh species that have the potential to in?uence lamprey–pollan interactions.
3: We applied stable isotope techniques to resolve both the movement patterns of lamprey and trophic interactions in this complex community. Recognizing that stable isotope studies are often hampered by high-levels of variability and uncertainty in the systems of interest, we employed novel Bayesian mixing models, which incorporate variability and uncertainty.
4: Stable isotope analyses identi?ed troutSalmo trutta and non-native breamAbramis brama as the main items in lamprey diet. Pollan only represented a major food source for lamprey between May and July.
5: Stable isotope ratios of carbon in tissues from 71 adult lamprey showed no evidence of marine carbon sources, strongly suggesting that Lough Neagh is host to a highly unusual, nonanadromous freshwater population. This ?nding marks out the Lough’s lamprey population as of particular scienti?c interest and enhances the conservation signi?cance of this feature of the Lough.
6: Synthesis and applications.Our Bayesian isotopic mixing models illustrate an unusual pattern of animal movement, enhancing conservation interest in an already threatened population. We have also revealed a complex relationship between lamprey and their food species that is suggestive of hyperpredation, whereby non-native species may sustain high lamprey populations that may in turn be detrimental to native pollan.Long-term conservation of lamprey and pollan in this system is likely to require management intervention, but in light of this exceptional complexity, no simple management options are currently supported. Conservation plans will require better characterization ofpopulation-level interactions and simulation modelling of interventions. More generally, our study demonstrates the importance of considering a full range of possible trophic interactions, particularly in complex ecosystems, and highlights Bayesian isotopic mixing models as powerful tools in resolving trophic relationships.
Key-words: Bayesian, conservation dilemma, Coregonus autumnalis, hyperpredation, Lampetra ?uviatilis, pollan, potamodromous, River lamprey, stable isotope analysis in R, stable isotope

Simulated predator extinctions: Predator identity affects survival and recruitment of oysters

The rate of species loss is increasing at a global scale, and human-induced extinctions are biased toward predator species. We examined the effects of predator extinctions on a foundation species, the eastern oyster (Crassostrea virginica). We performed a factorial experiment manipulating the presence and abundance of three of the most common predatory crabs, the blue crab (Callinectes sapidus), stone crab (Menippe mercenaria), and mud crab (Panopeus herbstii) in estuaries in the eastern United States. We tested the effects of species richness and identity of predators on juvenile oyster survival, oyster recruitment, and organic matter content of sediment. We also manipulated the density of each of the predators and controlled for the loss of biomass of species by maintaining a constant mass of predators in one set of treatments and simultaneously using an additive design. This design allowed us to test the density dependence of our results and test for functional compensation by other species. The identity of predator species, but not richness, affected oyster populations. The loss of blue crabs, alone or in combination with either of the other species, affected the survival rate of juvenile oysters. Blue crabs and stone crabs both affected oyster recruitment and sediment organic matter negatively. Mud crabs at higher than ambient densities, however, could fulfill some of the functions of blue and stone crabs, suggesting a level of ecological redundancy. Importantly, the strong effects of blue crabs in all processes measured no longer occurred when individuals were present at higher-than-ambient densities. Their role as dominant predator is, therefore, dependent on their density within the system and the density of other species within their guild (e.g., mud crabs). Our findings support the hypothesis that the effects of species loss at higher trophic levels are determined by predator identity and are subject to complex intraguild interactions that are largely density dependent. Understanding the role of biodiversity in ecosystem functioning or addressing practical concerns, such as loss of predators owing to overharvesting, remains complicated because accurate predictions require detailed knowledge of the system and should be drawn from sound experimental evidence, not based on observations or generalized models.

Can the spread of non-native oysters (Crassostrea gigas) at the early stages of population expansion be managed?

The Pacific oyster (Crassostrea gigas) was introduced into Strangford Lough, Northern Ireland in the 1970s. It was assumed that local environmental conditions would not facilitate successful reproduction. However, in the 1990s there were reports of C. gigas outside licensed aquaculture sites and this investigation set out to ascertain the current distribution, years of likely recruitment and population structure of the species. C. gigas were found distributed widely throughout the northern basin during surveys; the frequency distribution suggesting C. gigas is not recruiting every year. Establishment of feral populations of C. gigas elsewhere have linked to habitat change. A pilot cull was initiated to assess the success rate of early intervention. This paper demonstrates the potential benefits of responding rapidly to initial reports of non-native species in a way that may curtail establishment and expansion. The method advocated in simple and can be recommended to the appropriate regulatory authorities.

User behaviour, best practice and the risks of non-target exposure associated with anticoagulant rodenticide use

Usage of anticoagulant rodenticides (ARs) is an integral component of modern agriculture and is essential for the control of commensal rodent populations. However, the extensive deployment of ARs has led to widespread exposure of a range of non-target predatory birds and mammals to some compounds, in particular the second-generation anticoagulant rodenticides (SCARS). As a result, there has been considerable effort placed into devising voluntary best practice guidelines that increase the efficacy of rodent control and reduce the risk of non-target exposure. Currently, there is limited published information on actual practice amongst users or implementation of best practice. We assessed the behaviour of a typical group of users using an on-farm questionnaire survey. Most baited for rodents every year using SGARs. Most respondents were apparently aware of the risks of non-target exposure and adhered to some of the best practice recommendations but total compliance was rare. Our questionnaire revealed that users of first generation anticoagulant rodenticides rarely protected or checked bait stations, and so took little effort to prevent primary exposure of non-targets. Users almost never searched for and removed poisoned carcasses and many baited for prolonged periods or permanently. These factors are all likely to enhance the likelihood of primary and secondary exposure of non-target species. (C) 2010 Published by Elsevier Ltd.

Distinguishing between direct and indirect effects of predators in complex ecosystems

1. Global declines in biodiversity have stimulated much research into the consequences of species loss for ecosystems and the goods and services they provide. Species at higher trophic levels are at greater risk of human-induced extinction yet remarkably little is known about the effects of consumer species loss across multiple trophic levels in natural complex ecosystems. Previous studies have been criticized for lacking experimental realism and appropriate temporal scale, running for short periods that are not sufficient to detect many of the mechanisms operating in the field.
2. We manipulated the presence of two predator species and two groups of their prey (primary consumers) and measured their independent and interactive effects on primary producers in a natural marine benthic system. The presence of predators and their prey was manipulated in the field for 14 months to distinguish clearly the direct and indirect effects of predators on primary producers and to identify mechanisms driving responses.
3. We found that the loss of either predator species had indirect negative effects on species diversity and total cover of primary producers. These cascading effects of predator species loss were mediated by the presence of intermediate consumers. Moreover, the presence of different intermediate consumers, irrespective of the presence or absence of their predators, determined primary producer assemblage structure. We identified direct negative effects of predators on their prey and several indirect effects of predators on primary producers but not all interactions could have been predicted based on trophic level.
4. Our findings demonstrate the importance of trophic cascade effects coupled with non-trophic interactions when predicting the effects of loss of predator species on primary producers and consequently for ecosystem functioning. There is a pressing need for improved understanding of the effects of loss of consumers, based on realistic scenarios of diversity loss, to test conceptual frameworks linking predator diversity to variation in ecosystem functioning and for the protection of biodiversity, ecosystem functioning and related services.

Are richness patterns of common and rare species equally well explained by environmental variables?

We investigated relationships between richness patterns of rare and common grassland species and environmental factors, focussing on comparing the degree to which the richness patterns of rare and common species are determined by simple environmental variables. Using data collected in the Machair grassland of the Outer Hebrides of Scotland, we fitted spatial regression models using a suite of grazing, soil physicochemical and microtopographic covariates, to nested sub-assemblages of vascular and non-vascular species ranked according to rarity. As expected, we found that common species drive richness patterns, but rare vascular species had significantly stronger affinity for high richness areas. After correcting for the prevalence of individual species distributions, we found differences between common and rare species in 1) the amount of variation explained: richness patterns of common species were better summarised by simple environmental variables, 2) the associations of environmental variables with richness showed systematic trends between common and rare species with coefficient sign reversal for several factors, and 3) richness associations with rare environments: richness patterns of rare vascular species significantly matched rare environments but those of non-vascular species did not. Richness patterns of rare species, at least in this system, may be intrinsically less predictable than those of common species.

Emerging asymmetric interactions between forage and predator fisheries impose management trade-offs

A size and trait-based marine community model was used to investigate interactions, with potential implications for yields, when a fishery targeting forage fish species (whose main adult diet is zooplankton) co-occurs with a fishery targeting larger-sized predator species. Predicted effects on the size structure of the fish community, growth and recruitment of fishes, and yield from the fisheries were used to identify management trade-offs among the different fisheries. Results showed that moderate fishing on forage fishes imposed only small effects on predator fisheries, whereas predator fisheries could enhance yield from forage fisheries under some circumstances.

Estimating biomass, fishing mortality, and "total allowable discards" for surveyed non-target fish

Demersal fisheries targeting a few high-value species often catch and discard other "non-target" species. It is difficult to quantify the impact of this incidental mortality when population biomass of a non-target species is unknown. We calculate biomass for 14 demersal fish species in ICES Area VIIg (Celtic Sea) by applying species-and length-based catchability corrections to catch records from the Irish Groundfish Survey (IGFS). We then combine these biomass estimates with records of commercial discards (and landings for marketable non-target species) to calculate annual harvesting rates (HR) for each study species. Uncertainty is incorporated into estimates of both biomass andHR. Our survey-based HR estimates for cod and whiting compared well with HR-converted fishing mortality (F) estimates from analytical assessments for these two stocks. Of the non-target species tested, red gurnard (Chelidonichthys cuculus) recorded some annual HRs greater than those for cod or whiting; challenging "Pope's postulate" that F on non-target stocks in an assemblage will not exceed that on target stocks. We relate HR for each species to two corresponding maximum sustainable yield (MSY) reference levels; six non-target species (including three ray species) show annual HRs >= HRMSY. This result suggests that it may not be possible to conserve vulnerable non-target species when F is coupled to that of target species. Based on biomass, HR, and HRMSY, we estimate "total allowable catch" for each non-target species.

Benthic assemblages associated with native and non-native oysters are similar

Invasive species can impact native species and alter assemblage structure, which affects associated ecosystem functioning. The pervasive Pacific oyster, Crassostrea gigas, has been shown to affect the diversity and composition of many host ecosystems. We tested for effects of the presence of the invasive C. gigas on native assemblages by comparing them directly to assemblages associated with the declining native European oyster, Ostrea edulis. The presence of both oyster species was manipulated in intertidal and subtidal habitats and reefs were constructed at horizontal and vertical orientation to the substratum. After 12 months, species diversity and benthic assemblage structure between assemblages with C. gigas and O. edulis were similar, but differed between habitats and orientation, suggesting that both oyster species were functionally similar in terms of biodiversity facilitation. These findings support evidence, that non-native species could play an important role in maintaining biodiversity in systems with declining populations of native species.