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.

Spatial and temporal ecology of Scots pine ectomycorrhizas

Spatial analysis was used to explore the distribution of individual species in an ectomycorrhizal (ECM) fungal community to address: whether mycorrhizas of individual ECM fungal species were patchily distributed, and at what scale; and what the causes of this patchiness might be. Ectomycorrhizas were extracted from spatially explicit samples of the surface organic horizons of a pine plantation. The number of mycorrhizas of each ECM fungal species was recorded using morphotyping combined with internal transcribed spacer (ITS) sequencing. Semivariograms, kriging and cluster analyses were used to determine both the extent and scale of spatial autocorrelation in species abundances, potential interactions between species, and change over time. The mycorrhizas of some, but not all, ECM fungal species were patchily distributed and the size of patches differed between species. The relative abundance of individual ECM fungal species and the position of patches of ectomycorrhizas changed between years. Spatial and temporal analysis revealed a dynamic ECM fungal community with many interspecific interactions taking place, despite the homogeneity of the host community. The spatial pattern of mycorrhizas was influenced by the underlying distribution of fine roots, but local root density was in turn influenced by the presence of specific fungal species.

The effects of winter ice cover on the trophic ecology of whitefish (Coregonus lavaretus L.) in subarctic lakes

Lakes in Arctic and subarctic regions display extreme levels of seasonal variation in light, temperature and ice cover. Comparatively little is known regarding the effects of such seasonal variation on the diet and resource use of fish species inhabiting these systems. Variation in the diet of European whitefish Coregonus lavaretus (L.) during periods of ice cover in this region is often regarded as 'common knowledge'; however, this aspect of the species' ecology has not been examined empirically. Here, we outline the differences in invertebrate community structure, fish activity, and resource use of monomorphic whitefish populations between summer (August-September) and winter (February-March) in three subarctic lakes in Finnish Lapland. Benthic macroinvertebrate densities did not exhibit measurable differences between summer and winter. Zooplankton diversity and abundance, and activity levels of all fish species (measured as catch per unit effort) were lower in winter. The summer diet of C. lavaretus was typical of a generalist utilising a variety of prey sources. In winter, its dietary niche was significantly reduced, and the diet was dominated by chironomid larvae in all study sites. Pelagic productivity decreases during winter, and fish species inhabiting these systems are therefore restricted to feeding on benthic prey. Sampling time has strong effect on our understanding of resource utilisation by whitefish in subarctic lakes and should be taken into account in future studies of these systems. © 2012 John Wiley & Sons A/S.

The spatial ecology of the whiskered bat (Myotis mystacinus) at the western extreme of its range provides evidence of regional adaptation

Although widespread, the ecology of the whiskered bat, Myotis mystacinus in Europe remains poorly understood. Ireland is positioned at the most western extreme of this species' range. To ascertain the ecology of M. mystacinus at its geographic range extreme, the roosting behaviour, home range and habitat use of females in a maternity roost in Ireland was investigated by radio-tracking. M. mystacinus were active in a diversity of habitats: namely, mixed woodland, riparian vegetation, arable land and rough grassland. However, only mixed woodland and riparian habitats were selected as core foraging areas. This is in contrast to a previous study from Britain where only pasture was utilised but is in agreement with data from Slovakia, where woodland was also selected, whilst riparian areas were also utilised by this species in Germany. A high degree of overlap in the foraging areas of individuals was observed. A total of seven roosts were utilised by tracked bats and roost switching behaviour was observed. We discuss our contrasting results in respect to range limitations, regional variability in landscape structure and the composition of bat communities. The present results have implications for the conservation of M. mystacinus within Ireland and other parts of its range, highlighting the need for range wide ecological studies. Regional variability in the ecology of bats related to landscape factors is an important consideration for bat conservation and therefore must be incorporated into future management plans. (C) 2012 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved.

Adolescents' educational outcomes in a social ecology of parenting, family, and community risks in Northern Ireland

This study examines the influence of social ecological risks within the domains of parenting, family environment, and community in the prediction of educational outcomes for 770 adolescents (49% boys, 51% girls, M = 13.6 years, SD = 2.0) living in a setting of protracted political conflict, specifically working class areas of Belfast, Northern Ireland. Controlling for religious community, age, and gender, youths' lower academic achievement was associated with family environments characterized by high conflict and low cohesion. School behaviour problems were related to greater exposure to community violence, or sectarian and nonsectarian antisocial behaviour. Youths' expectations about educational attainment were undermined by conflict in the family environment and antisocial behaviour in the community, as well as parenting low in warmth and behavioural control. Findings underscore the importance of considering family and community contributions to youths' educational outcomes. Suggestions regarding targeted interventions toward promoting resilience are discussed, such as assessing both child and family functioning, developing multidimensional interventions for parents, and building community partnerships, among others.

Advancing impact prediction and hypothesis testing in invasion ecology using a comparative functional response approach

Invasion ecology urgently requires predictive methodologies that can forecast the ecological impacts of existing, emerging and potential invasive species. We argue that many ecologically damaging invaders are characterised by their more efficient use of resources. Consequently, comparison of the classical ‘functional response’ (relationship between resource use and availability) between invasive and trophically analogous native species may allow prediction of invader ecological impact. We review the utility of species trait comparisons and the history and context of the use of functional responses in invasion ecology, then present our framework for the use of comparative functional responses. We show that functional response analyses, by describing the resource use of species over a range of resource availabilities, avoids many pitfalls of ‘snapshot’ assessments of resource use. Our framework demonstrates how comparisons of invader and native functional responses, within and between Type II and III functional responses, allow testing of the likely population-level outcomes of invasions for affected species. Furthermore, we describe how recent studies support the predictive capacity of this method; for example, the invasive ‘bloody red shrimp’ Hemimysis anomala shows higher Type II functional responses than native mysids and this corroborates, and could have predicted, actual invader impacts in the field. The comparative functional response method can also be used to examine differences in the impact of two or more invaders, two or more populations of the same invader, and the abiotic (e.g. temperature) and biotic (e.g. parasitism) context-dependencies of invader impacts. Our framework may also address the previous lack of rigour in testing major hypotheses in invasion ecology, such as the ‘enemy release’ and ‘biotic resistance’ hypotheses, as our approach explicitly considers demographic consequences for impacted resources, such as native and invasive prey species. We also identify potential challenges in the application of comparative functional responses in invasion ecology. These include incorporation of numerical responses, multiple predator effects and trait-mediated indirect interactions, replacement versus non-replacement study designs and the inclusion of functional responses in risk assessment frameworks. In future, the generation of sufficient case studies for a meta-analysis could test the overall hypothesis that comparative functional responses can indeed predict invasive species impacts.

The predictive science of community ecology

Body mass measures provide a tantalizing tool for explaining both variation in emergent community-level patterns and as a mechanistic basis for fundamental processes such as metabolism, consumption and competition. The unification of body mass, abundance and food web (ecological network) structure in community ecology is an effective way to explore future scenarios of environmental change. However, constraints over the availability of data against which to validate model predictions limit the application of size-based approaches. Here, I explore issues over the use of body size for predicting interaction strengths and hence the dynamics of natural ecosystems. The advantages, disadvantages, opportunities and limitations of such approaches are explored. © 2011 The Author. Journal of Animal Ecology © 2011 British Ecological Society.

Geographies of Communality, Colonialism, and Capitalism: Ecology and the World-System

Drawing upon recent reworkings of world systems theory and Marx’s concept of metabolic rift, this paper attempts to ground early nineteenth-century Ireland more clearly within these metanarratives, which take the historical-ecological dynamics of the development of capitalism as their point of departure. In order to unravel the socio-spatial complexities of Irish agricultural production throughout this time, attention must be given to the prevalence of customary legal tenure, institutions of communal governance, and their interaction with the colonial apparatus, as an essential feature of Ireland’s historical geography often neglected by famine scholars. This spatially differentiated legacy of communality, embedded within a country-wide system of colonial rent, and burgeoning capitalist system of global trade, gave rise to profound regional differentiations and ecological contradictions, which became central to the distribution of distress during the Great Famine (1845-1852). Contrary to accounts which depict it as a case of discrete transition from feudalism to capitalism, Ireland’s pre-famine ecology must be understood through an analysis which emphasises these socio-spatial complexities. Consequently, this structure must be conceptualised as one in which communality, colonialism, and capitalism interact dynamically, and in varying stages of development and devolution, according to space and time.

Microbiology of sugar-rich environments: Diversity, ecology and system constraints

Microbial habitats that contain an excess of carbohydrate in the form of sugar are widespread in the microbial biosphere. Depending on the type of sugar, prevailing water activity and other substances present, sugar-rich environments can be highly dynamic or relatively stable, osmotically stressful, and/or destabilizing for macromolecular systems, and can thereby strongly impact the microbial ecology. Here, we review the microbiology of different high-sugar habitats, including their microbial diversity and physicochemical parameters, which act to impact microbial community assembly and constrain the ecosystem. Saturated sugar beet juice and floral nectar are used as case studies to explore the differences between the microbial ecologies of low and higher water-activity habitats respectively. Nectar is a paradigm of an open, dynamic and biodiverse habitat populated by many microbial taxa, often yeasts and bacteria such as, amongst many others, Metschnikowia spp. and Acinetobacter spp., respectively. By contrast, thick juice is a relatively stable, species-poor habitat and is typically dominated by a single, xerotolerant bacterium (Tetragenococcus halophilus). A number of high-sugar habitats contain chaotropic solutes (e.g. ethyl acetate, phenols, ethanol, fructose and glycerol) and hydrophobic stressors (e.g. ethyl octanoate, hexane, octanol and isoamyl acetate), all of which can induce chaotropicity-mediated stresses that inhibit or prevent multiplication of microbes. Additionally, temperature, pH, nutrition, microbial dispersion and habitat history can determine or constrain the microbiology of high-sugar milieux. Findings are discussed in relation to a number of unanswered scientific questions.

Towards a Critical Ecology of Child Development: Aligning the Theories of Bronfenbrenner and Bourdieu

Bronfenbrenner’s model of bio-ecological development has been utilized widely within the social sciences, in the field of human development, and in social work. Yet, while championing the rights of marginalised families and communities, Bronfenbrenner had under-theorized the role of power, agency and structure in shaping the ‘person-context’ interrelationship, life opportunities and social well-being. To respond to this deficit, this paper firstly outlines Bronfenbrenner’s ‘person, process, context, time’ model. Secondly, it then seeks to loosely align aspects of Bronfenbrenner’s model with Bourdieu’s analytical categories of habitus, field and capital. It is argued that these latter categories enable social workers to develop a critical ecology of child development, taking account of power and the interplay between agency and structure. The implications of the alignment for child and family social work are considered in the final section.

The organizational ecology of ethnic cleavages: The nonlinear effects of ethnic diversity on party system fragmentation

The conventional wisdom regarding party system fragmentation assumes that the effects of electoral systems and social cleavages are linear. However, recent work applying organizational ecology theories to the study of party systems has challenged the degree to which electoral system effects are linear. This paper applies such concepts to the study of social cleavages. Drawing from theories of organizational ecology and the experience of many ethnically diverse African party systems, I argue that the effects of ethnic diversity are nonlinear, with party system fragmentation increasing until reaching moderate levels of diversity before declining as diversity reaches extreme values. Examining this argument cross-nationally, the results show that accounting for nonlinearity in ethnic diversity effects significantly improves model fit.

Ecology of testate amoebae in an Amazonian peatland and development of a transfer function for palaeohydrological reconstruction

Tropical peatlands represent globally important carbon sinks with a unique biodiversity and are currently threatened by climate change and human activities. It is now imperative that proxy methods are developed to understand the ecohydrological dynamics of these systems and for testing peatland development models. Testate amoebae have been used as environmental indicators in ecological and palaeoecological studies of peatlands, primarily in ombrotrophic Sphagnum-dominated peatlands in the mid- and high-latitudes. We present the first ecological analysis of testate amoebae in a tropical peatland, a nutrient-poor domed bog in western (Peruvian) Amazonia. Litter samples were collected from different hydrological microforms (hummock to pool) along a transect from the edge to the interior of the peatland. We recorded 47 taxa from 21 genera. The most common taxa are Cryptodifflugia oviformis, Euglypha rotunda type, Phryganella acropodia, Pseudodifflugia fulva type and Trinema lineare. One species found only in the southern hemisphere, Argynnia spicata, is present. Arcella spp., Centropyxis aculeata and Lesqueresia spiralis are indicators of pools containing standing water. Canonical correspondence analysis and non-metric multidimensional scaling illustrate that water table depth is a significant control on the distribution of testate amoebae, similar to the results from mid- and high-latitude peatlands. A transfer function model for water table based on weighted averaging partial least-squares (WAPLS) regression is presented and performs well under cross-validation (r 2apparent=0.76,RMSE=4.29;r2jack=0.68,RMSEP=5.18. The transfer function was applied to a 1-m peat core, and sample-specific reconstruction errors were generated using bootstrapping. The reconstruction generally suggests near-surface water tables over the last 3,000 years, with a shift to drier conditions at c. cal. 1218-1273 AD