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.

Community convergence and recruitment of keystone species as performance indicators of artificial reefs

An experimental artificial reefwas constructed in Strangford Lough, Northern Ireland as part of trials to regenerate damaged biogenic reefs formed by the horse mussel Modiolus modiolus. Experimental reef plots were constructed using Pecten maximus shell as cultch. Clumps of live adult M. modiolus were translocated from nearby natural reefs into cultchwith a high profile (elevated cultch), cultch with a lowprofile (flattened cultch), as well as directly into the seafloor. The aim of the study was to test the hypothesis that translocated mussel clumps would increase habitat complexity thus accelerating community succession and enhancing natural recruitment of M. modiolus spat. These effects were predicted to be greater on elevated cultch due to greater protection from
predators and increased accessibility to food resources. Within the artificial reef array the translocated clumps had a significant positive effect on recruitment compared to cultch without mussels with average densities of spat settled on the translocated M. modiolus clumps ranging from 100 to 200 individuals m-2 compared to 4 to 52 spat m-2 on cultch without mussels. Recruitment of M. modiolus spat was also significantly higher on translocated horse mussels when compared to natural reefs where densities of 8–36 spat m-2 were recorded.
Reef elevation appeared to provide some degree of protection from predators but differences in translocated M. modiolus survival on the different elevation treatments were not significant. In total, 223 taxa were recorded 12 months after reef construction. The presence of translocated clumps ofM. modiolus was the main driver of the increases in faunal diversity and species abundance. Application of objective criteria to assess the performance of artificial reefs suggested that translocation of M. modiolus clumps alone achieved most of the restoration objectives. Consequently this pilot study demonstrates a straightforward and realistic intervention technique that could be used to kick start the regeneration and expansion of impacted mussel and similar biogenic reefs elsewhere.

Compositional Divergence and Convergence in Local Communities and Spatially Structured Landscapes

Community structure depends on both deterministic and stochastic processes. However, patterns of community dissimilarity (e.g. difference in species composition) are difficult to interpret in terms of the relative roles of these processes. Local communities can be more dissimilar (divergence) than, less dissimilar (convergence) than, or as dissimilar as a hypothetical control based on either null or neutral models. However, several mechanisms may result in the same pattern, or act concurrently to generate a pattern, and much research has recently been focusing on unravelling these mechanisms and their relative contributions. Using a simulation approach, we addressed the effect of a complex but realistic spatial structure in the distribution of the niche axis and we analysed patterns of species co-occurrence and beta diversity as measured by dissimilarity indices (e.g. Jaccard index) using either expectations under a null model or neutral dynamics (i.e., based on switching off the niche effect). The strength of niche processes, dispersal, and environmental noise strongly interacted so that niche-driven dynamics may result in local communities that either diverge or converge depending on the combination of these factors. Thus, a fundamental result is that, in real systems, interacting processes of community assembly can be disentangled only by measuring traits such as niche breadth and dispersal. The ability to detect the signal of the niche was also dependent on the spatial resolution of the sampling strategy, which must account for the multiple scale spatial patterns in the niche axis. Notably, some of the patterns we observed correspond to patterns of community dissimilarities previously observed in the field and suggest mechanistic explanations for them or the data required to solve them. Our framework offers a synthesis of the patterns of community dissimilarity produced by the interaction of deterministic and stochastic determinants of community assembly in a spatially explicit and complex context.

Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale

Extreme arid regions in the worlds' major deserts are typified by quartz pavement terrain. Cryptic hypolithic communities colonize the ventral surface of quartz rocks and this habitat is characterized by a relative lack of environmental and trophic complexity. Combined with readily identifiable major environmental stressors this provides a tractable model system for determining the relative role of stochastic and deterministic drivers in community assembly. Through analyzing an original, worldwide data set of 16S rRNA-gene defined bacterial communities from the most extreme deserts on the Earth, we show that functional assemblages within the communities were subject to different assembly influences. Null models applied to the photosynthetic assemblage revealed that stochastic processes exerted most effect on the assemblage, although the level of community dissimilarity varied between continents in a manner not always consistent with neutral models. The heterotrophic assemblages displayed signatures of niche processes across four continents, whereas in other cases they conformed to neutral predictions. Importantly, for continents where neutrality was either rejected or accepted, assembly drivers differed between the two functional groups. This study demonstrates that multi-trophic microbial systems may not be fully described by a single set of niche or neutral assembly rules and that stochasticity is likely a major determinant of such systems, with significant variation in the influence of these determinants on a global scale.

Taxonomic and functional diversity of farmland bird communities across Europe:Effects of biogeography and agricultural intensification

In eight European study sites (in Spain, Ireland, Netherlands, Germany, Poland, Estonia and Sweden), abundance of breeding farmland bird territories was obtained from 500 × 500 m survey plots (30 per area, N = 240) using the mapping method. Two analyses were performed: (I) a Canonical Correspondence Analysis of species abundance in relation to geographical location and variables measuring agricultural intensification at field and farm level to identify significant intensification variables and to estimate the fractions of total variance in bird abundance explained by geography and agricultural intensification; (II) several taxonomic and functional community indices were built and analysed using GLM in relation to the intensification variables found significant in the CCA. The geographical location of study sites alone explains nearly one fifth (19. 5%) of total variation in species abundance. The fraction of variance explained by agricultural intensification alone is much smaller (4. 3%), although significant. The intersection explains nearly two fifths (37. 8%) of variance in species abundance. Community indices are negatively affected by correlates of intensification like farm size and yield, whereas correlates of habitat availability and quality have positive effects on taxonomic and functional diversity of assemblages. Most of the purely geographical variation in farmland bird assemblage composition is associated to Mediterranean steppe species, reflecting the bio-geographical singularity of that assemblage and reinforcing the need to preserve this community. Taxonomic and functional diversity of farmland bird communities are negatively affected by agricultural intensification and positively affected by increasing farmland habitat availability and quality. © 2011 Springer Science+Business Media B.V.

Uses and abuses of fractal methodology in ecology

Fractals have found widespread application in a range of scientific fields, including ecology. This rapid growth has produced substantial new insights, but has also spawned confusion and a host of methodological problems. In this paper, we review the value of fractal methods, in particular for applications to spatial ecology, and outline potential pitfalls. Methods for measuring fractals in nature and generating fractal patterns for use in modelling are surveyed. We stress the limitations and the strengths of fractal models. Strictly speaking, no ecological pattern can be truly fractal, but fractal methods may nonetheless provide the most efficient tool available for describing and predicting ecological patterns at multiple scales.

Effects of environment and an introduced invertebrate species on the structure of benthic macroinvertebrate species at the catchment level

Biotic interactions such as predation and competition can influence aquatic communities at small spatial scales, but they are expected to be overridden by environmental factors at large scales. The continuing threat to freshwater biodiversity of biological invasions indicates that biotic factors do, however, have important structuring roles. In Irish rivers, the native amphipod Gammarus duebeni celticus has become locally extinct, ostensibly through differential predation by the more aggressive and introduced G. pulex. This mechanism explains impacts of G. pulex at within-river spatial scales on native macroinvertebrate community diversity, including declines in ephemeropterans, plecopterans, dipterans and oligochaetes. To determine if these patterns are predictable at larger spatial scales, we assessed patterns in native macroinvertebrate communities across river sites of the Erne catchment in 1998 and 1999, in conjunction with the distribution of G. pulex and G. d. celticus. In both years, G. pulex dominated invaded sites, whereas G. d. celticus occurred at low abundance in uninvaded sites. In both years, invaded sites had lower diversity and fewer pollution sensitive invertebrate species than un-invaded sites. Community ordination in 1998 showed that invaded sites had higher conductivity, smaller substrate particle size and comprised a lower proportion of pollution sensitive taxa including Ephemeroptera and Plecoptera. In contrast, in 1999, conductivity was the only variable explaining site ordination along axis 1, but was unable to separate sites with respect to invasion status. A second explanatory axis separated sites with respect to invasion status, with invaded sites having fewer taxa, including lower abundance of ephemeropterans, dipterans and plecopterans. Laboratory experiments examined the potential role of differential predation between the two Gammarus species in explaining these taxon specific patterns in the field. Survival of the ephemeropterans, Ephemerella ignita and Ecdyonurus venosus and the isopod, Asellus aquaticus, was lower when interacting with G. pulex than with G. d. celticus. This study indicates that G. putex may alter invertebrate community structure at scales beyond those detected within individual rivers. However, effects may be influenced by gradients in physico-chemistry, which may be temporal or depend on catchment characteristics. Invasions by amphipods have increased globally, thus comprehensive assessments of their impacts and of other aquatic invaders, may only be apparent when studies are conducted at a range of spatio-temporal scales.

A review of the status and decline in abundance of the Irish Hare (Lepus timidus hibernicus) in Northern Ireland

The Northern Ireland Hare Survey documented the distribution of the Irish Hare (Lepus timidus hibernicus). Historical game bag records and other, more contemporary, records of hare distribution were examined. These data indicate how numbers of L t. hibernicus may have changed over the last 140 years. The results of the Northern Ireland Hare Survey suggested that L. t. hibernicus was widespread throughout Northern Ireland. Current average densities are no more than 0.65 hares/km(2). Game bag records indicate that hare densities may have been much higher in the past, with a maximum of 138 hares/km(2) recorded on Crom Estate, Co. Fermanagh, in 1864. Evidence from hare distribution recorded during the Northern Ireland Rabbit Survey indicates that hare numbers declined between 1984 and 1994. Evidence from all sources suggests that L. t. hibernicus has declined in abundance substantially, with present total population estimates for Northern Ireland ranging from 8250 to 21000 individuals. Flushing data indicate that rushes and hedgerows are important diurnal resting areas for hares. While the principal reason for the decline in numbers of L. t. hibernicus in Northern Ireland is not clear, more species-rich pasture and provision of areas of cover, such as rushes, may arrest further declines, or indeed promote numbers of hares, particularly in lowland areas.

The abundance of HNCO and its use as a diagnostic of environment

Aims. We aim to investigate the chemistry and gas phase abundance of HNCO and the variation of the HNCO/CS abundance ratio as a diagnostic of the physics and chemistry in regions of massive star formation. Methods. A numerical-chemical model has been developed which self-consistently follows the chemical evolution of a hot core. The model comprises of two distinct stages. The first stage follows the isothermal, modified free-fall collapse of a molecular dark cloud. This is immediately followed by an increase in temperature which represents the switch on of a central massive star and the subsequent evolution of the chemistry in a hot, dense gas cloud (the hot core). During the collapse phase, gas species are allowed to accrete on to grain surfaces where they can participate in further reactions. During the hot core phase surface species thermally desorb back in to the ambient gas and further chemical evolution takes place. For comparison, the chemical network was also used to model a simple dark cloud and photodissociation regions. Results. Our investigation reveals that HNCO is inefficiently formed when only gas-phase formation pathways are considered in the chemical network with reaction rates consistent with existing laboratory data. This is particularly true at low temperatures but also in regions with temperatures up to ~200 K. Using currently measured gas phase reaction rates, obtaining the observed HNCO abundances requires its formation on grain surfaces – similar to other “hot core” species such as CH3OH. However our model shows that the gas phase HNCO in hot cores is not a simple direct product of the evaporation of grain mantles. We also show that the HNCO/CS abundance ratio varies as a function of time in hot cores and can match the range of values observed. This ratio is not unambiguously related to the ambient UV field as been suggested – our results are inconsistent with the hypothesis of Martín et al. (2008, ApJ, 678, 245). In addition, our results show that this ratio is extremely sensitive to the initial sulphur abundance. We find that the ratio grows monotonically with time with an absolute value which scales approximately linearly with the S abundance at early times.

Differential physico-chemical tolerances of amphipod species revealed by field transplantations

Physico-chemical regimes of river systems are major determinants of the distributions and relative abundances of macroinvertebrate taxa. Other factors, however, such as biotic interactions, may co-vary with changes in physico-chemistry and concomitant changes in community composition. Thus, direct cause and effect relationships may not always be established from field surveys. Equally, however, laboratory studies may suffer from lack of realism in extrapolation to the field. Here, we use balanced field transplantation experiments to elucidate the role of physico-chemical regime in determining the generally mutually exclusive distributions of two amphipod taxa, Gammarus (two species) and Crangonyx pseudogracilis. Within two river systems in Ireland, the former species dominate stretches of well oxygenated, high-quality water, whereas the latter dominates stretches of poorly oxygenated, low-quality water. G. pulex and G. duebeni celticus did not survive in bioassay tubes in areas dominated by C. pseudogracilis, which itself survived in tubes in such areas. However, both C. pseudogracilis and Gammarus spp. survived equally well in tubes in areas dominated by Gammarus spp. Physicochemical regime thus limits the movement of Gammarus spp. into C. pseudogracilis areas, but some other factor excludes C. pseudogracilis from Gammarus spp. areas. Since previous laboratory experiments showed high predation rates of Gammarus spp. on C. pseudogracilis, we propose that predation by the former causes exclusion of the latter. Hence, presumed effects of physico-chemical regime on macroinvertebrate presence/abundance may often require experimental field testing and appreciation of alternative explanations.

Distribution of the common lizard (Zootoca vivipara) and landscape favourability for the species in Northern Ireland

The common lizard (Zootoca vivipara) is Ireland’s only native reptile, forming a key part of the island’s biodiversity. However, there is a general paucity of distributional and abundance data for the species. In this study, we collated incidental records for common lizard sightings to define the distribution of the species in Northern Ireland. Maximum entropy modelling was employed to describe species-habitat associations. The resulting predicted landscape favourability was used to evaluate the current status of the species based on the distribution of its maximum potential range in relation to the degree of fragmentation of remaining suitable habitat. In common with previous studies in the Republic of Ireland, sightings were highly clustered indicating under-recording, observer bias, and fragmentation of suitable habitat. A total of 98 records were collated from 1905 to 2009. The species was recorded in 63 (ca. 34%) of 186 × 10 km Northern Irish grid squares. Lizard occurrence was strongly and positively associated with landscapes dominated by heathland, bog and coastal habitats. The single best approximating model correctly classified the presence of lizards in 84.2% of cases. Upland heath, lowland raised bog and sand dune systems are all subject to Habitat Action Plans in Northern Ireland and are threatened by conversion to agriculture, afforestation, invasive species encroachment and infrastructural development. Consequently, remaining common lizard populations are likely to be small, isolated and highly fragmented. Establishment of an ecological network to preserve connectivity of remaining heath and bog will not only benefit remaining common lizard populations but biodiversity in general.

Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2?kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of these were novel, and could be grouped into DNA families based upon sequence similarities. Significant inter-specific variation in abundance of cryptic repetitive DNA and DNA families was observed. Repbase scans show that a large proportion of cryptic repetitive DNA was identified as transposable elements (TEs). We argue that a large number of TEs and their transpositional activity may be linked to differential rates of DNA multiplication and recombination. This is likely to be an important factor explaining inter-specific variation in genome stability and hence microsatellite marker development success rates. Gastropods also differed significantly in the type of TEs classes (autonomous vs non-autonomous) observed. We propose that dissimilar transpositional mechanisms differentiate the TE classes in terms of their propensity for transposition, fixation and/or silencing. Consequently, the phylogenetic conservation of non-autonomous TEs, such as CvA, suggests that dispersal of these elements may have behaved as microsatellite-inducing elements. Results seem to indicate that, compared to autonomous, non-autonomous TEs maybe have a more active role in genome rearrangement processes. The implications of the findings for genomic rearrangement, stability and marker development are discussed.

The top-down mechanism for body-mass-abundance scaling

Scaling relationships between mean body masses and abundances of species in multitrophic communities continue to be a subject of intense research and debate. The top-down mechanism explored in this paper explains the frequently observed inverse linear relationship between body mass and abundance (i.e., constant biomass) in terms of a balancing of resource biomasses by behaviorally and evolutionarily adapting foragers, and the evolutionary response of resources to this foraging pressure. The mechanism is tested using an allometric, multitrophic community model with a complex food web structure. It is a statistical model describing the evolutionary and population dynamics of tens to hundreds of species in a uniform way. Particularities of the model are the detailed representation of the evolution and interaction of trophic traits to reproduce topological food web patterns, prey switching behavior modeled after experimental observations, and the evolutionary adaptation of attack rates. Model structure and design are discussed. For model states comparable to natural communities, we find that (1) the body-mass-abundance scaling does not depend on the allometric scaling exponent of physiological rates in the form expected from the energetic equivalence rule or other bottom-up theories; (2) the scaling exponent of abundance as a function of body mass is approximately -1, independent of the allometric exponent for physiological rates assumed; (3) removal of top-down control destroys this pattern, and energetic equivalence is recovered. We conclude that the top-down mechanism is active in the model, and that it is a viable alternative to bottom-up mechanisms for controlling body-mass-abundance relations in natural communities.

The ocean sunfish Mola mola: insights into distribution, abundance and behaviour in the Irish and Celtic Seas

Here we provide baseline data on the distribution and abundance of Mola mola within the Irish and Celtic Seas, made during aerial surveys from June to October during 2003-2005. These data were considered in conjunction with concurrent observations of three potential jellyfish prey species found throughout the region: Rhizostoma octopus, Chrysaora hysoscella and Cyanea capillata. A total area of 7850 km(2) was surveyed over the three years with an observed abundance of 68 sunfish giving a density of 0.98 ind/100 km(2). Although modest, these findings highlight that the species is more common than once thought around Britain and Ireland and an order of magnitude greater than the other apex jellyfish predator found in the region, the leatherback turtle (Dermochelys coriacea). furthermore, the distribution of sunfish sightings was inconsistent with the extensive aggregations of Rhizostoma octopus found throughout the study area. The modelled distributions of predator-prey co-occurrence (using data for all three jellyfish species) was less than the observed co-occurrence with the implication that neither jellyfish nor sunfish were randomly distributed but co-occurred more in the same areas than expected by chance. Finally, observed sunfish were typically small (similar to 1 in or less) and seen to either bask or actively swim at the surface.