Identifying optimal sites for natural recovery and restoration of impacted biogenic habitats in a special area of conservation using hydrodynamic and habitat suitability modelling

Selection of sites for successful restoration of impacted shellfish populations depends on understanding the dispersion capability and habitat requirements of the species involved. In Strangford Lough, Northern Ireland, the horse mussel (Modiolus modiolus) biogenic reefs cover only a fraction of their historical range with the remaining reefs badly damaged and requiring restoration. Previous experimental trials suggest that translocation of horse mussels accelerates reef recovery and has therefore been proposed as a suitable restoration technique. We used a series of coupled hydrodynamic and particle dispersal models to assess larval dispersion from remnant and translocated populations to identify suitable areas for adult live M. modiolus translocation in Strangford Lough, Northern Ireland. A maximum entropy model (MAXENT) was used to identify if dispersing larvae could reach habitat suitable for adult M. modiolus. From these we predicted if translocated mussels will reseed themselves or be able to act as larval sources for nearby reefs. The dispersal models showed that the remnant M. modiolus populations are largely self-recruiting with little connectivity between them. The majority of larvae settled near the sources and movement was largely dependent on the tides and not influenced by wind or waves. Higher reef elevation resulted in larvae being able to disperse further away from the release point. However, larval numbers away from the source population are likely to be too low for successful recruitment. There was also little connectivity between the Irish Sea and Strangford Lough as any larvae entering the Lough remained predominantly in the Strangford Narrows. The areas covered by these self-seeding populations are suitable for M. modiolus translocation according to the MAXENT model. As a result of this work and in conjunction with other field work we propose a combination of total protection of all remaining larval sources and small scale translocations onto suitable substrata in each of the identified self-recruiting areas.

Using particle dispersal models to assist in the conservation and recovery of the overexploited native oyster (Ostrea edulis) in an enclosed sea lough

Oyster populations around the world have seen catastrophic decline which has been largely attributed to overexploitation, disease and pollution. While considerable effort and resources have been implemented into restoring these important environmental engineers, the success of oyster populations is often limited by poor understanding of site-specific dispersal patterns of propagules. Water-borne transport is a key factor controlling or regulating the dispersal of the larval stage of benthic marine invertebrates which have limited mobility. The distribution of the native oyster Ostrea edulis in Strangford Lough, Northern Ireland, together with their densities and population structure at subtidal and intertidal sites has been documented at irregular intervals between 1997 and 2013. This paper revisits this historical data and considers whether different prevailing environmental conditions can be used to explain the distribution, densities and population structure of O. edulis in Strangford Lough. The approach adopted involved comparing predictive 2D hydrodynamic models coupled with particle tracking to simulate the dispersal of oyster larvae with historical and recent field records of the distribution of both subtidal and intertidal, populations since 1995. Results from the models support the hypothesis that commercial stocks of O. edulis introduced into Strangford Lough in the 1990s resulted in the re-establishment of wild populations of oysters in the Northern Basin which in turn provided a potential source of propagules for subtidal populations. These results highlight that strategic site selection (while inadvertent in the case of the introduced population in 1995) for the re-introduction of important shellfish species can significantly accelerate their recovery and restoration.

How can a knowledge of the past help to conserve the future? Biodiversity conservation and the relevance of long-term ecological studies

This paper evaluates how long-term records could and should be utilized in conservation policy and practice. Traditionally, there has been an extremely limited use of long-term ecological records (greater than 50 years) in biodiversity conservation. There are a number of reasons why such records tend to be discounted, including a perception of poor scale of resolution in both time and space, and the lack of accessibility of long temporal records to non-specialists. Probably more important, however, is the perception that even if suitable temporal records are available, their roles are purely descriptive, simply demonstrating what has occurred before in Earth’s history, and are of little use in the actual practice of conservation. This paper asks why this is the case and whether there is a place for the temporal record in conservation management. Key conservation initiatives related to extinctions, identification of regions of greatest diversity/threat, climate change and biological invasions are addressed. Examples of how a temporal record can add information that is of direct practicable applicability to these issues are highlighted. These include (i) the identification of species at the end of their evolutionary lifespan and therefore most at risk from extinction, (ii) the setting of realistic goals and targets for conservation ‘hotspots’, and (iii) the identification of various management tools for the maintenance/restoration of a desired biological state. For climate change conservation strategies, the use of long-term ecological records in testing the predictive power of species envelope models is highlighted, along with the potential of fossil records to examine the impact of sea-level rise. It is also argued that a long-term perspective is essential for the management of biological invasions, not least in determining when an invasive is not an invasive. The paper concludes that often inclusion of a long-term ecological perspective can provide a more scientifically defensible basis for conservation decisions than the one based only on contemporary records. The pivotal issue of this paper is not whether long-term records are of interest to conservation biologists, but how they can actually be utilized in conservation practice and policy.

"Angels and Demons in Cromwellian and Restoration Ireland: Heresy and the Supernatural"

This essay explores accounts of supernatural activity in Cromwellian and Restoration Ireland. Religious life in Cromwellian Ireland was driven by expectations of the unusual—including audible voices from heaven, material encounters with angels, and spiritual encounters with demons. Some conservative Protestants linked this activity to the development and dissemination of heretical belief, while some who had such encounters were confident that it was compatible with the Cromwellian religious mainstream. Crawford Gribben explores the flexibility in the discourse of the marvelous in Ireland and the ways in which the administration contributed to it, and the alignment of the supernatural with various confessional convictions and postures, as well as theological radicalism. After the Restoration, accounts of supernatural encounters were remembered as ghost stories, not as matters for theological debate, a cultural transition linked to the development of a historiography that has continued to invest the Irish Cromwellian past with Gothic tropes.

Spatial and Temporal Changes in Soil Organic Carbon Assessment using an Integrated Geostatistical and Compositional Data Analysis Approach

The Irish and UK governments, along with other countries, have made a commitment to limit the concentrations of greenhouse gases in the atmosphere by reducing emissions from the burning of fossil fuels. This can be achieved (in part) through increasing the sequestration of CO2 from the atmosphere including monitoring the amount stored in vegetation and soils. A large proportion of soil carbon is held within peat due to the relatively high carbon density of peat and organic-rich soils. This is particularly important for a country such as Ireland, where some 16% of the land surface is covered by peat. For Northern Ireland, it has been estimated that the total amount of carbon stored in vegetation is 4.4Mt compared to 386Mt stored within peat and soils. As a result it has become increasingly important to measure and monitor changes in stores of carbon in soils. The conservation and restoration of peat covered areas, although ongoing for many years, has become increasingly important. This is summed up in current EU policy outlined by the European Commission (2012) which seeks to assess the relative contributions of the different inputs and outputs of organic carbon and organic matter to and from soil. Results are presented from the EU-funded Tellus Border Soil Carbon Project (2011 to 2013) which aimed to improve current estimates of carbon in soil and peat across Northern Ireland and the bordering counties of the Republic of Ireland.
Historical reports and previous surveys provide baseline data. To monitor change in peat depth and soil organic carbon, these historical data are integrated with more recently acquired airborne geophysical (radiometric) data and ground-based geochemical data generated by two surveys, the Tellus Project (2004-2007: covering Northern Ireland) and the EU-funded Tellus Border project (2011-2013) covering the six bordering counties of the Republic of Ireland, Donegal, Sligo, Leitrim, Cavan, Monaghan and Louth. The concept being applied is that saturated organic-rich soil and peat attenuate gamma-radiation from underlying soils and rocks. This research uses the degree of spatial correlation (coregionalization) between peat depth, soil organic carbon (SOC) and the attenuation of the radiometric signal to update a limited sampling regime of ground-based measurements with remotely acquired data. To comply with the compositional nature of the SOC data (perturbations of loss on ignition [LOI] data), a compositional data analysis approach is investigated. Contemporaneous ground-based measurements allow corroboration for the updated mapped outputs. This provides a methodology that can be used to improve estimates of soil carbon with minimal impact to sensitive habitats (like peat bogs), but with maximum output of data and knowledge.

Carbon Sink Conservation and Global Justice: Benefiting, Free Riding and Non-Compliance

It is often assumed that in order to avoid the most severe consequences of global anthropogenic climate change we have to preserve our existing carbon sinks, such as for instance tropical forests. Global carbon sink conservation raises a host of normative issues, though, since it is debatable who should pay the costs of carbon sink conservation, who has the duty to protect which sinks, and how far the duty to conserve one’s carbon sinks actually extends, especially if it conflicts with other duties one might have. According to some, forested states like Ecuador have a duty to preserve their tropical forests while the rich states of the global North have a duty of fairness to compensate states like Ecuador for the costs they incur. My aim in this paper is to critically analyse this standard line of argument and to criticise its validity both internally (i.e. with regard to its normative conclusion based on its premises) and externally (i.e. with regard to the argument’s underlying assumptions and its lack of contextualisation). As I will argue, the duty to conserve one’s forests is only a particular instantiation of a wider, more general duty to contribute towards global climate justice for which the context in which one operates (e.g. whether other agents are complying with their duties of global climate justice or not) matters significantly.

Sub-fossil Insects and ecosystem dynamics in wetlands; implications for biodiversity and conservation.

We review the uses of fossil insects, particularly Coleoptera (beetles) and Chironomidae (non-biting midges) from ancient deposits to inform the study of wetland ecosystems and their ecological and restoration processes. In particular, we focus on two contrasting ecosystems, drawing upon research undertaken by us on British raised mire peats and shallow lake systems, one an essentially terrestrial ecosystem, the other aquatic, but in which wetland insects play an important and integral part. The study of raised mire peats suggests that faunal stability is a characteristic of these wetland systems, over what appear to be extensive periods of time (up to several millennia), whilst studies of shallow lake ecosystems over recent timescales indicates that faunal instability appears to be more common, usually driven by increasing eutrophication. Drawing upon a series of fossil Coleoptera records spanning several thousand years from Hatfield Moors, south Yorkshire, we reconstruct in some detail the mire’s ontogeny and fluctuations in site hydrology and vegetation cover, illustrating the intimate association between substrate, topography and peat development. A comparison between fossil and modern beetle populations indicates that the faunal characteristics of this mire and its adjacent neighbour, Thorne Moors, become established during the early phases of peat development, including its rare endemics, and that the faunal biodiversity on the sites today is dictated by complex site histories. The over-riding characteristic of these faunas is of stability over several thousand years, which has important implications for the restoration of degraded sites, especially those where refugial areas are limited. In contrast, analyses of fossil Chironomidae from shallow lakes allow researchers to track changes in limnological status and while attempts have been made to reconstruct changes in nutrient levels quantitatively, the chironomids respond indirectly to such changes, typically mediated through complex ecosystem dynamics such as changes in fish and/or macrophyte communities. These changes are illustrated via historic chironomid stratigraphies and diversity indices from a range of shallow lakes located across Britain: Slapton Ley, Frensham Great Pond, Fleet Pond, Kyre Pool and Barnes Loch. These sites have shown varying degrees of eutrophication over recent timescales which tends to be associated with a decline in chironomid diversity. While complex functional processes exist within these ecosystems, our evidence suggests that one of the key drivers in the loss of shallow lake chironomid diversity appears to be the loss of aquatic macrophytes. Overall, while chironomids do show a clear response to altered nutrient regimes, multi-proxy reconstructions are recommended for a clear interpretation of past change. We conclude that if we are to have a better understanding of biota at the ecosystem level we need to know more of the complex interactions between different insect groups as well as with other animal and plant communities. A palaeoecological approach is thus crucial in order to assess the role of insect groups in ecosystem processes, both in the recent past and over long time scales, and is essential for wetland managers and conservation organisations involved in long term management and restoration of wetland systems.

Applying species distribution modelling to identify areas of high conservation value for endangered species: A case study using Margaritifera margaritifera (L.)

The development and implementation of a population supplementation and restoration plan for any endangered species should involve an understanding of the species’ habitat requirements prior to the release of any captive bred individuals. The freshwater pearl mussel, Margaritifera margaritifera, has undergone dramatic declines over the last century and is now globally endangered. In Northern Ireland, the release of captive bred individuals is being used to support wild populations and repatriate the species in areas where it once existed. We employed a combination of maximum entropy modelling (MAXENT) and Generalized Linear Mixed Models (GLMM) to identify ecological parameters necessary to support wild populations using GIS-based landscape scale and ground-truthed habitat scale environmental parameters. The GIS-based landscape scale model suggested that mussel occurrence was associated with altitude and soil characteristics including the carbon, clay, sand, and silt content. Notably, mussels were associated with a relatively narrow band of variance indicating that M. margaritifera has a highly specific landscape niche. The ground-truthed habitat scale model suggested that mussel occurrence was associated with stable consolidated substrates, the extent of bankside trees, presence of indicative macrophyte species and fast flowing water. We propose a three phase conservation strategy for M. margaritifera identifying suitable areas within rivers that (i) have a high conservation value yet needing habitat restoration at a local level, (ii) sites for population supplementation of existing populations and (iii) sites for species reintroduction to rivers where the mussel historically occurred but is now locally extinct. A combined analytical approach including GIS-based landscape scale and ground-truthed habitat scale models provides a robust method by which suitable release sites can be identified for the population supplementation and restoration of an endangered species. Our results will be highly influential in the future management of M. margaritifera in Northern Ireland.

Quaternary pollen analysis: recent progress in palaeoecology and palaeoclimatology

During the last decade Quaternary pollen analysis has developed towards improved pollen-taxonomical precision, automated pollen identification and more rigorous definition of pollen assemblage zones. There have been significant efforts to model the spatial representation of pollen records in lake sediments which is important for more precise interpretation of the pollen records in terms of past vegetation patterns. We review the difficulties in matching modelled post-glacial plant migration patterns with pollen-based palaeorecords and discuss the potential of DNA analysis of pollen to investigate the ancestry and past migration pathways of the plants. In population ecology there has been an acceleration of the widely advocated conceptual advance of pollen-analytical research from vaguely defined ‘environmental reconstructions’ towards investigating more precisely defined ecological problems aligned with the current ecological theories. Examples of such research have included an increasing number of investigations about the ecological impacts of past disturbances, often integrating pollen records with other palaeoecological data. Such an approach has also been applied to incorporate a time perspective to the questions of ecosystem restoration, nature conservation and forest management. New lines of research are the use of pollen analysis to study long-term patterns of vegetation diversity, such as the role of glacial-age vegetation fragmentation as a cause of Amazonian rain forest diversity, and to investigate links between pollen richness and past plant diversity. Palaeoclimatological use of pollen records has become more quantitative and has included more precise and rigorous testing of pollen-climate calibration models with modern climate data. These tests show the approximate nature of the models and warn against a too straightforward climatic interpretation of the small-scale variation in reconstructions. Pollenbased climate reconstructions over the Late Glacial–early Holocene boundary have indicated that pollen-stratigraphical changes have been rapid with no evidence for response lags. This does not rule out the possibility of migrational disequilibrium, however, as the rapid changes may be mostly due to nonmigrational responses of existing vegetation. It is therefore difficult to assess whether the amplitude of reconstructed climate change reflects real climate change. Other outstanding problems remain the obscure relationship of pollen production and climate, the role of human impact and other nonclimatic factors, and nonanalogue situations.

A transposase-independent mechanism gives rise to precise excision of IS256 from insertion sites in Staphylococcus epidermidis.

The mobile element IS256 causes phase variation of biofilm formation in Staphylococcus epidermidis by insertion and precise excision from the icaADBC operon. Precise excision, i.e., removal of the target site duplications (TSDs) and restoration of the original DNA sequence, occurs rarely but independently of functional transposase. Instead, the integrity of the TSDs is crucial for precise excision. Excision increased significantly when the TSDs were brought into closer spatial proximity, suggesting that excision is a host-driven process that might involve most likely illegitimate recombination.

Can traditional harvesting methods for cockles be accommodated in a Special Area of Conservation?

The European Natura 2000 project attempts to balance conservation and exploitation by permitting activities that do not affect the conservation status of designated sites. Given the scale of Natura 2000, guidelines are needed to facilitate the drafting of simple site management plans. This need is particularly acute for traditional harvesting methods for which there is usually strong local opposition to the imposition of controls. These issues were examined in Strangford Lough, a special area of conservation where cockles have traditionally been harvested by hand-raking. Raking was found not to affect the ability of cockles to rebury. There were significant reductions in Zostera biomass when raking was carried out within eelgrass beds (a 90% reduction in biomass available to winter migrant birds from summer raking). Traditional harvesting methods could therefore be accepted in Strangford as long as Zostera beds are avoided. A relatively low intensity of harvesting activity in Strangford Lough probably reflects low cockle densities (average 91.8 m(-2)), with the most economically valuable individuals at some distance from points of access to the shore. An economically feasible management plan could sanction traditional harvesting and result in the implementation of more resource-intensive management only if increases in cockle stocks and market prices stimulate large increases in harvesting activity.

Lake restoration in terms of ecological resilience: a numerical study of biomanipulations under bistable conditions

An abstract version of the comprehensive aquatic simulation model (CASM) is found to exhibit bistability under intermediate loading of nutrient input, supporting the alternative-stable-states theory and field observations for shallow lakes. Our simulations of biomanipulations under the bistable conditions reveal that a reduction in the abundance of zooplanktivorous fish cannot switch the system from a turbid to a clear state. Rather, a direct reduction of phytoplankton and detritus was found to be most effective to make this switch in the present model. These results imply that multiple manipulations may be effective for practical restorations of lakes. We discuss the present results of biomanipulations in terms of ecological resilience in multivariable systems or natural systems.