Building Stone Condition Monitoring Using Specially Designed Compensated Optical Fiber Humidity Sensors

This paper presents the design and implementation of a novel optical fiber temperature compensated relative humidity (RH) sensor device, based on fiber Bragg gratings (FBGs) and developed specifically for monitoring water ingress leading to the deterioration of building stone. The performance of the sensor thus created, together with that of conventional sensors, was first assessed in the laboratory where they were characterized under experimental conditions of controlled wetting and drying cycles of limestone blocks, before being employed “in-the-field” to monitor actual building stone in a specially built wall. Although a new construction, this was built specifically using conservation methods similar to those employed in past centuries, to allow an accurate simulation of processes occurring with wetting and drying in the historic walls in the University of Oxford.

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.

Modelling distributional trends to inform conservation strategies for endangered species

Aim: Species loss has increased significantly over the last 1000 years and is ultimately attributed to the direct and indirect consequences of increased human population growth across the planet. A growing number of species are becoming endangered and require human intervention to prevent their local extirpation or complete extinction. Management strategies aimed at mitigating a species loss can benefit greatly from empirical approaches that indicate the rate of decline of a species providing objective information on the need for immediate conservation actions, e.g. captive breeding; however, this is rarely employed. The current study used a novel method to examine the distributional trends of a model endangered species, the freshwater pearl mussel, Margaritifera margaritifera (L.).
Location: United Kingdom and Republic of Ireland.
Methods: Using species presence data within 10-km grid squares since records began three-parameter logistic regression curves were fitted to extrapolate an estimated date of regional extinction.
Results: This study has shown that freshwater pearl mussel distribution has contracted since known historical records and outlier populations were lost first. Within the United Kingdom and Republic of Ireland, distribution loss has been greatest in Scotland, Northern Ireland, Wales and England, respectively, with the Republic of Ireland containing the highest relative proportion of M. margaritifera distribution, in 1998.
Main conclusions: This study provides empirical evidence that this species could become extinct throughout countries within the United Kingdom within 170 years under the current trends and emphasizes that regionally specific management strategies need to be implemented to prevent extirpation of this species.

Population enumeration and assessing conservation status in a widespread amphibian: A case study of Rana temporaria in Ireland

Global amphibian declines are a major element of the current biodiversity crisis. Monitoring changes in the distribution and abundance of target species is a basic component in conservation decision making and requires robust and repeatable sampling. For EU member states, surveillance of designated species, including the common frog Rana temporaria, is a formal requirement of the 'EC Habitats & Species Directive'. We deployed established methods for estimating frog population density at local water bodies and extrapolated these to the national and ecoregion scale. Spawn occurred at 49.4% of water bodies and 70.1% of independent 500-m survey squares. Using spawn mat area, we estimated the number of adult breeding females and subsequently the total population assuming a sex ratio of 1:1. A negative binomial model suggested that mean frog density was 23.5 frogsha [95% confidence interval (CI) 14.9-44.0] equating to 196M frogs (95%CI 124M-367M) throughout Ireland. A total of 86% of frogs bred in drainage ditches, which were a notably common feature of the landscape. The recorded distribution of the species did not change significantly between the last Article 17 reporting period (1993-2006) and the current period (2007-2011) throughout the Republic of Ireland. Recording effort was markedly lower in Northern Ireland, which led to an apparent decline in the recorded distribution. We highlight the need to coordinate biological surveys between adjacent political jurisdictions that share a common ecoregion to avoid apparent disparities in the quality of distributional information. Power analysis suggested that a reduced sample of 40-50 survey squares is sufficient to detect a 30% decline (consistent with the International Union for Conservation of Nature Category of 'Vulnerable') at 80% power providing guidance for minimizing future survey effort. Our results provin assessments for R. temporaria and other clump-spawning amphibians. 2013 The Zoological Society of London.

Restrospective genetic monitoring of the threatened Yellow marsh saxifrage (Saxifraga hirculus) reveals genetic erosion but provides valuable information for conservation strategies

Aim: Retrospective genetic monitoring, comparing genetic diversity of extant populations with historical samples, can provide valuable and often unique insights into evolutionary processes informing conservation strategies. The Yellow marsh saxifrage (Saxifraga hirculus) is listed as ‘critically endangered’ in Ireland with only two extant populations. We quantified genetic changes over time and identified genotypes in extant populations that could be used as founders for reintroductions to sites where the species is extinct.

Location: Ireland.

Methods: Samples were obtained from both locations where the species is currently found, including the most threatened site at the Garron Plateau, Co. Antrim, which held only 13 individuals during 2011. Herbarium samples covering the period from 1886 to 1957 were obtained including plants from the same area as the most threatened population, as well as three extinct populations. In total, 422 individuals (319 present-day and 103 historical) were genotyped at six microsatellite loci. Species distribution modelling was used to identify areas of potentially suitable habitat for reintroductions.

Results: Level of phenotypic diversity within the most threatened population was significantly lower in the present-day compared with historical samples but levels of observed heterozygosity and number of alleles, whilst reduced, did not differ significantly. However, Bayesian clustering analysis suggested gradual lineage replacement over time. All three measures of genetic diversity were generally lower at the most threatened population compared with the more substantial extant populations in Co. Mayo. Species distribution modelling suggested that habitat at one site where the species is extinct may be suitable for reintroduction.

Main conclusions: The dominant genetic lineage in the most threatened population is rare elsewhere; thus, care needs to be taken when formulating any potential reintroduction programme. Our findings highlight both the need for genetic monitoring of threatened populations, but also for its swift implementation before levels of diversity become critically low.

Control of biofilm growth through photodynamic treatments combined with chemical inhibitors: in vitro evaluation methods

The rock/atmosphere interface is inhabited by a complex microbial community including bacteria, algae and fungi. These communities are prominent biodeterioration agents and remarkably influence the status of stone monuments and buildings. Deeper comprehension of natural biodeterioration processes on stone surfaces has brought about a concept of complex microbial communities referred to as "subaerial biofilms". The practical implications of biofilm formation are that control strategies must be devised both for testing the susceptibility of the organisms within the biofilm and treating the established biofilm. Model multi-species biofilms associated with mineral surfaces that are frequently refractory to conventional treatment have been used as test targets. A combination of scanning microscopy with image analysis was applied along with traditional cultivation methods and fluorescent activity stains. Such a polyphasic approach allowed a comprehensive quantitative evaluation of the biofilm status and development. Effective treatment strategies incorporating chemical and physical agents have been demonstrated to prevent biofilm growth in vitro. Model biofilm growth on inorganic support was significantly reduced by a combination of PDT and biocides

Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake

The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).

Evaluating genetic traceability methods for captive-bred marine fish and their applications in fisheries management and wildlife forensics

Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in aquaculture production. Consequently, more captive-bred fish are released into the wild through accidental escape or deliberate releases. The increased mixing of captive-bred and wild fish may affect the ecological and/or genetic integrity of wild fish populations. Unambiguous identification tools for captive-bred fish will be highly valuable to manage risks (fisheries management) and tracing of escapees and seafood products (wildlife forensics). Using single nucleotide polymorphism (SNP) data from captive-bred and wild populations of Atlantic cod Gadus morhua L. and sole Solea solea L., we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive-bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterized the broodstock and escapees originated from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive-bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case-by-case strategy when choosing the best method.

Development of release methods for critically endangered freshwater pearl mussels (Margaritifera margaritifera)

Biodiversity loss is a global problem with freshwater bivalves considered amongst the most
endangered biota. The freshwater pearl mussel, Margaritifera margaritifera, is declining
throughout its range owing to habitat degradation and overexploitation. In most of its range,
populations are regarded as reproductively non-functional which has led to the development
of captive breeding programmes. A novel method of releasing M. margaritifera was trialled,
with captive-bred juveniles being released into the rivers caged in ‘mussels silos’ (protective
concrete domes with ventilation creating upwelling to ensure water through flow). We
released 240 juvenile mussels and survival and growth rates were monitored for 18 months
post-release for three size classes: A (13.01-20.00mm); B (10.01-13.00mm); and C (4.01-
10.00mm). We explicitly tested two experimental treatments; one where sediment was added
to each silo (allowing mussels to orientate and burrow) and one without sediment. Survival
by the end of the experiment at month 18 was significantly higher for the largest size class at
97% (though growth was lowest in this cohort), and lowest for the smallest size class at 61%
(though growth was highest in this cohort). Survival and growth were unaffected by the
experimental treatment suggesting that adding sediment offered no advantage. Growth was
positively correlated with both water temperature and the particle size of suspended solids
(both of which were collinear, peaking in summer). There are a large number of ex situ
breeding programmes for freshwater pearl mussels throughout Europe and our finding
suggest that the use of ‘mussel silos’ could be a useful tool to protecting juvenile mussels
allowing them to be released at a relatively early stage of development, minimising the risk of
domestication.