Characterization of polymorphic microsatellites for the rough periwinkle gastropod, Littorina saxatilis (Olivi, 1792) and their cross-amplification in four congeners.

Eight new microsatellite loci were characterized for Littorina saxatilis (Olivi, 1792) and tested for their cross-hybridization in congeners. All loci were polymorphic in Irish and Celtic Sea samples, with an average number of alleles per locus of 15 (range, 6–31). Observed and expected locus heterozygosities ranged from 26 to 85% and from 53 to 92%, respectively. Three loci showed excess homozygosity and significant departures from Hardy–Weinberg expectations in one sample, possibly due to null alleles, population structuring or inbreeding. No linkage disequilibrium was detected among loci within samples. A high degree of cross-hybridization was observed in closely related congeners and most loci were polymorphic. These markers will be useful for investigating population genetic diversity and connectivity in coastal populations, especially for marine reserve design.

Mammals and agri-environment schemes: hare haven or pest paradise?

1. Agri-environment schemes (AESs) are designed to create landscape-scale improvements in biodiversity. While the specific aims of AESs do not always include the enhancement of species of conservation concern, associated conservation strategies, such as the UK Biodiversity Action Plan, often rest on the assumption that AESs enhance environmental conditions and thereby improve the conservation status of target species. However, there is little evidence for the general efficacy of AESs in this respect. 2. To evaluate the effects of the Environmentally Sensitive Area (ESA) scheme, a widespread AES in Northern Ireland, a spotlight survey of the relative abundance of three mammal species, Irish hare Lepus timidus hibernicus, European rabbit Oryctolagus cuniculus and red fox Vulpes vulpes, was conducted. Of these, the Irish hare is a priority species for conservation action and the focus of a species action plan, while rabbit and fox are commonly considered agricultural pests. The effects of ESA designation and habitat on each species were assessed at 150 ESA and 50 non-ESA sites, matched for landscape characteristics. 3. The ESA scheme had no demonstrable effect on the abundance of Irish hares, and this agri-environment scheme did not target the landscape and habitat variables associated with hares. 4. In contrast, the abundance of rabbits and foxes was significantly greater within ESAs than the wider countryside. Agricultural factors such as reduced livestock stocking density, reduced overgrazing and field boundary enhancements may create more favourable conditions for both species. Aside from the implications for farm economics, the proliferation of rabbit populations within conservation areas may raise issues concerning the grazing of important plant communities, while increases in fox populations may adversely affect ground-nesting birds and other animal species of conservation concern. 5. Synthesis and applications: The abundance of rabbits and foxes corroborates recent work that suggests AESs may benefit common species but can not be relied upon to encourage rarer species. The Irish hare species action plan relies on agri-environment schemes to enhance the species’ status and realize the target of increasing the hare population by 2010 by promoting suitable habitat. However, the ESA scheme is unlikely to help in achieving these objectives. Targeted and evidence-based agri-environment prescriptions are clearly required in order to ensure the realization of species-specific conservation targets.

A rapid PCR-based assay for identification of cryptic Myotis spp (Myotis mystacinus, Myotis brandtii and Myotis alcathoe).

The development of a quick PCR-based method to distinguish European cryptic Myotis spp., Myotis mystacinus, Myotis brandtii and Myotis alcathoe is described. Primers were designed around species-specific single nucleotide polymorphisms (SNP’s) in the ND1 mitochondrial gene, and a pair of control primers was designed in the 12S mitochondrial gene. A multiplex of seven primer combinations produces clear species-specific bands using gel electrophoresis. Robustness of the method was tested on 33 M. mystacinus, 16 M. brandtii and 15 M. alcathoe samples from across the European range of these species. The method worked well on faecal samples collected from maternity roosts of M. mystacinus. The test is intended to aid collection of data on these species through a rapid and easy identification method with the ability to use DNA obtained from a range of sources including faecal matter.

Development and characterization of 10 polymorphic microsatellite loci for the blue shark, Prionace glauca, and their cross shark-species amplification.

Ten polymorphic nuclear microsatellite loci were developed from a microsatellite enriched genomic library of the blue shark, Prionace glauca. The utility of these markers for genetic studies of this globally distributed, heavily exploited, oceanic predator was assessed by screening 120 specimens sampled from six locations throughout the species’ range. Both moderately and highly polymorphic marker loci were identified. Three to 35 alleles were found to be segregating per locus (mean 10.1) with observed heterozygosities ranging from 24 to 91%. Evaluation of the cross-species amplification of these markers across 18 additional shark species indicates that these microsatellites are potentially useful for genetic studies of other species of conservation concern.

The conservation of bees: a global perspective

Bees are major pollinators of Angiosperms and therefore their apparent decline is of importance for humans and biodiversity. We synthesise results of 12 recent reviews to provide a global picture of the threats they face. Habitat loss is the major threat to bee diversity, whilst invasive species, emerging diseases, pesticide use, and climate change also have the potential to impact bee populations. We suggest that future conservation strategies need to prioritise (i) minimising habitat loss, (ii) making agricultural habitats bee-friendly, (iii) training scientists and the public in bee taxonomy and identification, (iv) basic autecological and population genetic studies to underpin conservation strategies, (v) assessing the value of DNA barcoding for bee conservation, (vi) determining the impact of invasive plants, animals, parasites and pathogens, and (vii) integrating this information to understand the potential impact of climate change on current bee diversity.

Uses of expertise:Sources, quotes, and voice in the reporting of genetics in the news

Science journalists call upon experts for background and for clarification and comment on scientific findings. This paper examines how science writers choose and use experts, and it focuses on several cases of reporting about genetics and behavior. Our research included two sources of data: interviews with 15 science reporters and three print media samples of coverage of genetics and behavior - alcoholism (between 1980-1995), homosexuality (in 1993 and 1995), and mental illness (between 1970-1995). Science reporters seek relevant and specific experts for nearly every story. Good sources are knowledgeable, are connected to prestigious institutions, are direct and articulate and don't overqualify statements, and they return phone calls. The mean number of experts quoted was 2.8 per story, differing for alcoholism (3.5), homosexuality (2.8), and mental illness (2.6). Researchers and scientists predominated among experts quoted. Quotes were used to provide context, give legitimization, as explication, to provide a kind of balance, and to outline implications. For the homosexuality sample, a significantly greater percentage of activists and advocates were quoted (21 percent compared with 5 percent and 1 percent in other samples, X <0.0001). "Lay" quotes for alcoholism and mental illness were minimal. Except for homosexuality, whose advocates are organized, those "affected" do not have a voice in genetics news stories.

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.

Threats and knowledge gaps for ecosystem services provided by kelp forests: a northeast Atlantic perspective.

Kelp forests along temperate and polar coastlines represent some of most diverse and productive habitats on the Earth. Here, we synthesize information from >60 years of research on the structure and functioning of kelp forest habitats in European waters, with particular emphasis on the coasts of UK and Ireland, which represents an important biogeographic transition zone that is subjected to multiple threats and stressors. We collated existing data on kelp distribution and abundance and reanalyzed these data to describe the structure of kelp forests along a spatial gradient spanning more than 10° of latitude. We then examined ecological goods and services provided by kelp forests, including elevated secondary production, nutrient cycling, energy capture and flow, coastal defense, direct applications, and biodiversity repositories, before discussing current and future threats posed to kelp forests and identifying key knowledge gaps. Recent evidence unequivocally demonstrates that the structure of kelp forests in the NE Atlantic is changing in response to climate- and non-climate-related stressors, which will have major implications for the structure and functioning of coastal ecosystems. However, kelp-dominated habitats along much of the NE Atlantic coastline have been chronically understudied over recent decades in comparison with other regions such as Australasia and North America. The paucity of field-based research currently impedes our ability to conserve and manage these important ecosystems. Targeted observational and experimental research conducted over large spatial and temporal scales is urgently needed to address these knowledge gaps.

Production and Processing of Spider Silk Proteins

Natural spider silk fibers have impressive mechanical properties (outperforming many man-made fibers) and are, moreover, biocompatible, biodegradable, and produced under benign conditions (using water as a solvent at ambient temperature). The problems associated with harvesting natural spider silks inspired us to devise a method to produce spider silk-like proteins biotechnologically (the first subject tackled in this highlight); we subsequently discuss their processing into various materials morphologies, and some potential technical and biomedical applications.

A rapid PCR-based assay for identification of cryptic Myotis spp. (M. mystacinus, M. brandtii and M. alcathoe)

The development of a quick PCR-based method to distinguish European cryptic Myotis spp., Myotis mystacinus, Myotis brandtii and Myotis alcathoe is described. Primers were designed around species-specific single nucleotide polymorphisms (SNP's) in the ND1 mitochondrial gene, and a pair of control primers was designed in the 12S mitochondrial gene. A multiplex of seven primer combinations produces clear species-specific bands using gel electrophoresis. Robustness of the method was tested on 33 M. mystacinus, 16 M. brandtii and 15 M. alcathoe samples from across the European range of these species. The method worked well on faecal samples collected from maternity roosts of M. mystacinus. The test is intended to aid collection of data on these species through a rapid and easy identification method with the ability to use DNA obtained from a range of sources including faecal matter.

Isolation and characterization of eight polymorphic microsatellite loci for Natterer's bat, Myotis nattereri (Vespertilionidae, Chiroptera)

Eight new microsatellite loci were isolated and characterized for the Natterer's bat Myotis nattereri from a microsatellite-enriched genomic library. The usefulness of these markers was assessed by screening a sample comprising 100 specimens collected from throughout the species range in Europe. Both moderately and highly polymorphic loci were identified with 3-17 alleles segregating per locus (mean 8.1 SE +/- A 0.048). No evidence for departure from HWE or linkage disequilibrium among loci was observed. These markers will provide a valuable addition to the molecular toolbox currently available for studies of population genetic structure, parentage and social organisation of M. nattereri and related species.

Slopes of Avian Species-Area Relationships, Human Population Density, and Environmental Factors

There is increasing interest in how humans influence spatial patterns in biodiversity. One of the most frequently noted and marked of these patterns is the increase in species richness with area, the species-area relationship (SAR). SARs are used for a number of conservation purposes, including predicting extinction rates, setting conservation targets, and identifying biodiversity hotspots. Such applications can be improved by a detailed understanding of the factors promoting spatial variation in the slope of SARs, which is currently the subject of a vigorous debate. Moreover, very few studies have considered the anthropogenic influences on the slopes of SARs; this is particularly surprising given that in much of the world areas with high human population density are typically those with a high number of species, which generates conservation conflicts. Here we determine correlates of spatial variation in the slopes of species-area relationships, using the British avifauna as a case study. Whilst we focus on human population density, a widely used index of human activities, we also take into account (1) the rate of increase in habitat heterogeneity with increasing area, which is frequently proposed to drive SARs, (2) environmental energy availability, which may influence SARs by affecting species occupancy patterns, and (3) species richness. We consider environmental variables measured at both local (10 km x 10 km) and regional (290 km x 290 km) spatial grains, but find that the former consistently provides a better fit to the data. In our case study, the effect of species richness on the slope SARs appears to be scale dependent, being negative at local scales but positive at regional scales. In univariate tests, the slope of the SAR correlates negatively with human population density and environmental energy availability, and positively with the rate of increase in habitat heterogeneity. We conducted two sets of multiple regression analyses, with and without species richness as a predictor. When species richness is included it exerts a dominant effect, but when it is excluded temperature has the dominant effect on the slope of the SAR, and the effects of other predictors are marginal.

The imprint of the geographical, evolutionary and ecological context on species-area relationships

Species-area relationships (SAR) are fundamental in the understanding of biodiversity patterns and of critical importance for predicting species extinction risk worldwide. Despite the enormous attention given to SAR in the form of many individual analyses, little attempt has been made to synthesize these studies. We conducted a quantitative meta-analysis of 794 SAR, comprising a wide span of organisms, habitats and locations. We identified factors reflecting both pattern-based and dynamic approaches to SAR and tested whether these factors leave significant imprints on the slope and strength of SAR. Our analysis revealed that SAR are significantly affected by variables characterizing the sampling scheme, the spatial scale, and the types of organisms or habitats involved. We found that steeper SAR are generated at lower latitudes and by larger organisms. SAR varied significantly between nested and independent sampling schemes and between major ecosystem types, but not generally between the terrestrial and the aquatic realm. Both the fit and the slope of the SAR were scale-dependent. We conclude that factors dynamically regulating species richness at different spatial scales strongly affect the shape of SAR. We highlight important consequences of this systematic variation in SAR for ecological theory, conservation management and extinction risk predictions.

Lack of genetic structure and evidence for long-distance dispersal in ash (Fraxinus excelsior) populations under threat from an emergent fungal pathogen: implications for restorative planting

Genetic analysis on populations of European ash (Fraxinus excelsior) throughout Ireland was carried out to determine the levels and patterns of genetic diversity in naturally seeded trees in ash woodlands and hedgerows, with the aim of informing conservation and replanting strategies in the face of potential loss of trees as a result of ash dieback. Samples from 33 sites across Northern Ireland and three sites in the Republic of Ireland were genotyped for eight nuclear and ten chloroplast microsatellites. Levels of diversity were high (mean A R = 10.53; mean H O = 0.709; mean H E = 0.765) and were similar to those in Great Britain and continental Europe, whilst levels of population genetic differentiation based on nuclear microsatellites were extremely low (Φ ST = 0.0131). Levels of inbreeding (mean F IS = 0.067) were significantly lower than those reported for populations from Great Britain. Fine-scale analysis of seed dispersal indicated potential for dispersal over hundreds of metres. Our results suggest that ash woodlands across Ireland could be treated as a single management unit, and thus native material from anywhere in Ireland could be used as a source for replanting. In addition, high potential for dispersal has implications for recolonization processes post-ash dieback (Chalara fraxinea) infection, and could aid in our assessment of the capacity of ash to shift its range in response to global climate change.

Genetic provenance and best practice woodland management: a case study in native alder (Alnus glutinosa)

In recent years, the native woodlands of Europe, including those of Britain and Ireland, have increasingly come under threat from a range of biotic and abiotic factors, and are therefore a conservation priority demanding careful management in order to realise their inherent ecological and cultural benefits. Because the distribution of genetic variation across populations and regions is increasingly considered an important component of woodland management, we carried out a population genetic analysis on black alder (Alnus glutinosa) across Northern Ireland in order to inform “best practice” strategies. Our findings suggest that populations harbour high levels of genetic diversity, with very little differentiation between populations. Significant F IS values were observed in over half of the populations analysed, however, which could reflect inbreeding as a result of the patchy occurrence of alder in Northern Ireland, with scattered, favourable damp habitats being largely isolated from each other by extensive tracts of farmland. Although there is no genetic evidence to support the broad-scale implementation of tree seed zones along the lines of those proposed for native woodlands in Great Britain, we suggest that the localised occurrence of rare chloroplast haplotypes should be taken into account on a case-by-case basis. This, coupled with the identification of populations containing high genetic diversity and that are broadly representative of the region as a whole, will provide a sound genetic basis for woodland management, both in alder and more generally for species that exhibit low levels of genetic differentiation.