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).

Gene-associated markers provide tools for tackling illegal fishing and false eco-certification

Illegal, Unreported and Unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using gene-associated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93-100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. Our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.

Culturing freshwater pearl mussel Margaritifera margaritifera: a breakthrough in the conservation of an endangered species.

1. The freshwater pearl mussel Margaritifera margaritifera L. is globally endangered and is threatened by commercial exploitation, pollution and habitat loss throughout its range. Captive breeding would be a valuable tool in enhancing the status of M. margaritifera in the UK. 2. We have developed a semi-natural system for successfully infecting juvenile brown trout with glochidial M. margaritifera, and culturing juvenile mussels in experimental tanks where glochidial M. margaritifera can excyst from fish gills and settle into sediment. 3. Infected fish had less than 1% mortality. Levels of infection varied among fish. Two yearly cohorts of juvenile M. margaritifera were identified from samples of sediment taken from each experimental tank. Individuals range in size from 1.4 mm (2000 cohort) to >3 mm in length (1999 cohort). 4. The number of juvenile M. margaritifera present in the two experimental tanks are estimated to be between 3600 (tank A) and 0 (tank B) for the putative 1999 cohort and between 6000 (tank A) and 13 000 (tank B) for the putative 2000 cohort. 5. This pioneering method for large-scale cultivation of juvenile M. margaritifera is intermediate between the release of infected fish into rivers and the intensive cultivation systems developed in continental Europe and the USA for other species of unionid. This is the first time that large numbers of M. margaritifera have been cultured and represents a significant breakthrough in the conservation of this globally endangered Red Data List species. The method is straightforward and is most cost-effective when undertaken alongside established hatchery processes.

COMMUNICATION AND GREEK ENVIRONMENTAL ORGANISATIONS: MEANS OF COMMUNICATION AND INFLUENCING FACTORS

A basic operational objective of any environmental organisation is to raise awareness among the public on issues of environmental protection, through the dissemination of knowledge and experience to local communities, so that the conservation and ecologically sound management of natural resources can acquire a local dimension. This can be achieved either through interventions directed at the State, mainly in relation to its legislative function, or by encouraging citizens to change or improve their attitude regarding environmental matters. In order to ensure a successful outcome and the efficient functioning of any organisation, a feeling of mutual trust and understanding should exist between the latter and its various audiences, i.e. the State and society. A basic ingredient of this balance between the organisation, the broader public and the State is effective communication and activity planning. As a way of contributing to the exploration of this process, this paper describes the means of communication used by Greek environmental organisations, and presents, through a non-linear model, the differentiation amongst them, in conjunction with aspects of the profile of those running each organisation and other indicators, such as the years in operation and the membership figures in each sampled organisation. The paper concludes by arguing that the diversification of communication means is related to the head person's years as a member of the organisation and the extent of its total membership. Another important finding is that the more the involvement in activities within the organisation, the less differentiation we observe amongst the employed means of communication.

European hare (Lepus europaeus) invasion ecology: Implication for the conservation of the endemic Irish hare (Lepus timidus hibernicus)

European hare Lepus europaeus populations have undergone recent declines but the species has successfully naturalised in many countries outside its native range. It was introduced to Ireland during the mid-late nineteenth century for field sport and is now well established in Northern Ireland. The native Irish hare Lepus timidus hibernicus is an endemic subspecies of mountain hare L. timidus and has attracted major conservation concern following a long-term population decline during the twentieth century and is one of the highest priority species for conservation action in Ireland. Little is known about the European hare in Ireland or whether it poses a significant threat to the native mountain hare subspecies by compromising its ecological security or genetic integrity. We review the invasion ecology of the European hare and examine evidence for interspecific competition with the mountain hare for habitat space and food resources, interspecific hybridisation, disease and parasite transmission and possible impacts of climate change. We also examine the impact that introduced hares can have on native non-lagomorph species. We conclude that the European hare is an emerging and significant threat to the conservation status of the native Irish hare. Invasive mammal species have been successfully eradicated from Ireland before and immediate action is often the only opportunity for cost-effective eradication. An urgent call is issued for further research whilst the need for a European hare invasive Species Action Plan (iSAP) and Eradication strategy are discussed.

Patterns of use of natural health products by Ontario seniors

A random dialing telephone survey of 1,071 60+ year-olds in 4 Ontario communities identified 553 (52%) users of natural health products. Mean age was 72 yrs (min-max:60-95); 76% were female. The most frequently reported natural health products were: echinacea (27%), glucosamine (26%), garlic (20%), ginkgo biloba (10%), St. John's wort (5%), ginseng (5%), flax seed oil (3%), evening primrose oil (2%), devil's claw (2%), saw palmetto (2%). Natural source vitamin use was reported by 24% of users, and 6% reporting using herbal teas. 51% of users used 2 or more herbal products and 8% used 5 or more products. 19% of herbal users also used a conventional prescription drug to manage the same health problem as the herbal product. The reported range of monthly expenditures for these products varied from a few cents (grew their own) to $288 (CAN). Thirty-five percent of users did not know the price of at least one of their natural products. Of the 75% of respondents willing to disclose their annual household income ($CAN), 20 had an income of $46,000. The widespread use and potential for significant expenditure of limited resources would suggest that more study is required into the efficacy, safety and value of these products.