Barry J. McMahon

How and why should we implement genomics into conservation

Conservation genetics has provided important information into the dynamics of endangered populations. The rapid development of genomic methods has posed an important question, namely where do genetics and genomics sit in relation to their application in the conservation of species? Although genetics can answer a number of relevant questions related to conservation, the argument for the application of genomics is not yet fully exploited. Here, we explore the transition and rationale for the move from genetic to genomic research in conservation biology and the utility of such research. We explore the idea of a ‘conservation prior’ and how this can be determined by genomic data and used in the management of populations. We depict three different conservation scenarios and describe how genomic data can drive management action in each situation. We conclude that the most effective applications of genomics will be to inform stakeholders with the aim of avoiding ‘emergency room conservation’.

A Blueprint to Evaluate One Health

One Health (OH) positions health professionals as agents for change and provides a platform to manage determinants of health that are often not comprehensively captured in medicine or public health alone. However, due to the organization of societies and disciplines, and the sectoral allocation of resources, the development of transdisciplinary approaches requires effort and perseverance. Therefore, there is a need to provide evidence on the added value of OH for governments, researchers, funding bodies, and stakeholders. This paper outlines a conceptual framework of what OH approaches can encompass and the added values they can provide. The framework was developed during a workshop conducted by the “Network for Evaluation of One Health,” an Action funded by the European Cooperation in Science and Technology. By systematically describing the various aspects of OH, we provide the basis for measuring and monitoring the integration of disciplines, sectors, and stakeholders in health initiatives. The framework identifies the social, economic, and environmental drivers leading to integrated approaches to health and illustrates how these evoke characteristic OH operations, i.e., thinking, planning, and working, and require supporting infrastructures to allow learning, sharing, and systemic organization. It also describes the OH outcomes (i.e., sustainability, health and welfare, interspecies equity and stewardship, effectiveness, and efficiency), which are not possible to obtain through sectoral approaches alone, and their alignment with aspects of sustainable development based on society, environment, and economy.

Antimicrobial resistant bacteria in wild mammals and birds: a coincidence or cause for concern?

BackgroundThe emergence and dissemination of antimicrobial resistance (AMR) is a growing concern to public and animal health. The contribution attributable to wildlife remains unclear. In this study two unrelated wildlife species herring gulls (Larus argentatus) and a hybrid deer (Cervus elaphus x Cervus nippon) were investigated for the presence of Escherichia coli expressing an AMR phenotype.FindingsBacterial isolates resistant to β-lactam compounds were identified in both animal species and the production of functional β-lactamase was confirmed using nitrocefin. The prevalence of resistant isolates was higher in herring gulls (87%) compared to deer (31%). Resistance to this class of antibiotic was found only in non-pathogenic E. coli in herring gulls and in both pathogenic and non-pathogenic E. coli strains in deer.ConclusionsThe presence of AMR in wildlife has implications for public health, food safety and potable water source protection among others.

Antimicrobial Resistance in Wildlife: Implications for Public Health

The emergence and spread of antimicrobial‐resistant (AMR) bacteria in natural environments is a major concern with serious implications for human and animal health. The aim of this study was to determine the prevalence of AMR Escherichia coli (E. coli) in wild birds and mammalian species. Thirty faecal samples were collected from each of the following wildlife species: herring gulls (Larus argentatus), black‐headed gulls (Larus ridibundus), lesser black‐back gulls (Larus fuscus), hybrid deer species (Cervus elaphus x Cervus nippon) and twenty‐six from starlings (Sturnus vulgaris). A total of 115 E. coli isolates were isolated from 81 of 146 samples. Confirmed E. coli isolates were tested for their susceptibility to seven antimicrobial agents by disc diffusion. In total, 5.4% (8/146) of samples exhibited multidrug‐resistant phenotypes. The phylogenetic group and AMR‐encoding genes of all multidrug resistance isolates were determined by PCR. Tetracycline‐, ampicillin‐ and streptomycin‐resistant isolates were the most common resistant phenotypes. The following genes were identified in E. coli: blaTEM, strA, tet(A) and tet(B). Plasmids were identified in all samples that exhibited multidrug‐resistant phenotypes. This study indicates that wild birds and mammals may function as important host reservoirs and potential vectors for the spread of resistant bacteria and genetic determinants of AMR.

Antibiotic resistance patterns in Escherichia coli from gulls in nine European countries

Background The prevalence of antibiotic resistant faecal indicator bacteria from humans and food production animals has increased over the last decades. In Europe, resistance levels in Escherichia coli from these sources show a south-to-north gradient, with more widespread resistance in the Mediterranean region compared to northern Europe. Recent studies show that resistance levels can be high also in wildlife, but it is unknown to what extent resistance levels in nature conform to the patterns observed in human-associated bacteria. Methods To test this, we collected 3,158 faecal samples from breeding gulls (Larus sp.) from nine European countries and tested 2,210 randomly isolated E. coli for resistance against 10 antibiotics commonly used in human and veterinary medicine. Results Overall, 31.5% of the gull E. coli isolates were resistant to ≥1 antibiotic, but with considerable variation between countries: highest levels of isolates resistant to ≥1 antibiotic were observed in Spain (61.2%) and lowest levels in Denmark (8.3%). For each tested antibiotic, the Iberian countries were either the countries with the highest levels or in the upper range in between-country comparisons, while northern countries generally had a lower proportion of resistant E. coli isolates, thereby resembling the gradient of resistance seen in human and food animal sources. Conclusion We propose that gulls may serve as a sentinel of environmental levels of antibiotic resistant E. coli to complement studies of human-associated microbiota.

Don't forget to look down - collaborative approaches to predator conservation

Finding effective ways of conserving large carnivores is widely recognised as a priority in conservation. However, there is disagreement about the most effective way to do this, with some favouring top‐down ‘command and control’ approaches and others favouring collaboration. Arguments for coercive top‐down approaches have been presented elsewhere; here we present arguments for collaboration. In many parts of the developed world, flexibility of approach is built into the legislation, so that conservation objectives are balanced with other legitimate goals. In the developing world, limited resources, poverty and weak governance mean that collaborative approaches are likely to play a particularly important part in carnivore conservation. In general, coercive policies may lead to the deterioration of political legitimacy and potentially to non‐compliance issues such as illegal killing, whereas collaborative approaches may lead to psychological ownership, enhanced trust, learning, and better social outcomes. Sustainable hunting/trapping plays a crucial part in the conservation and management of many large carnivores. There are many different models for how to conserve carnivores effectively across the world, research is now required to reduce uncertainty and examine the effectiveness of these approaches in different contexts.

Identifying set-aside features for bird conservation and management in northeast Iberian pseudo-steppes

Capsule Set‐aside (land temporally removed from agricultural production) features and their regional locations influence steppe‐bird species of conservation concern in Catalonia. Aims To identify set‐aside features important to the ecology of four ground nesting species, namely Little Bustard Tetrax tetrax, Stone‐curlew Burhinus oedicnemus, Greater Short‐toed Lark Calandrella brachydactyla and Calandra Lark Melanocorypha calandra. Methods Set‐aside fields were surveyed in four regions of Catalonia (northeast of Spain) for the selected species during the 2004 and 2005 breeding seasons. Set‐aside habitat descriptors (e.g. size, vegetation structure) were collected. Ordination plots and information theoretic methods were used to assess the relationship between the selected bird species, set‐aside features and the regions. Results The region where the set‐aside was located had a strong effect on the abundance of the selected species. In addition, vegetation coverage, field shape of set‐aside and surrounding natural habitats were critical features, but with contrasting effects on the different species. Conclusion Populations of the selected species of conservation concern could be improved by effective management of set‐aside. As selected species responded differently, we recommend that management at local level should take into account the conservation value at a regional level of the protected area for each of the selected species.

Development of a Sustainably-Competitive Agriculture

The need for both Competitiveness and Sustainability, the two primary overarching goals of EU policy, present the agri-food sector with a unique set of formidable challenges and uncertainties. These point to the need for development of new, quality-focused models for agriculture and food production that are sustainably-competitive. The design criteria for the concept are outlined and developed within the context of an agronomic model for multifunctional, grass-based cattle production systems. This model highlights the importance of harnessing the benefits of functional biodiversity within two key epicenters of the system in order to realise both agronomic and environmental – and hence economic – advantage. Whilst much of the knowledge needed to implement the described model already exists, the functionality of biologically complex rumen and pasture processes within the two key system epicenters, represent the two main pillars of an innovation-driven research programme that is needed to provide fundamental new knowledge necessary to underpin practical development of the model.

An assessment of bird species within Irish agricultural landscapes using the Field Boundary Evaluation and Grading System

Capsule The Field Boundary Evaluation and Grading System (FBEGS) is a useful predictor of bird populations found in field boundaries located in southeast Ireland. Aims To assess the potential of FBEGS to evaluate the ecological quality of field boundaries in agricultural ecosystems and as a tool for the measurement of bird populations within field boundaries. Methods Surveys of bird populations were made in selected field boundaries on 50 farms in southeast Ireland in winter and during the breeding season. FBEGS surveys were also carried out on field boundaries to assess ecological quality. glms were fitted to assess the utility of the FBEGS Index as a predictor of bird populations. Results The FBEGS Index was an effective predictor of bird populations in the breeding season, but had limited use in predicting bird populations in winter. Within the overall FBEGS Index, the Associated Features score was a good predictor for populations in both the winter and breeding seasons. In addition, the Boundary Structural score of the field boundary was also an accurate predictor of birds in the breeding season. Conclusion The FBEGS Index has high potential for predicting the effect that changes in the farmed landscape will have on bird populations.

A comparison of winter bird communities in agricultural grassland and cereal habitats in Ireland: implications for Common Agricultural Policy reform

Capsule In winter, grassland sites had greater bird numbers compared to winter cereals, but a number of species of conservation concern were exclusively recorded on winter cereals. Aims To compare the winter bird communities in grassland and winter cereal fields. Methods Grassland and winter cereal fields were surveyed for overwintering birds in a landscape of mixed grassland and arable agriculture. Results Generalized Linear Models demonstrated that total bird abundance, the mean abundance of the majority of ecological groups and that of several common species, were significantly greater in grassland compared with winter cereal fields. However, a number of species of conservation concern, e.g. Skylark Aluda arvensis, were observed only on winter cereal fields. Only a minority of bird variables showed a positive response to field size. Of these, total bird species richness and the Shannon and Simpsons diversity indices showed positive significant responses to increasing field size, which may alternatively and perhaps more correctly be interpreted as a positive response to field boundary density within the farmed landscape. Conclusions Farmland habitats are important for the provision of overwintering resources for birds, and policy directed towards bird conservation should target the management of locally significant habitat types. The implications of these findings are discussed in light of the proposed revision of the Common Agricultural Policy in 2014, particularly the proposed measure for crop diversification.