Pseudo-nitzschia in New Zealand and the role of DNA probes and immunoassays in refining marine biotoxin monitoring programmes

Domoic acid (DA) was first detected in shellfish in New Zealand after the implementation of a comprehensive biotoxin monitoring programme for amnesic, paralytic, diarrhetic and neurotoxic shellfish toxins, following a suspected neurotoxic shellfish poisoning (NSP) event in early 1993. Both phytoplankton monitoring and shellfish flesh testing programmes have led to an extensive database which has helped link species of Pseudo-nitzschia to specific DA outbreaks. In 1994, P. pungens and P. turgidula were associated with DA contamination of shellfish, and cultured isolates of these species proved to be toxin producers. During 1996 the use of species-specific ribosomal RNA (rRNA)-targeted oligonucleotide probes and DA immunoassays led to the discovery of toxin production by P. fraudulenta, and showed the nontoxic P. heimii to be a major bloom former. Pseudo-nitzschia delicatissima, P. pseudodelicatissima and P. multiseries, also identified using rRNA-targeted probes, have been linked to DA contamination of New Zealand shellfish; P. australis is the main cause of DA in scallops. The relative amnesic shellfish poisoning (ASP) risk associated with different species, largely determined by DA immunoassays of cultured isolates, is now used by some regulators to refine risk assessments. Species identification is therefore vital so that shellfish growers, and health and industry officials, can make safe and economically sound harvesting decisions. The development and field trialling of DNA probes is proving invaluable in this context.     

Monitoring and management of the endangered Cape mountain zebra Equus zebra zebra in the Western Cape, South Africa

De Hoop Nature Reserve and a neighbouring conservancy contain the most genetically diverse subpopulation of the Endangered (IUCN) Cape mountain zebra ( Equus zebra zebra Linnaeus 1758). Although vital for the long-term stability of the meta-population, the population had received limited monitoring post-1999. We summarize data obtained during a population monitoring programme established in 2005. Ninety-nine individuals were identified indicating a decline in annual population growth from 6.6% (1995–1999) to 4.5% (1999–2005). The population was male biased and the deficit of females is likely to have prevented additional breeding herd formation resulting in excess nonbreeding males. These animals are currently of limited reproductive value to the meta-population and may be contributing to the decline in reproductive potential at De Hoop by competing for limited resources. One solution may be to translocate 'excess' males to reinforce existing small populations or establish new populations with females from elsewhere provided that a minimum of 78 animals is maintained at De Hoop to limit genetic loss. Population monitoring and effective management strategies for the De Hoop population and the meta-population are vital to ensure the long-term survival of Cape mountain zebra and for the success of other species recovery programmes.     

Protecting Free-Living Dormice: Molecular Identification of Cestode Parasites in Captive Dormice (Muscardinus avellanarius) Destined for Reintroduction

The success of any population translocation programme relies heavily on the measures implemented to control and monitor the spread of disease. Without these measures, programmes run the risk of releasing immunologically naïve species or, more dangerously, introducing novel infectious agents to native populations. As a precaution, a reintroduction programme for the common or hazel dormouse, Muscardinus avellanarius, in England screens dormice before release following captive breeding. Using PCR sequencing of a range of genes, we tested whether the same species of tapeworm(s) were present in captive and free-living dormice. Whilst only Rodentolepis straminea were identified in free-living dormice, cestode ova found in a captive individual produced a molecular match closely related to Hymenolepis microstoma and a previously unrecorded Rodentolepis species. To prevent putting at risk the free-living population, we recommended the continued treatment of dormice showing tapeworm infection before release. Our work demonstrates how molecular techniques can be used to inform reintroduction programmes, reduce risk from disease and increase chances of reintroduction success.

     

Genotype by environment interactions in forest tree breeding: review of methodology and perspectives on research and application

Genotype by environment interaction (G×E) refers to the comparative performances of genotypes differing among environments, representing differences in genotype rankings or differences in the level of expression of genetic differences among environments. G×E can reduce heritability and overall genetic gain, unless breeding programmes are structured to address different categories of environments. Understanding the impact of G×E, the role of environments in generating G×E and the problems and opportunities is vital to efficient breeding programme design and deployment of genetic material. We review the current main analytical methods for identifying G×E: factor analytic models, biplot analysis and reaction norm. We also review biological and statistical evidence of G×E for growth, form and wood properties in forest species of global economic importance, including some pines, eucalypts, Douglas-fir, spruces and some poplars. Among these species, high levels of G×E tend to be reported for growth traits, with low levels of G×E for form traits and wood properties. Finally, we discuss possible ways of exploiting G×E to maximise genetic gain in forest tree breeding. Characterising the role of environments in generating interactions is seen as the basic platform, allowing efficient testing of candidate genotypes. We discuss the importance of level-of-expression interaction, relative to rank-change interaction, as being greater than in many past reports, especially for deployment decisions. We examine the impacts of G×E on tree breeding, some environmental factors that cause G×E and the strategies for dealing with G×E in tree breeding, and the future role of genomics.     

Protecting Free-Living Dormice: Molecular Identification of Cestode Parasites in Captive Dormice (<Emphasis Type="Italic">Muscardinus avellanarius</Emphasis>) Destined for Reintroduction

The success of any population translocation programme relies heavily on the measures implemented to control and monitor the spread of disease. Without these measures, programmes run the risk of releasing immunologically naïve species or, more dangerously, introducing novel infectious agents to native populations. As a precaution, a reintroduction programme for the common or hazel dormouse, Muscardinus avellanarius, in England screens dormice before release following captive breeding. Using PCR sequencing of a range of genes, we tested whether the same species of tapeworm(s) were present in captive and free-living dormice. Whilst only Rodentolepis straminea were identified in free-living dormice, cestode ova found in a captive individual produced a molecular match closely related to Hymenolepis microstoma and a previously unrecorded Rodentolepis species. To prevent putting at risk the free-living population, we recommended the continued treatment of dormice showing tapeworm infection before release. Our work demonstrates how molecular techniques can be used to inform reintroduction programmes, reduce risk from disease and increase chances of reintroduction success.     

The impact of data precision on the effectiveness of alien plant control programmes: a case study from a protected area

Successful long-term invasive alien plant control programmes rely on alien plant distribution and abundance data to assess, prioritise, implement and monitor the efficacy of the programme. Here we assess the impact of data accuracy using the alien plant programme in Table Mountain National Park, South Africa. A systematic plot-based survey method was carried out to assess the distribution of alien plants in the park at a fine scale (systematic sampling). Alien plant richness, total area invaded and the degree of spatial overlap in species’ presence were compared between the systematic sample and a protected area (PA) managers’ dataset (collated from collective observations by park visitors, rangers and managers) and Working for Water (WfW) project data (data collected for the planning and implementation of the alien plant clearing programme) using a range of confusion matrix-based statistics to assess similarity and error rates between the datasets. A total of 106 alien plant taxa were detected across the three datasets, 12 in PA manager’s data, 23 in WfW data and 101 in the systematic survey. Overall, there was substantive disagreement between the datasets on the distribution of alien plants. For example both management datasets estimated species’ hectare coverage at orders of magnitude greater than indicated by systematic sampling. The inaccuracy of manager data has direct negative implications for funding allocation, which currently appears to be in excess of what is required. We recommend that contrary to perception, fine-scale surveys are a cost-effective way to inform long-term monitoring programmes and improve programme effectiveness.     

Valuing biodiversity and nature conservation at a local level

At a time where much of the discussion about major issues in nature conservation is necessarily undertaken at a global level, it is still important to consider the needs of the smaller organizations who do much of the grass roots work in the protection of wildlife and biodiversity. This study focuses on one such group, and examines how the contingent valuation method can be used to help to inform its decisions relating to the management of its portfolio of reserves in order to maximize benefits to its members. This paper argues that at a local level, where actions will not have significant global effects, contingent valuation methodology can inform decisions by assessing the value of additional reserves or particular conservation programmes to members in terms of their willingness to pay to acquire or implement them.     

Mathematical models and lymphatic filariasis control: monitoring and evaluating interventions

Monitoring and evaluation are crucially important to the scientific management of any mass parasite control programme. Monitoring enables the effectiveness of implemented actions to be assessed and necessary adaptations to be identified; it also determines when management objectives are achieved. Parasite transmission models can provide a scientific template for informing the optimal design of such monitoring programmes. Here, we illustrate the usefulness of using a model-based approach for monitoring and evaluating anti-parasite interventions and discuss issues that need addressing. We focus on the use of such an approach for the control and/or elimination of the vector-borne parasitic disease, lymphatic filariasis.     

Why monitoring often fails to inform adaptive management: a case study

Monitoring that facilitates adaptive management requires us to link observed changes in resource condition with management actions. Here, we present a case study to discuss how monitoring should be undertaken so it can facilitate adaptive management. Drawing on monitoring data collected by landholders as part of an incentive programme for native vegetation conservation on private land, we examined whether it was possible to determine to what extent changes in native vegetation condition were affected by funded management actions. Using a simple statistical technique (linear regression), we were unable to find strong links between the intended natural resource management (NRM) outcomes and funded management actions because (i) we could only use data from 22% of the 55 monitored sites as most data sheets were incomplete; (ii) sampling was undertaken in different seasons making it difficult to distinguish change due to management from change due to natural variability; and (iii) management actions were recorded in a generic way only, and not monitored through time, thus making it difficult to link observed changes in vegetation condition to on‐ground management. We suggest that monitoring programmes will only inform adaptive management where NRM bodies can prosecute (i) sampling designs that enable change as a result of management to be distinguished from change due to natural variability, and (ii) protocols that provide consistent data capture between sites and through time.     

Capacity of large-scale, long-term biodiversity monitoring programmes to detect trends in species prevalence

There is a critical need for monitoring programmes to assess change or trends in species status to inform conservation. A key aspect in developing such programmes is evaluating their statistical power—the ability to detect a real change. Here we examine the capacity of a broad-scale biodiversity monitoring programme in Alberta, Canada to measure changes in species prevalence. Using observed variation in detectability and prevalence for 252 species monitored at 85 sites, we simulated 3% annual declines and evaluated sample size (6 different sizes) and length of monitoring (5 different durations) necessary to detect change with a 90% certainty (power) at an α of 0.1. Our results suggest that after four monitoring cycles (e.g., 20 years for a 5-year cycle) a power of 90% can be expected for 99% of species when monitoring 1,625 sites, 65% of species for 300 sites, 27% of species for 75 sites, and 8% of species for 25 sites. We found that 66% detectability and 50% prevalence were needed to ensure that 3% annual change is detected at 50 sites over a 20-year period. Our results demonstrate that broad-scale monitoring programmes cannot effectively detect trends in all species at all spatial scales. The time period and spatial scale necessary to detect a real change at a specified level needs to be provided to stakeholders to ensure the short-term success of biodiversity monitoring programmes and to ensure that the most robust indicators of biodiversity are selected.     

The business of biodiversity – What is needed for biodiversity markets to work

There has been considerable discussion in Australia about market-based initiatives with the potential to bring effective incentives and greater investment for farmers and other land managers to promote biodiversity conservation. These initiatives include biodiversity trading markets (also termed the nature repair market), stewardship schemes, certification programmes, sustainability frameworks, and natural capital accounting. We welcome these discussions and believe these initiatives would be true advances if they bring much greater investment in conservation and stronger protection and recovery of biodiversity. However, we also have major concerns about the integrity and scientific credibility of some of these initiatives. In this article, we discuss why it is critical that such initiatives both carefully define biodiversity and determine what elements of biodiversity are to be targeted in conservation efforts. We also discuss the fundamental importance of appropriate and agreed biodiversity metrics, as well as the critical need for rigorous, well designed and independent biodiversity monitoring. To ensure that initiatives like biodiversity trading markets, stewardship schemes, certification programmes, sustainability frameworks and natural capital accounting are rigorous, non-corruptible and actually deliver what they are intended to do, they will need to be underpinned by appropriate programme designs. This includes robust and transparent governance structures, high-quality monitoring and timely reporting of key metrics.     

The African Waterfowl Census: review and development of an international monitoring programme

Dodman, T. 2000. The African Waterfowl Census: review and development of an international monitoring programme. Ostrich 71 (1 &2):95.

The African Waterfowl Census (AFWC) is now in its sixth year of operation as a coordinated wetland monitoring programme for sub-Saharan Africa. A comprehensive review of the AFWC took place in 1995 and 1996, including a widely-circulated questionnaire and a special meeting in Senegal. The results from this review process are being used to develop the programme as a lasting tool for wetland conservation and management in Africa. This paper summarises these results. The AFWC currently involves about 25 countries, which all submit data annually to enable waterbird numbers and distribution to be viewed at regional and international levels. On a national level, results are used variably for the identification and designation of Wetlands of International importance (Ramsar Sites), for standard wetland monitoring programmes, for wetland and species management actions and for setting hunting quotas. In some countries, large networks have already been established, comprising scientists, managers and local volunteers. Priorities for the future operation of the AFWC include: a) the establishment of a Steering Committee with representation from all regions; b) election of National Coordinators in all countries; c) national and regional training initiatives; d) a field guide to African waterbirds and basic monitoring exercises; e) involving local communities in basic monitoring exercises; and f) increasing the use of results, especially in support of the Bonn and Ramsar Conventions. The AFWC is uniquely placed to help countries meet obligations under the Agreement on the Conservation of African-Eurasian Migratory Waterbirds (AEWA) under the Bonn Convention. Increased collaboration and information exchange between National Coordinators and others will lead to a greater knowledge of wetland networks important for migratory waterbirds. This in turn will help in the identification of conservation priorities for particular species, for threatened wetlands that form vital components of migration networks and for threatened wetland habitats.     

Combining data‐derived priors with postrelease monitoring data to predict persistence of reintroduced populations

Monitoring is an essential part of reintroduction programs, but many years of data may be needed to obtain reliable population projections. This duration can potentially be reduced by incorporating prior information on expected vital rates (survival and fecundity) when making inferences from monitoring data. The prior distributions for these parameters can be derived from data for previous reintroductions, but it is important to account for site‐to‐site variation. We evaluated whether such informative priors improved our ability to estimate the finite rate of increase (λ) of the North Island robin (Petroica longipes) population reintroduced to Tawharanui Regional Park, New Zealand. We assessed how precision improved with each year of postrelease data added, comparing models that used informative or uninformative priors. The population grew from about 22 to 80 individuals from 2007 to 2016, with λ estimated to be 1.23 if density dependence was included in the model and 1.13 otherwise. Under either model, 7 years of data were required before the lower 95% credible limit for λ was > 1, giving confidence that the population would persist. The informative priors did not reduce this requirement. Data‐derived priors are useful before reintroduction because they allow λ to be estimated in advance. However, in the case examined here, the value of the priors was overwhelmed once site‐specific monitoring data became available. The Bayesian method presented is logical for reintroduced populations. It allows prior information (used to inform prerelease decisions) to be integrated with postrelease monitoring. This makes full use of the data for ongoing management decisions. However, if the priors properly account for site‐to‐site variation, they may have little predictive value compared with the site‐specific data. This value will depend on the degree of site‐to‐site variation as well as the quality of the data.     

Computer tomographic investigation of subcutaneous adipose tissue as an indicator of body composition

Background  

Modern computer tomography (CT) equipment can be used to acquire whole-body data from large animals such as pigs in minutes or less. In some circumstances, computer assisted analysis of the resulting image data can identify and measure anatomical features. The thickness of subcutaneous adipose tissue at a specific site measured by ultrasound, is used in the pig industry to assess adiposity and inform management decisions that have an impact on reproduction, food conversion performance and sow longevity. The measurement site, called "P2", is used throughout the industry. We propose that CT can be used to measure subcutaneous adipose tissue thickness and identify novel measurement sites that can be used as predictors of general adiposity.     

Challenges for biodiversity monitoring using citizen science in transitioning social–ecological systems

Biodiversity monitoring requires sound data collection over large temporal and spatial scales in order to inform policy and conservation management. Citizen science programmes, if designed appropriately, can make valuable contributions to data collection and analyses. Moreover, citizen science has potential for both environmental education and civic participation. Recommendations on effective citizen science are available in the literature, but most existing work has come from relatively rich, industrialized countries. By contrast, there is very little knowledge on citizen science projects in transitioning economic, social and cultural settings. This paper seeks to adjust this deficit by contributing insights from our attempt to initiate a new monitoring scheme in Romania. We draw on our experience of conducting workshops, training events and camps to strengthen citizen engagement in a butterfly monitoring scheme, and discussions with many stakeholders engaged in other monitoring programmes inside and outside of Europe. We highlight four general themes that are worth considering when initiating new citizen science projects in socio-economically challenging settings: (i) engaging citizens requires a combination of formal and informal support; (ii) a culture of volunteering requires education as well as building capacity and confidence; (iii) citizen science needs active integration of both national experts and local stakeholders; and (iv) successful monitoring schemes require effective leadership. We conclude that particular attention should be paid to the cultural legacies of the target area.     

Using the natural capital index framework as a scalable aggregation methodology for regional biodiversity indicators

There is an increasing need for aggregated biodiversity indicators to inform policy decisions at all levels from local to global. Despite their similar policy goals, low-level (e.g. local, regional) and high-level (e.g. continental, global) indicator development is generally performed independently, and the resulting indicators are often incompatible both in their structure and data requirements. In this paper we focus on a particularly flexible aggregation framework originally developed for global assessments, the Natural Capital Index. We show that with the use of appropriate fine-scale data, the NCI framework can be applied in low-level policy contexts as well. To support this statement, we show that several established low-level indicators are essentially conforming to the NCI framework, and can be seen as existing low-level NCI implementations. The concept is illustrated with an implementation for Hungary, and the potential advantages and shortcomings of low level NCI implementations are discussed. NCI-based low level indicators can be implemented in any region, where a local indicator of ecological quality is systematically surveyed. Given the recent surge in monitoring activities worldwide, fuelled by global change and reporting obligations, fine-scale NCI implementations can become important additions to existing ecological state indicators useful in a wide range of local and regional policy contexts.     

Integrating genomic selection into dairy cattle breeding programmes: a review

Extensive genetic progress has been achieved in dairy cattle populations on many traits of economic importance because of efficient breeding programmes. Success of these programmes has relied on progeny testing of the best young males to accurately assess their genetic merit and hence their potential for breeding. Over the last few years, the integration of dense genomic information into statistical tools used to make selection decisions, commonly referred to as genomic selection, has enabled gains in predicting accuracy of breeding values for young animals without own performance. The possibility to select animals at an early stage allows defining new breeding strategies aimed at boosting genetic progress while reducing costs. The first objective of this article was to review methods used to model and optimize breeding schemes integrating genomic selection and to discuss their relative advantages and limitations. The second objective was to summarize the main results and perspectives on the use of genomic selection in practical breeding schemes, on the basis of the example of dairy cattle populations. Two main designs of breeding programmes integrating genomic selection were studied in dairy cattle. Genomic selection can be used either for pre-selecting males to be progeny tested or for selecting males to be used as active sires in the population. The first option produces moderate genetic gains without changing the structure of breeding programmes. The second option leads to large genetic gains, up to double those of conventional schemes because of a major reduction in the mean generation interval, but it requires greater changes in breeding programme structure. The literature suggests that genomic selection becomes more attractive when it is coupled with embryo transfer technologies to further increase selection intensity on the dam-to-sire pathway. The use of genomic information also offers new opportunities to improve preservation of genetic variation. However, recent simulation studies have shown that putting constraints on genomic inbreeding rates for defining optimal contributions of breeding animals could significantly reduce achievable genetic gain. Finally, the article summarizes the potential of genomic selection to include new traits in the breeding goal to meet societal demands regarding animal health and environmental efficiency in animal production.     

Some new approaches to conservation monitoring of British breeding birds

It is important to monitor bird populations both in their own right and as indicators of the general health of wildlife habitats. The objectives of the British Trust for Ornithology's Integrated Population Monitoring programme relate to breeding bird populations in Britain and Ireland and involve the estimation of demographic parameters as well as assessment of numbers. Current programmes for monitoring bird numbers cover the majority of British species; it would be feasible to monitor most of the rest. A new Breeding Bird Survey has been developed to provide effective coverage of all regions and all major habitats in Britain through random sampling, allowing for the marked geographical variation in volunteer observer density. The final choice of a random sample stratified by observer density (with some professional support in regions with few volunteer observers) was based on comparison with alternative stratifications, using data from a 2-year pilot study to assess the number of species adequately covered under various alternatives. A method of assessing whether or not targets are being achieved at any time has been developed: it involves looking back through the data at intervals of 1-year, 4-year, 16-year and longer spans. It will be possible to refine this by incorporating environmental and density-dependent effects into predictive models. The method is illustrated here using Common Birds Census data. We discuss associated problems of statistical inference and of taking decisions under uncertainty. The data provide evidence for large declines in some species, particularly in farmland; the value of birds as general indicators of habitat health is clear. The results of monitoring can be used to illuminate possible causes of problems and to guide both practical steps to ameliorate the problems and research aimed at better understanding the causes. Examples of such research are discussed.     

Interpreting coral reef monitoring data: A guide for improved management decisions

Coral reef monitoring programmes exist in all regions of the world, recording reef attributes such as coral cover, fish biomass and macroalgal cover. Given the cost of such monitoring programs, and the degraded state of many of the world’s reefs, understanding how reef monitoring data can be used to shape management decisions for coral reefs is a high priority. However, there is no general guide to understanding the ecological implications of the data in a format that can trigger a management response. We attempt to provide such a guide for interpreting the temporal trends in 41 coral reef monitoring attributes, recorded by seven of the largest reef monitoring programmes. We show that only a small subset of these attributes is required to identify the stressors that have impacted a reef (i.e. provide a diagnosis), as well as to estimate the likely recovery potential (prognosis). Two of the most useful indicators, turf algal canopy height and coral colony growth rate are not commonly measured, and we strongly recommend their inclusion in reef monitoring. The diagnosis and prognosis system that we have developed may help guide management actions and provides a foundation for further development as biological and ecological insights continue to grow.