• Experimentally testing the accuracy of an extinction estimator: Solow's optimal linear estimation model

      Clements, Christopher F.; Worsfold, Nicholas T.; Warren, Philip H.; Collen, Ben; Clark, Nick; Blackburn, Tim M.; Petchey, Owen L.; Butler, Simon; University of Sheffield; University of York; et al. (Wiley Blackwell, 2013)
      Mathematical methods for inferring time to extinction have been widely applied but poorly tested. Optimal linear estimation (also called the 'Weibull' or 'Weibull extreme value' model) infers time to extinction from a temporal distribution of species sightings. Previous studies have suggested optimal linear estimation provides accurate estimates of extinction time for some species; however, an in-depth test of the technique is lacking. The use of data from wild populations to gauge the error associated with estimations is often limited by very approximate estimates of the actual extinction date and poor sighting records. Microcosms provide a system in which the accuracy of estimations can be tested against known extinction dates, whilst incorporating a variety of extinction rates created by changing environmental conditions, species identity and species richness. We present the first use of experimental microcosm data to exhaustively test the accuracy of one sighting-based method of inferring time of extinction under a range of search efforts, search regimes, sighting frequencies and extinction rates. Our results show that the accuracy of optimal linear estimation can be affected by both observer-controlled parameters, such as change in search effort, and inherent features of the system, such as species identity. Whilst optimal linear estimation provides generally accurate and precise estimates, the technique is susceptible to both overestimation and underestimation of extinction date. Microcosm experiments provide a framework within which the accuracy of extinction predictors can be clearly gauged. Variables such as search effort, search regularity and species identity can significantly affect the accuracy of estimates and should be taken into account when testing extinction predictors in the future.
    • A framework for assessing threats and benefits to species responding to climate change

      Thomas, Chris D.; Hill, Jane K.; Anderson, Barbara J.; Bailey, Sallie; Beale, Colin M.; Bradbury, Richard B.; Bulman, Caroline R.; Crick, Humphrey Q. P.; Eigenbrod, Felix; Griffiths, Hannah M.; et al. (Wiley Blackwell, 2011-04)
      Current national and international frameworks for assessing threats to species have not been developed in the context of climate change, and are not framed in a way that recognises new opportunities that arise from climate change. The framework presented here separates the threats and benefits of climate change for individual species. Threat is assessed by the level of climate-related decline within a species’ recently occupied (e.g. pre-1970s) historical distribution, based on observed (e.g. repeat census) and/or projected changes (e.g. modelled bioclimate space). Benefits are assessed in terms of observed and/or projected increases outside the recently occupied historical range. Exacerbating factors (e.g. small population size, low dispersal capacity) that might increase levels of threat or limit expansion in response to climate change are taken into consideration within the framework. Protocols are also used to identify levels of confidence (and hence research and/or monitoring needs) in each species’ assessment.
    • From citizen science to policy development on the coral reefs of Jamaica

      Crabbe, M. James C. (Hindawi Publishing Corporation, 2012)
      This paper explores the application of citizen science to help generation of scientific data and capacity-building, and so underpin scientific ideas and policy development in the area of coral reef management, on the coral reefs of Jamaica. From 2000 to 2008, ninety Earthwatch volunteers were trained in coral reef data acquisition and analysis and made over 6,000 measurements on fringing reef sites along the north coast of Jamaica. Their work showed that while recruitment of small corals is returning after the major bleaching event of 2005, larger corals are not necessarily so resilient and so need careful management if the reefs are to survive such major extreme events. These findings were used in the development of an action plan for Jamaican coral reefs, presented to the Jamaican National Environmental Protection Agency. It was agreed that a number of themes and tactics need to be implemented in order to facilitate coral reef conservation in the Caribbean. The use of volunteers and citizen scientists from both developed and developing countries can help in forging links which can assist in data collection and analysis and, ultimately, in ecosystem management and policy development.
    • Global warming and coral reefs: modelling the effect of temperature on Acropora Palmata colony growth

      Crabbe, M. James C. (Elsevier, 2007)
      Data on colony growth of the branching coral Acropora palmata from fringing reefs off Discovery Bay on the north coast of Jamaica have been obtained over the period 2002-2007 using underwater photography and image analysis by both SCUBA and remotely using an ROV incorporating twin lasers. Growth modelling shows that while logarithmic growth is an approximate model for growth, a 3:3 rational polynomial function provides a significantly better fit to growth data for this coral species. Over the period 2002-2007, involving several cycles of sea surface temperature (SST) change, the rate of growth of A. palmata was largely proportional to rate of change of SST, with R(2)=0.935. These results have implications for the influence of global warming and climate change on coral reef ecosystems.
    • A hard instrument goes soft: the implications of the Convention on Biological Diversity's current trajectory

      Harrop, Stuart R.; Pritchard, Diana J. (Elsevier, 2011)
      The relentless loss of biological diversity, which will have a direct impact on human society and degrade ecosystem buffers against the extremes of climate perturbation, requires a strong global governance response. Of the numerous international legal instruments relating to the protection of nature, the Convention on Biological Diversity (CBD) is the most comprehensive. This paper examines its current emphasis on global biodiversity targets to extend our understanding of its trajectory, and its evolving nature as an instrument of global governance. We review CBD documents, and early examinations of its emergent character, in the context of the distinction between hard and soft law approaches, and combine analysis on the issue of targets from the literature on development, climate change and conservation biology. We emphasise that the CBD, created as a hard law instrument with a framework character, had the clear facility to develop subsidiary hard law instruments in the form of protocols but has not significantly followed this route.
    • Hurricanes and coral bleaching linked to changes in coral recruitment in Tobago

      Mallela, Jennie; Crabbe, M. James C. (Elsevier, 2009)
      Knowledge of coral recruitment patterns helps us understand how reefs react following major disturbances and provides us with an early warning system for predicting future reef health problems. The authors have reconstructed and interpreted historical and modern-day recruitment patterns, using a combination of growth modelling and in situ recruitment experiments, in order to understand how hurricanes, storms and bleaching events have influenced coral recruitment on the Caribbean coastline of Tobago. Whilst Tobago does not lie within the main hurricane belt results indicate that regional hurricane events negatively impact coral recruitment patterns in the Southern Caribbean. The results indicate that despite multiple large-scale disturbances corals are still recruiting on Tobago’s marginal reef systems, albeit in low numbers.
    • Identifying management needs for sustainable coral-reef ecosystems

      Crabbe, M. James C.; Martinez, Edwin; Garcia, Christiana; Chub, Juan; Castro, Leonardo; Guy, Jason (ProQuest, 2009)
      In 2007, it was developed with the aid of the Earthwatch Institute and the Oak Foundation a capacity-building program in southern Belize to address issues of marine reserve management underpinned by science. The first component included group discussions on important issues related to the management of the reserves and review of scientific papers, strategic plans, and action plans. The second component included field research in the Sapodilla Cayes Marine Reserve and the Port Honduras Marine Reserve. The project’s overall objectives and outcomes were to increase the participants’ capacity to lead and educate regarding sustainable development and to promote networking among organizations that manage marine resources, enhancing their collective influence over policy decisions. From that program, the project group developed the concepts and management protocols for coral-reef sustainability elucidated below.
    • The importance of religion in shaping volcanic risk perception in Italy, with special reference to Vesuvius and Etna

      Chester, David K.; Duncan, Angus M.; Dibben, Christopher J.L.; University of Liverpool; University of Bedfordshire; University of St. Andrews (Elsevier, 2008)
      With the exception of societies that are relatively untouched by modernism, the academic consensus holds that since the Eighteenth Century Enlightenment popular perception of divine responsibility for disasters has been progressively replaced by a perspective that views losses as resulting from the effects of extreme natural events upon vulnerable human populations. Nature is considered to be de-moralised. By means of examples of volcanic eruptions that have occurred over the past one hundred and fifty years and which transcend place, culture and faith tradition, the present authors have maintained a contrasting position, by arguing that religious perspectives are still important features of the ways in which people in many societies perceive volcanic eruptions. In the present paper it is argued that religious terms of reference have been and remain vital elements in the perceptions held by a significant proportion of the population in southern Italy when confronted by volcanic eruptions, particularly those that have occurred on Vesuvius and Etna. Within the context of what is termed popular Catholicism, the development of distinctive religious responses in pre-industrial times is first described.
    • The influence of extreme climate events on models of coral colony recruitment and survival in the Caribbean

      Crabbe, M. James C. (Scientific Research Publishing, 2012)
      Knowledge of coral recruitment patterns helps us understand how reefs react following major disturbances and provides us with an early warning system for predicting future reef health problems. We have reconstructed and interpreted historical and modern-day recruitment patterns, using growth modeling, in order to understand how hurricanes, storms and bleaching events have influenced coral recruitment in the Caribbean. The results indicate that regional hurricane events negatively impact coral recruitment patterns in the Caribbean, from the south in Tobago to more northerly areas in Belize and Jamaica. However, despite multiple large-scale disturbances, corals are still recruiting to marginal reef systems, and to the Mesoamerican Barrier reef off the coast of Belize. While recruitment and initial growth since the Caribbean-wide bleaching event of 2005 has been successful for Colpophylia natans at the sites studied in North Jamaica, medium and large sized colonies of this species have decreased in numbers since the bleaching event at most sites, except where the rugosity is highest, at Dairy Bull reef.
    • Influence of macroalgal cover on coral colony growth rates on fringing reefs of Discovery Bay, Jamaica: a letter report

      Crabbe, M. James C. (Bentham Open, 2008)
      This study investigated the hypothesis that alterations in macroalgal cover significantly influenced the growth rates of coral colonies on the fringing reefs of Discovery Bay, Jamaica. For colonies of Montastrea annularis, Porites astreoides, and Sidastrea siderea, radial growth rates were significantly (p<0.02) higher at Dairy Bull (where Diadema antillarum had removed macroalgal cover) than at either M1 or Rio Bueno (where there was c. 80% macroalgal cover). For colonies of Colpophyllia natans and Montastrea fankseii, radial growth rates were significantly (p<0.02) higher at Dairy Bull than at Rio Bueno. It has been suggested that macroalgal shading as well as contact is a significant inhibitor of coral growth, and our results are in accord with that hypothesis. These studies suggest that marine park managers should foster macroalgal predation wherever possible, in order to limit the irreversible decline of coral reefs.
    • Lack of recruitment of non-branching corals in Discovery Bay is linked to severe storms

      Crabbe, M. James C.; Mendes, Judith M.; Warner, George F. (University of Miami - Rosenstiel School of Marine and Atmospheric Science, 2002)
      We developed a rational polynomial function model for coral colony growth which proved a better fit than exponential logistic, Gompertz, and von Bertalanffy models. We tested the models with published coral weight growth data, and with new growth band data with Montastraea annularis samples. There was good correlation (r = 0.92, P < 0.01) between rates of growth and the degree of the polynomial, and this related to coral morphology, where n = 1 for non-branching corals, n = 2 for plate coral and n = 3 for branching species. We used this model to verify growth rates when we measured the surface areas and calculated recruitment dates of 438 non-branching corals in sites around Discovery Bay, Jamaica. Recruitment was significantly lower in 1980, 1951 and 1944 than in other years since 1940. This low recruitment coincided with the severest storms since 1940. There was a significant negative correlation (r = −0.72, P < 0.01) between recruitment estimates and storm severity. The severest storms resulted in significantly (P < 0.002) lower recruitment estimates. We show here that severe storm damage not only destroys branching corals, it also results in limiting non-branching coral recruitment.
    • Linking the ceramic industry, creativity and education in Jingdezhen, China: given at the First British Ceramics Biennial Conference Artists into Industry at the Wedgwood Museum in Stoke-on-Trent, October 2009

      Crabbe, M. James C. (Intellect, 2009)
      From 3 October to 13 December 2009, Stoke-on-Trent hosted the first British Ceramics Biennial. This grew from the legacy of the Stoke Ceramics Festival, setting ambitious aims as a festival and as an ongoing part of the city. A conference on ‘Artists into Industry’ at the Wedgwood Museum formed an important part of the Festival, where this article was presented.
    • Local understandings of conservation in southeastern Mexico and their implications for community-based conservation as an alternative paradigm

      Reyes-Garcia, Victoria; Ruiz-Mallen, Isabel; Porter-Bolland, Luciana; Garcia-Frapolli, Eduardo; Ellis, Edward A.; Mendez, Maria-Elena; Pritchard, Diana J.; Sanchez-Gonzalez, Maria-Consuelo; Institucio Catalana de Recerca i Estudis Avancats; Centro de Investigaciones en Ecosistemas; et al. (Wiley, 2013-08)
      Since the 1990s national and international programs have aimed to legitimize local conservation initiatives that might provide an alternative to the formal systems of state-managed or otherwise externally driven protected areas. We used discourse analysis (130 semistructured interviews with key informants) and descriptive statistics (679 surveys) to compare local perceptions of and experiences with state-driven versus community-driven conservation initiatives. We conducted our research in 6 communities in southeastern Mexico. Formalization of local conservation initiatives did not seem to be based on local knowledge and practices. Although interviewees thought community-based initiatives generated less conflict than statemanaged conservation initiatives, the community-based initiatives conformed to the biodiversity conservation paradigm that emphasizes restricted use of and access to resources. This restrictive approach to community-based conservation in Mexico, promoted through state and international conservation organizations, increased the area of protected land and had local support but was not built on locally relevant and multifunctional landscapes, a model that community-based conservation is assumed to advance.
    • Magnaporthe oryzae populations adapted to finger millet and rice exhibit distinctive patterns of genetic diversity, sexuality and host interaction

      Takan, J.P.; Chipili, J.; Muthumeenakshi, S.; Talbot, N.J.; Manyasa, E.O.; Bandyopadhyay, R.; Sere, Y.; Nutsugah, S.K.; Talhinhas, Pedro; Hossain, M.; et al. (Humana Press, 2012-02)
    • Mount Etna, Sicily : landscape evolution and hazard responses in the pre-industrial era

      Chester, David K.; Duncan, Angus M.; University of Bedfordshire (2010)
    • A novel method for the transport and analysis of genetic material from polyps and zooxanthellae of scleractinian corals

      Crabbe, M. James C. (Elsevier, 2003)
      We have developed a new simple method for transport, storage, and analysis of genetic material from the corals Agaricia agaricites, Dendrogyra cylindrica, Eusmilia ancora, Meandrina meandrites, Montastrea annularis, Porites astreoides, Porites furcata, Porites porites, and Siderastrea siderea at room temperature. All species yielded sufficient DNA from a single FTA® card (19 μg–43 ng) for subsequent PCR amplification of both coral and zooxanthellar DNA. The D1 and D2 variable region of the large subunit rRNA gene (LSUrDNA) was amplified from the DNA of P. furcata and S. siderea by PCR. Electrophoresis yielded two major DNA bands: an 800-base pair (bp) DNA, which represented the coral ribosomal RNA (rRNA) gene, and a 600-bp DNA, which represented the zooxanthellar srRNA gene. Extraction of DNA from the bands yielded between 290 μg total DNA (S. siderea coral DNA) and 9 μg total DNA (P. furcata zooxanthellar DNA). The ability to transport and store genetic material from scleractinian corals without resort to laboratory facilities in the field allows for the molecular study of a far wider range and variety of coral sites than have been studied to date.
    • Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments: a systems biological analysis

      Luo, R.; Wei, H.; Ye, L.; Wang, K.; Chen, F.; Luo, L.; Liu, L.; Li, Y.; Crabbe, M. James C.; Jin, L.; et al. (HighWire Press, 2009-01-20)
    • Preferential regulation of stably expressed genes in the human genome suggests a widespread expression buffering role of microRNAs

      Yang, Zhen; Dong, Dong; Zhang, Zhaolei; Crabbe, M. James C.; Wang, Li; Zhong, Yang (BioMed Central, 2012)
      In this study, we comprehensively explored the stably expressed genes (SE genes) and fluctuant genes (FL genes) in the human genome by a meta-analysis of large scale microarray data. We found that these genes have distinct function distributions. miRNA targets are shown to be significantly enriched in SE genes by using propensity analysis of miRNA regulation, supporting the hypothesis that miRNAs can buffer whole genome expression fluctuation. The expression-buffering effect of miRNA is independent of the target site number within the 3'-untranslated region. In addition, we found that gene expression fluctuation is positively correlated with the number of transcription factor binding sites in the promoter region, which suggests that coordination between transcription factors and miRNAs leads to balanced responses to external perturbations.