Professor Richard Griffiths

Article

• Labisko, J. et al. (2019). Endemic, endangered, and evolutionarily significant: Cryptic lineages in Seychelles’ frogs. Biological Journal of the Linnean Society [Online]. Available at: https://doi.org/10.1093/biolinnean/bly183.
  Abstract View in KAR View full text
  Cryptic diversity that corresponds with island origin has been previously reported in the endemic, geographically restricted sooglossid frogs of the Seychelles archipelago. The evolutionary pattern has not been fully explored, and given current amphibian declines and the increased extinction risk faced by island species, we sought to identify evolutionarily significant units (ESUs) to address conservation concerns for these highly threatened anurans. We obtained genetic data for two mitochondrial (mtDNA) and four nuclear (nuDNA) genes from all known populations of sooglossid frog (the islands of Mahé, Praslin, and Silhouette) to perform phylogenetic analyses and construct nuDNA haplotype networks. Bayesian and maximum likelihood analyses of mtDNA support monophyly and molecular differentiation of populations in all species that occur on multiple islands. Haplotype networks using statistical parsimony revealed multiple high-frequency haplotypes shared between islands and taxa, in addition to numerous geographically distinct (island-specific) haplotypes for each species. We consider each island-specific population of sooglossid frog as an ESU and advise conservation managers to do likewise. Furthermore, our results identify each island lineage as a candidate species, evidence for which is supported by Bayesian Poisson Tree Processes analyses of mtDNA, and independent analyses of mtDNA and nuDNA using the multispecies coalescent. Our findings add to the growing understanding of the biogeography and hidden diversity within this globally important region.
• Zhou, M. et al. (2019). Removal models accounting for temporary emigration. Biometrics [Online] 75:24-35. Available at: https://doi.org/10.1111/biom.12961.
  Abstract View in KAR View full text
  Removal of protected species from sites scheduled for development is often a legal requirement in order to minimize the loss of biodiversity. The assumption of closure in the classic removal model will be violated if individuals become temporarily undetectable, a phenomenon commonly exhibited by reptiles and amphibians. Temporary emigration can be modeled using a multievent framework with a partial hidden process, where the underlying state process describes the movement pattern of animals between the survey area and an area outside of the study. We present a multievent removal model within a robust design framework which allows for individuals becoming temporarily unavailable for detection. We demonstrate how to investigate parameter redundancy in the model. Results suggest the use of the robust design and certain forms of constraints overcome issues of parameter redundancy. We show which combinations of parameters are estimable when the robust design reduces to a single secondary capture occasion within each primary sampling period. Additionally, we explore the benefit of the robust design on the precision of parameters using simulation. We demonstrate that the use of the robust design is highly recommended when sampling removal data. We apply our model to removal data of common lizards, Zootoca vivipara, and for this application precision of parameter estimates is further improved using an integrated model.
• Rosa, G. et al. (2019). Sex‐biased disease dynamics increase extinction risk by impairing population recovery. Animal Conservation [Online]. Available at: http://dx.doi.org/10.1111/acv.12502.
  Abstract View in KAR
  The periodicity of life‐cycle events (phenology) modulates host availability to pathogens in a repeatable pattern. The effects of sexual differences in host phenology have been little explored in wildlife epidemiological studies. A recent series of ranavirosis outbreaks led to serious declines of Boscas’ newt populations at Serra da Estrela (Portugal). The peculiar phenology of this species, in which a large number of females remain in the aquatic habitat after the breeding season, turns it into a suitable model to test how sex‐biased mortality can affect host population persistence in the context of infectious diseases. We investigated how the phenology of Bosca's newt (i.e. biased number of females) mediated the impact of Ranavirus. We then evaluated the risk of extinction of the population under different scenarios of sex‐biased mortality using a population viability analysis. Two newt populations (one subject to yearly outbreaks and a comparative site where outbreaks have not been recorded) were tracked for trends over time following emergence of ranaviral disease, allowing us to assess the differential impact of the disease on both sexes. In addition to a significant decline in abundance of adult newts, our data suggest that phenology can affect disease dynamics indirectly, leading to reduction in females and a reversal of the sex ratio of the breeding population. Our models suggest that female‐biased mortality does not exacerbate Ranavirus‐driven population declines in the short‐term, but is likely to have a deleterious impact during the recovery process once the lethal effect of disease is removed from the system.
• Barata, I., Silva, E. and Griffiths, R. (2018). Predictors of abundance of a rare bromeliad-dwelling frog (Crossodactylodes itambe) in the Espinhaço Mountain Range of Brazil. Journal of Herpetology [Online] 52:321-326. Available at: http://dx.doi.org/10.1670/17-183.
  Abstract View in KAR
  Although tank bromeliads are used by many anuran species, bromeligenous frogs (species strictly dependent on bromeliads for reproduction) occur less frequently and are poorly understood. Crossodactylodes are small frogs confined to bromeliads where they lay their eggs and complete their life cycle without leaving the plant. The genus comprises five species and there is little information on their natural history. We focused on Crossodactylodes itambe – a species confined to a single summit of <0.5 km2 at 1700 m above sea level in the Espinhaço Mountain Range of Brazil. We surveyed frogs in 75 individual bromeliads during two consecutive years and we used a Generalized Linear Model to investigate the drivers of species abundance related to habitat structure and local climate. We recorded 446 adults, 267 tadpoles and 40 juveniles over the two years. Most bromeliads contained one adult frog and the mean number of tadpoles was 2-3. The structure of bromeliads influenced species abundance more than local climate. We found that bromeliad size, volume of central tank, and presence/absence of invertebrates and water influenced abundance of frogs. Abundance increased in larger bromeliads at higher elevation. Changes in the structure and size of bromeliads might therefore affect abundance. We provide the first species assessment and evaluation of threat categories for this poorly known species.
• Mahoney, P. et al. (2018). The Biorhythm of Human Skeletal Growth. Journal of Anatomy [Online] 232:26-38. Available at: http://onlinelibrary.wiley.com/doi/10.1111/joa.12709/full.
  Abstract View in KAR View full text
  Evidence of a periodic biorhythm is retained in tooth enamel in the form of Retzius lines. The periodicity of Retzius lines (RP) correlates with body mass and the scheduling of life history events when compared between some mammalian species. The correlation has led to the development of the inter-specific Havers-Halberg Oscillation (HHO) hypothesis, which holds great potential for studying aspects of a fossil species biology from teeth. Yet, our understanding of if, or how the HHO relates to human skeletal growth is limited. The goal here is to explore associations between the biorhythm and two hard tissues that form at different times during human ontogeny, within the context of the HHO. First, we investigate the relationship of RP to permanent molar enamel thickness and the underlying daily rate that ameloblasts secrete enamel during childhood. Following this, we develop preliminary research conducted on small samples of adult human bone by testing associations between RP, adult femoral length (as a proxy for attained adult stature), and cortical osteocyte lacunae density (as a proxy for the rate of osteocyte proliferation). Results reveal RP is positively correlated with enamel thickness, negatively correlated with femoral length, but weakly associated with the rate of enamel secretion and osteocyte proliferation. These new data imply that a slower biorhythm predicts thicker enamel for children but shorter stature for adults. Our results develop the intra-specific HHO hypothesis suggesting that there is a common underlying systemic biorhythm that has a role in the final products of human enamel and bone growth.
• Harper, L. et al. (2018). Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds. Hydrobiologia [Online]. Available at: https://doi.org/10.1007/s10750-018-3750-5.
  Abstract View in KAR View full text
  Environmental DNA (eDNA) analysis is a rapid, non-invasive, cost-efficient biodiversity monitoring tool with enormous potential to inform aquatic conservation and management. Development is ongoing, with strong commercial interest, and new uses are continually being discovered. General applications of eDNA and guidelines for best practice in freshwater systems have been established, but habitat-specific assessments are lacking. Ponds are highly diverse, yet understudied systems that could benefit from eDNA monitoring. However, eDNA applications in ponds and methodological constraints specific to these environments remain unaddressed. Following a stakeholder workshop in 2017, researchers combined knowledge and expertise to review these applications and challenges that must be addressed for the future and consistency of eDNA monitoring in ponds. The greatest challenges for pond eDNA surveys are representative sampling, eDNA capture, and potential PCR inhibition. We provide recommendations for sampling, eDNA capture, inhibition testing, and laboratory practice, which should aid new and ongoing eDNA projects in ponds. If implemented, these recommendations will contribute towards an eventual broad standardisation of eDNA research and practice, with room to tailor workflows for optimal analysis and different applications. Such standardisation will provide more robust, comparable, and ecologically meaningful data to enable effective conservation and management of pond biodiversity.
• Nash, D. and Griffiths, R. (2018). Ranging behaviour of adders (Vipera berus) translocated from a development site. Herpetological Journal [Online] 28:155-159. Available at: https://thebhs.org/publications/the-herpetological-journal/volume-28-number-4-october-2018/1852-04-ranging-behaviour-of-adders-i-vipera-berus-i-translocated-from-a-development-site.
  Abstract View in KAR View full text
  Translocation of animals from sites scheduled for development is a widespread but controversial intervention to resolve human-wildlife conflicts. Indeed, reptiles are very frequently the subject of such translocations, but there is a paucity of information on the fate of such animals or how their behaviour compares to residents. In 2014, a population of adders (Vipera berus) was translocated from a development site in Essex, UK. A sample of snakes was fitted with external radio tags and tracked for a period of 10 days during the spring. This exercise was repeated during the summer using a combination of translocated and resident individuals. Translocated males exhibited significantly greater average daily movements than resident conspecifics. Furthermore, all translocated males undertook long-distance, unidirectional movements away from the release site. In contrast, all translocated females remained within 50 m of the point of release. One of the males returned to the donor site, crossing large areas of unsuitable habitat in doing so. Translocated males also maintained significantly larger total ranges than resident conspecifics. No differences in range sizes were observed between translocated and resident females. The dispersal of male snakes from the release site may increase the risk of mortality of translocated snakes and reduces the likelihood of establishing a new population. Interventions to encourage the establishment of new home ranges within the boundaries of release sites may include mechanisms to prevent dispersal immediately following release.
• Worthington, H. et al. (2018). Estimation of population size when capture probability depends on individual state. Journal of Agricultural, Biological, and Environmental Statistics [Online]. Available at: https://doi.org/10.1007/s13253-018-00347-x.
  Abstract View in KAR View full text
  We develop a multi-state model to estimate the size of a closed population from
  capture–recapture studies. We consider the case where capture–recapture data are not of
  a simple binary form, but where the state of an individual is also recorded upon every
  capture as a discrete variable. The proposed multi-state model can be regarded as a
  generalisation of the commonly applied set of closed population models to a multi-state
  form. The model allows for heterogeneity within the capture probabilities associated with
  each state while also permitting individuals to move between the different discrete states.
  A closed-form expression for the likelihood is presented in terms of a set of sufficient
  statistics. The link between existing models for capture heterogeneity is established,
  and simulation is used to show that the estimate of population size can be biased when
  movement between states is not accounted for. The proposed unconditional approach is
  also compared to a conditional approach to assess estimation bias. The model derived
  in this paper is motivated by a real ecological data set on great crested newts, Triturus
  cristatus.
• Buxton, A., Groombridge, J. and Griffiths, R. (2018). Comparison of two Citizen Scientist Methods for Collecting Pond Water Samples for Environmental DNA Studies. Ctizen Science: Theory and Practice [Online] 3:2. Available at: https://doi.org/10.5334/cstp.151.
  Abstract View in KAR View full text
  The use of environmental DNA (eDNA) for the survey of aquatic species offers a wide range of benefits over conventional surveys and has begun to be used by citizen scientists. One advantage of eDNA over conventional survey protocols is the comparative ease with which samples can be collected over a wide geographic area by citizen scientists. However, eDNA collection protocols vary widely between different studies, promoting a need to identify an optimum method. Collection protocols include ethanol precipitation and various filtration methods including those that use electronic vacuum or peristaltic pumps, hand pumps or syringes to capture eDNA on a membrane. We compare the effectiveness of two eDNA collection methods suitable for use by citizen scientists: glass-microfiber syringe filtration and ethanol precipitation. Paired samples of water were analysed for great crested newt (Triturus cristatus) DNA using (1) a laboratory tank experiment using different dilutions of water inoculated with newt DNA; and (2) by sampling naturally colonised ponds. Although syringe filters consistently yielded greater DNA extract concentrations in the tank experiments, this was not the case in samples collected from the field where no difference between the two methods was identified. Clearly, properties within the water – such as algae and particulate matter - can influence the amount of DNA captured by the two methods, so the sampling protocol of choice will depend on the design and goals of the study.
• Robinson, J. et al. (2018). Supplying the wildlife trade as a livelihood strategy in a biodiversity hotspot. Ecology and Society [Online] 23:13. Available at: https://doi.org/10.5751/ES-09821-230113.
  Abstract View in KAR View full text
  Much of the global wildlife trade is sourced from biodiversity-rich developing countries. These often have high levels of poverty and habitat loss, particularly in rural areas where many depend on natural resources. However, wildlife collection may incentivize local people to conserve habitats that support their livelihoods. Here we examined the contribution of the commercial collection of live animals to rural livelihoods in Madagascar, one of the world’s most important biodiversity hotspots. Using questionnaires, we investigated the prevalence, profitability relative to other livelihood activities, and local importance of the trade, and its capacity to provide incentives for conservation. Thirteen percent of households were engaged in live animal collection in the study area (~5% trapped reptiles and amphibians and the remainder trapped invertebrates). This formed part of a diverse livelihood strategy, and was more profitable than other activities (in terms of returns per unit of effort), with median earnings of ~US$100 per season (~25% of Gross National Income per year). However, trapping was part-time, usually undertaken by poorer members of the community, and often perceived as opportunistic, risky, and financially unreliable. Further, trappers and nontrappers held similar perceptions regarding conservation, suggesting wildlife trade currently does not incentivize enhanced stewardship of traded species and their habitats. Our study brings together a range of methodologies to present the most comprehensive insights into livelihoods and conservation in poor rural communities involved in the commercial collection of live animals to supply international trade. This improved understanding of the wider socioeconomic dimensions of wildlife trade can inform policy and management interventions for both the threats and opportunities associated with global trade in biodiversity both in Madagascar and more generally.
• Buxton, A., Groombridge, J. and Griffiths, R. (2018). Seasonal variation in environmental DNA detection in sediment and water samples. PlosOne [Online] 13:e0191737. Available at: https://doi.org/10.1371/journal.pone.0191737.
  Abstract View in KAR View full text
  The use of aquatic environmental DNA (eDNA) to detect the presence of species depends
  on the seasonal activity of the species in the sampled habitat. eDNA may persist in sediments
  for longer than it does in water, and analysing sediment could potentially extend the
  seasonal window for species assessment. Using the great crested newt as a model, we
  compare how detection probability changes across the seasons in eDNA samples collected
  from both pond water and pond sediments. Detection of both aquatic and sedimentary
  eDNA varied through the year, peaking in the summer (July), with its lowest point in the winter
  (January): in all seasons, detection probability of eDNA from water exceeded that from
  sediment. Detection probability of eDNA also varied between study areas, and according to
  great crested newt habitat suitability and sediment type. As aquatic and sedimentary eDNA
  show the same seasonal fluctuations, the patterns observed in both sample types likely
  reflect current or recent presence of the target species. However, given the low detection
  probabilities found in the autumn and winter we would not recommend using either aquatic
  or sedimentary eDNA for year-round sampling without further refinement and testing of the
  methods.
• Robinson, J. et al. (2018). Wildlife supply chains in Madagascar from local collection to global export. Biological Conservation [Online] 226:144-152. Available at: https://doi.org/10.1016/j.biocon.2018.07.027.
  Abstract View in KAR
  International trade in wildlife is a complex multi-billion dollar industry. To supply it, many animals are extracted from the wild, sourced from biodiversity-rich, developing countries. Whilst the trade has far-reaching implications for wildlife protection, there is limited information regarding the socio-economic implications in supply countries. Consequently, a better understanding of the costs and benefits of wildlife supply chains, for both livelihoods and conservation, is required to enhance wildlife trade management and inform its regulation. Using Madagascar as a case study, we used value chain analysis to explore the operation of legal wildlife trade on a national scale; we estimate the number of actors involved, the scale, value and profit distribution along the chain, and explore management options. We find that the supply of wildlife provided economic benefits to a number of actors, from local collectors, to intermediaries, exporters and national authorities. CITES-listed reptiles and amphibians comprised a substantial proportion of the quantity and value of live animal exports with a total minimum export value of 230,795USD per year. Sales prices of reptiles and amphibians increased over 100-fold between local collectors and exporters, with exporters capturing ~92% of final export price (or 57% when their costs are deducted). However, exporters shouldered the largest costs and financial risks. Local collectors obtained ~1.4% of the final sales price, and opportunities for poverty alleviation and incentives for sustainable management from the trade appear to be limited. Promoting collective management of species harvests at the local level may enhance conservation and livelihood benefits. However, this approach requires consideration of property rights and land-tenure systems. The complex and informal nature of some wildlife supply chains make the design and implementation of policy instruments aimed at enhancing conservation and livelihoods challenging. Nevertheless, value chain analysis provides a mechanism by which management actions can be more precisely targeted.
• Austen, G. et al. (2017). Species identification by conservation practitioners using online images: accuracy and agreement between experts. PeerJ [Online]. Available at: https://doi.org/10.7717/peerj.4157.
  Abstract View in KAR View full text
  Emerging technologies have led to an increase in species observations being recorded via digital images. Such visual records are easily shared, and are often uploaded to online communities when help is required to identify or validate species. Although this is common practice, little is known about the accuracy of species identification from such images. Using online images of newts that are native and non-native to the UK, this study asked holders of great crested newt (Triturus cristatus) licences (issued by UK authorities to permit surveying for this species) to sort these images into groups, and to assign species names to those groups. All of these experts identified the native species, but agreement among these participants was low, with some being cautious in committing to definitive identifications. Individuals’ accuracy was also independent of both their experience and self-assessed ability. Furthermore, mean accuracy was not uniform across species (69–96%). These findings demonstrate the difficulty of accurate identification of newts from a single image, and that expert judgements are variable, even within the same knowledgeable community. We suggest that identification decisions should be made on multiple images and verified by more than one expert, which could improve the reliability of species data.
• Buxton, A., Groombridge, J. and Griffiths, R. (2017). Is the detection of aquatic environmental DNA influenced by substrate type? PLOS ONE [Online] 12:e0183371. Available at: http://dx.doi.org/10.1371/journal.pone.0183371.
  Abstract View in KAR View full text
  The use of environmental DNA (eDNA) to assess the presence-absence of rare, cryptic or invasive species is hindered by a poor understanding of the factors that can remove DNA from the system. In aquatic systems, eDNA can be transported out either horizontally in water flows or vertically by incorporation into the sediment. Equally, eDNA may be broken down by various biotic and abiotic processes if the target organism leaves the system. We use occupancy modelling and a replicated mesocosm experiment to examine how detection probability of eDNA changes once the target species is no longer present. We hypothesise that detection probability falls faster with a sediment which has a large number of DNA binding sites such as topsoil or clay, over lower DNA binding capacity substrates such as sand. Water removed from ponds containing the target species (the great crested newt) initially showed high detection probabilities, but these fell to between 40% and 60% over the first 10 days and to between 10% and 22% by day 15: eDNA remained detectable at very low levels until day 22. Very little difference in detection was observed between the control group (no substrate) and the sand substrate. A small reduction in detection probability was observed between the control and clay substrates, but this was not significant. However, a highly significant reduction in detection probability was observed with a topsoil substrate. This result is likely to have stemmed from increased levels of PCR inhibition, suggesting that incorporation of DNA into the sediment is of only limited importance. Surveys of aquatic species using eDNA clearly need to take account of substrate type as well as other environmental factors when collecting samples, analysing data and interpreting the results
• Meredith, H. et al. (2017). Practitioner and scientist perceptions of successful amphibian conservation. Conservation Biology [Online] 32:366-375. Available at: http://dx.doi.org/10.1111/cobi.13005.
  Abstract View in KAR View full text
  Conservation requires successful outcomes. However, success is perceived in many different ways depending on the desired outcome, which can vary according to numerous factors. We analysed perceptions of success among 355 scientists and practitioners working on amphibian conservation from over 150 organisations in more than 50 countries. Respondents identified four types of success: species and habitat improvements (84% of respondents); effective programme management (36%); outreach initiatives such as education and public engagement (25%); and the application of science-based conservation (15%). The most significant factor influencing overall perceived success was reducing threats. Capacity building was rated least important. Perceptions were influenced by experience, professional affiliation, involvement in conservation practice, and country of residence. More experienced conservation practitioners associated success with improvements to species and habitats, and less so with education and engagement initiatives. Whilst science-based conservation was rated as important, this factor declined in importance as the number of programmes a respondent participated in increased, particularly amongst those from Less Economically Developed Countries. The ultimate measure of conservation success – population recovery – may be difficult to measure in many amphibians, difficult to relate to the conservation actions intended to drive it, and difficult to achieve within conventional funding timeframes. The relaunched Amphibian Conservation Action Plan provides a framework for capturing lower-level processes and outcomes, identifying gaps, and measuring progress.
• Buxton, A. et al. (2017). Seasonal variation in environmental DNA in relation to population size and environmental factors. Scientific Reports [Online] 7:46294. Available at: http://dx.doi.org/10.1038/srep46294.
  Abstract View in KAR View full text
  Analysing DNA that organisms release into the environment (environmental DNA, or eDNA) has
  enormous potential for assessing rare and cryptic species. At present the method is only reliably used
  to assess the presence-absence of species in natural environments, as seasonal influences on eDNA in
  relation to presence, abundance, life stages and seasonal behaviours are poorly understood. A naturally
  colonised, replicated pond system was used to show how seasonal changes in eDNA were influenced
  by abundance of adults and larvae of great crested newts (Triturus cristatus). Peaks in eDNA were
  observed in early June when adult breeding was coming to an end, and between mid-July and mid-
  August corresponding to a peak in newt larval abundance. Changes in adult body condition associated
  with reproduction also influenced eDNA concentrations, as did temperature (but not rainfall or UV).
  eDNA concentration fell rapidly as larvae metamorphosed and left the ponds. eDNA concentration
  may therefore reflect relative abundance in different ponds, although environmental factors can affect
  the concentrations observed. Nevertheless, eDNA surveys may still represent an improvement over
  unadjusted counts which are widely used in population assessments but have unreliable relationships
  with population size.
• Barata, I., Griffiths, R. and Ridout, M. (2017). The power of monitoring: optimizing survey designs to detect occupancy changes in a rare amphibian population. Scientific Reports [Online] 7:1-9. Available at: http://dx.doi.org/10.1038/s41598-017-16534-8.
  Abstract View in KAR View full text
  Biodiversity conservation requires reliable species assessments and rigorously designed surveys.
  However, determining the survey effort required to reliably detect population change can be
  challenging for rare, cryptic and elusive species. We used a tropical bromeliad-dwelling frog as a model
  system to explore a cost-effective sampling design that optimizes the chances of detecting a population
  decline. Relatively few sampling visits were needed to estimate occupancy and detectability with good
  precision, and to detect a 30% change in occupancy with 80% power. Detectability was influenced
  by observer expertise, which therefore also had an effect on the sampling design – less experienced
  observers require more sampling visits to detect the species. Even when the sampling design provides
  precise parameter estimates, only moderate to large changes in occupancy will be detected with
  reliable power. Detecting a population change of 15% or less requires a large number of sites to be
  surveyed, which might be unachievable for range-restricted species occurring at relatively few sites.
  Unless there is high initial occupancy, rare and cryptic species will be particularly challenging when it
  comes to detecting small population changes. This may be a particular issue for long-term monitoring of
  amphibians which often display low detectability and wide natural fluctuations.
• Ward, R. et al. (2017). Optimising monitoring efforts for secretive snakes: a comparison of occupancy and N-mixture models for assessment of population status. Scientific Reports [MS Excel] 7. Available at: http://dx.doi.org/10.1038/s41598-017-18343-5.
  Abstract View in KAR View full text
  A fifth of reptiles are Data Deficient; many due to unknown population status. Monitoring snake populations can be demanding due to crypsis and low population densities, with insufficient recaptures for abundance estimation via Capture-Mark-Recapture. Alternatively, binomial N-mixture models enable abundance estimation from count data without individual identification, but have rarely been successfully applied to snake populations. We evaluated the suitability of occupancy and N-mixture methods for monitoring an insular population of grass snakes (Natrix helvetica) and considered covariates influencing detection, occupancy and abundance within remaining habitat. Snakes were elusive, with detectability increasing with survey effort (mean: 0.33 ± 0.06 s.e.m.). The probability of a transect being occupied was moderate (mean per kilometre: 0.44 ± 0.19 s.e.m.) and increased with transect length. Abundance estimates indicate a small threatened population associated to our transects (mean: 39, 95% CI: 20–169). Power analysis indicated that the survey effort required to detect occupancy declines would be prohibitive. Occupancy models fitted well, whereas N-mixture models showed poor fit, provided little extra information over occupancy models and were at greater risk of closure violation. Therefore we suggest occupancy models are more appropriate for monitoring snakes and other elusive species, but that population trends may go undetected.
• Pasmans, F. et al. (2017). Future of keeping pet reptiles and amphibians:towards integrating animal welfare, human health and environmental sustainability. Veterinary Record [Online] 181. Available at: http://doi: 10.1136/vr.104296.
  Abstract View in KAR
  The keeping of exotic pets is currently under debate and governments of several countries are increasingly exploring the regulation, or even the banning, of exotic pet keeping. Major concerns are issues of public health and safety, animal welfare and biodiversity conservation. The keeping of reptiles and amphibians in captivity encompasses all the potential issues identified with keeping exotic pets, and many of those relating to traditional domestic pets. Within the context of risks posed by pets in general, the authors argue for the responsible and sustainable keeping
  of reptile and amphibian pets by private persons, based on scientific evidence and on the authors' own expertise (veterinary medicine, captive husbandry, conservation biology).
• Rosa, G. et al. (2017). Impact of asynchronous emergence of two lethal pathogens on amphibian assemblages. Scientific Reports [Online]:43260. Available at: http://dx.doi.org/10.1038/srep43260.
  Abstract View in KAR View full text
  Emerging diseases have been increasingly associated with population declines, with co-infections
  exhibiting many types of interactions. The chytrid fungus (Batrachochytrium dendrobatidis) and
  ranaviruses have extraordinarily broad host ranges, however co-infection dynamics have been largely
  overlooked. We investigated the pattern of co-occurrence of these two pathogens in an amphibian
  assemblage in Serra da Estrela (Portugal). The detection of chytridiomycosis in Portugal was linked
  to population declines of midwife-toads (Alytes obstetricans). The asynchronous and subsequent
  emergence of a second pathogen - ranavirus - caused episodes of lethal ranavirosis. Chytrid effects
  were limited to high altitudes and a single host, while ranavirus was highly pathogenic across multiple
  hosts, life-stages and altitudinal range. This new strain (Portuguese newt and toad ranavirus – member
  of the CMTV clade) caused annual mass die-offs, similar in host range and rapidity of declines to other
  locations in Iberia affected by CMTV-like ranaviruses. However, ranavirus was not always associated
  with disease, mortality and declines, contrasting with previous reports on Iberian CMTV-like ranavirosis.
  We found little evidence that pre-existing chytrid emergence was associated with ranavirus and the
  emergence of ranavirosis. Despite the lack of cumulative or amplified effects, ranavirus drove declines
  of host assemblages and changed host community composition and structure, posing a grave threat to
  all amphibian populations.
• Griffiths, R. (2017). Which amphibians should qualify for the ark? Animal Conservation [Online] 20:120-121. Available at: http://dx.doi.org/10.1111/acv.12348.
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• Matechou, E. et al. (2016). Open models for removal data. Annals of Applied Statistics [Online]. Available at: http://dx.doi.org/10.1214/16-AOAS949.
  Abstract View in KAR View full text
  Individuals of protected species, such as amphibians and reptiles, often need to be removed from sites before development commences. Usually, the population is considered to be closed. All individuals are assumed to i) be present and available for detection at the start of the study period and ii) remain at the site until the end of the study, unless they are detected. However, the assumption of population closure is not always valid. We present new removal models which allow for population renewal through birth and/or immigration, and population depletion through sampling as well as through death/emigration. When appropriate, productivity may be estimated and a Bayesian approach allows the estimation of the probability of total population depletion. We demonstrate the performance of the models using data on common lizards, Zootoca vivipara, and great crested newts, Triturus cristatus.
• Wombwell, E. et al. (2016). Detection of Batrachochytrium dendrobatidis in amphibians imported into the UK for the pet trade. EcoHealth [Online]. Available at: http://dx.doi.org/10.1007/s10393-016-1138-4.
  Abstract View in KAR View full text
  There is increasing evidence that the global spread of the fungal pathogen Batrachochytrium dendrobatidis (Bd) has been facilitated by the international trade in amphibians. Bd was first detected in the UK in 2004, and has since been detected in multiple wild amphibian populations. Most amphibians imported into the UK for the pet trade from outside the European Union enter the country via Heathrow Animal Reception Centre (HARC), where Bd positive animals have been previously detected. Data on the volume, diversity and origin of imported amphibians were collected for 59 consignments arriving at HARC between November 2009 and June 2012, along with a surveillance study to investigate the prevalence of Bd in these animals. Forty three amphibian genera were recorded, originating from 12 countries. It was estimated that 5000 – 7000 amphibians are imported through HARC into the UK annually for the pet trade. Bd was detected in consignments from the USA and Tanzania, in six genera, resulting in an overall prevalence of 3.6%. This suggests that imported amphibians are a source of Bd within the international pet trade.
• Lewis, B., Griffiths, R. and Wilkinson, J. (2016). Population status of great crested newts (Triturus cristatus) at sites subjected to development mitigation. Herpetological Journal [Online] 27:133-142. Available at: https://www.thebhs.org/publications/the-herpetological-journal/volume-27-number-2-april-2017/1006-02-population-status-of-great-crested-newts-i-triturus-cristatus-i-at-sites-subjected-to-development-mitigation.
  Abstract View in KAR View full text
  Increasing development of natural habitats frequently causes conflict with the conservation of protected species. Consequently, interventions that attempt to mitigate the impact of development are becoming increasingly commonplace. We used four approaches to assess the effectiveness of development mitigation on a species subject to widespread development pressures in Europe – the great crested newt (Triturus cristatus). Firstly, a systematic evidence review revealed eleven published studies of great crested newt populations at development sites. None provided conclusive evidence that the mitigation carried out was effective in maintaining populations. Secondly, less than half of 406 mitigation licence project files examined contained reports of results. Of those that did, only 16 provided post-development population assessments. These included one extinct population, and 10 ‘small’ populations. Thirdly, standardised population assessments were carried out at 18 sites in England, at least six years after the initial mitigation was completed. Although newt populations persisted at most of these sites, there was evidence of an overall decline, with extinctions occurring at four sites. Fourthly, although the annual cost of mitigation for great crested newts in England is estimated at between £20-43 million, information on the status of populations and habitats makes it difficult to assess whether this is cost-effective for either conservation or development. The quality and quantity of available data make it difficult to assign reasons for population changes at mitigation sites, but the study highlighted four general issues concerning mitigation practice: (1) presence of non-viable populations pre-mitigation; (2) inadequate mitigation interventions and site management; (3) cumulative impacts of further developments; and (4) emergence of new threats post-mitigation. Nevertheless, it is possible that some mitigation activities may have unforeseen and undocumented benefits, such as providing green spaces and biodiversity enhancement in urban areas.
• Hudson, M. et al. (2016). Dynamics and genetics of a disease driven species decline to near extinction: lessons for conservation. Scientific reports [Online]:30772. Available at: http://dx.doi.org/10.1038/srep30772.
  Abstract View in KAR View full text
  Amphibian chytridiomycosis has caused precipitous declines in hundreds of species worldwide. By
  tracking mountain chicken (Leptodactylus fallax) populations before, during and after the emergence of
  chytridiomycosis, we quantified the real-time species level impacts of this disease. We report a rangewide
  species decline amongst the fastest ever recorded, with a loss of over 85% of the population in
  fewer than 18 months on Dominica and near extinction on Montserrat. Genetic diversity declined in the
  wild, but emergency measures to establish a captive assurance population captured a representative
  sample of genetic diversity from Montserrat. If the Convention on Biological Diversity’s targets are
  to be met, it is important to evaluate the reasons why they appear consistently unattainable. The
  emergence of chytridiomycosis in the mountain chicken was predictable, but the decline could not
  be prevented. There is an urgent need to build mitigation capacity where amphibians are at risk from
  chytridiomycosis.
• Austen, G. et al. (2016). Species identification by experts and non-experts: comparing images from field guides. Scientific Reports [Online] 6. Available at: http://dx.doi.org/10.1038/srep33634.
  Abstract View in KAR View full text
  Accurate species identification is fundamental when recording ecological data. However, the ability to correctly identify organisms visually is rarely questioned. We investigated how experts and non-experts compared in the identification of bumblebees, a group of insects of considerable conservation concern. Experts and non-experts were asked whether two concurrent bumblebee images depicted the same or two different species. Overall accuracy was below 60% and comparable for experts and non-experts. However, experts were more consistent in their answers when the same images were repeated, and more cautious in committing to a definitive answer. Our findings demonstrate the difficulty of correctly identifying bumblebees using images from field guides. Such error rates need to be accounted for when interpreting species data, whether or not they have been collected by experts. We suggest that investigation of how experts and non-experts make observations should be incorporated into study design, and could be used to improve training in species identification.
• Hudson, M. et al. (2016). In-situ itraconazole treatment improves survival rate during an amphibian chytridiomycosis epidemic. Biological Conservation [Online] 195:37-45. Available at: http://dx.doi.org/10.1016/j.biocon.2015.12.041.
  Abstract View in KAR
  The emerging infectious disease, amphibian chytridiomycosis caused by the fungus Batrachochytrium dendrobatidis (Bd), threatens hundreds of amphibian species globally. In the absence of field-based mitigation methods, the Amphibian Conservation Action Plan advocates captive assurance programmes to prevent extinction from this infectious disease. Unfortunately, with the cooperation of the entire global zoo community, the International Union for the Conservation of Nature Amphibian Ark estimates only 50 species could be saved. Clearly, if catastrophic losses are to be averted, alternative mitigation techniques need to be developed. There has been an absence of trialling laboratory proven interventions for chytridiomycosis in field settings, which must change in order to allow informed management decisions for highly threatened amphibian populations. We tested the in-situ treatment of individual mountain chicken frogs (Leptodactylus fallax) using the antifungal drug, itraconazole. Multi-state mark–recapture analysis showed increased probability of survival and loss of Bd infection for treated frogs compared to untreated animals. There was evidence of a prophylactic effect of treatment as, during the treatment period, infection probability was lower for treated animals than untreated animals. Whilst long term, post-treatment increase in survival was not observed, a deterministic population model estimated antifungal treatment would extend time to extinction of the population from 49 to 124 weeks, an approximated 60% increase. In-situ treatment of individuals could, therefore, be a useful short-term measure to augment other conservation actions for amphibian species threatened by chytridiomycosis or to facilitate population survival during periods of high disease risk.
• Griffiths, R. et al. (2015). Science, statistics and surveys: a herpetological perspective. Journal of Applied Ecology [Online] 52:1413-1417. Available at: http://dx.doi.org/10.1111/1365-2664.12463.
  View in KAR View full text
• Robinson, J. et al. (2015). Dynamics of the global trade in live reptiles: Shifting trends in production and consequences for sustainability. Biological Conservation [Online] 184:42-50. Available at: http://dx.doi.org/10.1016/j.biocon.2014.12.019.
  Abstract View in KAR
  Biodiversity-rich countries provide wildlife for the exotic pet trade, but the implications of this for conservation, sustainable use and livelihoods remain poorly understood. CITES Appendix II import data from 1996 to 2012 were used to analyse spatial and temporal trends in live reptiles, a group comprising a substantial component of the commercial wildlife trade. Between 2001 and 2012 the trade declined by a third. The decrease was greatest in wild-caught reptiles (70%), but imports in captive-bred reptiles also decreased (40%), due to reduced trade in green iguanas. Imports originating from captive sources comprised about half of the total trade over the period. In contrast, there was a nearly 50-fold increase in imports of ranched reptiles, dominated by royal pythons from sub-Saharan Africa, but including a recent upsurge of ranched turtles from South America and Asia. Additionally, the proportion of reptiles sourced from ‘range countries’ (where species naturally occur in the wild) declined. Numbers of reptiles captive-bred within consumer countries to supply domestic markets are difficult to obtain, but may be impacting international trade. Captive breeding may ease collection pressure on wild populations, but might also divert benefit flows, impacting local livelihoods. Ranching may benefit livelihoods and have low impacts on natural populations, but along with captive breeding, could be detrimental if loopholes allow wild animals to be exported as ranched. Given the shift from wild to ranched reptiles, more information is required on the benefits and impacts of commercial ranching operations for traded reptile species.
• Harding, G., Griffiths, R. and Pavajeau, L. (2015). Developments in amphibian captive breeding and reintroduction programs. Conservation Biology [Online] 30:340-349. Available at: http://dx.doi.org/10.1111/cobi.12612.
  Abstract View in KAR
  Captive breeding and reintroduction remain high profile but controversial conservation interventions.
  It is important to understand how such programs develop and respond to strategic conservation initiatives.
  We analyzed the contribution to conservation made by amphibian captive breeding and reintroduction
  since the launch of the International Union for Conservation of Nature (IUCN) Amphibian Conservation
  Action Plan (ACAP) in 2007. We assembled data on amphibian captive breeding and reintroduction from a
  variety of sources including the Amphibian Ark database and the IUCN Red List. We also carried out systematic
  searches of Web of Science, JSTOR, and Google Scholar for relevant literature. Relative to data collected from
  1966 to 2006, the number of species involved in captive breeding and reintroduction projects increased by
  57% in the 7 years since release of the ACAP. However, there have been relatively few new reintroductions over
  this period; most programs have focused on securing captive-assurance populations (i.e., species taken into
  captivity as a precaution against extinctions in the wild) and conservation-related research. There has been
  a shift to a broader representation of frogs, salamanders, and caecilians within programs and an increasing
  emphasis on threatened species. There has been a relative increase of species in programs from Central
  and South America and the Caribbean, where amphibian biodiversity is high. About half of the programs
  involve zoos and aquaria with a similar proportion represented in specialist facilities run by governmental or
  nongovernmental agencies. Despite successful reintroduction often being regarded as the ultimate milestone
  for such programs, the irreversibility of many current threats to amphibians may make this an impractical
  goal. Instead, research on captive assurance populations may be needed to develop imaginative solutions to
  enable amphibians to survive alongside current, emerging, and future threats.
• Maldonado, J. et al. (2015). Phylogeography and Conservation Genetics of the Common Wall Lizard, Podarcis muralis, on Islands at Its Northern Range. PLOS ONE [Online] 10:e0117113. Available at: http://doi.org/10.1371/journal.pone.0117113.
  Abstract View in KAR View full text
  Populations at range limits are often characterized by lower genetic diversity, increased genetic isolation and differentiation relative to populations at the core of geographical ranges. Furthermore, it is increasingly recognized that populations situated at range limits might be the result of human introductions rather than natural dispersal. It is therefore important to document the origin and genetic diversity of marginal populations to establish conservation priorities. In this study, we investigate the phylogeography and genetic structure of peripheral populations of the common European wall lizard, Podarcis muralis, on Jersey (Channel Islands, UK) and in the Chausey archipelago. We sequenced a fragment of the mitochondrial cytochrome b gene in 200 individuals of P. muralis to infer the phylogeography of the island populations using Bayesian approaches. We also genotyped 484 individuals from 21 populations at 10 polymorphic microsatellite loci to evaluate the genetic structure and diversity of island and mainland (Western France) populations. We detected four unique haplotypes in the island populations that formed a sub-clade within the Western France clade. There was a significant reduction in genetic diversity (HO, HE and AR) of the island populations in relation to the mainland. The small fragmented island populations at the northern range margin of the common wall lizard distribution are most likely native, with genetic differentiation reflecting isolation following sea level increase approximately 7000 BP. Genetic diversity is lower on islands than in marginal populations on the mainland, potentially as a result of early founder effects or long-term isolation. The combination of restriction to specific localities and an inability to expand their range into adjacent suitable locations might make the island populations more vulnerable to extinction.
• Germano, J. et al. (2015). Mitigation-driven translocations: are we moving wildlife in the right direction? Frontiers in Ecology and the Environment [Online] 13:100-105. Available at: http://www.dx.doi.org/10.1890/140137.
  Abstract View in KAR View full text
  Despite rapid growth in the field of reintroduction biology, many lessons learned from scientific research are not being applied to translocations initiated when human land-use conflicts with persistence of a species. Mitigation-driven translocations outnumber and receive better funding than science-based conservation translocations worldwide, yet their conservation benefit is unclear. As mitigation releases are economically motivated, outcomes may diverge greatly from releases designed to serve the biological needs of species. Translocation as a regulatory tool may be ill-fitted to biologically mitigate environmental damage wrought by development. Evidence suggests that many mitigation-driven translocations fail, though application of scientific principles and best-practices could likely increase success. Furthermore, lack of transparency and documentation of outcomes hinder efforts to understand the scope of the problem. If mitigation-driven translocations continue unabated as a part of the growing billion-dollar ecological consulting industry, it is imperative that the scale and effects of these releases are reported and evaluated.
• Robinson, J. et al. (2015). Captive reptile mortality rates in the home and implications for the wildlife trade. PLoS ONE [Online] 10:e0141460. Available at: http://www.dx.doi.org/10.1371/journal.pone.0141460.
  Abstract View in KAR View full text
  The trade in wildlife and keeping of exotic pets is subject to varying levels of national and international regulation and is a topic often attracting controversy. Reptiles are popular exotic pets and comprise a substantial component of the live animal trade. High mortality of traded animals raises welfare concerns, and also has implications for conservation if collection from the wild is required to meet demand. Mortality of reptiles can occur at any stage of the trade chain from collector to consumer. However, there is limited information on mortality rates of reptiles across trade chains, particularly amongst final consumers in the home. We investigated mortality rates of reptiles amongst consumers using a specialised technique for asking sensitive questions, additive Randomised Response Technique (aRRT), as well as direct questioning (DQ). Overall, 3.6% of snakes, chelonians and lizards died within one year of acquisition. Boas and pythons had the lowest reported mortality rates of 1.9% and chameleons had the highest at 28.2%. More than 97% of snakes, 87% of lizards and 69% of chelonians acquired by respondents over five years were reported to be captive bred and results suggest that mortality rates may be lowest for captive bred individuals. Estimates of mortality from aRRT and DQ did not differ significantly which is in line with our findings that respondents did not find questions about reptile mortality to be sensitive. This research suggests that captive reptile mortality in the home is rather low, and identifies those taxa where further effort could be made to reduce mortality rates
• Dawson, J. et al. (2015). Assessing the global zoo response to the amphibian crisis through 20-year trends in captive collections. Conservation Biology [Online] 30:82-91. Available at: http://dx.doi.org/10.1111/cobi.12563.
  Abstract View in KAR
  Global amphibian declines are one of the biggest challenges currently facing the conservation
  community, and captive breeding is one way to address this crisis. Using information from the International
  Species Information System zoo network, we examined trends in global zoo amphibian holdings across
  species, zoo region, and species geographical region of origin from 1994 to 2014. These trends were compared
  before and after the 2004 Global Amphibian Assessment to assess whether any changes occurred and whether
  zoo amphibian conservation effort had increased. The numbers of globally threatened species (GTS) and
  their proportional representation in global zoo holdings increased and this rate of increase was significantly
  greater after 2004. North American, European, and Oceanian GTS were best represented in zoos globally, and
  proportions of Oceanian GTS held increased the most since 2004. South American and Asian GTS had the
  lowest proportional representation in zoos. At a regional zoo level, European zoos held the lowest proportions
  of GTS, and this proportion did not increase after 2004. Since 1994, the number of species held in viable
  populations has increased, and these species are distributed among more institutions. However, as of 2014,
  zoos held 6.2% of globally threatened amphibians, a much smaller figure than for other vertebrate groups and
  one that falls considerably short of the number of species for which ex situ management may be desirable.
  Although the increased effort zoos have put into amphibian conservation over the past 20 years is encouraging,
  more focus is needed on ex situ conservation priority species. This includes building expertise and capacity
  in countries that hold them and tracking existing conservation efforts if the evidence-based approach to
  amphibian conservation planning at a global level is to be further developed.
• Carpenter, A. et al. (2014). A review of the international trade in amphibians:the types, levels and dynamics of trade in CITES-listed species. Oryx [Online] 48:565-574. Available at: http://dx.doi.org/10.1017/S0030605312001627.
  Abstract View in KAR
  Globally, amphibians face many potential threats,
  including international trade. However, there is a lack of
  knowledge regarding the types, levels and dynamics of the
  amphibian trade at the global scale. This study reviewed
  the trade in CITES-listed species between 1976 and 2007.
  Four main trade groups (eggs, skins, meat and individuals)
  were identified. Trade in amphibian leather focused on
  Hoplobatrachus tigerinus (5,572 individuals), whereas trade
  in eggs focused on Ambystoma mexicanum (6,027 eggs).
  However, for the entire study period (1976–2007), trade in
  skins and eggs was small compared with trade in meat
  and live animals. The meat trade was estimated to be worth
  .USD 111 million, whereas the trade in live animals was
  estimated to be worth .USD 11.5 million in only three of
  the genera involved. Trade dynamics have changed as a
  result of changes in legislation, such as a ban on H. tigerinus
  exports from Bangladesh for meat. Within the live trade
  22 species categorized as either Critically Endangered or
  Endangered were traded during the study period, and these
  require greater attention. International trade and potential
  conservation benefits are affected by countries supplying
  captive-bred individuals to their domestic markets as this
  trade goes unrecorded. However, this study only investigated
  trade in species listed by CITES, and other species may
  comprise a significant additional component of international
  trade. The trade in amphibians is dynamic, and
  changes in both the types of trade and the species concerned
  were identified over the study period. Conservation concerns
  have multiplied from issues concerning population
  depletions to include indirect impacts associated with
  disease, predation and competition, which requires a
  reappraisal of data capture and reporting.
• Biggs, J. et al. (2014). Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus). Biological Conservation [Online] 183:19-28. Available at: http://dx.doi.org/10.1016/j.biocon.2014.11.029.
  Abstract View in KAR
  The use of environmental DNA (eDNA) is rapidly emerging as a potentially valuable survey technique for
  rare or hard to survey freshwater organisms. For the great crested newt (Triturus cristatus) in the UK, the
  substantial cost and manpower requirements of traditional survey methods have hampered attempts to
  assess the status of the species. We tested whether eDNA could provide the basis for a national citizen
  science-based monitoring programme for great crested newts by (i) comparing the effectiveness of eDNA
  monitoring with torch counts, bottle trapping and egg searches and (ii) assessing the ability of volunteers
  to collect eDNA samples throughout the newt’s UK range. In 35 ponds visited four times through the
  breeding season, eDNA detected newts on 139 out of 140 visits, a 99.3% detection rate. Bottle traps, torch
  counts and egg searches were significantly less effective, detecting newts 76%, 75% and 44% of the time.
  eDNA was less successful at predicting newt abundance being positively, but weakly, correlated with
  counts of the number of newts. Volunteers successfully collected eDNA samples across the UK with
  219 of 239 sites (91.3%) correctly identified as supporting newts. 8.7% of sites generated false negatives,
  either because of very small newt populations or practical difficulties in sample collection. There were no
  false positives. Overall, we conclude that eDNA is a highly effective survey method and could be used as
  the basis for a national great crested newt monitoring programme.
• Sutherland, W. et al. (2013). Conservation practice could benefit from routine testing and publication of management outcomes. Conservation Evidence 10:1-3.
  Abstract View in KAR View full text
  Effective conservation requires a step change in the way practitioners can contribute to science and
  can have access to research outputs. The journal Conservation Evidence was established in 2004 to
  help practitioners surmount several obstacles they face when attempting to document the effects of
  their conservation actions scientifically. It is easily and freely accessible online. It is free to publish in
  and it enables global communication of the effects of practical trials and experiments, which are
  virtually impossible to get published in most scientific journals. The driving force behind
  Conservation Evidence is the need to generate and share scientific information about the effects of
  interventions.
• Griffiths, R. and Dos Santos, M. (2012). Trends in conservation biology: Progress or procrastination in a new millennium? Biological Conservation [Online] 153:153-158. Available at: http://dx.doi.org/10.1016/j.biocon.2012.05.011.
  Abstract View in KAR
  Since the 1990s the number of papers published by four mainstream conservation journals (Conservation
  Biology, Biological Conservation, Biodiversity and Conservation and Oryx) has increased by 133%. The main
  subject areas of research have not changed over time, with population biology, habitat change, community
  ecology and species conservation remaining the most popular topics. Equally, mammals, birds, invertebrates
  and plants have remained the most popular taxa, and – surprisingly – the number of papers
  dealing with general or global issues or using molecular approaches has remained low. Although collaboration
  increased over time, most conservation biology is still conducted by researchers working in
  developed countries. Most research published from developing countries in the 1990s did not have a local
  researcher as co-author. This trend has now been reversed, although there is only marginal evidence of an
  increase in collaboration between authors from developed and developing countries. Although conservation
  science has undergone dramatic technological changes as we have moved into the new millennium,
  published research remains rooted within the cultural traditions of developed countries, with a continuing
  emphasis on charismatic taxa.
• Sewell, D. et al. (2012). When Is a Species Declining? Optimizing Survey Effort to Detect Population Changes in Reptiles. PLoS ONE [Online] 7. Available at: http://dx.doi.org/10.1371/journal.pone.0043387.
  Abstract View in KAR
  Biodiversity monitoring programs need to be designed so that population changes can be detected reliably. This can be problematical for species that are cryptic and have imperfect detection. We used occupancy modeling and power analysis to optimize the survey design for reptile monitoring programs in the UK. Surveys were carried out six times a year in 2009–2010 at multiple sites. Four out of the six species – grass snake, adder, common lizard, slow-worm –were encountered during every survey from March-September. The exceptions were the two rarest species ­– sand lizard and smooth snake – which were not encountered in July 2009 and March 2010 respectively. The most frequently encountered and most easily detected species was the slow-worm. For the four widespread reptile species in the UK, three to four survey visits that used a combination of directed transect walks and artificial cover objects resulted in 95% certainty that a species would be detected if present. Using artificial cover objects was an effective detection method for most species, considerably increased the detection rate of some, and reduced misidentifications. To achieve an 85% power to detect a decline in any of the four widespread species when the true decline is 15%, three surveys at a total of 886 sampling sites, or four surveys at a total of 688 sites would be required. The sampling effort needed reduces to 212 sites surveyed three times, or 167 sites surveyed four times, if the target is to detect a true decline of 30% with the same power. The results obtained can be used to refine reptile survey protocols in the UK and elsewhere. On a wider scale, the occupancy study design approach can be used to optimize survey effort and help set targets for conservation outcomes for regional or national biodiversity assessments.
• Taylor, M. et al. (2012). Evidence for evolutionary distinctiveness of a newly discovered population of sooglossid frogs on Praslin Island, Seychelles. Conservation Genetics [Online] 13:557-566. Available at: http://doi.org/10.1007/s10592-011-0307-9.
  Abstract View in KAR
  Amidst a worldwide decline in amphibian populations, those species endemic to islands remain an important focus for conservation efforts. The Sooglossidae are a family of frog species endemic to the Seychelles islands that are believed to have evolved in isolation for approximately 75 million years. Formerly thought to inhabit just two Seychelles islands (Mahé and Silhouette), a third population was discovered on Praslin in 2009. Phylogenetic analysis based on 438 bp of mitochondrial 16S rRNA suggests that the Praslin population is most closely related to Sooglossus sechellensis from Silhouette, and identifies these as two separate clades which together sit distinct from the population on Mahé. An average of 4.06% uncorrected pairwise sequence divergence between the Praslin and Silhouette populations suggests substantial evolutionary divergence rather than recent introduction. Discriminant function analysis also revealed differences in morphology in frogs from Praslin and Mahé. DNA sequences of two Praslin specimens group more closely with the Mahé population, indicating some shared haplotypes that suggest recent secondary contact. Tests for a genetic signature of recent population expansion on either island were not significant. Our results suggest substantial evolutionary divergence between the three populations of S. sechellensis, most likely following isolation due to changes in sea level in the Indian Ocean. Whilst further genetic sampling and ecological studies are needed, our initial phylogenetic analyses suggest that the sooglossid population on Praslin should be managed as an evolutionarily significant unit to retain the uniqueness of its genetic diversity and its evolutionary trajectory within this ancient family of amphibians.
• Griffiths, R. et al. (2011). Engineering a future for amphibians under climate change. Journal of Applied Ecology [Online] 48:487-492. Available at: http://dx.doi.org/10.1111/j.1365-2664.2010.01942.x.
  Abstract View in KAR
  1.?Altered global climates in the 21st century pose serious threats for biological systems and practical actions are needed to mount a response for species at risk. 2.?We identify management actions from across the world and from diverse disciplines that are applicable to minimizing loss of amphibian biodiversity under climate change. Actions were grouped under three thematic areas of intervention: (i) installation of microclimate and microhabitat refuges; (ii) enhancement and restoration of breeding sites; and (iii) manipulation of hydroperiod or water levels at breeding sites. 3.?Synthesis and applications. There are currently few meaningful management actions that will tangibly impact the pervasive threat of climate change on amphibians. A host of potentially useful but poorly tested actions could be incorporated into local or regional management plans, programmes and activities for amphibians. Examples include: installation of irrigation sprayers to manipulate water potentials at breeding sites; retention or supplementation of natural and artificial shelters (e.g. logs, cover boards) to reduce desiccation and thermal stress; manipulation of canopy cover over ponds to reduce water temperature; and, creation of hydrologoically diverse wetland habitats capable of supporting larval development under variable rainfall regimes. We encourage researchers and managers to design, test and scale up new initiatives to respond to this emerging crisis.
• Griffiths, R. and Di Minin, E. (2011). Viability analysis of a threatened amphibian population: modelling the past, present and future. Ecography [Online] 34:162-169. Available at: http://dx.doi.org/10.1111/j.1600-0587.2010.06263.x.
  Abstract View in KAR
  Conservation actions that have maintained populations in the past may not necessarily do so in the future. Population viability analysis provides one tool for exploring the impact of management actions on large temporal scales. However, there are relatively few long-term data sets that provide the demographic and environmental data demanded by such models. Using a 37-yr data set, we used RAMAS Metapop to model the persistence of natterjack toads Epidalea (Bufo) calamita on a heathland in southern Britain. A retrospective analysis showed that the best fit between the predicted population trajectories and the real population was when the management carried out was modelled as an increase in K of 150 toads yr?1. However, even if ongoing management continues to improve K by a further 40–60 toads yr?1 over the next 50 yr, the population still has an extinction risk of at least 60% if other factors remain unchanged. Sensitivity analyses and simulated management scenarios indicated that the population was most sensitive to changes in the survival of juvenile (i.e. 1–2 yr old) toads. In addition, if the frequency and severity of pond desiccation increases, the risk of extinction was predicted to increase as a result of reduced recruitment. Low levels of extinction risk occurred irrespective of K when juvenile survival was enhanced in combination with low frequency and severity of pond desiccation. The models suggest that populations that are responding to management against a background of natural fluctuations may remain vulnerable to extinction for several decades. These extinction risks may increase if habitat management fails to offset reductions in recruitment and juvenile survival caused by environmental change.
• Tapley, B., Griffiths, R. and Bride, I. (2011). Dynamics of the trade in reptiles and amphibians within the United Kingdom over a ten-year period. The Herpetological Journal 21:27-34.
  Abstract View in KAR
  This study compared the trade in reptiles and amphibians in the United Kingdom between 1992–3 and 2004–5. In particular,
  the impacts of captive breeding and colour and pattern morphs on price structures were examined. The number of amphibian
  and reptile species in the trade more than doubled over this period, and less than a third of the species traded were common to
  both trading periods. More traded species were listed by CITES in 1992–3 than in 2004–5. Taking into account inflation, the
  study showed that the price of all groups of reptiles and amphibians recorded increased over the ten-year period, and that some
  snake species had done so dramatically when colour and pattern morphs were considered. The price change of chelonians was
  probably the result of responses to changes in various trade regulations. Price increases for amphibians seemed to represent
  their increased popularity, coupled with the overhead costs of captive breeding on a commercial scale being transferred to the
  hobbyist. The increased popularity of captive-bred colour and pattern morphs could alleviate pressure on wild stocks. On the
  other hand, as such animals are predominantly being produced outside their countries of origin, no benefits accrue to local
  people and trade could undermine sustainable use programmes for wild animals.

Conference or workshop item

• Austen, G. et al. (2016). Reliability of experts in species identification: are images enough? in: British Ecological Society / Cambridge Conservation Initiative.
  View in KAR
• Austen, G. et al. (2015). Earning your stripes: Does expertise improve the ability to match bumblebee images in identification guides? in: 27th International Congress for Conservation Biology and 4th European Congress for Conservation Biology.
  View in KAR

Datasets / databases

• Austen, G. et al. (2018). Species identification by conservation practitioners using online images: accuracy and agreement between experts. [MS Excel file]. Available at: http://dx.doi.org/10.7717/peerj.4157.
  Abstract View in KAR View full text
  Emerging technologies have led to an increase in species observations being recorded via digital images. Such visual records are easily shared, and are often uploaded to online communities when help is required to identify or validate species. Although this is common practice, little is known about the accuracy of species identification from such images. Using online images of newts that are native and non-native to the UK, this study asked holders of great crested newt (Triturus cristatus) licences (issued by UK authorities to permit surveying for this species) to sort these images into groups, and to assign species names to those groups. All of these experts identified the native species, but agreement among these participants was low, with some being cautious in committing to definitive identifications. Individuals’ accuracy was also independent of both their experience and self-assessed ability. Furthermore, mean accuracy was not uniform across species (69–96%). These findings demonstrate the difficulty of accurate identification of newts from a single image, and that expert judgements are variable, even within the same knowledgeable community. We suggest that identification decisions should be made on multiple images and verified by more than one expert, which could improve the reliability of species data.
• Austen, G. et al. (2016). Species identification by experts and non-experts: comparing images from field guides. [Electronic deposit (Excel)].
  Abstract View in KAR View full text
  Accurate species identification is fundamental when recording ecological data. However, the ability to correctly identify organisms visually is rarely questioned. We investigated how experts and non-experts compared in the identification of bumblebees, a group of insects of considerable conservation concern. Experts and non-experts were asked whether two concurrent bumblebee images depicted the same or two different species. Overall accuracy was below 60% and comparable for experts and non-experts. However, experts were more consistent in their answers when the same images were repeated, and more cautious in committing to a definitive answer. Our findings demonstrate the difficulty of correctly identifying bumblebees using images from field guides. Such error rates need to be accounted for when interpreting species data, whether or not they have been collected by experts. We suggest that investigation of how experts and non-experts make observations should be incorporated into study design, and could be used to improve training in species identification.
• Robinson, J. et al. (2015). Captive reptile mortality rates in the home and implications for the wildlife trade. [Data file].
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Monograph

• Bormpoudakis, D. et al. (2016). Developing models to estimate the occurrence in the English countryside of Great Crested Newts, a protected species under the Habitats Directive. Defra. Available at: http://randd.defra.gov.uk/Default.aspx?Menu=Menu&Module=More&Location=None&ProjectID=19272&FromSearch=Y&Publisher=1&SearchText=WC1108&SortString=ProjectCode&SortOrder=Asc&Paging=10.
  Abstract View in KAR
  The great crested newt is a European Protected Species (EPS) with a widespread distribution within Great Britain. This results in the species frequently coming into conflict with development. Consequently, decision-makers in local government and licensing authorities face complex issues when it comes to reconciling development and conservation. New approaches are therefore needed to ensure that conservation decisions are based upon the best available science. The project set out to evaluate new potential approaches to these issues using three work packages: (1) Develop, test and compare species distribution models (SDMs) for great crested newts; (2) Building on these models, develop a methodology for assessing the impact of a plan or project on the local conservation status of great crested newts; and (3) End-user testing to assess model applications and fitness for purpose. Defra commissioned the project with additional funding from Natural Resources Wales, and together with Natural England and JNCC, also provided guidance.
  GLM models developed using eDNA presence-absence data for a small area of Kent provided a good prediction of the county-wide distribution of the species. GLM models developed for Cheshire and Lincolnshire using eDNA data yielded weaker models. Equally, the Kent model did not reliably fit Cheshire and Lancashire, suggesting that the predictor variables vary geographically.
  Maxent and ensemble models yielded good fits to county-wide distributions but poor fits to the localised eDNA data in all three counties. These models may have utility at a broad scale, but cannot account for absences at a local scale. Equally, some important variables at a local scale cannot be obtained through GIS layers and need to be obtained through field surveys. Constructing models for different scales therefore requires different modelling tools and different types of predictor variables.
  Maxent models of the national distribution of great crested newts in England gave predictions that were broadly consistent with current knowledge and can be used to calculate potential areas of occupancy.
  A framework for assigning and measuring Favourable Reference Values (FRVs) for great crested newts at different scales was developed using both an ‘equilibrium’ (=’no net change’) approach and FRVs set using baseline data according to other criteria. These principles were combined with SDMs and connectivity analysis of five case studies. The case studies combine both real and hypothetical data, and illustrate how a modelling approach can be used to identify important areas of newt habitat, identify connectivity between ponds, predict potential impacts of development, and design and evaluate mitigation measures.
  Three end-user consultation exercises showed that there was considerable interest and enthusiasm for the development and application of SDMs across a range of applications and stakeholders. Concerns were expressed over the quality and quantity of data available for modelling using current data-flow systems; the predictive power of models; and the potential for model outputs to be misused. Challenges that need to be addressed include training, expertise and building capacity, enhancing the regulatory framework for protected species, and the improvement and centralisation of data management systems.
  Species Distribution Models (SDMs) provide an objective and evidence-based tool for use within decision-making processes involving great crested newts. They have the potential to identify priority areas for conservation, target survey effort, assess the impacts of development, and assign Favourable Reference Values for the species. However, great crested newt records and habitat data are currently dispersed across multiple recording systems and vary in quality and quantity. A well-integrated data management system is required if SDMs are to make the best use of available information.

Forthcoming

• Worthington, H. et al. (2019). Estimating Abundance from Multiple Sampling Capture-Recapture Data via a Multi-State Multi-Period Stopover Model. Annals of Applied Statistics.
  Abstract View in KAR
  Capture-recapture studies often involve collecting data on numerous capture occasions over a relatively short period of time. For many study species, this process is repeated, for example annually, resulting in capture information spanning multiple sampling periods. To account for the different temporal scales, the robust design class of models have traditionally been applied providing a frame-work in which to analyse all of the available capture data in a single likelihood expression. However, these models typically require strong
  constraints, either the assumption of closure within a sampling period (the closed robust design) or conditioning on the number of individuals captured within a sampling period (the open robust design). For real datasets these assumptions may not be appropriate. We develop a general modelling structure that requires neither assumption by explicitly modelling the movement of individuals into the population both within and between the sampling periods, which in turn permits the estimation of abundance within a single consistent framework. The exibility of the novel model structure is further demonstrated by including the computationally challenging case of multi-state data where there is individual time-varying discrete covariate information. We derive an efficient likelihood expression for the new multi-state multi-period stopover model using the hidden Markov model framework. We demonstrate the signfi�cant improvement in parameter estimation using our new modelling approach in terms of both the multi-period and multi-state components through both a simulation study and a real dataset relating to the protected species of great crested newts, Triturus cristatus."