Portrait of Professor Jim Groombridge

Professor Jim Groombridge

Professor of Biodiversity Conservation
Programme Convenor for Conservation Project Management

About

Professor Jim Groombridge’s research interests lie primarily in population restoration, population and disease ecology, conservation genetics, genomics, and the geographical processes that determine the distribution of biodiversity. A central focus is the theoretical and practical aspects of endangered species conservation and the application of population, genetic, morphological and phylogeographic studies to enhance understanding of the biological processes that guide the conservation trajectory of endangered species. Alongside this work, he also utilises similar approaches to understand the evolutionary processes of invasive alien species, many of which can be expected to have population profiles that show strong population growth following initial small population size at foundation. These two themes are complementary: indeed, much of what we can learn about how populations of invasive alien species function can be applied to the conservation of endangered species.

Jim’s background of conservation work on island species in the Indian Ocean (Mauritius and Seychelles) and the Pacific (Hawaiian islands) has combined the practice of field monitoring and population recovery techniques with the more theoretical approaches of evolutionary phylogenetics and conservation genetics at the population level.

His research group focuses on the evolution, population genetics and conservation of endangered populations, with a particular emphasis on endemic island species. Islands are justifiably celebrated as living laboratories for evolutionary studies as well as a focus for efforts to conserve their biodiversity. Valuable insights for conservation can be gained from studying island endemics in view of their history of isolation from ancestral mainland populations, together with the problems they can encounter from invasive alien species and diseases.

Jim’s work is supported by his research group, who primarily work out of the Conservation Genetics Lab.

Professor Jim Groombridge is a member of the Durrell Institute of Conservation and Ecology

Research interests

Professor Groombridge’s genetics research group focuses on conservation genetics, genomics, disease ecology and ecological and evolutionary studies involving endangered species, invasive alien species and other wildlife populations, as well as extinct species and reconstruction of evolutionary history amongst species and populations using molecular DNA markers.

For detailed information on the group, research projects, funding, members, collaborations and facilities visit the laboratory webpage.

Teaching

Undergraduate (BSc in Wildlife Conservation)

  • DI521: Saving Endangered Species
  • DI503: Evolutionary Genetics and Conservation

Postgraduate (MSc in Conservation Biology)

  • DI1001: Multidisciplinary Perspectives on Conservation
  • DI836: Integrated Species Conservation and Management

Supervision

A scholarship is currently available to work with Professor Groombridge on the project 'How does supplemental feeding effect demography and reproductive fitness in endangered bird species on Mauritius?' Further details can be found here.  

Current PhD / research students

  • Hadi Al-Hikmani: Population and conservation genetics of Arabian leopards
  • Kate Allberry: How is environmental change influencing the movement of Malaysia's apex predators in wildlife corridors?
  • Debbie Fogell: Molecular evolution of beak and feather disease virus in endangered Mauritius parakeets
  • Jessica Haysom: Borneo's arboreal mammals: diversity and vulnerability to habitat change
  • Anna Jemmett: Conservation of Mongolia's Wild Camels (Camelus ferus)
  • Jack Slattery: Feasibility of reintroducing the red-billed chough (Pyrrhocorax pyrrhocorax) to Kent
  • Helena Turner: Population status and conservation of the critically endangered Bermuda rock lizard (Plestiodon Longirostris).

Professional

External Examiner for MSc in Biodiversity, Conservation and Management, University of Oxford (2015-2018)

Publications

Showing 50 of 91 total publications in the Kent Academic Repository. View all publications.

Article

  • van de Crommenacker, J., Bunbury, N., Jackson, H., Nupen, L., Wanless, R., Fleischer-Dogley, F., Groombridge, J. and Warren, B. (2019). Rapid loss of flight in the Aldabra white-throated rail. PLoS ONE [Online]. Available at: https://doi.org/10.1371/journal.pone.0226064.
    Flight loss has evolved independently in numerous island bird lineages worldwide, and particularly in rails (Rallidae). The Aldabra white-throated rail (Dryolimnas [cuvieri] aldabranus) is the last surviving flightless bird in the western Indian Ocean, and the only living flightless subspecies within Dryolimnas cuvieri, which is otherwise volant across its extant range. Such a difference in flight capacity among populations of a single species is unusual, and could be due to rapid evolution of flight loss, or greater evolutionary divergence than can readily be detected by traditional taxonomic approaches. Here we used genetic and morphological analyses to investigate evolutionary trajectories of living and extinct Dryolimnas cuvieri subspecies. Our data places D. [c.] aldabranus among the most rapid documented avian flight loss cases (within an estimated maximum of 80,000–130,000 years). However, the unusual intraspecific variability in flight capacity within D. cuvieri is best explained by levels of genetic divergence, which exceed those documented between other volant taxa versus flightless close relatives, all of which have full species status. Our results also support consideration of Dryolimnas [cuvieri] aldabranus as sufficiently evolutionary distinct from D. c. cuvieri to warrant management as an evolutionary significant unit. Trait variability among closely related lineages should be considered when assessing conservation status, particularly for traits known to influence vulnerability to extinction (e.g. flightlessness).
  • White, R., Strubbe, D., Dallimer, M., Davies, Z., Davis, A., Edelaar, P., Groombridge, J., Jackson, H., Menchetti, M., Mori, E., Nikolov, B., Pârâu, L., Pečnikar, Ž, Pett, T., Reino, L., Tollington, S., Turbé, A. and Shwartz, A. (2019). Assessing the ecological and societal impacts of alien parrots in Europe using a transparent and inclusive evidence-mapping scheme. NeoBiota [Online]. Available at: https://doi.org/10.3897/neobiota.48.34222.
    Globally, the number of invasive alien species (IAS) continues to increase, and management and policy responses typically need to be adopted before conclusive empirical evidence on their environmental and socioeconomic impacts are available. Consequently, numerous protocols exist for assessing IAS impacts, and differ considerably in which evidence they include. However, inclusive strategies for building a transparent evidence base underlying IAS impact assessments are lacking, potentially affecting our ability to reliably identify priority IAS. Using alien parrots in Europe as a case study, here we apply an evidence-mapping scheme to classify impact evidence and evaluate the consequences of accepting different subsets of available evidence on impact assessment outcomes. We collected environmental and socioeconomic impact data in multiple languages using a “wiki-review” process, comprising a systematic evidence search and an online editing and consultation phase. Evidence was classified by parrot species, impact category (e.g. infrastructure), geographical area (e.g. native range), source type (e.g. peer-review), study design (e.g. experimental), and impact direction (deleterious, beneficial and no impact). Our comprehensive database comprised 386 impact entries from 233 sources. Most evidence was anecdotal (50%). 42% of entries reported damage to agriculture (mainly in native ranges), while within Europe most entries concerned interspecific competition (39%). We demonstrate that the types of evidence included in assessments can strongly influence impact severity scores. For example, including evidence from the native range or anecdotal evidence resulted in an overall switch from minimal-moderate to moderate-major overall impact scores. We advise using such an evidence-mapping approach to create an inclusive and updatable database as the foundation for more transparent IAS impact assessments. When openly shared, such evidence-mapping can help better inform IAS research, management and policy.
  • Fogell, D., Groombridge, J., Tollington, S., Canessa, S., Henshaw, S., Zuel, N., Jones, C., Greenwood, A. and Ewen, J. (2019). Hygiene and biosecurity protocols reduce infection prevalence but do not improve fledging success in an endangered parrot. Scientific Reports [Online]. Available at: https://doi.org/10.1038/s41598-019-41323-w.
    Emerging Infectious Diseases (EIDs) are recognised as global extinction drivers of threatened species. Unfortunately, biodiversity managers have few tested solutions to manage them when often the desperate need for solutions necessitates a response. Here we test in situ biosecurity protocols to assess the efficacy of managing Psittacine beak and feather disease (PBFD), one of the most common and emergent viral diseases in wild parrots (Psittaciformes) that is currently affecting numerous threatened species globally. In response to an outbreak of PBFD in Mauritius “echo” parakeets (Psittacula eques), managers implemented a set of biosecurity protocols to limit transmission and impact of Beak and feather disease virus (BFDV). Here we used a reciprocal design experiment on the wild population to test whether BFDV management reduced viral prevalence and viral load, and improved nestling body condition and fledge success. Whilst management reduced the probability of nestling infection by approximately 11% there was no observed impact on BFDV load and nestling body condition. In contrast to expectations there was lower fledge success in nests with added BFDV biosecurity (83% in untreated vs. 79% in treated nests). Our results clearly illustrate that management for wildlife conservation should be critically evaluated through targeted monitoring and experimental manipulation, and this evaluation should always focus on the fundamental objective of conservation.
  • Tollington, S., Ewen, J., Newton, J., McGill, R., Smith, D., Henshaw, A., Fogell, D., Tatayah, V., Greenwood, A., Jones, C. and Groombridge, J. (2019). Individual consumption of supplemental food as a predictor of reproductive performance and viral infection intensity. Journal of Applied Ecology [Online] 56:594-603. Available at: https://doi.org/10.1111/1365-2664.13303.
    1. Supplemental food is often provided to threatened species in order to maintain or enhance reproductive fitness and thus population growth. However, its impact on individual reproductive fitness is rarely evaluated, despite being associated with both positive and negative consequences.

    2. We used stable isotope analyses to characterise the relative proportional consumption of supplemental food and quantitative polymerase chain reaction to assess beak and feather disease viral infection intensity among parakeets. Life- history and nest- site data from a long-term monitoring effort was incorporated.

    3. Older females benefitted the most from supplemental feeding; demonstrated by a greater reproductive uplift than younger females. There were no strong predictors of viral infection levels among nestlings.

    4. Reproductive fitness, measured by the number of fledglings produced per brood, was positively associated with proportional dietary content of supplemental food among adult parakeets and breeding pairs that nested closer to feeding stations consumed more supplemental food than those nesting further away.

    5. Synthesis and applications. Our study demonstrates that supplementary feeding can lead to an overall increase in population growth. However, by characterising individual consumption, we also reveal subtle patterns of use and differential benefits on reproductive fitness within a population. Manipulating the delivery of supplemental food may help to reduce demand on finite resources or target the proportion of a population that derives the most benefit, but is associated with trade-offs in fecundity. For example, the use of and access to feeding stations could potentially be targeted towards specific individuals, or positioned in the habitats most deficient in native food. However, increasing reproductive fitness in one component of the population may be accompanied by a decrease in another. This knowledge can be incorporated into adaptive management strategies that aim to fulfil specific objectives associated with species recovery and long-term viability as long as the relative importance of each objective is be considered.
  • Labisko, J., Griffiths, R., Chong-Seng, L., Bunbury, N., Maddock, S., Bradfield, K., Taylor, M. and Groombridge, J. (2019). Endemic, endangered, and evolutionarily significant: Cryptic lineages in Seychelles’ frogs. Biological Journal of the Linnean Society [Online] 126:417-435. Available at: https://doi.org/10.1093/biolinnean/bly183.
    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.
  • Jones, C., Jackson, H., McGowan, R., Hume, J., Forshaw, J., Tatayah, V., Winters, R. and Groombridge, J. (2019). A parakeet specimen held at National Museums Scotland is a unique skin of the extinct Reunion Parakeet Psittacula eques eques: a reply to Cheke and Jansen (2016). Ibis [Online] 161:230-238. Available at: http://dx.doi.org/10.1111/ibi.12673.
  • Tollington, S., Ewen, J., Newton, J., McGill, R., Smith, D., Henshaw, A., Fogell, D., Tatayah, V., Greenwood, A., Jones, C., Groombridge, J. and Thompson, D. (2018). Individual consumption of supplemental food as a predictor of reproductive performance and viral infection intensity. Journal of Applied Ecology [Online] 56:1-10. Available at: https://doi.org/10.1111/1365-2664.13303.
    1. Supplemental food is often provided to threatened species in order to maintain or enhance reproductive fitness and thus population growth. However, its impact on individual reproductive fitness is rarely evaluated, despite being associated with both positive and negative consequences.
    2. We used stable isotope analyses to characterise the relative proportional consumption of supplemental food and quantitative polymerase chain reaction to assess beak and feather disease viral infection intensity among parakeets. Life-history and nest-site data from a long-term monitoring effort was incorporated.
    3. Older females benefitted the most from supplemental feeding; demonstrated by a greater reproductive uplift than younger females. There were no strong predictors of viral infection levels among nestlings.
    4. Reproductive fitness, measured by the number of fledglings produced per brood, was positively associated with proportional dietary content of supplemental food among adult parakeets and breeding pairs that nested closer to feeding stations consumed more supplemental food than those nesting further away.
    5. Synthesis and applications. Our study demonstrates that supplementary feeding can lead to an overall increase in population growth. However, by characterising individual consumption, we also reveal subtle patterns of use and differential benefits on reproductive fitness within a population. Manipulating the delivery of supplemental food may help to reduce demand on finite resources or target the proportion of a population that derives the most benefit, but is associated with trade-offs in fecundity. For example, the use of and access to feeding stations
    could potentially be targeted towards specific individuals, or positioned in the habitats most deficient in native food. However, increasing reproductive fitness in one component of the population may be accompanied by a decrease in another. This knowledge can be incorporated into adaptive management strategies that aim to fulfil specific objectives associated with species recovery and long-term viability as long as the relative importance of each objective is be considered.
  • Aziz, M., Smith, O., Barlow, A., Tollington, S., Islam, M. and Groombridge, J. (2018). Do rivers influence fine-scale population genetic structure of tigers in the Sundarbans?. Conservation Genetics [Online] 29:1137-1151. Available at: https://doi.org/10.1007/s10592-018-1084-5.
    Global tiger Panthera tigris populations mostly survive within the geographically fragmented forest patches, thereby limited genetic exchange between isolated populations. Assessing the genetic status of these populations can reveal the effects of dispersal barriers and provide critical insights to guide future conservation actions. Using non-invasively collected biological samples, we investigated fine-scale genetic structure of tigers in the Sundarbans mangrove forests intersected by the complex river systems, and which holds one of the largest global tiger populations. We genotyped 52 tiger samples at 10 polymorphic microsatellite loci, and sequenced 33 of them for a total of 1263 base-pairs at four mitochondrial gene fragments. Microsatellite analyses exhibit a signature of fine-scale genetic structure, which might have been the consequence of limited tiger dispersal due to wide rivers across the Sundarbans. Similarly, mitochondrial data show a historic pattern of population isolation that might be due to wider rivers across the entire Sundarbans shared by Bangladesh and India. Given the intrinsic nature of the mangrove habitat embedded with numerous rivers, increased commercial traffic and human activities may further impede tiger dispersal across wide rivers, escalating further genetic isolation of the Sundarbans tigers.
  • Mounce, H., Warren, C., McGowan, C., Paxton, E. and Groombridge, J. (2018). Extinction risk and conservation options for Maui Parrotbill, an endangered Hawaiian honeycreeper. Journal of Fish and Wildlife Management [Online] 9:367-382. Available at: https://doi.org/10.3996/072017-JFWM-059.
    Extinction rates for island birds around the world have been historically high. For forest passerines, the Hawaiian archipelago has suffered some of the highest extinction rates and reintroduction is a conservation tool that can be used to prevent the extinction of some of the remaining endangered species. Population viability analyses can be used to assess risks to vulnerable populations and evaluate the relative benefits of conservation strategies. Here we present a population viability analysis to assess the long-term viability for Maui parrotbill(s) (Kiwikiu) Pseudonestor xanthophrys, a federally endangered passerine on the Hawaiian island of Maui. Contrary to indications from population monitoring, our results indicate Maui parrotbills may be unlikely to persist beyond 25 years. Our modeling suggests female mortality as a primary factor driving this decline. To evaluate and compare management options involving captive rearing and translocation strategies we made a female-only stage-structured, meta-population simulation model. Due to the low reproductive potential of Maui parrotbills in captivity, the number of individuals (~ 20% of the global population) needed to source a reintroduction solely from captive reared birds is unrealistic. A reintroduction strategy that incorporates a minimal contribution from captivity and instead translocates mostly wild individuals was found to be the most feasible management option. Habitat is being restored on leeward east Maui, which may provide more favorable climate and habitat conditions and promote increased reproductive output. Our model provides managers with benchmarks for fecundity and survival needed to ensure reintroduction success, and highlights the importance of establishing a new population in potentially favorable habitat to ensure long-term persistence.
  • Fogell, D., Martin, R., Bunbury, N., Lawson, B., Sells, J., McKeand, A., Tatayah, V., Trung, C. and Groombridge, J. (2018). Trade and conservation implications of new beak and feather disease virus detection in native and introduced parrots. Conservation Biology [Online] 32:1325-1335. Available at: https://doi.org/10.1111/cobi.13214.
    Psittacine beak and feather disease (PBFD), caused by Beak and feather disease virus (BFDV), has spread rapidly around the world, raising concerns for threatened species conservation and biosecurity risks associated with the global pet bird trade. BFDV has been reported in several wild parrot populations, but data is lacking for many taxa and geographical areas with high parrot endemism. This data deficit impedes the development of strategies to mitigate the threats posed by BFDV. We aimed to advance understanding of BFDV distribution in many data deficient areas and determine phylogenetic and biogeographic associations of the virus from five parrot species in Africa, the Indian Ocean islands, Asia and Europe. BFDV was detected in eight countries where it was not known to occur previously, indicating the virus is more widely distributed than currently recognised. We document for the first time the presence of BFDV in wild populations of the highly traded and invasive Psittacula krameri within its native range in Asia and Africa. BFDV was detected among introduced 15 P. krameri on the Indian Ocean islands of Mauritius and the Seychelles, raising concerns for island endemic species in the region. Examination of the phylogenetic relationships between viral sequences, including those detected among wild-sourced parrots seized from illegal trade in Western Africa, revealed likely pathways of transmission between populations. A close degree of phylogenetic relatedness between viral variants from geographically distant populations suggests recent introductions, likely driven by global trade. These findings highlight the need for effective regulation of international trade in live parrots, particularly in regions with high parrot endemism or vulnerable taxa where P. krameri could act as a reservoir host.
  • 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.
    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.
  • 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.
    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.
  • Davies, O., Huggins, A., Begue, J., Groombridge, J., Jones, C., Norfolk, D., Steward, P., Tatayah, V., Zuël, N. and Ewen, J. (2017). Reintroduction or natural colonisation? Using cost-distance analysis to inform decisions about Rodrigues Island Fody and Warbler reintroductions. Animal Conservation [Online] 21:110-119. Available at: http://dx.doi.org/10.1111/acv.12378.
    When making decisions about reintroducing a species, practitioners need to consider whether the release site contains habitat suitable for those species, whether past extinction drivers have been remedied and whether reintroduction is the best option for the species to recolonise the release site. These concerns are captured within two paradigms; the habitat and metapopulation paradigms. We use cost-distance analysis to assess the need for reintroduction of two bird species, Rodrigues Fody and Rodrigues Warbler, to Anse Quitor reserve on Rodrigues Island, testing hypotheses based on these underlying paradigms. Given a lack of detailed field studies of dispersal across the landscape on either species we rely on expert judgement. Our results show that experts believe Rodrigues Fody will naturally colonise Anse Quitor but that Rodrigues Warbler may not, at least within a time frame of 10 years. This information and treatment of expert judgement allows greater justification in reintroduction planning. Our method shows one way to assist in reintroduction decision making in poorly studied systems.
  • Booth Jones, K., Nicoll, M., Raisin, C., Dawson, D., Hipperson, H., Horsburgh, G., Groombridge, J., Ismar, S., Sweet, P., Jones, C., Tatayah, V., Ruhomaun, K. and Norris, K. (2017). Widespread gene flow between oceans in a pelagic seabird species complex. Molecular Ecology [Online] 26:5716-5728. Available at: http://dx.doi.org/10.1111/mec.14330.
    Global-scale gene flow is an important concern in conservation biology as it has the potential to either increase or decrease genetic diversity in species and populations. Although many studies focus on the gene flow between different populations of a single species, the potential for gene flow and introgression between species is understudied, particularly in seabirds. The only well studied example of a mixed-species, hybridising population of petrels exists on Round Island, in the Indian Ocean. Previous research assumed that Round Island represents a point of secondary contact between Atlantic (Pterodroma arminjoniana) and Pacific species (P. neglecta and P. heraldica). This study uses microsatellite genotyping and tracking data to address the possibility of between-species hybridisation occurring outside the Indian Ocean. Dispersal and gene flow spanning three oceans was demonstrated between the species in this complex. Analysis of migration rates estimated using BAYESASS revealed unidirectional movement of petrels from the Atlantic and Pacific into the Indian Ocean. Conversely, STRUCTURE analysis revealed gene-flow between species of the Atlantic and Pacific Oceans, with potential three-way hybrids occurring outside the Indian Ocean. Additionally, geolocation tracking of Round Island petrels revealed two individuals travelling to the Atlantic and Pacific. These results suggest that inter-specific hybrids in Pterodroma petrels are more common than was previously assumed. This study is the first of its kind to investigate gene flow between populations of closely related Procellariform species on a global scale, demonstrating the need for consideration of widespread migration and hybridisation in the conservation of threatened seabirds.
  • Aziz, M., Tollington, S., Barlow, A., Greenwood, C., Goodrich, J., Smith, O., Shamsuddoha, M., Islam, M. and Groombridge, J. (2017). Using non-invasively collected genetic data to estimate density and population size of tigers in the Bangladesh Sundarbans. Global Ecology and Conservation [Online] 12:272-282. Available at: http://dx.doi.org/10.1016/j.gecco.2017.09.002.
    Population density is a key parameter to monitor endangered carnivores in the wild. The photographic capture-recapture method has been widely used for decades to monitor tigers, Panthera tigris, however the application of this method in the Sundarbans tiger landscape is challenging due to logistical difficulties. Therefore, we carried out molecular analyses of DNA contained in non-invasively collected genetic samples to assess the tiger population in the Bangladesh Sundarbans within a spatially explicit capture-recapture (SECR) framework. By surveying four representative sample areas totalling 1,994 km2 of the Bangladesh Sundarbans, we collected 440 suspected tiger scat and hair samples. Genetic screening of these samples provided 233 authenticated tiger samples, which we attempted to amplify at 10 highly polymorphic microsatellite loci. Of these, 105 samples were successfully amplified, representing 45 unique genotype profiles. The capture-recapture analyses of these unique genotypes within the SECR model provided a density estimate of 2.85 ± SE 0.44 tigers/100 km2 (95% CI: 1.99-3.71 tigers/100 km2) for the area sampled, and an estimate of 121 tigers (95% CI: 84-158 tigers) for the total area of the Bangladesh Sundarbans. We demonstrate that this non-invasive genetic surveillance can be an additional approach for monitoring tiger populations in a landscape where camera-trapping is challenging.
  • 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.
    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
  • Buxton, A., Groombridge, J., Zakaria, N. and Griffiths, R. (2017). Seasonal variation in environmental DNA in relation to population size and environmentalfactors. Scientific Reports [Online] 7:46294. Available at: https://www.nature.com/articles/srep46294.
    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.
  • Buxton, A., Groombridge, J., Zakaria, N. and Griffiths, R. (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.
    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.
  • Aziz, M., Tollington, S., Barlow, A., Goodrich, J., Shamsuddoha, M., Islam, M. and Groombridge, J. (2016). Investigating patterns of tiger and prey poaching in the Bangladesh Sundarbans: Implications for improved management. Global Ecology and Conservation [Online] 9:70-81. Available at: http://dx.doi.org/10.1016/j.gecco.2016.12.001.
    Poaching of tigers and their key prey threatens the survival of tigers across their range. This
    study investigated the methods, intensity, and driving factors of tiger and prey poaching
    in the Sundarbans Reserved Forest of Bangladesh, to help better design and direct future
    management interventions. The study identified a range of snaring methods used to catch
    prey and an approach to killing tigers by poisoning prey carcasses with a Carbofuran
    pesticide. We recorded six poisoned baits set to kill tigers and 1427 snare loops in 56
    snare sets to kill tiger prey. With an average of 23 snare loops/snare set, this is equivalent
    to an estimated 6268 snare loops across the Sundarbans or 147 snare loops/100 km2.
    Poachers selected sites that tended to be away from guard posts, and close to river banks,
    but were not influenced by protected area status or distance to the forest boundary. The
    current poaching pressure is likely to have contributed to a recent decline in relative tiger
    abundance. We recommend using better regulation of Carbofuran use across tiger range
    countries, and using remote camera traps set up around snares and poisoned baits to help
    authorities identify poachers for arrest. This study demonstrates a simple approach to
    investigating the methods, intensity and distribution of poaching, that could be replicated
    across all tiger landscapes to better direct mitigating actions and monitor changes in threat
    levels over time.
  • Fogell, D., Martin, R. and Groombridge, J. (2016). Beak and feather disease virus in wild and captive parrots: an analysis of geographic and taxonomic distribution and methodological trends. Archives of Virology [Online]:1-16. Available at: http://www.dx.doi.org/10.1007/s00705-016-2871-2.
    Psittacine beak and feather disease (PBFD) has emerged in recent years as a major threat to wild parrot populations and is an increasing concern to aviculturists and managers of captive populations. Pathological and serological tests for screening for the presence of beak and feather disease virus (BFDV) are a critical component of efforts to manage the disease and of epidemiological studies. Since the disease was first reported in the mid-1970s, screening for BFDV has been conducted in numerous wild and captive populations. However, at present, there is no current and readily accessible synthesis of screening efforts and their results. Here, we consolidate information collected from 83 PBFD- and BFDV-based publications on the primary screening methods being used and identify important knowledge gaps regarding potential global disease hotspots. We present trends in research intensity in this field and critically discuss advances in screening techniques and their applications to both aviculture and to the management of threatened wild populations. Finally, we provide an overview of estimates of BFDV prevalence in captive and wild flocks alongside a complete list of all psittacine species in which the virus has been confirmed. Our evaluation highlights the need for standardised diagnostic tests and more emphasis on studies of wild populations, particularly in view of the intrinsic connection between global trade in companion birds and the spread of novel BFDV strains into wild populations. Increased emphasis should be placed on the screening of captive and wild parrot populations within their countries of origin across the Americas, Africa and Asia.
  • Jackson, H., Bunbury, N., Przelomska, N. and Groombridge, J. (2016). Evolutionary distinctiveness and historical decline in genetic diversity in the Seychelles Black Parrot Coracopsis nigra barklyi. Ibis [Online]:1-15. Available at: http://dx.doi.org/10.1111/ibi.12343.
    Island endemic species are acutely vulnerable to extinction as a result of stochastic and human impacts. Conservation of unique island biodiversity is high priority, and an understanding of the evolutionary history of vulnerable island species is important to inform conservation management. The Seychelles Black Parrot Coracopsis nigra barklyi is an island endemic threatened with extinction. The total population of 520–900 individu- als is restricted to the 38-km2 island of Praslin, and it is one of the last few remaining endemic island parrots that survive in the Indian Ocean. We combined mitochondrial and microsatellite DNA markers with morphological data to examine the evolutionary distinctiveness of C. n. barklyi within Coracopsis, and to compare levels of genetic diver- sity between historical and contemporary specimens. Phylogenetic analyses revealed C. n. barklyi as sister to the remaining three C. nigra subspecies, and discriminant func- tion analysis suggested the Seychelles Black Parrot is the smallest of the four subspecies. Higher levels of genetic diversity were observed in historical specimens, whereas only one mtDNA haplotype was observed in the contemporary specimens, suggesting that C. n. barklyi has lost genetic diversity as a consequence of substantial recent population decline. This study provides a first insight into the evolutionary, genetic and morphologi- cal processes that have shaped C. n. barklyi and provides an important perspective on this parrot’s current genetic status to guide its future conservation management. Further ecological studies are essential but we suggest that C. n. barklyi should be managed as an evolutionary significant unit to conserve its unique evolutionary pathway
  • Bobadilla Suarez, M., Ewen, J., Groombridge, J., Beckmann, K., Shotton, J., Masters, N., Hopkins, T. and Sainsbury, A. (2015). Using Qualitative Disease Risk Analysis for Herpetofauna Conservation Translocations Transgressing Ecological and Geographical Barriers. EcoHealth [Online] 14:47-60. Available at: https://doi.org/10.1007/s10393-015-1086-4.
    Through the exploration of disease risk analysis methods employed for four different UK herpetofauna translocations, we illustrate how disease hazards can be identified, and how the risk of disease can be analysed. Where ecological or geographical barriers between source and destination sites exist, parasite populations are likely to differ in identity or strain between the two sites, elevating the risk from disease and increasing the number and category of hazards requiring analysis. Simplification of the translocation pathway through the avoidance of these barriers reduces the risk from disease. The disease risk analysis tool is intended to aid conservation practitioners in decision making relating to disease hazards prior to implementation of a translocation.
  • Tollington, S., Turbe, A., Rabitsch, W., Groombridge, J., Scalera, R., Essl, F., Roy, H. and Shwartz, A. (2015). Making the EU legislation on invasive species a conservation success. Conservation Letters [Online] 10:112-120. Available at: https://doi.org/10.1111/conl.12214.
    The European Union’s (EU) new legislation concerning Invasive Alien Species (IAS) is a ground-breaking and commendable attempt to set a common standard for combating IAS across political jurisdictions at a multinational scale. However, the regulation, underpinned by a list of IAS of Union concern, affords Member States a degree of operational flexibility and its successful implementation will be dictated by appropriate national enforcement and resource use. In evaluating this EU legislation, we provide pragmatic recommendations based upon a geo-political analysis of the pan-European capabilities to combat IAS and discuss measures to avoid the risk that the regulation will promote a piecemeal response by stakeholders instead of a truly collaborative effort. We highlight a major deficit in the funding mechanisms to support a comprehensive implementation of the legislation and stress the importance of consultation with the broader scientific community, including with key stakeholders, businesses and the general public. Our recommendations will create incentives for industries, raise awareness among citizens and stakeholders, and help establish a social norm for the EU and further afield. The legislation offers a collaborative Europe the chance to demonstrate its commitment to tackling the problems of IAS and to achieve a successful conservation breakthrough of international importance.
  • Crommenacker, J., Bourgeois, Y., Warren, B., Jackson, H., Fleischer-Dogley, F., Groombridge, J. and Bunbury, N. (2015). Using molecular tools to guide management of invasive alien species: assessing the genetic impact of a recently introduced island bird population. Diversity and Distributions [Online] 21:1414-1427. Available at: http://dx.doi.org/10.1111/ddi.12364.
    Aim: Biological invasions are a major threat to island biodiversity and are responsible for a large proportion of species declines and extinctions worldwide.
    The process of hybridization between invasive and native species is a major factor that contributes to the loss of endemic genetic diversity. The issue of hybridization is often overlooked in the management of introduced species because morphological evidence of hybridization may be difficult to recognize
    in the field. Molecular techniques, however, facilitate identification of specific hybridization events and assessment of the direction and timing of introgression. We use molecular markers to track hybridization in a population of an island endemic bird, the Aldabra fody (Foudia aldabrana), following the recent discovery of a co-occurring population of non-native Madagascar fodies (Foudia madagascariensis).

    Location: Aldabra Atoll, Seychelles.

    Methods: We combine phylogenetic analyses of mitochondrial and nuclear markers to assess whether hybridization has occurred between F. madagascariensis
    and F. aldabrana on Aldabra. Using coalescence models and comparing different hybridization scenarios, we estimate the timing of such events and confirm the geographic origin of F. madagascariensis.

    Results: Our analyses confirm a recent hybridization event between the two species of Foudia, and we find evidence that the invasive F. madagascariensis
    originate from the neighbouring island of Assumption, where they were introduced in the 1970s.

    Main conclusions: Our results validate the threat of losing the unique genetic diversity of F. aldabrana through admixture due to recent invasion of F. madagascariensis. We show that molecular analyses can be a valuable tool in formulating strategies for the management of invasive birds.
  • Jackson, H., Strubbe, D., Tollington, S., Prys-Jones, R., Matthysen, E. and Groombridge, J. (2015). Ancestral origins and invasion pathways in a globally invasive bird correlate with climate and influences from bird trade. Molecular Ecology [Online] 24:4269-4285. Available at: http://doi.org/10.1111/mec.13307.
    Invasive species present a major threat to global biodiversity. Understanding genetic patterns and evolutionary processes that reinforce successful establishment is para- mount for elucidating mechanisms underlying biological invasions. Among birds, the ring-necked parakeet (Psittacula krameri) is one of the most successful invasive spe- cies, established in over 35 countries. However, little is known about the evolutionary genetic origins of this species and what population genetic signatures tell us about patterns of invasion. We reveal the ancestral origins of populations across the invasive range and explore the potential influence of climate and propagule pressure from the pet trade on observed genetic patterns. Ring-necked parakeet samples representing the ancestral native range (n = 96) were collected from museum specimens, and modern samples from the invasive range (n = 855) were gathered from across Europe, Mauritius and Seychelles, and sequenced for two mitochondrial DNA markers comprising 868 bp of cytochrome b and control region, and genotyped at 10 microsatellite loci. Invasive populations comprise birds that originate predominantly from Pakistan and northern areas of India. Haplotypes associated with more northerly distribution limits in the ancestral native range were more prevalent in invasive populations in Europe, and the predominance of Asian haplotypes in Europe is consistent with the higher number of Asian birds transported by the pet trade outside the native range. Success- ful establishment of invasive species is likely to be underpinned by a combination of environmental and anthropogenic influences.
  • Strubbe, D., Jackson, H., Groombridge, J. and Matthysen, E. (2015). Invasion success of a global avian invader is explained by within-taxon niche structure and association with humans in the native range. Diversity and Distributions [Online] 21:675-685. Available at: http://dx.doi.org/10.1111/ddi.12325.
    Aim To mitigate the threat invasive species pose to ecosystem functioning, reli- able risk assessment is paramount. Spatially explicit predictions of invasion risk obtained through bioclimatic envelope models calibrated with native species distribution data can play a critical role in invasive species management. Fore- casts of invasion risk to novel environments, however, remain controversial. Here, we assess how species’ association with human-modified habitats in the native range and within-taxon niche structure shape the distribution of invasive populations at biogeographical scales and influence the reliability of predictions of invasion risk.
    Location Africa, Asia and Europe.
    Methods We use ~1200 native and invasive ring-necked parakeet (Psittacula krameri) occurrences and associated data on establishment success in combi- nation with mtDNA-based phylogeographic structure to assess niche dynam- ics during biological invasion and to generate predictions of invasion risk. Niche dynamics were quantified in a gridded environmental space while bioclimatic models were created using the biomod2 ensemble modelling framework.
    Results Ring-necked parakeets show considerable niche expansion into climates colder than their native range. Only when incorporating a measure of human modification of habitats within the native range do bioclimatic envelope mod- els yield credible predictions of invasion risk for parakeets across Europe. Inva- sion risk derived from models that account for differing niche requirements of phylogeographic lineages and those that do not achieve similar statistical accu- racy, but there are pronounced differences in areas predicted to be susceptible for invasion.
    Main conclusions Information on within-taxon niche structure and especially association with humans in the native range can substantially improve predic- tive models of invasion risk. To provide policymakers with robust predictions of invasion risk, including these factors into bioclimatic envelope models is recommended.
  • Tollington, S., Greenwood, A., Jones, C., Hoeck, P., Chowrimootoo, A., Smith, D., Richards, H., Tatayah, V. and Groombridge, J. (2015). Detailed monitoring of a small but recovering population reveals sublethal effects of disease and unexpected interactions with supplemental feeding. Journal of Animal Ecology [Online] 84:969-977. Available at: http://dx.doi.org/10.1111/1365-2656.12348.
    Infectious diseases are widely recognized to have substantial impact on wildlife populations. These impacts are sometimes exacerbated in small endangered populations, and therefore, the success of conservation reintroductions to aid the recovery of such species can be seriously threatened by outbreaks of infectious disease. Intensive management strategies associated with conservation reintroductions can further compound these negative effects in such populations.
    Exploring the sublethal effects of disease outbreaks among natural populations is challenging and requires longitudinal, individual life-history data on patterns of reproductive success and other indicators of individual fitness.
    Long-term monitoring data concerning detailed reproductive information of the reintroduced Mauritius parakeet (Psittacula echo) population collected before, during and after a disease outbreak was investigated.
    Deleterious effects of an outbreak of beak and feather disease virus (BFDV) were revealed on hatch success, but these effects were remarkably short-lived and disproportionately associated with breeding pairs which took supplemental food. Individual BFDV infection status was not predicted by any genetic, environmental or conservation management factors and was not associated with any of our measures of immune function, perhaps suggesting immunological impairment. Experimental immunostimulation using the PHA (phytohaemagglutinin assay) challenge technique did, however, provoke a significant cellular immune response.
    We illustrate the resilience of this bottlenecked and once critically endangered, island-endemic species to an epidemic outbreak of BFDV and highlight the value of systematic monitoring in revealing inconspicuous but nonetheless substantial ecological interactions. Our study demonstrates that the emergence of such an infectious disease in a population ordinarily associated with increased susceptibility does not necessarily lead to deleterious impacts on population growth and that negative effects on reproductive fitness can be short-lived.
  • Maldonado, J., Michaelides, S., Cornish, N., Griffiths, R., Groombridge, J., Zajac, N., Walters, G., Aubret, F., While, G. and Uller, T. (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.
    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.
  • Mounce, H., Raisin, C., Leonard, D., Wickenden, H., Swinnerton, K. and Groombridge, J. (2015). Spatial genetic architecture of the critically-endangered Maui Parrotbill (Pseudonestor xanthophrys): management considerations for reintroduction strategies. Conservation Genetics [Online] 16:71-84. Available at: http://doi.org/10.1007/s10592-014-0641-9.
    Conservation translocations are an important tool to circumvent extinctions on oceanic islands. A thorough understanding of all components of a species’ biology, including genetic diversity and structure, can maximize their likelihood of success. The Maui Parrotbill (Pseudonestor xanthophrys) is an endangered Hawaiian honeycreeper endemic to the island of Maui. With a population of approximately 500 individuals restricted to 50 km2 of habitat, this species is at high risk of extinction. Using nuclear and mitochondrial DNA, this study quantified the levels of genetic diversity and structure in wild and captive parrotbill populations, and compared these genetic patterns to those observed within levels of contemporary and historical nuclear diversity derived from 100-year old museum samples. Substantial differences in the effective population sizes estimated between contemporary and historical parrotbill populations highlight the impact that introduced disease had on this species just before the turn of the century. Contemporary parrotbill diversity was low (global F st = 0.056), and there has been a 96 % reduction in genetic effective population size between contemporary and historical samples. This should not eliminate a conservation translocation (or reintroduction) as a viable recovery option. Measures of population differentiation (pairwise F st and R st ) between different sections of the current population on either side of the Koolau Gap suggest that current genetic structure may be the result of this topographic barrier to gene flow. These data can enable the design of a conservation translocation strategy that is tailored to the patterns of genetic structure across the species’ range.
  • Mori, E., Ancillotto, L., Groombridge, J., Howard, T., Smith, V. and Menchetti, M. (2015). Macroparasites of introduced parakeets in Italy: a possible role for parasite-mediated competition. Parasitology Research [Online] 114:3277-3281. Available at: http://doi.org/10.1007/s00436-015-4548-2.
    Alien species are considered a cause of biodiversity loss throughout the world. An important but often overlooked
    form of competition with native species is the parasite-mediated one. Introduced species may bring their own parasites
    from their native ranges (spillover) or get native parasites from native species, thus increasing the parasites’ spread and
    transmission risk (spillback). Thus, a complete knowledge of parasites hosted by introduced species is important to assess
    and to possibly prevent impacts. Ring-necked and monk parakeets have been introduced in many European countries,
    where they established a number of alien reproductive populations. We sampled 21 ring-necked parakeets and 7 monk
    parakeets from Italy and identified 35 arthropod ectoparasites belonging to five species. Amongst those, one species was
    native to India (Neopsittaconirmus lybartota), where alien populations of ring-necked parakeet may have been originated,
    and one species from South America (Paragoniocotes fulvofasciatus), which is typically found of the monk parakeet
    in its native range. The other three species of arthropod parasites were native to Italy and commonly found on native species,
    suggesting the possibility of spillback processes.
  • Jackson, H., Jones, C., Agapow, P., Tatayah, V. and Groombridge, J. (2015). Micro-evolutionary diversification among Indian Ocean parrots: temporal and spatial changes in phylogenetic diversity as a consequence of extinction and invasion. Ibis [Online] 157:496-510. Available at: http://doi.org/10.1111/ibi.12275.
    Almost 90% of global bird extinctions have occurred on islands. The loss of endemic spe- cies from island systems can dramatically alter evolutionary trajectories of insular species biodiversity, resulting in a loss of evolutionary diversity important for species adaptation to changing environments. The Western Indian Ocean islands have been the scene of evolution for a large number of endemic parrots. Since their discovery in the 16th cen- tury, many of these parrots have become extinct or have declined in numbers. Alongside the extinction of species, a number of the Indian Ocean islands have experienced coloni- zation by highly invasive parrots, such as the Ring-necked Parakeet Psittacula krameri. Such extinctions and invasions can, on an evolutionary timescale, drive changes in spe- cies composition, genetic diversity and turnover in phylogenetic diversity, all of which can have important impacts on species potential for adaptation to changing environmen- tal and climatic conditions. Using mtDNA cytochrome b data, we resolve the taxonomic placement of three extinct Indian Ocean parrots: the Rodrigues Psittacula exsul, Sey- chelles Psittacula wardi and Reunion Parakeets Psittacula eques. This case study quantifies how the extinction of these species has resulted in lost historical endemic phylogenetic diversity and reduced levels of species richness, and illustrates how it is being replaced by non-endemic invasive forms such as the Ring-necked Parakeet. Finally, we use our phylogenetic framework to identify and recommend a number of phylogenetically appro- priate ecological replacements for the extinct parrots. Such replacements may be intro- duced once invasive forms have been cleared, to rejuvenate ecosystem function and restore lost phylogenetic diversity.
  • Ewen, J., Walker, L., Canessa, S. and Groombridge, J. (2014). Improving supplementary feeding in species conservation. Conservation Biology [Online] 29:341-349. Available at: http://doi.org/10.1111/cobi.12410.
    Supplementary feeding is often a knee-jerk reaction to population declines, and its application is not critically evaluated, leading to polarized views among managers on its usefulness. Here, we advocate a more strategic approach to supplementary feeding so that the choice to use it is clearly justified over, or in combination with, other management actions and the predicted consequences are then critically assessed following implementation. We propose combining methods from a set of specialist disciplines that will allow critical evaluation of the need, benefit, and risks of food supplementation. Through the use of nutritional ecology, population ecology, and structured decision making, conservation managers can make better choices about what and how to feed by estimating consequences on population recovery across a range of possible actions. This structured approach also informs targeted monitoring and more clearly allows supplementary feeding to be integrated in recovery plans and reduces the risk of inefficient decisions. In New Zealand, managers of the endangered Hihi (Notiomystis cincta) often rely on supplementary feeding to support reintroduced populations. On Kapiti island the reintroduced Hihi population has responded well to food supplementation, but the logistics of providing an increasing demand recently outstretched management capacity. To decide whether and how the feeding regime should be revised, managers used a structured decision making approach informed by population responses to alternative feeding regimes. The decision was made to reduce the spatial distribution of feeders and invest saved time in increasing volume of food delivered into a smaller core area. The approach used allowed a transparent and defendable management decision in regard to supplementary feeding, reflecting the multiple objectives of managers and their priorities.
  • Mounce, H., Iknayan, K., Leonard, D., Swinnerton, K. and Groombridge, J. (2014). Management implications derived from long term re-sight data: annual survival of the Maui Parrotbill Pseudonestor xanthophrys. Bird Conservation International [Online] 24:316-326. Available at: http://doi.org/10.1017/S0959270913000476.
  • Buckland, S., Cole, N., Groombridge, J., Küpper, C., Burke, T., Dawson, D., Gallagher, L. and Harris, S. (2014). High Risks of Losing Genetic Diversity in an Endemic Mauritian Gecko: Implications for Conservation. PLoS ONE [Online]:e93387. Available at: http://doi.org/10.1371/journal.pone.0093387.
    Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations.
  • Bristol, R., Fraser, I., Groombridge, J. and Veríssimo, D. (2014). An economic analysis of species conservation and translocation for island communities: the Seychelles paradise flycatchers as a case study. Journal of Environmental Economics and Policy [Online] 3:237-252. Available at: http://doi.org/10.1080/21606544.2014.886531.
    In this paper we introduce a methodology for assessing the economic justification for translocation–conservation programmes for critically endangered species. We demonstrate our methodology by presenting an economic analysis of the critically endangered Seychelles paradise flycatcher (Terpsiphone corvina) (hereafter SPF). To do this we first estimated the critical amenity value of the forest that currently supports the SPF. Results support the maintenance of the forest, which in turn implies that the existing population of SPF needs to be protected so as to achieve species conservation objectives. Next we conducted a benefit–cost analysis of the translocation, showing that the development of a second population yields net economic benefits. By employing the methodology presented we can conclude that our analysis indicates that current conservation and translocation actions to support the SPF are economically justified.
  • Bristol, R., Tucker, R., Dawson, D., Horsburgh, G., Prys-Jones, R., Frantz, A., Krupa, A., Shah, N., Burke, T. and Groombridge, J. (2013). Comparison of historical bottleneck effects and genetic consequences of re-introduction in a critically endangered island passerine. Molecular Ecology [Online] 22:4644-4662. Available at: http://dx.doi.org/10.1111/mec.12429.
    Re-introduction is an important tool for recovering endangered species; however, the magnitude of genetic consequences for re-introduced populations remains largely unknown, in particular the relative impacts of historical population bottlenecks compared to those induced by conservation management. We characterize 14 microsatellite loci developed for the Seychelles paradise flycatcher and use them to quantify temporal and spatial measures of genetic variation across a 134-year time frame encompassing a historical bottleneck that reduced the species to ~28 individuals in the 1960s, through the initial stages of recovery and across a second contemporary conservation-introduction-induced bottleneck. We then evaluate the relative impacts of the two bottlenecks, and finally apply our findings to inform broader re-introduction strategy. We find a temporal trend of significant decrease in standard measures of genetic diversity across the historical bottleneck, but only a nonsignificant downward trend in number of alleles across the contemporary bottleneck. However, accounting for the different timescales of the two bottlenecks (~40 historical generations versus <1 contemporary generation), the loss of genetic diversity per generation is greater across the contemporary bottleneck. Historically, the flycatcher population was genetically structured; however, extinction on four of five islands has resulted in a homogeneous contemporary population. We conclude that severe historical bottlenecks can leave a large footprint in terms of sheer quantity of genetic diversity lost. However, severely depleted genetic diversity does not render a species immune to further genetic erosion upon re-introduction. In some cases, the loss of genetic diversity per generation can, initially at least, be greater across re-introduction-induced bottlenecks.
  • Tollington, S., Jones, C., Greenwood, A., Tatayah, V., Raisin, C., Burke, T., Dawson, D. and Groombridge, J. (2013). Long-term, fine-scale temporal patterns of genetic diversity in the restored Mauritius parakeet reveal genetic impacts of management and associated demographic effects on reintroduction programmes. Biological Conservation [Online] 161:28-38. Available at: http://dx.doi.org/10.1016/j.biocon.2013.02.013.
    Threatened populations of birds are often restored after bottleneck events by using reintroduction techniques. Whilst population numbers are often increased by using such measures, the long-term genetic effects of reintroductions and post-release management of the resulting populations are frequently overlooked. We identify an overall declining trend in population-wide estimates of genetic diversity over two decades since the initial recovery of the population from the most severe part of this species’ bottleneck. Additionally, by incorporating the genotypes of known founding individuals into population viability simulations, we evaluate the genetic effects of population management under various scenarios at both the metapopulation and subpopulation levels. We reveal that whilst population augmentation has led to increased genetic homogenisation among subpopulations, significant differentiation still exists. Simulations predict that even with a low level of natural dispersal leading to gene-flow this differentiation could be ameliorated. We conclude by offering a number of key recommendations relating to post-recovery management of reintroduced bird populations which support the encouragement of individual dispersal using established management techniques such as artificial nest-site provisioning.
  • Bristol, R., Fabre, P., Irestedt, M., Jønsson, K., Shah, N., Tatayah, V., Warren, B. and Groombridge, J. (2013). Molecular phylogeny of the Indian Ocean Terpsiphone paradise flycatchers: Undetected evolutionary diversity revealed amongst island populations. Molecular Phylogenetics and Evolution [Online] 67:336-347. Available at: http://doi.org/10.1016/j.ympev.2013.01.019.
    We construct a molecular phylogeny of Terpsiphone flycatchers of the Indian Ocean and use this to investigate their evolutionary relationships. A total of 4.4 kb of mitochondrial (cyt-b, ND3, ND2, control region) and nuclear (G3PDH, MC1R) sequence data were obtained from all species, sub-species and island populations of the region.

    Colonisation of the western Indian Ocean has been within the last two million years and greatly postdates the formation of the older islands of the region. A minimum of two independent continent-island colonisation events must have taken place in order to explain the current distribution and phylogenetic placement of Terpsiphone in this region. While five well-diverged Indian Ocean clades are detected, the relationship between them is unclear. Short intermodal branches are indicative of rapid range expansion across the region, masking exact routes and chronology of colonisation.

    The Indian Ocean Terpsiphone taxa fall into five well supported clades, two of which (the Seychelles paradise flycatcher and the Mascarene paradise flycatcher) correspond with currently recognised species, whilst a further three (within the Madagascar paradise flycatcher) are not entirely predicted by taxonomy, and are neither consistent with distance-based nor island age-based models of colonisation. We identify the four non-Mascarene clades as Evolutionarily Significant Units (ESUs), while the Mascarene paradise flycatcher contains two ESUs corresponding to the Mauritius and Réunion subspecies. All six ESUs are sufficiently diverged to be worthy of management as if they were separate species.

    This phylogenetic reconstruction highlights the importance of sub-specific molecular phylogenetic reconstructions in complex island archipelago settings in clarifying phylogenetic history and ESUs that may otherwise be overlooked and inadvertently lost. Our phylogenetic reconstruction has identified hidden pockets of evolutionary distinctiveness, which provide a valuable platform upon which to re-evaluate investment of conservation resources within the Terpsiphone flycatchers of the Indian Ocean.
  • Simpson, S., Blampied, N., Peniche, G., Dozières, A., Blackett, T., Coleman, S., Cornish, N. and Groombridge, J. (2013). Genetic structure of introduced populations: 120-year-old DNA footprint of historic introduction in an insular small mammal population. Ecology and Evolution [Online] 3:614-628. Available at: http://doi.org/10.1002/ece3.486.
    Wildlife populations have been introduced to new areas by people for centuries, but this human-mediated movement can disrupt natural patterns of genetic structure by altering patterns of gene flow. Insular populations are particularly prone to these influences due to limited opportunities for natural dispersal onto islands. Consequently, understanding how genetic patterns develop in island populations is important, particularly given that islands are frequently havens for protected wildlife. We examined the evolutionary origins and extent of genetic structure within the introduced island population of red squirrels (Sciurus vulgaris) on the Channel Island of Jersey using mitochondrial DNA (mtDNA) control region sequence and nuclear microsatellite genotypes. Our findings reveal two different genetic origins and a genetic architecture reflective of the introductions 120 years ago. Genetic structure is marked within the maternally inherited mtDNA, indicating slow dispersal of female squirrels. However, nuclear markers detected only weak genetic structure, indicating substantially greater male dispersal. Data from both mitochondrial and nuclear markers support historic records that squirrels from England were introduced to the west of the island and those from mainland Europe to the east. Although some level of dispersal and introgression across the island between the two introductions is evident, there has not yet been sufficient gene flow to erase this historic genetic “footprint.” We also investigated if inbreeding has contributed to high observed levels of disease, but found no association. Genetic footprints of introductions can persist for considerable periods of time and beyond traditional timeframes of wildlife management.
  • Mounce, H., Leonard, D., Swinnerton, K., Becker, C., Berthold, L., Iknayan, K. and Groombridge, J. (2013). Determining productivity of Maui Parrotbills, an endangered Hawaiian honeycreeper. Journal of Field Ornithology [Online] 84:32-39. Available at: http://doi.org/10.1111/jofo.12003.
    Maui Parrotbills (Pseudonestor xanthophrys), critically endangered Hawaiian honeycreepers endemic to the island of Maui, are restricted to a single population of ?500 individuals located in remote, mountainous terrain. From January to June 2006–2011, we located nests and fledglings in the Hanawi Natural Area Reserve (NAR) in east Maui, Hawaii, to document nest success and annual reproductive success. Nest success is a commonly used measure of productivity and is a central component of many demographic studies. Annual reproductive success is less frequently documented because greater effort is required to monitor the reproductive success of breeding pairs through time. However, for species whose nests are difficult to locate or access, such as Maui Parrotbills, the presence or absence of fledged young may provide a more accurate measure of breeding success than monitoring nests. During our study, we located and determined the outcome of 30 nests to document nest success, and monitored 106 territories for the presence or absence of fledglings to calculate annual reproductive success. Nest success probability was 19% (N= 30) and seasonal nest success was 46%. During our monitoring efforts, 49 of 106 breeding pairs produced a single fledged young. Because parrotbills typically have single egg clutches and only re-nest after nests fail, the presence or absence of a fledgling is an indication of a pair's overall reproductive success for a breeding season. Based on the number of fledglings per pair, our estimate of annual reproductive success was 46%, confirming our initial productivity estimate from nests. Thus, our results indicate that the two methods, determining annual reproductive success by monitoring fledglings and calculating nest success, provide similar estimates of annual productivity for Maui Parrotbills. Based on our estimates, the parrotbill population appears to be demographically stable. However, our productivity estimate was based only on the population at Hanawi, an area representing just 3% of the total range of parrotbills. Thus, our results may not accurately reflect the status of parrotbills over their entire range.

Thesis

  • Sells, J. (2017). Adaptive Potential and Signatures of Natural Selection in the Globally Introduced Ringneck Parakeet Psittacula Krameri.
    Anthropogenic impact, through animal trade, climate change, habitat fragmentation and globalisation, is a principal cause of global species redistributions and community rearrangements. Species introduced accidently or intentionally to non-native ranges may adapt to survive and proliferate, and native species threatened by environmental change may need to adapt in situ, or track more tolerable conditions through extra-range dispersal. Under both scenarios, we must facilitate greater understanding of the mechanisms that underlie adaptation within a complexity of ecosystem dynamics, which in turn will inform management strategies for both introduced species, and preserving biodiversity. Here, I explore mechanisms that support adaptive potential to rapid environmental change across taxa, and model them to the introduced ringneck parakeet Psittacula krameri. This species has recently successfully traversed extensive climate gradients in establishing introduced global populations. Some of this success may be attributable to morphological, behavioural, physiological or phenological adaptations, and therefore the species represents an opportunity for exploring rapid adaptation. I initially review the navigation of dispersal and invasive pathways, and the importance of specific character traits toward adaptive potential, before identifying genetic and non-genetic adaptive mechanisms (pertinent across taxa) that may help explain observed establishment and population growth of the ringneck parakeet. Mutations as the basis for an evolutionary adaptive response are examined, alongside the significance that the origin and extent of such polymorphisms may have toward a rapid adaptive response. I consider the role of selective sweeps and polygenic models as genetic processes for an adaptive response, alongside non-genetic mechanisms such as phenotypic plasticity and epigenetics that may better support rapid adaptation. Finally, I assess avian literature to interpret genetic and plastic responses as explanations for adaptive potential
  • Ward, R. (2017). Status and Conservation of the Grass Snake in Jersey.
    Global biodiversity losses are being driven by anthropogenic pressures; the most pervasive of which is habitat loss resulting in fragmentation and population isolation. These issues are prevalent throughout Europe due to high intensity agriculture and increasing human population densities. Limitations imposed by resources and the secretive lifestyles of many species hinder the ability of conservationists to undertake status assessments and identify conservation actions. This thesis investigates the threats to an isolated population of grass snakes Natrix helvetica on the island of Jersey, providing recommendations for conservation management and recovery, whilst testing the suitability of tools for monitoring cryptic species. Grass snakes were historically widespread throughout Jersey; however, anthropogenic influences have restricted their distribution to the west and southwest. Furthermore, recent monitoring efforts have detected few individuals and their status is unknown.
    Intensive surveys to locate individuals combined with occupancy and N-mixture (abundance) models identified continued occupancy of semi-natural sites in the island's west and southwest, but also highlighted poor detectability of the species unless utilising a large survey effort. Therefore, a large amount of effort is required to determine absence of snakes, and declines in the population cannot be detected with reasonable power. Occupancy models were more reliable than N-mixture models, particularly due to the risks of closure violation when estimating abundance. Nonetheless, N-mixture models estimated an abundance of 48 snakes (95% CI: 23?1279) across the study sites. Radio-tracking also provided evidence for low detection rates. Additionally snakes demonstrated small ranges (mean: 2.48 ha ± 3.54 SD), site fidelity, preferences for ranges close to paths and compost heaps, but avoided crossing roads. Snakes were positively associated with structurally complex habitats including rough grassland, dense scrub and gorse at multiple spatial scales, but negatively with open and wooded habitats.
    Species distribution modelling indicated similar habitat preferences to radio-tracking and poor suitability of agricultural habitats. Areas close to amphibian prey populations were also suitable whereas those with high road densities were not. A fifth of Jersey contained priority conservation areas, however almost 90% of these areas do not receive statutory protection. Those in the west and southwest should be prioritised for protection due to their proximity to extant subpopulations. Mitochondrial genes identified the population to belong to a western lineage of grass snakes Natrix helvetica helvetica, with a probable natural colonisation prior to separation from northwest France. Within Jersey, microsatellite markers identified three subpopulations, with significant differentiation between snakes in the south and west. This coincides with a dense urban area, through which connectivity needs improvement.
    The Jersey grass snake population can be classified as regionally Vulnerable (D2) under IUCN guidelines. The study illustrates how nature reserves are important for maintaining isolated subpopulations and the potential avenues by which statutory protection, sympathetic management practices and efforts to improve inter-reserve connectivity can contribute to conservation objectives.
  • Aziz, M. (2017). Population Status, Threats, and Evolutionary Conservation Genetics of Bengal Tigers in the Sundarbans of Bangladesh.
    The Sundarbans is a Tiger Conservation Landscape of global priority that supports one of the most important tiger populations across their current range. In Bangladesh, Sundarbans is the last stronghold of the critically endangered tiger, therefore conserving this flagship species will help to ensure the long-term future of the Sundarbans which has been providing significant economic and ecosystem services to human communities for centuries. However, scientific information is lacking on many aspects of the Sundarbans tigers, including population and genetic status, and detailed patterns of tiger and prey poaching. The objectives of this study were therefore to improve the knowledge base to help design better management strategies for long-term persistence of the Sundarbans tigers. As a consequence of challenges faced in applying conventional census methods in the Sundarbans mangrove habitat, a non-invasive genetic approach was applied to collect samples that were then screened using polymorphic microsatellite markers to estimate density and population size of tigers within the spatially explicit capture-recapture model. DNA analyses provided reasonable population estimates, indicating that a non-invasive genetic approach is a viable method for monitoring tigers and can be applied to monitor tiger populations elsewhere. Bayesian and Maximum likelihood inferences using mitochondrial DNA sequences supported a polyphyletic relationship between tiger population in the Sundarbans and the populations in central India. Together, microsatellite and mitochondrial DNA analyses revealed a signal of fine-scale genetic structure and significant genetic differentiation on a spatial scale which is probably the consequence of limited tiger dispersal due to the presence of wide rivers in the Sundarbans landscape. Systematic field survey across sample areas detected a range of snaring methods used to catch tiger prey and evidence of killing tigers by poisoning prey carcasses with the Carbofuran pesticide. Spatial analysis showed that poachers selected sites that tended to be further away from guard posts, and close to river banks. Based on these results, a range of future management interventions were recommended including the reduction of water-based commercial and resource collection activities to allow tiger dispersal, and regulation of Carbofuran and snare materials to better tackle tiger and prey poaching in the Sundarbans.
  • Rice, C. (2016). Abundance, Impacts and Resident Perceptions of Non-Native Common Pheasants (Phasianus Colchicus) in Jersey, UK Channel Islands.
    Few species are able to establish themselves in a non-native range and expand their population to
    become a wide-ranging invasive. However, for those that are able to, their negative environmental
    impacts include widespread predation of native flora and fauna, competition and spread of
    parasites and disease. The common pheasant (Phasianus colchicus), a native of central Asia, has
    been the subject of introductions for recreational hunting across the globe for hundreds of years.
    Today, millions of birds are released annually and rural habitats managed to better accommodate
    them. These mass introductions have prompted much research regarding the effects of pheasant
    populations in areas where they are released at high densities. However, little is known about the
    effects of naturalised populations of pheasants in areas where they are neither released nor their
    habitat managed. To fill this knowledge gap and to aid management, this study seeks to investigate
    the naturalised population of common pheasants on the Bailiwick of Jersey, UK Channel Islands.
    Through an extensive programme of field surveys, this research enables a better understanding of
    the impacts of this non-native species on native wildlife and agriculture. Distance sampling was
    used to provide density and abundance estimates of Jersey's pheasant population and Breeding
    Bird Survey data, provided by the British Trust for Ornithology, were also used to investigate
    population trends over time. Summer habitat preferences were also investigated and, to
    complement these findings and further inform management, an online questionnaire to analyse
    local perceptions of pheasants and their impacts was conducted. Pheasant density estimates ranged from 9.5 to 16.6 pheasants per km2, with a total island-wide population of 1011-1780
    pheasants. Highest concentrations were seen in the southeast (St. Clement) and northwest (St.
    Ouen) of the island and the lowest concentrations in the southwest (St. Brelade), with pheasants
    showing a preference for fields that contained shoots, mustard and bare ground. The long-term
    data revealed an overall decreasing but oscillating population trend since 2002. Residents of Jersey
    perceive pheasants as having negative impacts on farmland birds, herpetofauna and crops, with
    some respondents witnessing predation of reptiles and amphibians, all of which are protected
    species. Despite this, pheasants are generally well received by residents with the majority 'agreeing'
    or 'strongly agreeing' that pheasants add to the appeal of the countryside and that they enjoy
    having pheasants in Jersey. Pheasants are also considered to have a positive impact on birds of prey
    and are credited for the rise in marsh harrier (Circus aeruginosus) and buzzard (Buteo buteo)
    numbers. Arable farmers displayed the most adverse opinions of pheasants and were significantly
    more likely to view pheasants as negative for arable crops. The percentages of residents who
    believe pheasants should be protected by legislation and those who do not are almost equal.
    Specifically, arable farmers were generally in favour of removing pheasant protection, whereas
    game shooters polarise this view. The successful management of any invasive species or their
    impacts relies on monitoring populations, examining their trends, and understanding their habitat
    use. To this end, this study provides the baseline data required for future decisions on pheasant
    management by policy makers in Jersey.
  • Labisko, J. (2016). Evolutionary Relationships of the Sooglossid Frogs of Seychelles’.
  • Worswick, G. (2016). A Population Genetic Study of Pasqueflower: In Situ and Ex Situ Conservation Genetics of a Vulnerable UK Plant Species.
    The population genetic structure of the vulnerable UK plant species Anemone pulsatilla L. reflects geographic patterns of historical range fragmentation and the influence of population decline and restoration intervention. Positive spatial auto-correlation of natural in situ populations of A. pulsatilla lends support to a scenario for genetic drift (i.e. random drift of allelic frequencies) driving the emergence of population genetic structure as a consequence of fragmentation. Multivariate and STRUCTURE analysis estimates the partitioning of genetic variation among four natural population genetic clusters (broadly defined by geographical regions of the species’ range) and a fifth, highly differentiated, genetic cluster defined by introduced genotypes of unverifiable genetic origin to the casually augmented AN population. It is recommended that restoration intervention (i.e. to augment declining populations or introduce populations to enhance gene flow) source propagules for introduction from within the local population genetic cluster in order to maximise the potential for introduction/exchange of locally adaptive genetic variation.
    The existing ex situ gene conservation strategy for A. pulsatilla can be predicted to under-represent the species’ natural genetic variability due to limited sampling effort. At a minimum, a representative ex situ gene conservation strategy for the safeguard of A. pulsatilla UK variability should aim to capture representative accessions from the most diverse population/s of each of the four natural population genetic clusters. It is also recommended that the six native AN genotypes are sampled for ex situ conservation due to a disproportionately high level of unique genetic variation. A pilot study of regenerated ex situ accessions supports a prediction that the following factors act on genetic diversity: (a) survivorship; (b) number of generation removed from the wild; (c) effective population size.
  • Mounce, H. (2015). Recovery of the Endangered Maui Parrotbill (Kiwikiu, Pseudonestor Xanthophrys).
    Species recovery programs are tasked with reversing the declines of
    threatened and endangered species and mitigating the threats to their populations.
    These goals must be accomplished in the face of a human dominated global
    landscape where habitat destruction and alteration is still increasing at an alarming
    rate. Hawaii, as common on many islands, has one of the highest historical
    extinction rates in the world. Here I use the Maui Parrotbill (Kiwikiu; Pseudonestor
    xanthophrys) to explore population demographics, genetics, population viability,
    and recovery options for one of Hawaii’s most critically endangered passerines (Maui
    Island endemic, pop. ~500). The accurate estimation of key demographic parameters
    is invaluable for making decisions about the management of endangered wildlife.
    Due to the challenges of data collection on a rare and cryptic species that inhabits
    remote terrain, such estimates are often difficult to obtain and reliable basic
    demographic data was not before available for parrotbills. First I look at parrotbill
    productivity estimates through both nest success and annual reproductive success
    measures. Secondly, I look at annual survival based on an 18 year encounter history.
    These studies both suggest population limitations may be coming from fecundity,
    and juvenile and female survival. Maui Parrotbill once inhabited a variety of forest
    types throughout Maui Nui but are now restricted to a single strip of wet forest 40-50
    km2 in size. I quantified the levels of contemporary genetic diversity and structure in
    wild and captive Kiwikiu populations, and compared these genetic patterns to those
    observed within historical nuclear diversity derived from 100-year old museum
    samples enabling the design of a conservation translocation strategy that is tailored
    to the patterns of genetic structure across the species’ range. Lastly, I combine
    these data into a comprehensive population viability model to assess the risks to this
    population and evaluate the impacts of recovery options to the overall viability
    trajectory of a species. In planning for a reintroduction of parrotbills to areas of
    their former range, this model provides managers with demographic benchmarks
    that the new population will need to meet in order for the reintroduction to be
    successful.
  • Jackson, H. (2015). Evolutionary Conservation Genetics of Invasive and Endemic Parrots.
    The world is now thought to have entered into a sixth mass extinction event, which unlike previous mass extinctions, is entirely driven by human impacts. The early colonisation of humans has led to as many as a thousand endemic bird species becoming extinct, while increasing human mediated transport of species around the world has led to invasive species becoming one of the largest global conservation challenges of today. Studies in molecular ecology can help us to unravel how evolutionary processes are important for informing conservation and invasion biology by understanding genetic mechanisms that enable populations to grow and adapt in a changing world. As genetic diversity is essential for the persistence of populations, this thesis aims to understand how species respond, at a genetic level, to human-driven events such as the reduction of a population to a small size, or the introduction of a species into a novel environment. The findings demonstrate the important use of genetic markers for phylogenetic reconstruction and understanding population structure. These phylogenetic reconstructions examine taxonomic distinctiveness and patterns of evolution, and allow the identification of ancestral origins for invasive ring-necked parakeets. Evidence from genetic phylogroups, trade data and drivers of population growth, highlight how multiple introductions and patterns of climate matching between the native and invasive ranges of ring-necked parakeets, are mechanisms for invasion success. In contrast to mild genetic bottleneck effects, high levels of diversity and the avoidance of problems associated with small population size within populations of invasive ring-necked parakeet, the endemic Seychelles black parrot exhibited a reduction in population size and reduced levels of genetic diversity over time. Moreover, the inclusion of new genetic data for a number of extinct parrot species enabled an examination of the loss of broader scale phylogenetic diversity, important for ecosystem function, as a result of extinctions of endemic species and invasions of ring-necked parakeets. The findings from this thesis have already been applied to conservation and invasion biology by contributing to the reclassification of the endemic Seychelles black parrot, and to improving the ability of ecological niche models to predict areas suitable for future invasions of ring-necked parakeets. Furthermore they provide a novel approach to identifying potential candidates as ecological replacements to restore ecosystem function and lost phylogenetic diversity.

Forthcoming

  • Fogell, D. (2019). Measuring the Effects of Supplementary Feeding and Biosecurity on the Trajectory of a Threatened Avian Population.
    When faced with emerging infectious diseases in wild populations, conservationists are often forced to respond rapidly, with decisions based in uncertainty. Clear decision-making processes are rarely followed and subsequent monitoring and evaluation as to the efficacy of the chosen solution is often neglected. This thesis interrogates the interaction between disease transmission and population management solutions for the recovery of the endangered Mauritius parakeet (Psittacula eques), with a particular focus on nest sites, supplementary feeding hoppers and biosecurity. Beak and feather disease virus (BFDV; Circoviridae), the etiological agent of Psittacine beak and feather disease (PBFD), is widely infectious and fatal. PBFD is considered the most common viral disease in wild parrots and was first detected in Mauritius parakeets in 2005. Here I apply a combination of field-based experiments and molecular genetic techniques to screen both host and environmental DNA for BFDV, alongside observational, demographic and breeding data to address three key research questions. I assess the influence of (i) the wildlife trade in the global spread of BFDV, (ii) artificial nest sites and supplementary feeding hoppers on the prevalence of BFDV in Mauritius parakeets, and (iii) sociality at supplementary feeding hoppers on the transmission of BFDV. The key aim of this thesis is to provide practical and implementable management solutions that are relevant to any conservationists managing wild populations affected by BFDV.

    I detected BFDV in wild parrots from eight new countries, as well as from birds seized from illegal trafficking. Phylogenetic associations between geographically distant regions highlight the impacts of the wildlife trade in the spread of infectious disease globally. With regards to population management, I found that there is currently no observable relationship between nest site placement and either BFDV prevalence or fecundity, but the relationship between BFDV prevalence and nest altitude may be of greater relevance under future climate change scenarios. Whilst biosecurity protocols applied at nest sites successfully reduced BFDV prevalence in nestlings, upscaled disinfection of hoppers had no significant effect. However, both forms of biosecurity unintentionally and significantly hindered Mauritius parakeet breeding success. Finally, I determined that the relationship between BFDV prevalence and hoppers was better attributed to the artificially altered frequency of social interaction between individuals at these centralised hubs.

    These results have both increased our knowledge of BFDV occurrence globally, covering some highly biodiverse but data deficient regions, and provided an evidence-based approach to the evaluation of in situ pathogen management. Management for wildlife conservation should be critically evaluated through targeted monitoring and experimental manipulation, and this evaluation should always focus on the fundamental objective of conservation.
  • Buxton, A., Groombridge, J. and Griffiths, R. (2018). Comparison of two Citizen Scientist Methods for Collecting Pond Water Samples for Environmental DNA Studies. Citizen Science: Theory and Practice [Online] 3. Available at: http://dx.doi.org/10.5334/cstp.151.
    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.
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