Professor Jim Groombridge
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.
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.
Undergraduate (BSc in Wildlife Conservation)
Postgraduate (MSc in Conservation Biology)
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).
External Examiner for MSc in Biodiversity, Conservation and Management, University of Oxford (2015-2018)
Showing 50 of 78 total publications in the Kent Academic Repository. View all publications.
Fogell, D. et al. (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 âechoâ 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.
Jones, C. et al. (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. et al. (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. et al. (2019). Endemic, endangered, and evolutionarily significant: Cryptic lineages in Seychellesâ frogs. Biological Journal of the Linnean Society [Online]. 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 MahÃ©, 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.
Fogell, D. et al. (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.
Mounce, H. et al. (2018). Extinction risk and conservation options for Maui Parrotbill, an endangered Hawaiian honeycreeper. Journal of Fish and Wildlife Management [Online]. 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.
Tollington, S. et al. (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. et al. (2018). Do rivers influence fine-scale population genetic structure of tigers in the Sundarbans? Conservation Genetics [Online]:1-15. 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 1,263 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.
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
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 â 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. et al. (2017). Seasonal variation in environmental DNA in relation to population size and environmental factors. Scientific Reports [Online] 7:46294. Available at: http://dx.doi.org/10.1038/srep46294.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. et al. (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 Â± 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.
Booth Jones, K. et al. (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.
Davies, O. et al. (2017). Reintroduction or natural colonisation? Using cost-distance analysis to inform decisions about Rodrigues Island Fody and Warbler reintroductions. Animal Conservation [Online]. 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.
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
Aziz, M. et al. (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. et al. (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 520â900 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 parrotâs 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
Crommenacker, J. et al. (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.
Tollington, S. et al. (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.
Bobadilla Suarez, M. et al. (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.
Maldonado, J. et al. (2015). Phylogeography and Conservation Genetics of the Common Wall Lizard, Podarcis muralis, on Islands at Its Northern Range. PLOS ONE [Online] 10:e0117113. Available at: http://doi.org/10.1371/journal.pone.0117113.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.
Strubbe, D. et al. (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 speciesâ 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. et al. (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 Unionâs (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.
Mori, E. et al. (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 parasitesâ 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.
Mounce, H. et al. (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 speciesâ 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 speciesâ range.
Jackson, H. et al. (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.
Jackson, H. et al. (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.
Bristol, R. et al. (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 translocationâconservation 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 benefitâcost 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.
Mounce, H. et al. (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. et al. (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.
Ewen, J. et al. (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.
Black, S., Groombridge, J. and Jones, C. (2013). Using Better Management Thinking to Improve Conservation Effectiveness. ISRN Biodiversity [Online] 2013:1-8. Available at: http://doi.org/10.1155/2013/784701.The current paradigm for effective management in biodiversity conservation programmes is dominated by three broad streams of thinking: (i) traditional âcommand-and-controlâ approaches which are commonly observed in, but are not exclusive to, bureaucratic government-administered conservation, (ii) more recent notions of âadaptive management,â and (iii) emerging âgood practiceâ management frameworks for conservation. Other variations on these themes suggested by the literature tend to endorse additions or enhancement to one or more of these approaches. We argue that instead a more fundamental alternative approach to conservation management is required, based on âsystems thinking.â The systems thinking approach should encompass (i) an understanding of natural systems, (ii) a sense of how human behaviour is influenced, (iii) an understanding of how knowledge should inform decision-making and problem solving, and (iv) an approach based on an understanding of variation in natural systems. Our argument is that the current paradigms of conservation management fail to address these four fundamentals and therefore do not represent the most effective way to manage conservation programmes. We suggest that the challenge for the conservation community is so great that conservation managers should seriously consider better ways of designing and managing programmes, setting goals, making decisions, and encouraging learning and improvement.
Simpson, S. et al. (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 âfootprint.â 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.
Buckland, S. et al. (2013). Isolation and characterisation of Mauritius lowland day gecko Phelsuma guimbeaui microsatellite loci. Conservation Genetics Resources [Online] 5:1013-1018. Available at: http://doi.org/10.1007/s12686-013-9957-x.We isolated 315 sequences from a Phelsuma guimbeaui microsatellite-enriched genomic library. Primer sets were designed for 44 loci and used to genotype 29 unrelated individuals belonging to a population in the west of Mauritius. All the loci were polymorphic and the number of alleles ranged from 6 to 34. Mean observed and expected heterozygosity varied from 0.29 to 1.00 and 0.48 to 0.97, respectively. Thirteen loci displayed evidence of deviation from HardyâWeinberg equilibrium, of which 11 also had an estimated null allele frequency ?10 %. The microsatellite loci will be used to evaluate the population structure and genetic diversity of P. guimbeaui in Mauritius.
Bristol, R. et al. (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. et al. (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 speciesâ 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.
Jackson, H., Morgan, B. and Groombridge, J. (2013). How closely do measures of mitochondrial DNA control region diversity reflect recent trajectories of population decline in birds? Conservation Genetics [Online] 14:1291-1296. Available at: http://dx.doi.org/10.1007/s10592-013-0514-7.Monitoring levels of genetic diversity in wild- life species is important for understanding population sta- tus and trajectory. Knowledge of the distribution and level of genetic diversity in a population is essential to inform conservation management, and help alleviate detrimental genetic impacts associated with recent population bottle- necking. Mitochondrial DNA (mtDNA) markers such as the control region have become a common means of sur- veying for within-population genetic diversity and detect- ing signatures of recent population decline. Nevertheless, little attention has been given to examining the mtDNA control regionâs sensitivity and performance at detecting instances of population decline. We review genetic studies of bird populations published since 1993 that have used the mtDNA control region and reported haplotype diversity, number of haplotypes and nucleotide diversity as measures of within-population variability. We examined the extent to which these measures reflect differences in known demo- graphic parameters such as current population size, severity of any recent bottleneck and IUCN Red List status.Overall, significant relationships were observed between two measures of genetic diversity (haplotype diversity and the number of haplotypes), and population size across a number of comparisons. Both measures gave a more accurate reflection of recent population history in com- parison to nucleotide diversity, for which no significant associations were found. Importantly, levels of diversity only correlated with demographic declines where popula- tion sizes were known to have fallen below 500 individu- als. This finding suggests that measures of mtDNA control region diversity should be used with a degree of caution when inferring demographic history, particularly bottle- neck events at population sizes above N = 500.
Bristol, R. et al. (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 RÃ©union 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.
Mounce, H. et al. (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 2006â2011, 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.
Groombridge, J. et al. (2012). Dynamic colonization exchanges between continents and islands drive diversification in paradise-flycatchers (Terpsiphone, Monarchidae). Journal of Biogeography [Online] 39:1900-1918. Available at: http://dx.doi.org/10.1111/j.1365-2699.2012.02744.x.Aim? We use parametric biogeographical reconstruction based on an extensive DNA sequence dataset to characterize the spatio-temporal pattern of colonization of the Old World monarch flycatchers (Monarchidae). We then use this framework to examine the role of dispersal and colonization in their evolutionary diversification and to compare plumages between island and continental Terpsiphone species.
Taylor, M. et al. (2012). Evidence for evolutionary distinctiveness of a newly discovered population of sooglossid frogs on Praslin Island, Seychelles. Conservation Genetics [Online] 13:557-566. Available at: http://doi.org/10.1007/s10592-011-0307-9.Amidst a worldwide decline in amphibian populations, those species endemic to islands remain an important focus for conservation efforts. The Sooglossidae are a family of frog species endemic to the Seychelles islands that are believed to have evolved in isolation for approximately 75 million years. Formerly thought to inhabit just two Seychelles islands (MahÃ© and Silhouette), a third population was discovered on Praslin in 2009. Phylogenetic analysis based on 438 bp of mitochondrial 16S rRNA suggests that the Praslin population is most closely related to Sooglossus sechellensis from Silhouette, and identifies these as two separate clades which together sit distinct from the population on MahÃ©. An average of 4.06% uncorrected pairwise sequence divergence between the Praslin and Silhouette populations suggests substantial evolutionary divergence rather than recent introduction. Discriminant function analysis also revealed differences in morphology in frogs from Praslin and MahÃ©. DNA sequences of two Praslin specimens group more closely with the MahÃ© population, indicating some shared haplotypes that suggest recent secondary contact. Tests for a genetic signature of recent population expansion on either island were not significant. Our results suggest substantial evolutionary divergence between the three populations of S. sechellensis, most likely following isolation due to changes in sea level in the Indian Ocean. Whilst further genetic sampling and ecological studies are needed, our initial phylogenetic analyses suggest that the sooglossid population on Praslin should be managed as an evolutionarily significant unit to retain the uniqueness of its genetic diversity and its evolutionary trajectory within this ancient family of amphibians.
Kundu, S. et al. (2012). Tracking Viral Evolution during a Disease Outreak: the Rapid and Complete Selective Sweep of a Circovirus in the Endangered Echo Parakeet. Journal of Virology [Online] 86:5221-5221. Available at: http://dx.doi.org/10.1128/JVI.06504-11.Circoviruses are amongst the smallest and simplest of all viruses, but are relatively poorly characterised. Here, we intensively sampled two sympatric parrot populations from Mauritius over a period of 11 years and screened for the circovirus Beak and Feather Disease Virus. During the sampling period a severe outbreak of Psittacine Beak and Feather Disease, which is caused by Beak and Feather Disease Virus, occurred in Echo parakeets. Consequently, this dataset presents an ideal system to study the evolution of a pathogen in a natural population and to understand the adaptive changes that cause outbreaks. Unexpectedly, we discovered that the outbreak was most likely caused by changes in functionally important regions of the normally conserved replicase gene and not the immunogenic capsid. Moreover, these mutations were completely fixed in the Echo parakeet host population very shortly after the outbreak. Several capsid alleles were linked to the replicase outbreak allele suggesting that whilst the key changes occurred in the latter, the scope of the outbreak and the selective sweep may have been influenced by positive selection in the capsid. We found evidence for viral transmission between the two host populations though evidence for the invasive species as the source of the outbreak was equivocal. Finally, the high evolutionary rate that we estimated shows how rapidly new variation can arise in Beak and Feather Disease Virus and is consistent with recent results from other small single-stranded DNA viruses.
Paredes, U. et al. (2012). Micro-CT X-rays do not fragment DNA in preserved bird skins. Journal of Zoological Systematics and Evolutionary Research [Online] 50:247-250. Available at: http://doi.org/10.1111/j.1439-0469.2012.00657.x.Most zoological systematics studies are currently based on morphological features, molecular traits or a combination of both to reconstruct animalsâ phylogenetic history. Increasingly, morphological studies of museum specimens are using X-ray computed tomography to visualize internal morphology, because of its ânon-destructiveâ nature. However, it is not known whether CT can fragment the size of DNA extracted from museum specimens, as has been demonstrated to occur in living cells. This question is of paramount importance for collections based research because X-rays may reduce the amount of data obtainable from specimens. In our study, we tested whether exposure of museum bird skins to typical CT X-ray energies (for visualization of the skeleton) increased DNA strand fragmentation, a key factor for the success of downstream molecular applications. For the present study, we extracted DNA from shavings of 24 prepared and dried bird skins (100+ years) footpads before and after CT scanning. The pre- and post-CT fragmentation profiles were assessed using a capillary electrophoresis high-precision instrument (Agilent Bioanalyzer). Comparison of the most common strand length in each DNA sample (relative mass) revealed no significant difference unexposed and exposed tissue (paired t-test p = 0.463). In conclusion, we found no further quantifiable degradation of DNA strand length under standard X-ray exposure obtained from our bird skins sample. Differences in museum preservation techniques probably had a greater effect on variation of pre-CT DNA fragmentation.
Pickles, R. et al. (2012). Genetic diversity and population structure in the endangered giant otter, Pteronura brasiliensis. Conservation Genetics [Online] 13:235-245. Available at: http://doi.org/10.1007/s10592-011-0279-9.We assessed levels of genetic diversity and investigated patterns of population structure in three remnant populations of the endangered giant otter, Pteronura brasiliensis, using microsatellite loci. All populations displayed moderate to low levels of heterozygosity and allelic richness (H O 0.56â0.57, A R 4.00â5.15) and effective population sizes were low (N E 10.8â54) although only the ItÃ©nez population exhibited the signature of a genetic bottleneck. Population structure analyses revealed a pattern in which the populations of the Upper Amazon, Orinoco and Essequibo drainages comprised partially differentiated segments of a northern South American metapopulation, whereas the population of the ItÃ©nez appeared isolated. The observed patterns are congruent with previous mitochondrial DNA analysis which suggested the ItÃ©nez and northern South American groups constitute two evolutionary significant units. The results presented here should be considered in planning future policies aiming to manage the recovery of the giant otter across its range.
Raisin, C. et al. (2012). Genetic consequences of intensive conservation management for the Mauritius parakeet. Conservation Genetics [Online] 13:707-715. Available at: http://doi.org/10.1007/s10592-012-0319-0.For conservation managers tasked with recovering threatened species, genetic structure can exacerbate the rate of loss of genetic diversity because alleles unique to a sub-population are more likely to be lost by the effects of random genetic drift than if a population is panmictic. Given that intensive management techniques commonly used to recover threatened species frequently involve movement of individuals within and between populations, managers need to be aware not only of pre-existing levels of genetic structure but also of the potential effects that intensive management might have on these patterns. The Mauritius parakeet (Psittacula echo) has been the subject of an intensive conservation programme, involving translocation and reintroduction that has recovered the population from less than 20 individuals in 1987 to approximately 500 in 2010. Analysis of genotype data derived from 18 microsatellite markers developed for this species reveals a clear signal of structure in the population before intensive management began, but which subsequently disappears following management intervention. This study illustrates the impacts that conservation management can have on the genetic structure of an island endemic population and demonstrates how translocations or reintroductions can benefit populations of endangered species by reducing the risk of loss of genetic diversity.
Black, S., Meredith, H. and Groombridge, J. (2011). Biodiversity conservation: Applying new criteria to assess excellence. Total Quality Management & Business Excellence [Online] 22:1165-1178. Available at: http://doi.org/10.1080/14783363.2011.624766.Biodiversity conservation is a discipline that has developed from amateur pursuits by wildlife enthusiasts in the 1960s to today's complex community of multi-national NGOs, government agencies and research institutions. The conservation sector is largely funded by government grants, private donations and sponsorship, and unsurprisingly faces increasing scrutiny in the current economic downturn. Furthermore, the observed failure to halt the decline of biodiversity provides additional pressure to organisations. In this context, business excellence models which have been utilised across many other sectors for evaluation, benchmarking and improvement planning could prove valuable in influencing the effectiveness of conservation management. This paper presents a sector-specific Conservation Excellence Model which describes how conservation managers can better understand how scientific processes and results can be aligned with financial and organisational measures of success. The relevance of the model is illustrated through evaluation of two well-documented species conservation programmes, and experience of adapting the assessment process to evaluate a field-based conservation programme is also presented. The potential benefits of using the Conservation Excellence Model include improved objective setting, more effective measures of biological success and clearer evaluation of conservation processes. The paper illustrates how assessment models can support improvement in organisations still unfamiliar with concepts of excellence.
Black, S., Groombridge, J. and Jones, C. (2011). Leadership and conservation effectiveness: finding a better way to lead. Conservation Letters [Online] 4:329-339. Available at: http://dx.doi.org/10.1111/j.1755-263X.2011.00184.x.Conservation practitioners and academics have highlighted leadership as an important component for conservation programs, but the attributes of effective leaders are not yet clearly defined. We identify a leadership approach that enables a conservation organization to be more effective in achieving positive results. An analysis of successful and unsuccessful species conservation programs consistently reveals contrasting leadership approaches. Successful approaches resonate strongly with both the characteristics of species conservation and established leadership theory in mainstream management literature. We describe the practices identified in successful species conservation programs to provide the basis for a new understanding of conservation leadership using established management theory. The traits of a successful conservation leader include: an ability to share a clear, long-term vision; orientation toward âhands-onâ management; an ability to switch thinking between the big picture and the detail; and a willingness to encourage learning, improvement, and receptiveness to alternative solutions. Activities in the conservation sector are typically influenced by factors beyond the control of managers. Conversely, a leadership approach is under managersâ direct control and has an impact on attainment of results. Effective leadership is one factor that should not be left to chance but should be considered seriously for its impact on achievement in biodiversity conservation.
Groombridge, J. et al. (2012). Genetic Consequences of Reintroductions and Insights from Population History. in: Ewen, J. G. et al. eds. Reintroduction Biology: Integrating Science and Management. John Wiley and Sons, pp. 395-440. Available at: http://dx.doi.org/10.1002/9781444355833.ch12.
White, R. et al. (2019). Assessing the ecological and societal impacts of alien parrots in Europe using a transparent and inclusive evidence-mapping scheme. NeoBiota.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 âwiki-reviewâ 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.