Ecological immunology and genetic diversity of the endangered Mauritius parakeet

Studies of avian ecological immunology attempt to describe the biotic and abiotic factors which explain natural variation in immune function within and among free-living bird species. Understanding this variation and the trade-offs associated with maintaining appropriate immune defences and individual life history variables has important implications for the conservation of endangered species, many of which are characterised by small population size and reduced genetic diversity. Such species often display increased susceptibility to infectious diseases as a result of inbreeding depression and are prone to the effects of novel parasites and pathogens. This thesis aims to explain the variation in immune function in the endangered, island-endemic Mauritius parakeet (Psittacula echo), a species which has passed through a considerable population bottleneck but now thrives by virtue of ongoing conservation management despite the presence of a highly infectious disease. Identifying the ecological, environmental and genetic elements which define individual immunity offers the potential to predict the survival probability of juvenile individuals in a disease landscape thereby representing an exciting prospect for the field of conservation reintroduction biology. Interactions among indices of immune function are investigated at the individual level for Mauritius parakeets and also at the species level with the sympatrically occurring and non-native Indian ringneck parakeet (Psittacula krameri). Patterns of species-level genetic diversity of the Mauritius parakeet spanning two decades are examined and interspecies variation in immune function and genetic diversity is explored. Productivity and survival of Mauritius parakeets is summarised during and after a disease outbreak and an in depth analysis of the predictors of infection status and immunocompetence in this species is offered. This study highlights the complexity of the immune system and the challenges faced when trying to characterise it among individuals in an ecological context. I reveal a declining trend in species-level genetic diversity among Mauritius parakeets due to low natural dispersal demonstrating the importance of adaptively managing endangered species. I illustrate how, as a result of population bottlenecks or contrasting evolutionary histories that the Mauritius parakeet displays an attenuated immune function when compared to the Indian ringneck parakeet. I find no evidence to suggest that genetic diversity or inbreeding predicts disease infection in Mauritius parakeet nestlings and finally I use long-term monitoring data to cherry pick suitable individuals for reintroduction

Phylogeography of Panthera tigris in the mangrove forest of the Sundarbans

Tigers Panthera tigris in the Sundarbans represent the only population adapted to living in mangrove forest habitat. Several studies, based on limited morphological and genetic data, have described the population as being differentiated from the Bengal tiger subspecies P. tigris tigris. The phylogenetic ancestry of the Sundarbans population has also remained poorly understood. We generated 1263 bp of mtDNA sequences across 4 mtDNA genes for 33 tiger samples from the Bangladesh Sundarbans and compared these with 33 mtDNA haplotypes known from all subspecies of extant tigers. We detected 3 haplotypes within the Sundarbans tigers, of which one is unique to this population and the remaining 2 are shared with tiger populations inhabiting central Indian landscapes. Phylogenetic analyses using maximum likelihood and Bayesian inferences supported the Sundarbans tigers as being paraphyletic, indicating a close phylogenetic relationship with other populations of Bengal tigers, from which the Sundarbans population diverged around 26000 yr ago. Our phylogenetic analyses, together with evidence of ecological adaptation to the unique mangrove habitat, indicate that the Sundarbans population should be recognised as a separate management unit. We recommend that conservation management must focus on sustaining this representative tiger population adapted to mangrove habitat while at the same time recognising that trans-boundary conservation efforts through reintroduction or exchange of individuals, to enhance genetic diversity, might be needed in the future as a last resort for population recovery

Hygiene and biosecurity protocols reduce infection prevalence but do not improve fledging success in an endangered parrot

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

Assessing the assessments: evaluation of four impact assessment protocols for invasive alien species

Aim: Effective policy and management responses to the multiple threats posed by invasive alien species (IAS) rely on the ability to assess their impacts before conclusive empirical evidence is available. A plethora of different IAS risk and/or impact assessment protocols have been proposed, but it remains unclear whether, how and why the outcomes of such assessment protocols may differ. Location: Europe. Methods: Here, we present an in-depth evaluation and informed assessment of the consistency of four prominent protocols for assessing IAS impacts (EICAT, GISS, Harmonia and NNRA), using two non-native parrots in Europe: the widespread ring-necked parakeet (Psittacula krameri) and the rapidly spreading monk parakeet (Myiopsitta monachus). Results: Our findings show that the procedures used to assess impacts may influence assessment outcomes. We find that robust IAS prioritization can be obtained by assessing species based on their most severe documented impacts, as all protocols yield consistent outcomes across impact categories. Additive impact scoring offers complementary, more subtle information that may be especially relevant for guiding management decisions regarding already established invasive alien species. Such management decisions will also strongly benefit from consensus approaches that reduce disagreement between experts, fostering the uptake of scientific advice into policy-making decisions. Main conclusions: Invasive alien species assessments should take advantage of the capacity of consensus assessments to consolidate discussion and agreement between experts. Our results suggest that decision-makers could use the assessment protocol most fit for their purpose, on the condition they apply a precautionary approach by considering the most severe impacts only. We also recommend that screening for high-impact IAS should be performed on a more robust basis than current ad hoc practices, at least using the easiest assessment protocols and reporting confidence scores.This study is a joint effort from a workshop organized under COST European Cooperation in Science and Technology Actions Parrotnet (ES1304) and Alien Challenge (TD1209). We would also like to thank two anonymous referees for helpful comments on an earlier version of this manuscript. D.S is currently funded by a Marie Skłodowska‐Curie Action under the Horizon 2020 call (H2020‐MSCA‐IF‐2015, grant number 706318) and acknowledges the Danish National Research Foundation for support to the Center for Macroecology, Evolution and Climate (grant number DNRF96). J.C.S. was supported by funds from the Ministry of Economy and Competitivity, Spanish Research Council (CGL‐2016‐79568‐C3‐3‐P)

Tollington et al JAPPL2018_00567

Individual based data with variables of proportional supplemental food consumption, viral load and reproductive output

Data from: Quantifying the damage caused by fruit bats to backyard lychee trees in Mauritius and evaluating the benefits of protective netting

The Mauritius fruit bat (Pteropus niger) has been the subject of repeated culling campaigns, apparently in response to pressure from the fruit-growing industry concerned over damage to commercially valuable orchard crops such as lychees. More than 31,000 fruit-bearing lychee trees also exist in private backyards making this an issue pertinent to a wide cross-section of the Mauritian general public and not just those involved in commercial fruit production. The level of damage caused by bats to fruit crops is often debated and the low number of robust damage assessment studies hampers mitigation efforts. During the fruiting season of 2016/2017, we assessed the damage among backyard lychee trees attributable to fruit bats and other causes around Vacoas-Phoenix, Central Mauritius and evaluated the impact of using protective netting as a mitigation strategy. Fruit yield from panicles that were protected from depredation by nylon netting was approximately one third greater than that from unprotected panicles. We suspect that fruit bats were responsible for approximately 42% of the total damage but illustrate the difficulties in attributing damage to a single cause in such assessments. Although we demonstrate the value of protective netting we recognize that barriers to implementation exist and that a more holistic approach that incorporates crop protection, forest restoration strategies and addresses negative public attitudes towards bats in general is required to ensure the persistence of this endemic species

Quantifying the biodiversity value of repeatedly logged rainforests: gradient and comparative approaches from Borneo

There is substantial variation in the reported effects of logging on tropical forest fauna. In addition to inherent variation in disturbance sensitivity amongst taxa, another contributing factor is that most studies use comparative analyses of unlogged versus logged forests, which cannot fully account for heterogeneity in disturbance as well as underlying environmental gradients. To better understand how logging affects biodiversity we examined changes in bat assemblages across a disturbance gradient ranging from old growth to forest logged several times. In one of the first evaluations of repeatedly logged forest, we use both comparative and gradient analyses to reveal substantial signals in assemblage change in response to habitat alteration. Despite multiple rounds of extraction in the most degraded forest, neither approach revealed a definitive effect of logging on site-based richness. However, each approach generated insight into assemblage compositional responses to forest degradation. Structural differences were evident between old growth and repeatedly logged forest, and depauperate assemblages characterized degraded sites with low, open canopy. Ordinations identified species that best contributed to the signal of assemblage change, and also key associated forest structure variables. Models of trap-based abundance confirmed the importance of forest height in determining assemblage change, but also the role of tree cavity availability in supporting forest specialists, indicating that efforts to supplement this resource could aid restoration. Whilst highlighting the ecological importance of unlogged stands, we show that heavily degraded forests – even those that have been repeatedly logged – still hold some potential value for tropical biota, and could have a role in conservation

Making the EU legislation on invasive species a conservation success: invasive alien species policy in Europe

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

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

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