Biological, Earth and Environmental Sciences - Doctoral Theses

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Nurturing blue growth: enabling sustainable development of emerging marine sectors
(University College Cork, 2024) Giannoumis, Jessica; Wheeler, Andrew; Dooley, Lawrence; Cummins, Valerie
Current marine resource exploitation practices and management are unsustainable as resource degradation is ongoing and coastal regions struggle to realise sustainable development of marine resources. The key topic of this research is expanding knowledge on the reconciliation of environmental and economic models regarding the sustainable development of marine resources through the EU-introduced concept of blue growth. In the context of this research, blue growth refers to the sustainable development of marine resources, generating livelihoods, and securing well-being from innovation in emerging marine sectors. Blue growth development attracted interest across Europe and beyond, as the utilisation of marine resources is viewed as an opportunity to meet climate change obligations, enable a transition away from finite resources, and creating employment opportunities, thereby enabling long-term regional economic development. Blue growth development initially focused on the development of five emerging marine sectors with economic growth potential including coastal tourism, aquaculture, ocean renewable energy including offshore wind development, seabed mining, and marine biotechnology. Yet, EU coastal regions struggle with the realisation of blue growth as they received limited guidance from the European Commission on what blue growth is and what successful blue growth development looks like. This highlights a need to investigate what nurtures blue growth to enable coastal regions to realise their blue growth potential. This qualitative and interdisciplinary research focuses on the potential of blue growth in coastal regions focusing on the development of emerging marine sectors. In the context of this research, a region refers to coastal regions with common economic activities and characteristics, such as access to regionally specific marine resources, and common administrative characteristics such as specific political and governmental functions, e.g., regional economic development policies. Within the scope of this research, emerging sectors refer to rapidly growing industries utilising innovative technologies to enable sustainable development of regions, job creation, and technological advancement. This research investigates the manifestation and effectiveness of an EU intervention, the ProtoAtlantic project which includes regions of Orkney (SCT), Cork (IRE), Brest (FR), Porto (PT), and Las Palmas (SP) and two in-depth cases in Norway and Scotland. ProtoAtlantic was a Interreg Atlantic Area project, initially funded from November 2017 to October 2020, due to Covid-19, the project was extended to October 2021. The study harnessed an opportunity to engage with a wide range of multiple stakeholders representing stakeholders from government, industry, and academia. Data collection from the ProtoAtlantic cases included extensive desktop research and policy analysis of marine and generic development strategies in each case, analysis of regional blue growth stakeholder workshops which were carried out in each region, as well as analysis of additional material provided through the ProtoAtlantic project such as the outcomes of the ProtoAtlantic accelerator programme, and semi-structured interviews with nine regional stakeholders. The two deep dive cases included the offshore wind sector development around the DeepWind cluster in Scotland and the Norwegian aquaculture sector. Data collection from the in-depth cases included extensive desktop research and policy analysis of marine development strategies with particular focus on offshore wind development in Scotland and aquaculture development in Norway, in addition to 32 semi-structured interviews. To date, limited scientific attention has been paid to blue growth realisation from a marine governance perspective. Even less research has been undertaken to understand blue growth development from a business perspective. The research aim was to expand on how economic opportunities can catalyse sustainable development in a marine context. By achieving economic sustainability, coastal communities may consequently be in a better position to achieve environmental and social sustainability. The findings of this research address this research gap and provide practical contributions on how decisionmakers in coastal regions can nurture and realise their regional blue growth potential. In-depth analysis found that blue growth requires a systems approach which enables the integration of blue growth antecedents, this has been lacking from current marine management approaches. Furthermore, the study found that economic development approaches to marine resource management can secure well-being of coastal communities and ensure sustainable practices to marine resource utilisation. This research offers a modification of Ostrom’s Social-Ecological Systems framework, the expansions of the framework provide insight into collective action, the role of technology development, and the need for bespoke regional approaches to identify and realise blue growth. This research examines the role of regional stakeholders, the need for entrepreneurial activity and clustering activities in driving blue growth development and offers recommendations for policymakers and decisionmakers in coastal regions to nurture blue growth adoption and development. This research also presents a Practitioner’s Guide to Blue Growth which offers relevant questions to enable practitioners and intermediaries in the identification and realisation of their regional blue growth potential.
A multi-method approach to understanding the ecology of harbour porpoise in Irish waters
(University College Cork, 2023) Todd, Nicole R. E.; Jessopp, Mark John; Rogan, Emer; Kavanagh, Ailbhe; Irish Research Council
Small coastal cetaceans are often some of the most threatened species by anthropogenic and climate change impacts. Distribution and behavioural patterns can be difficult to determine for these wide-ranging, cryptic species that spend a limited amount of time at the surface, making direct observation difficult. Harbour porpoise (Phocoena phocoena phocoena, Linnaeus, 1758) is protected across European waters, listed under Annex II of the EU Habitats Directive, requiring Special Areas of Conservation (SAC) for their conservation. Despite its protected status, harbour porpoise are a relatively understudied species. It is therefore important to determine long-term habitat use patterns to ensure effective conservation is put in place. This research uses long-term passive acoustic monitoring (PAM) to increase our understanding of harbour porpoise habitat use in Irish waters. Firstly, feeding buzzes and spatial-orientation echolocation clicks of harbour porpoise were differentiated within a 9-year PAM dataset from northwest Ireland (Chapter 2). The spatio-temporal distribution of foraging behaviour was investigated using Generalized Additive Models (GAMs), at multiple temporal scales. The research identified clear interannual and seasonal variation, with peak foraging buzzes detected in autumn, as well as highlighting a negative impact of construction related activities in the area. A new PAM monitoring network was also established in an SAC designated for harbour porpoise in southwest Ireland, over a 3-year period. GAMs were used to examine harbour porpoise occurrence and foraging behaviour in relation to intra-site differences in habitat use and environmental variables (Chapter 5). Harbour porpoise were detected year-round within the SAC, with seasonal trends in occurrence and foraging behaviour observed, with peak detections in the late autumn and winter reflecting similar trends from Broadhaven Bay (Chapter 2). Clear preferences in habitat use were identified, with porpoise occurrence and foraging varying across small spatial scales, as well as across diel, tidal, and lunar cycles. This research also noted an overall decline in acoustic detections across the monitoring period, reflecting wider population trends in Irish waters that bears further investigation. An in-field comparison of a widely used PAM tool, the C-POD (Cetacean POrpoise Detector) with its recently developed successor the F-POD (Full waveform capture POD) was conducted, providing timely insights into the integration of this new equipment into acoustic monitoring programmes (Chapter 3). The F-POD recorded twice the amount of harbour porpoise detections compared to a co-deployed C-POD. GAMs highlighted similar patterns of harbour porpoise occurrence, however, in contrast to the F-POD, the C-POD failed to detect sufficient foraging rates to identify temporal trends in foraging behaviour. This work suggests that the switch to F-PODs will likely have minimal effect on our understanding of seasonal patterns of occurrence but may improve our understanding of foraging. Following on from this finding, an in-field playback experiment was conducted to determine the detection probability and effective detection radius/area (EDR/EDA) of three commonly used PAM devices, the C-POD, the F-POD, along with a continuous recording hydrophone (SoundTrap) (Chapter 4). The SoundTrap detected porpoise playbacks at the greatest distance, followed by the F-POD. The C-POD detection range was considerably less than the other two PAM devices. The type of harbour porpoise echolocation (spatial orientation clicks versus buzzes) was also found to influence the detection range, with clicks detected at a closer range across all devices. Understanding how this range of PAM devices compare provides valuable information to enable robust comparison of studies and inform appropriate planning of acoustic monitoring programmes. Collectively, the research has significantly enhanced our knowledge of acoustic monitoring methodologies and identified key harbour porpoise habitat use patterns. The findings can inform more effective conservation management of harbour porpoise at a national and international level. Additionally, this research contributes valuable insights to inform the designation of protected areas to cover important feeding habitats, and ensure targeted protections are put in place in the future.
The use of translocation as a conservation tool in the protection of dhub (Uromastyx aegyptia leptieni) against urbanisation in the Emirate of Dubai, United Arab Emirates
(University College Cork, 2023) O'Donovan, Declan; Ramsay, Ruth; O'Halloran, John
The UAE is described as hyperarid desert environment with mean maximum temperatures reaching 43.9 °C in July and mean minimum of 12.6 °C in January. It lies between 22°30’ and 26°10’N and 51° and 56°25’E. The Emirate of Dubai, the second largest Emirate in the United Arab Emirates is a fast-evolving metropolitan city that has changed from a small trading hub in the Arabian Gulf to an economy based on tourism and the provision of novel and luxurious experiences. Urbanisation pressures within Dubai, where almost 80% of the population now live in an urban setting, have increased dramatically over the last number of years. The resident population grew by over 173% in the 10 years to 2021 to approximately 3,478,300. To cater for residents and tourists alike, new roads, places to live and social and recreational activities have been developed and are being planned. As a result, previous areas of natural desert have been destroyed to make way for the continued development of the Emirate. It is imperative that procedures and protocols are put in place to protect the biodiversity of the affected lands. The current study was carried out between October 2014 and December 2017 with intermittent data collection of environmental data until December 2019. The primary focus was on two sites, Wadi Al Safa (WAS - N 25.088360° and E 55.282707°) and Mugatrah (MUG - N 24.812233° and E 55.248874°) within the Emirate of Dubai. The study looked at various factors affecting the survival of the spiny tailed lizard, Uromastyx aegyptia leptieni (dhub), one of the 72 species of herpetofauna considered native to the UAE. Dhub are a diurnal, fossorial species listed on Appendix II of CITES and listed as VU on the UAE National Red List of Herpetofauna. Using dhub as a flagship species should help to raise awareness about the fragility of the desert environment, the current threats faced by the dhub and other species, and to gather vital information that could aid in potential translocation efforts. Analysis of video data collected with CCTV cameras found that dhub are inherently a sedentary species, spending more than 80% of observed time below surface. When they did emerge, 14% of the emerged time was spent in sedentary behaviours, usually basking at the burrow or nearby on the gravel or a raised bush. The most active periods were in the spring and particularly March and April. During this time, dhub showed a unimodal burrow emergence pattern with a peak between 12:00 and 14:00. However, during the hottest months, dhub exhibited a bimodal activity pattern and usually went into their burrows between 11:00 and 13:00 before emerging and spending the majority of the time outside basking. The orientation of burrows revealed a distinct westerly direction, in contrast to previous research on dhub in Saudi Arabia where burrows predominantly faced southwest or southeast. In Israel, no specific orientation was identified. However, in the Wadi Al Safa site, there was a notable variation in orientation between seasons. The deployment of Radio Frequency Identification (RFID) traps showed that several different dhub could enter or leave the burrow throughout the day. The mean travel distance for all dhub over the study period (recorded as being the distance the animal moved from its first capture burrow to the furthest of the RFID traps), was similar at 128.8 m (SEM 11.0) for females and 113.0 m (SEM 10.4) for males. As the ultimate goal of the current study was to develop a mitigation translocation procedure for dhub, this information will allow field workers to decide on stocking densities of dhub, the number, spacing and dimensions of artificial or natural burrows to complete the translocation. In a desert environment, a species’ ability to use and avoid extreme temperatures is vital to its survival. Without knowing the range of temperatures, a dhub can tolerate, the ability to plan translocations is hindered. As such, the study also demonstrated, through the use of copper analogues, that the operative temperature Te (the environmental temperature range for the species) range was ± 19 °C (a low of 19 °C in Winter to a high of 38 °C in Summer). Internal burrow temperature data collected between June through to September showed the daily temperatures did not fall below 34.5 °C in June or rise above 37.5 °C. Foraging was the most active behaviour dhub engaged in with a mean time of 9:00 minutes for males and 6:00 minutes for females. There were a confirmed 8 forage plant species (all perennials) recorded across both sites while another 12 forage species were recorded which had been confirmed from other studies as forage plants. This indicates that there were sufficient forage resources for the dhub if grazing from larger herbivores such as camels, goats and gazelle species is controlled. The next most active behaviour was burrow cleaning with females spending less time (mean 1:35 ± SE=0:10 minutes) engaged in this than males (1:51 ± SE=0:15 minutes). Burrow cleaning was observed at some stage every day and was probably under-represented time wise in the data since the behaviour could not be observed once the dhub went sub-surface. A major part of any translocation is health monitoring. There were differences between the 25(OH)D levels across both sites, possibly due to overgrazing and exposure times to UV-B. If human levels of Vit D were used as the reference values, then 30% (N=7) of dhub in MUG in 2015 would be considered deficient (<25 nmol/L) and the remaining 70% (N=17) would be insufficient (<75 nmol/L ) and only 40% (N=19) of dhub from WAS would be considered to have a sufficient level. Vitamin D levels were slightly better in 2016, when 74% (N=47) of dhub sampled in WAS would be considered sufficient or higher, while 71% (N=21) of dhub in MUG would have been considered to have insufficient levels of Vit D3. Further studies on the correct levels of 25(OH)D in dhub blood need to be investigated especially as many reference intervals used in veterinary practice are determined from captive animals and may not reflect the wild situation. This study has shown how dhub can be successfully translocated if required. The study has also demonstrated what the consequences for the dub are if it is not done correctly. While large-scale translocations are theoretically feasible, careful consideration of various factors and insights gained from this study, such as dhub behaviour, potential travel distances, burrow orientation, vegetation needs for food and shelter, and health monitoring, is crucial. This comprehensive approach is essential to guarantee the success of any translocation project and subsequent enforced protection measures.
Lead toxicity in Mute swans: Cygnus olor (Gmelin)
(University College Cork, 1987) O'Halloran, John; Myers, A. A.
Lead toxicity in Mute swans Cygnus olor (Gmelin) was investigated. Two methods for the assessment of lead exposure were used: (1) blood lead level and (2) free red blood cell protoporphyrin. An accurate estimation of haemoglobin was found to be a prerequisite to determining lead exposure. A measurement of haemoglobin based on converting all haem species to alkaline haematin was found to give accurate and reproducible results. Variation in blood lead during the diel cycle in caged birds was investigated. Blood lead levels in a flock of Mute swans at a coarse-fish angling site were examined over a two year period. Forty-two percent of blood samples (n = 870) from this site were shown to have elevated lead. X-ray examination of swans revealed the source of contamination to be ingested lead pellets. Post mortem examination showed that 68% (n = 101) of all Mute swans examined died from lead poisoning. Two sources of lead were identified: spent gunshot and lost or discarded anglers' weights. Biochemical and haematological aspects of swan blood were also investigated. Reference haematological and biochemical values were established from 'normal' healthy Mute swans. These reference values were used as a baseline against which changes in lead poisoned birds could be measured. Moulting and immaturity were identified as causing natural variation, while acute lead poisoning was found to increase protoporphyrin, cholesterol and two serum enzymes: lactate dehydrogenase and aspartate amino transferase. Hypochromic anaemia was noted in swans suffering from acute lead poisoning. The possible role of lead in causing other sub-lethal effects, for example collisions, is also discussed.
Monitoring mammals in airfield environments; a case study of the Irish hare at Dublin Airport
(University College Cork, 2022) Ball, Samantha; Butler, Fidelma; Caravaggi, Anthony; Irish Research Council for Science, Engineering and Technology; Dublin Airport
The number of reported wildlife-aircraft collisions (i.e., strikes) with mammal species is increasing globally with severe consequences for passenger safety, industry economics and wildlife populations. Despite this, little research has been conducted on the class Mammalia in airfield environments, with strike mitigation research efforts predominantly focused on avian species. This thesis addresses some of the wildlife hazard issues faced by the aviation industry, specifically looking to mammal species. The thesis focuses on developing ecological survey methods for mammals in airfields and exploring the role of ecological data in informing strike risk. The Irish hare (Lepus timidus hibernicus) population at Dublin airport is used as a population case study to assess survey methods in an airport environment, throughout. As little is known about mammal strikes on a global scale, strike records with mammals from available literature and national aviation authorities are collated in chapter 1. These data highlighted that mammal strikes are widespread and identify 42 mammal families involved in strike events in 47 countries and demonstrate that reported mammal strike events have been increasing by up to 68% annually. Looking to mammal management measures on a European scale for chapter 2, the most successful mammal mitigation measures were identified as: (i) the management of watercourses within the airfield; (ii) the implementation of specific grass cutting regimes (94.4%) and (iii) the management of waste products at the airfield so as not to attract or sustain wildlife (93.8%). Utilising historical strike data in chapter 3, it was demonstrated that hare strikes have been increasing by an average of 14% annually at Dublin Airport with over 340 recorded wildlife strikes since 1997. The kinetic energy of such an event (10,576 J) is substantial enough to inflict damage to the landing gear of an aircraft, although this has never been reported to have occurred. As the basis of effective wildlife management practices necessitates reliable estimates of the population size, design and model-based distance sampling methods were compared, alongside Random Encounter Modelling, to establish ecological survey methods suitable for monitoring mammals in airfields for chapter 5. Population estimates ranged from 29 (SE ± 9) to 133 (SE ± 19) individuals, with the most robust model (nocturnal line transects), estimating a population size of 118 (SE ± 21) hares at Dublin Airport. A concern regarding mammal strike events is not only the strike event itself, but the secondary strike risk with a predatory or scavenger species. Camera trap surveys were utilised to identify secondary strike risk in chapter 4. It was identified that birds take an average of 2 hours and 23 minutes to detect a mammal carcass following a replicated strike event at Dublin Airport and an average of 11 hours 40 minutes for mammal species to detect a carcass. These data indicate that current clean-up practices at Dublin Airport (i.e., immediate clean-up and closing of the runway to facilitate clean-up operations) are likely adequate for reducing the likelihood of a secondary strike event. This thesis presents some of the first data collected through remote monitoring methods (camera traps/ GPS trackers) to inform of airside wildlife hazard. These methods, in addition to overlap analysis and cross correlation functions have demonstrated that recorded strike times are closely associated with hares’ circadian activity and largely dissociated with aircraft movements (chapter 6). Additionally, data collected via GPS tracking devices in chapter 7 demonstrated that the hares at Dublin Airport have an average home range size of 0.28 km2 (±SD 0.1 km2), based on 95% Kernal Density Utilisation Distribution. What’s more, it is demonstrated that the hares incorporate active area habitat types (i.e., runways and taxiways) into their home ranges with up to 13% of one individual’s movements incorporating these areas. These data have fed directly into the Wildlife Hazard Management Plan at Dublin Airport and instigated targeted strike mitigation measures. Throughout this thesis, the importance of ecological data for informing strike risk and mammal management in airfield environments is highlighted. While the Irish hare is used as a case study for ecological field methods in airfield environments, this thesis also broadly demonstrates the extent of mammal related issued at airfields worldwide. Thus, although here the focus is on a specific species at a specific airport, the developed methodologies are suitable for cohort of terrestrial mammals inhabiting airfield environments worldwide.

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