Biological, Earth and Environmental Sciences - Masters by Research Theses
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Item Assessment of the American crocodile (Crocodylus acutus) population in Ambergris caye, Belize(University College Cork, 2024) Ó Mórdha, Ciarán; Collins, Courtney; Ramsay, Ruth; Summers, Chris; Manzi, Christina; Crocodile Specialist Group; European Crocodile NetworkAmerican crocodiles (Crocodylus acutus) have the second largest global distribution of all extant crocodilians, ranging from South Florida through Hispaniola, Cuba, and Jamaica, along the Caribbean coast from southern Mexico to Venezuela, and along the Pacific coast from Mexico to Peru. The species is considered Vulnerable by the IUCN throughout its range, with habitat loss currently a major threat facing the species in parts of its range, including Belize. In Belize, C. acutus is found throughout the coastal zone. Ambergris caye, the country’s largest and most densely populated caye, is inhabited by C. acutus, but its present status there is poorly understood. The aim of this study was to address these data gaps by assessing the status and life history of C. acutus on Ambergris caye and comparing this information with that from other areas within the species’ range to inform the development of a local American crocodile management plan. During 19 nocturnal eyeshine surveys covering 171.5 km of shoreline on Ambergris caye carried out between May and September 2023, 199 American crocodiles were observed, an encounter rate of 1.16 crocodiles/km consisting of 22% adults, 10% subadults, 16% juveniles, 22% yearlings/hatchlings and 30% whose size class could not be determined. These results were similar to those of previous surveys carried out in 2010-2011, but with a higher encounter rate in 2023, suggesting a stable, if not slowly increasing, population. Crocodile nests were located by visiting previously identified nest sites, conducting additional surveys by boat and drone, and utilising social media to investigate reports of nesting activity by residents. A total 9 nests were found during the study. More than half (56%) of these were concentrated along the sand banks adjacent to the caye’s three sewage treatment ponds. Utilizing the 13 years of crocodile capture data (n=865) collected by ACES Wildlife Rescue in Ambergris caye, this study investigated growth rates, morphometrics, and sexual size dimorphism of the local crocodile population. Analysis revealed the growth rate (total length [TL]) of 115 crocodiles averaged 0.045 ± 0.027 cm/day. The growth rates found in adults differed by sex, with females (n=20) exhibiting a slightly lower average growth rate (0.039 ± 0.028 cm/day) compared to males (n=47) (0.048 ± 0.028 cm/day); however, the difference was not statistically significant. Notably, as total length (TL) increased with age, growth rates slowed more significantly in females than in males, with no significant relationship observed between TL and growth rates in males. Morphometric analysis encompassed 332 juveniles (TL<120cm), 25 female sub-adults (120≤ TL<180 cm), 31 male sub-adults (120≤ TL<180 cm), 40 female adults (TL≥180 cm) and 62 male adults (TL≥180 cm). Allometric relationships between TL and dorscal cranial length (DCL), snout length (SL), snout vent length anterior (SVLa) and snout vent length posterior (SVLp) revealed both positive and negative associations, all of which followed linear regressions. The dorsal cranial length to cranial width ratio (DCL: CW) of 2.7 to 4.2 indicates a broad-snouted skull morphotype akin to that observed in other island populations of C. acutus in the Yucatan region. The sexual dimorphism index of 1.07 toward males suggests a relatively minor disparity between the TL of males and females on Ambergris caye, indicating less pronounced sexual dimorphism compared to other populations of C. acutus. The sex ratio 2.39(M):1.0(F) was biased towards males. While Ambergris caye, likely the most human-populated caye in Belize, faces increasing development, pollution, and human-crocodile interactions, it may harbor one of the largest and most stable American crocodile populations in the country. The encounter rate of 1.16 on Ambergris caye is notably higher than that reported for nearby Turneffe atoll (0.34 in 2009) and the Belizean cayes overall (0.43 in 2000), suggesting this population is among the most robust in Belize. However, the study’s findings indicate that insufficient nesting habitat could pose a risk to the long-term stability of the population if not addressed through targeted conservation efforts. To mitigate this risk, it is imperative to conduct annual surveys to ascertain long-term population trends. Additionally, implementing protective measures for nests and intensifying surveys within the Bacalar Chico National Park and Marine Reserve to investigate nesting activity are vital steps in formulating a robust species management plan. Addressing these research gaps will not only enhance our understanding of the ecology of C. acutus in Belize but also inform targeted conservation efforts essential for safeguarding this population's viability and ecological role in the region.Item Exploring the application of eDNA for intraspecific studies of the Shannon bottlenose dolphins (Tursiops truncatus Montagu, 1821): a preliminary study(University College Cork, 2024) McKee, Jack; Rogan, Emer; Mirimin, Luca; Biodiversa+; Environmental Protection Agency; National Parks and Wildlife ServiceWith the recent advancements in molecular technologies, environmental DNA (eDNA) has become an especially useful tool for biodiversity monitoring. More recently, eDNA has been investigated as a tool to obtain fine scale molecular information such as individuals’ mitochondrial DNA (mtDNA) haplotypes. This study examines the capabilities of eDNA in enhancing our understanding and monitoring of the well-studied Shannon Estuary bottlenose dolphin (Tursiops truncatus) population. Water samples taken from the fluke print of dolphins were filtered using two different filter types Sterivex (~1.5L) and Waterra (~50L) species-specific qPCR was used to detect bottlenose dolphins’ eDNA, as well as conventional PCR to amplify a 543bp haplotype region to identify known haplotypes from eDNA samples. These same water samples were also used for a metabarcoding analysis of fish species in an attempt to better understand potential prey species. Bottlenose dolphin eDNA was successfully detected in 44% of the samples using Sterivex filers and 61% using Waterra filters. The two haplotypes known from the Shannon estuary population (Ire1 and 2) were also successfully identified using Dlp1.5 and Dlp8G primers, and putative fish prey species were successfully obtained by both filter methodologies. The effectiveness of both sample acquisition approaches was compared and their implementation in further eDNA studies considered. The results of this study add to the evidence that eDNA is a promising non-invasive method for monitoring both presence/absence and genetic diversity of bottlenose dolphins.Item Assessment of the effectiveness of SuperFifty® Prime in preventing cold stress in pepper (Capsicum annuum cv. Kurtovska Kapija)(University College Cork, 2024) Mahony, Cian; Henriques, Rossana; Jansen, Marcel A. K.; BioAtlantisThe occurrence of abiotic stress is becoming increasingly common as climate change progresses, and this poses a major challenge for agriculture. Plant Biostimulants are a new form of abiotic stress management which induces the plants natural defence systems in a process known as “molecular priming”. SuperFifty® Prime is a highly concentrated A. nodosum extract (500g/L) which has been proven to mitigate the detrimental effects of different abiotic stressors. Peppers were chosen for this experiment (Capsicum annuum) as they are a commercially important crop with an extremely low tolerance to cold conditions. In this project we aimed to investigate how a priming and recovery application of SuperFifty® Prime on a cold sensitive crop helped avoid and mitigate the damage caused by cold and uncover the molecular mechanisms behind this protection. At the physiological level, the results showed that two applications of SuperFifty® Prime improved plant performance as demonstrated by monitoring the following parameters: fresh weight, electrolyte leakage, chlorophyll content, flavonoid content and the occurrence of necrotic tissue. The application of SuperFifty® Prime also improved plant recovery after the cold stress event. At final harvest, there was no significant difference in yield parameters between Primed Cold-Treated and Unprimed Untreated plants. At the molecular level, five genes of interest were selected. Three of these genes; ICE 1, CBF 1 and COR 314, are part of most studied cold signalling pathway known as the ICE-CBF-COR transcriptional cascade. The two other selected genes; PAL 1 and CHS 1, are important for flavonoid production. A similar pattern of expression was observed for all five genes with a clear difference between Primed and Unprimed Cold-Treated plants. Expression of ICE 1 and COR 314 are also upregulated in Primed Untreated plants, despite these plants not experiencing cold stress inducing conditions. Based on the evidence from this experiment, two applications of SuperFifty® Prime improved yield and productivity in Primed Cold- Treated plants and has the potential to improve grower incomes in areas affected by cold stress.Item The influence of community-defined land use plans and de facto land use practices on the relative abundance and distribution of large wild mammals in a community-based Wildlife Management Area in southern Tanzania(University College Cork, 2023) Duggan, Lily; Killeen, Gerry; Butler, Fidelma; Mombo, Felister; AXA Research FundThis study investigates the relationship between community-defined land use plans and de facto land use practices, and the influence of the latter on the relative abundance and distribution of large wild mammals in a community-based Wildlife Management Area (WMA) adjacent to Nyerere National Park (NNP) in southern Tanzania. The WMA model represents a relatively new approach to community-based conservation in Tanzania, in which local villages set aside part of their land for wildlife conservation and manage that resource collectively, so that their stakeholder communities can leverage economic and social benefits from income-generating activities like tourism. The Ifakara-Lupiro-Mangula (ILUMA) WMA acts as a key buffer zone between the fully domesticated habitats of the villages to the north and west, and Nyerere National Park to the east. All observed signs of wildlife and human activity were recorded across 32 locations inside ILUMA and in the permanent settlements and national park that border it to the west and east, respectively. For the great majority of wild mammal species, surveys around water bodies within a 2km radius of suitable camping locations proved more sensitive than those along transects between them. The latter transect surveys were only more sensitive for Sable and Spotted Hyena, which are known to routinely commute considerable distances across their home ranges, and for Greater Kudu that seldom drink surface water. Across much of ILUMA WMA, in areas where agreed land use plans were not adhered to, rampant cattle herding and land clearing for cultivation of rice and other tillage crops were associated with reductions in wildlife richness and biodiversity, as well as overall ecosystem integrity. Many unauthorised human activities were recorded inside ILUMA, such as livestock herding, charcoal burning and agriculture, and, where they occur at a high density, wildlife populations are negatively affected. Although all these activities impact wildlife to some degree, cattle herding had the most severe negative effect on wildlife (Species Richness, P=0.002, Simpson’s Index of Diversity, P=0.0022) and ecosystem integrity (P <<0.0001). Nevertheless, several well-managed authorised human settlements within the WMA, where fishing is the primary authorised livelihood, support thriving wildlife populations and pristine land cover, so human settlement per se was not found to be associated with reductions of any of these composite indices (P≥0.4532), except for the novel subjective natural ecosystem integrity index (P=0.0256). Correspondingly, the best conserved parts of the WMA were those closest to the national park to the east and the fishing villages to the north, where compliance with agreed land use plans is highest. Overall, this study illustrates how well-managed WMAs can host resident local communities undertaking selective and appropriately regulated natural resource extraction activities, while maintaining a rich and diverse local wildlife population and acting as an effective buffer zone between fully domesticated areas of human habitation and pristine environments such as national parks. Furthermore, this study also developed and evaluated a novel method for synthesizing consensus subjective impressions of the investigators and intuitively expressing them in semi-quantitative format as a readily interpreted subjective natural ecosystem integrity index that accounts for all aspects of land use, wildlife and human activities. Crucially, however, this alternative to statistical syntheses of extensive, formally collected survey data is intuitively accessible to all manner of stakeholders, including relevant communities, and should be far better suited to routine programmatic monitoring through participatory approaches.Item Blood host preferences and competitive inter-species dynamics within an African malaria vector species complex inferred from signs of animal activity around aquatic larval habitats distributed across a gradient of fully domesticated to fully pristine ecosystems in southern Tanzania(University College Cork, 2023) Walsh, Katrina; Killeen, Gerard; Butler, Fidelma; Kaindoa, Emmanuel; AXA Research Fund; University College CorkThe effectiveness of current first-choice vector control interventions on the semi-zoophagic vector Anopheles arabiensis are limited, among other things, by insecticide resistance and their ability to acquire non-human bloodmeals. Across much of southern Tanzania, in areas where humans and cattle are readily available, it is the predominant member sibling species of the Anopheles gambiae complex. However, little is known about its population dynamics or blood utilization behaviours in pristine natural ecosystems, where these known preferred hosts are scarce or completely absent. This study investigated larval habitat occupancy and species composition of the An. gambiae complex, together with the availability of various potential mammalian blood host species, across a gradient of fully domesticated to fully pristine ecosystems in southern Tanzania. Potential aquatic habitats were surveyed at 40 locations encompassing permanent human settlements, a community-owned Wildlife Management Area with varying degrees of human activity, and Nyerere National Park (NNP), which had very little. To investigate the effects of potential host availability on the species composition of the complex, all direct observations, tracks and signs of humans, livestock and wild animals observed around the surveyed larval habitats were recorded in parallel. The resulting data were analysed by logistic regression using generalized linear mixed models. Odds of habitat occupancy by An. gambiae complex larvae decreased by 62% (P<0.0001) across the full range of natural ecosystem integrities observed, from fully domesticated to completely pristine areas, suggesting that the availability of suitable blood hosts had a modest effect on overall habitat utilization by this taxon. However, while only An. arabiensis, a key vector of residual malaria transmission, was found in fully domesticated ecosystems, its non-vector sibling species An. quadriannulatus also occurred in conserved areas and dominated the most pristine natural ecosystems. The proportion of An. arabiensis versus An. quadriannulatus was positively associated with the number of times humans and/or cattle (P=0.0007) were detected at a location and negatively associated with distance inside NNP and away from human settlements (P<0.0001). Nevertheless, An. arabiensis was found even in absolute pristine environments that were >40km away from any signs of human or livestock, suggesting this species can survive on blood from one or more wild animal species. High proportions of An. quadriannulatus inside NNP were positively associated with the number of times impala were detected (P<0.0001), suggesting they may be a preferred blood source for this non-vector, giving it a competitive advantage over An. arabiensis where this antelope is abundant. Despite being detected less frequently, bushpig were also positively associated with high proportions of An. quadriannulatus, suggesting they provide a second preferred blood source, particularly in the miombo woodlands of the buffer zone where impala were scarce. Overall, it seems that the availability of preferred hosts influences the competitive balance between these sibling species and that refugia populations of An. arabiensis can persist in wild areas, thus presenting both challenges and opportunities for control interventions: While such refuge populations deep inside pristine conservation area may confound attempts to repeat historical successes with eliminating this species from areas outside its natural range, it may also constitute a reservoir of diverse, unselected genomes with original wild-type insecticide susceptibility traits that could repopulate areas around human settlements that had otherwise been considered lost from the natural gene pool.