Biological, Earth and Environmental Sciences

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Accelerating animal energetics: High dive costs in a small seabird disrupt the dynamic body acceleration - energy expenditure relationship
(The Company of Biologists, 2022-05-20) Ste Marie, Eric; Grémillet, David; Fort, Jérôme; Patterson, Allison; Brisson-Curadeau, Émile; Clairbaux, Manon; Perret, Samuel; Speakman, John; Elliott, Kyle H.; Conseil National de la Recherche Scientifique; Institut Polaire Français Paul Emile Victor; Agence Nationale de la Recherche; Natural Sciences and Engineering Research Council of Canada; Government of Canada
Accelerometry has been widely used to estimate energy expenditure in a broad array of terrestrial and aquatic species. However, a recent reappraisal of the method showed that relationships between dynamic body acceleration (DBA) and energy expenditure weaken as the proportion of non-mechanical costs increase. Aquatic air breathing species often exemplify this pattern, as buoyancy, thermoregulation and other physiological mechanisms disproportionately affect oxygen consumption during dives. Combining biologging with the doubly-labelled water method, we simultaneously recorded daily energy expenditure (DEE) and triaxial acceleration in one of the world's smallest wing-propelled breath-hold divers, the dovekie (Alle alle). These data were used to estimate the activity-specific costs of flying and diving and to test whether overall dynamic body acceleration (ODBA) is a reliable predictor of DEE in this abundant seabird. Average DEE for chick-rearing dovekies was 604±119 kJ/d across both sampling years. Despite recording lower stroke frequencies for diving than for flying (in line with allometric predictions for auks), dive costs were estimated to surpass flight costs in our sample of birds (flying: 7.24, diving: 9.37 X BMR). As expected, ODBA was not an effective predictor of DEE in this species. However, accelerometer-derived time budgets did accurately estimate DEE in dovekies. This work represents an empirical example of how the apparent energetic costs of buoyancy and thermoregulation limit the effectiveness of ODBA as the sole predictor of overall energy expenditure in small shallow-diving endotherms.
Acoustic activity across a seabird colony reflects patterns of within-colony flight rather than nest density
(Wiley, 2019-05-18) Arneill, Gavin E.; Critchley, Emma Jane; Wischnewski, Saskia; Jessopp, Mark J.; Quinn, John L.; Department of Culture, Heritage and the Gaeltacht; Petroleum Infrastructure Programme, PIP, Ireland
Passive acoustic monitoring is increasingly being used as a cost‐effective way to study wildlife populations, especially those that are difficult to census using conventional methods. Burrow‐nesting seabirds are among the most threatened birds globally, but they are also one of the most challenging taxa to census, making them prime candidates for research into such automated monitoring platforms. Passive acoustic monitoring has the potential to determine presence/absence or quantify burrow‐nesting populations, but its effectiveness remains unclear. We compared passive acoustic monitoring, tape‐playbacks and GPS tracking data to investigate the ability of passive acoustic monitoring to capture unbiased estimates of within‐colony variation in nest density for the Manx Shearwater Puffinus puffinus. Variation in acoustic activity across 12 study plots on an island colony was examined in relation to burrow density and environmental factors across 2 years. As predicted fewer calls were recorded when wind speed was high, and on moon‐lit nights, but there was no correlation between acoustic activity and the density of breeding birds within the plots as determined by tape‐playback surveys. Instead, acoustic indices correlated positively with spatial variation in the in‐colony flight activity of breeding individuals detected by GPS. Although passive acoustic monitoring has enormous potential in avian conservation, our results highlight the importance of understanding behaviour when using passive acoustic monitoring to estimate density and distribution.
Acoustic behaviour, ecology and social structure of bottlenose dolphins (Tursiops truncatus, Montagu 1821) in the North Atlantic
(University College Cork, 2014) Englund, Anneli; Rogan, Emer; Ingram, Simon N.; Irish Research Council for Science Engineering and Technology; National Parks and Wildlife Service, Ireland; Zoology, Ecology and Plant Science, College of Science, Engineering and Food Science, University College Cork
Communication is important for social and other behavioural interactions in most marine mammal species. The bottlenose dolphin (Tursiops truncatus, Montagu, 1821) is a highly social species that use whistles as communication calls to express identity and to initiate and maintain contact between socially interactive individuals. In this thesis, the degree of variability in whistle behaviour and whistle characteristics was examined between different habitats on a range of spatial scales. The whistle characteristics that best discriminated between different communities were investigated, along with exploration of whistle variation in relation to habitat type, levels of social interaction and relatedness. Finally, the use and variability of individually distinctive calls (signature whistles) within and between Irish and US waters were also examined. Relatively high levels of whistle variation were found within a genetically and socially isolated population of dolphins in the Shannon Estuary, reflecting the need for individual identification and distinctive whistles in a population with long term site fidelity and high levels of social cohesion. Variation between reproductively separate communities in Irish waters was relatively small except between animals in inshore compared with continental shelf waters. The greatest differences in whistle structure overall were evident between dolphins using inshore and offshore US waters, likely reflecting social isolation of the two distinct ecotypes that occur in these waters but also variation in behaviour or habitat conditions. Variation found among inshore communities in US waters reflected similarities in habitat use and levels of social interaction. These findings suggest that vocal variation is socially mediated, behaviourally maintained and dependent on levels of social contact between individuals. The findings contribute to our understanding of the interaction of factors influencing vocalisation behaviour in this behaviourally complex and ecologically plastic species.
Adaptive responses of animals to climate change are most likely insufficient
(Nature Publishing Group, 2019-07-23) Radchuk, Viktoriia; Reed, Thomas E.; Teplitsky, Céline; van de Pol, Martijn; Charmantier, Anne; Hassall, Christopher; Adamík, Peter; Adriaensen, Frank; Ahola, Markus P.; Arcese, Peter; Miguel Avilés, Jesús; Balbontin, Javier; Berg, Karl S.; Borras, Antoni; Burthe, Sarah; Clobert, Jean; Dehnhard, Nina; de Lope, Florentino; Dhondt, André A.; Dingemanse, Niels J.; Doi, Hideyuki; Eeva, Tapio; Fickel, Joerns; Filella, Iolanda; Fossøy, Frode; Goodenough, Anne E.; Hall, Stephen J. G.; Hansson, Bengt; Harris, Michael; Hasselquist, Dennis; Hickler, Thomas; Joshi, Jasmin; Kharouba, Heather; Martínez, Juan Gabriel; Mihoub, Jean-Baptiste; Mills, James A.; Molina-Morales, Mercedes; Moksnes, Arne; Ozgul, Arpat; Parejo, Deseada; Pilard, Philippe; Poisbleau, Maud; Rousset, Francois; Rödel, Mark-Oliver; Scott, David; Senar, Juan Carlos; Stefanescu, Constanti; Stokke, Bård G.; Kusano, Tamotsu; Tarka, Maja; Tarwater, Corey E.; Thonicke, Kirsten; Thorley, Jack; Wilting, Andreas; Tryjanowski, Piotr; Merilä, Juha; Sheldon, Ben C.; Pape Møller, Anders; Matthysen, Erik; Janzen, Fredric; Dobson, F. Stephen; Visser, Marcel E.; Beissinger, Steven R.; Courtiol, Alexandre; Kramer-Schadt, Stephanie; European Research Council; Ministry of Economy and Competitivity; Svenska Forskningsrådet Formas; Consejo Superior de Investigaciones Científicas; National Science Foundation; Academy of Finland; U.S. Department of Energy
Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.
Adaptive strategies of sponges to deoxygenated oceans
(John Wiley & Sons, Inc., 2021-12-01) Micaroni, Valerio; Strano, Francesca; McAllen, Rob; Woods, Lisa; Turner, John; Harman, Luke; Bell, James J.; National Parks and Wildlife Service
Ocean deoxygenation is one of the major consequences of climate change. In coastal waters, this process can be exacerbated by eutrophication, which is contributing to an alarming increase in the so-called ‘dead zones’ globally. Despite its severity, the effect of reduced dissolved oxygen has only been studied for a very limited number of organisms, compared to other climate change impacts such as ocean acidification and warming. Here, we experimentally assessed the response of sponges to moderate and severe simulated hypoxic events. We ran three laboratory experiments on four species from two different temperate oceans (NE Atlantic and SW Pacific). Sponges were exposed to a total of five hypoxic treatments, with increasing severity (3.3, 1.6, 0.5, 0.4 and 0.13 mg O2 L−1, over 7–12-days). We found that sponges are generally very tolerant of hypoxia. All the sponges survived in the experimental conditions, except Polymastia crocea, which showed significant mortality at the lowest oxygen concentration (0.13 mg O2 L−1, lethal median time: 286 h). In all species except Suberites carnosus, hypoxic conditions do not significantly affect respiration rate down to 0.4 mg O2 L−1, showing that sponges can uptake oxygen at very low concentrations in the surrounding environment. Importantly, sponges displayed species-specific phenotypic modifications in response to the hypoxic treatments, including physiological, morphological and behavioural changes. This phenotypic plasticity likely represents an adaptive strategy to live in reduced or low oxygen water. Our results also show that a single sponge species (i.e., Suberites australiensis) can display different strategies at different oxygen concentrations. Compared to other sessile organisms, sponges generally showed higher tolerance to hypoxia, suggesting that sponges could be favoured and survive in future deoxygenated oceans.
Age-dependent effects of moderate differences in environmental predictability forecasted by climate change, experimental evidence from a short-lived lizard (Zootoca vivipara)
(Springer Nature, 2019-10-29) Masó, G.; Kaufmann, Joshka; Clavero, H.; Fitze, P. S.; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; Spanish Ministry of Education and Science
Whether and how differences in environmental predictability affect life-history traits is controversial and may depend on mean environmental conditions. Solid evidence for effects of environmental predictability are lacking and thus, the consequences of the currently observed and forecasted climate-change induced reduction of precipitation predictability are largely unknown. Here we experimentally tested whether and how changes in the predictability of precipitation affect growth, reproduction, and survival of common lizard Zootoca vivipara. Precipitation predictability affected all three age classes. While adults were able to compensate the treatment effects, yearlings and juvenile females were not able to compensate negative effects of less predictable precipitation on growth and body condition, respectively. Differences among the age-classes’ response reflect differences (among age-classes) in the sensitivity to environmental predictability. Moreover, effects of environmental predictability depended on mean environmental conditions. This indicates that integrating differences in environmental sensitivity, and changes in averages and the predictability of climatic variables will be key to understand whether species are able to cope with the current climatic change.
Aggregate potential of Irish south coast offshore palaeovalleys
(University College Cork, 2021-04-28) O'Mahony, Evan; Wheeler, Andrew; Lim, Aaron; Science Foundation Ireland; Petroleum Infrastructure Programme (PIP)
The southern shelf of offshore Ireland possesses many developed marine based resources such as hydrocarbons and commercial fisheries. Increasing knowledge of the seabed and the processes that cause large scale variation to the morphology and sedimentology is crucial in determining marine aggregate resource potential on the south coast. Qualitative data was processed using a multiproxy geophysical and sedimentological approach, creating detailed seabed maps using bathymetric data supported by ground truthing sedimentsamples. Surficial sediment deposits display a close fit to industry standard aggregates but considerable temporal variance at depth from vibrocore analysis shows variable marine reworking over time. Marine processes off the south coast diminish the aggregate quality of reworked fluvio-glacial deposits as evidence of increased marine reworking causes the replacement of favorable coarse-grained deposits with shell fragments. The southern shelf, at depth shows potential for marine aggregate exploration but variance within the extractable near surface deposits deems it too variable and accurate prediction of areas with high aggregate yield is diminished.
Agrobacterium mediated CRISPR Cas9 genetic engineering of Solanum tuberosum
(University College Cork, 2020) Barrett, Dylan; Doyle Prestwich, Barbara; Lettice, Eoin
Global populations are continuing to rise and so too does the strain on the food production and agriculture industry. We are constantly in pursuit of new sustainable ways to feed the ever-increasing population. Genetic engineering of crop plants may prove to be a crucial tool in providing healthy sustainable food sources. The main aim of the project was to create an INDEL in The Rhamnose:beta-solanine/beta-chaconine rhamnosyltransferase (SGT3) gene region in Solanum tuberosum using Agrobacterium mediated CRISPR Cas9 genetic engineering. Sterol glycoside transferase (SGT) genes are involved in the biosynthetic pathway of glycoalkaloids in potatoes. This is a food safety issue which can result in reduced yields. In addition, the goal was to investigate the role of pre-transformation treatments on transformation efficiency. To that end, the effects of different wavelengths of light produced by light-emitting diodes on potatoes were examined in order to design a pre-transformation treatment. Red light and combinations of red and blue light were shown to have a significant positive impact on plant growth rate. Eight bacterial isolates from the soil rhizosphere were successfully isolated, identified and the volatile organic compounds produced by these bacterial isolates were measured in order to design a pre-transformation treatment. Six of the isolates were shown to produce known growth promoters through gas-chromatography mass-spectrometry and four of the isolates had a significant positive impact on plant growth rate in co-cultivation experiments. The role of heat shock treatment in transformation efficiency was also investigated. LED treatment with red-blue light (ratio of 3:1) and heat shock treatments were shown to increase Agrobacterium transformation efficiency in gus histochemical staining experiments. Finally, this project aimed to design guide RNA to target the SGT3 gene and transform Agrobacterium with the CRISPR vectors in order to successfully create a knockout in Solanum tuberosum. Three guide RNAs to target the SGT3 DNA were successfully designed and validated using an in vitro cleavage of SGT3 DNA by CRISPR/Cas9 ribonucleoprotein complex, however, it is unclear whether an in vivo knockout has been created due to the activity of the Agrobacterium-mediated CRISPR Cas9 transformation.
Allometric analysis sheds light on the systematics and ontogeny of anurognathid pterosaurs
(Taylor & Francis, 2022-03-03) Yang, Zixiao; Benton, Michael J.; Hone, David W. E.; Xu, Xing; McNamara, Maria E.; Jiang, Baoyu; National Natural Science Foundation of China; Chinese Academy of Sciences; China Scholarship Council; Nanjing University
Anurognathids are a clade of non-pterodactyloid pterosaurs with generally conservative morphology, but specializations as insectivores. They are represented by a disparate collection of adult and juvenile specimens that range in wingspan from ∼0.24–1 m. There have been concerns about the extent to which ontogenetic variation might affect phylogenetic inference, and indeed how aspects of their ontogeny might relate to the distinctive anurognathid adult morphology. Here we perform allometric analysis on 23 key skeletal dimensions in 13 anurognathid specimens. Our results show that all anurognathids share a common growth trajectory in most dimensions, and that ontogeny affects variation in a minority of characters commonly used in phylogenetic analysis. Excluding these ontogeny-related characters, a new taxon, Cascocauda rong gen. et sp. nov., is established. Based on the ontogenetically corrected dataset, our phylogenetic analysis supports Anurognathidae as the sister-group of Breviquartossa and reveals a general trend of tail reduction in the clade. Allometric growth suggests the anurognathid lifestyle remained consistent throughout ontogeny, maintaining a highly maneuverable flight style by near-isometric development in the wing, small prey (i.e., insects), by strong negative allometry in the skull, and an arboreal habit by strong positive allometry in the claws. This specialized lifestyle suggests retention of plesiomorphic juvenile traits into later ontogeny and facilitated morphological stasis by stabilizing selection during over 40 million years of evolution in the group.
Alternative migratory tactics in brown trout (Salmo trutta) are underpinned by divergent regulation of metabolic but not neurological genes
(Wiley, 2021-06-02) Wynne, Robert; Archer, Louise C.; Hutton, Stephen A.; Harman, Luke; Gargan, Patrick; Moran, Peter A.; Dillane, Eileen; Coughlan, Jamie; Cross, Thomas F.; McGinnity, Philip; Colgan, Thomas J.; Reed, Thomas E.; Horizon 2020; European Research Council; Science Foundation Ireland; Marine Institute, Ireland; Government of Ireland
The occurrence of alternative morphs within populations is common, but the underlying molecular mechanisms remain poorly understood. Many animals, for example, exhibit facultative migration, where two or more alternative migratory tactics (AMTs) coexist within populations. In certain salmonid species, some individuals remain in natal rivers all their lives, while others (in particular, females) migrate to sea for a period of marine growth. Here, we performed transcriptional profiling (“RNA-seq”) of the brain and liver of male and female brown trout to understand the genes and processes that differentiate between migratory and residency morphs (AMT-associated genes) and how they may differ in expression between the sexes. We found tissue-specific differences with a greater number of genes expressed differentially in the liver (n = 867 genes) compared with the brain (n = 10) between the morphs. Genes with increased expression in resident livers were enriched for Gene Ontology terms associated with metabolic processes, highlighting key molecular–genetic pathways underlying the energetic requirements associated with divergent migratory tactics. In contrast, smolt-biased genes were enriched for biological processes such as response to cytokines, suggestive of possible immune function differences between smolts and residents. Finally, we identified evidence of sex-biased gene expression for AMT-associated genes in the liver (n = 12) but not the brain. Collectively, our results provide insights into tissue-specific gene expression underlying the production of alternative life histories within and between the sexes, and point toward a key role for metabolic processes in the liver in mediating divergent physiological trajectories of migrants versus residents.
Amplicon sequencing of 42 nuclear loci supports directional gene flow between South Pacific populations of a hydrothermal vent limpet
(John Wiley and Sons Ltd, 2019-05-06) Plouviez, Sophie; LaBella, Abigail Leavitt; Weisrock, David W.; von Meijenfeldt, F. A. Bastiaan; Ball, Bernard; Neigel, Joseph E.; Van Dover, Cindy L.; National Science Foundation; Nautilus Minerals, Inc.; Duke University; Schure‐Beijerinck‐Popping Fonds; Royal Dutch Academy of Arts and Sciences
In the past few decades, population genetics and phylogeographic studies have improved our knowledge of connectivity and population demography in marine environments. Studies of deep‐sea hydrothermal vent populations have identified barriers to gene flow, hybrid zones, and demographic events, such as historical population expansions and contractions. These deep‐sea studies, however, used few loci, which limit the amount of information they provided for coalescent analysis and thus our ability to confidently test complex population dynamics scenarios. In this study, we investigated population structure, demographic history, and gene flow directionality among four Western Pacific hydrothermal vent populations of the vent limpet Lepetodrilus aff. schrolli. These vent sites are located in the Manus and Lau back‐arc basins, currently of great interest for deep‐sea mineral extraction. A total of 42 loci were sequenced from each individual using high‐throughput amplicon sequencing. Amplicon sequences were analyzed using both genetic variant clustering methods and evolutionary coalescent approaches. Like most previously investigated vent species in the South Pacific, L. aff. schrolli showed no genetic structure within basins but significant differentiation between basins. We inferred significant directional gene flow from Manus Basin to Lau Basin, with low to no gene flow in the opposite direction. This study is one of the very few marine population studies using >10 loci for coalescent analysis and serves as a guide for future marine population studies.
Anadromy in brown trout (Salmo trutta): A review of the relative roles of genes and environmental factors and the implications for management and conservation
(Troubador Publishing Ltd., 2016-10) Ferguson, Andy; Reed, Thomas E.; McGinnity, Philip; Prodöhl, Paolo A.; Harris, Graham; European Research Council; Horizon 2020
While many brown trout (Salmo trutta) populations spend their entire life cycle in freshwater, especially as river-lake migrants or river residents, others show facultative anadromy. That is, some trout migrate to sea while other individuals of the same population remain within their natal river. Sea trout can give rise to resident offspring and vice versa, although there is a strong tendency to track the parental life history. Anadromy delivers better feeding and thus larger size, which results in higher fecundity in females, enhanced mate choice, and other reproductive benefits. River residence, more prevalent in males as anadromy conveys fewer benefits, can give higher survival and avoids the energy expenditure required by anadromy. Overall, the costs and benefits of anadromy versus residency, measured in terms of survival and reproduction, are finely balanced and small changes to the cost-benefit equation can lead to evolutionary changes in life history. The decision to be anadromous or resident is a quantitative threshold trait, controlled by multiple genes and environmental factors. The dichotomous nature of the trait is postulated to be the result of the environmentally influenced physiological condition (e.g. energy status) relative to a genetically determined threshold. Anadromy ensues when an individual’s condition fails to meet the threshold level, which varies between sexes and among individuals and populations. Environmental factors and genetic architecture may also directly influence life history, e.g., by altering gene expression. A strong genetic influence on the anadromy decision means that facultative anadromy can be altered by natural selection driven by changes such as differential exploitation, stocking with farm-reared brown trout, partial barriers to migration, and changes in climate, and freshwater and marine productivity, together with parasite, pathogen and predator abundance resulting in reduced marine survival and growth. Further studies of the factors determining life history choice, together with multiple population estimates of heritability and differential reproductive success (fitness), are required to understand fully the impact of natural and anthropogenic environmental changes on sea trout dynamics.
Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment
(John Wiley & Sons, Inc., 2019-05-10) Ferguson, Andrew; Reed, Thomas E.; Cross, Tom F.; McGinnity, Philip; Prodöhl, Paulo A.; European Research Council; Science Foundation Ireland; Marine Institute; Inland Fisheries Ireland; Environmental Protection Agency; Horizon 2020
Brown trout Salmo trutta is endemic to Europe, western Asia, north‐western Africa and is a prominent member of freshwater and coastal marine fish faunas. The species shows two resident (river‐resident, lake‐resident) and three main facultative migratory life histories (downstream–upstream within a river system, fluvial–adfluvial potamodromous; to and from a lake, lacustrine–adfluvial (inlet)–allucustrine (outlet) potamodromous; to and from the sea, anadromous). River‐residency v. migration is a balance between enhanced feeding and thus growth advantages of migration to a particular habitat v. the costs of potentially greater mortality and energy expenditure. Fluvial–adfluvial migration usually has less feeding improvement, but less mortality risk, than lacustrine–adfluvial–allacustrine and anadromous, but the latter vary among catchments as to which is favoured. Indirect evidence suggests that around 50% of the variability in S. trutta migration v. residency, among individuals within a population, is due to genetic variance. This dichotomous decision can best be explained by the threshold‐trait model of quantitative genetics. Thus, an individual's physiological condition (e.g., energy status) as regulated by environmental factors, genes and non‐genetic parental effects, acts as the cue. The magnitude of this cue relative to a genetically predetermined individual threshold, governs whether it will migrate or sexually mature as a river‐resident. This decision threshold occurs early in life and, if the choice is to migrate, a second threshold probably follows determining the age and timing of migration. Migration destination (mainstem river, lake, or sea) also appears to be genetically programmed. Decisions to migrate and ultimate destination result in a number of subsequent consequential changes such as parr–smolt transformation, sexual maturity and return migration. Strong associations with one or a few genes have been found for most aspects of the migratory syndrome and indirect evidence supports genetic involvement in all parts. Thus, migratory and resident life histories potentially evolve as a result of natural and anthropogenic environmental changes, which alter relative survival and reproduction. Knowledge of genetic determinants of the various components of migration in S. trutta lags substantially behind that of Oncorhynchus mykiss and other salmonids. Identification of genetic markers linked to migration components and especially to the migration–residency decision, is a prerequisite for facilitating detailed empirical studies. In order to predict effectively, through modelling, the effects of environmental changes, quantification of the relative fitness of different migratory traits and of their heritabilities, across a range of environmental conditions, is also urgently required in the face of the increasing pace of such changes.
Anthropogenic disturbance in a changing environment: modelling lifetime reproductive success to predict the consequences of multiple stressors on a migratory population
(Wiley, 2019-08-30) Pirotta, Enrico; Mangel, Marc; Costa, Daniel P.; Goldbogen, Jeremy; Harwood, John; Hin, Vincent; Irvine, Ladd M.; Mate, Bruce R.; McHuron, Elizabeth A.; Palacios, Daniel M.; Schwarz, Lisa K.; New, Leslie; Office of Naval Research; European Research Council; International Association of Oil and Gas Producers
Animals make behavioural and reproductive decisions that maximise their lifetime reproductive success, and thus their fitness, in light of periodic and stochastic variability of the environment. Modelling the variation of an individual's energy levels formalises this tradeoff and helps to quantify the population-level consequences of stressors (e.g. disturbance from human activities and environmental change) that can affect behaviour or physiology. In this study, we develop a dynamic state variable model for the spatially explicit behaviour, physiology and reproduction of a female, long-lived, migratory marine vertebrate. The model can be used to investigate the spatio-temporal patterns of behaviour and reproduction that allow an individual to maximise its overall reproductive output. We parametrised the model for eastern North Pacific blue whales Balaenoptera musculus, and used it to predict the effects of changing environmental conditions and increasing human disturbance on the population's vital rates. In baseline conditions, the model output had high fidelity to observed energy dynamics, movement patterns and reproductive strategies. Simulated scenarios suggested that environmental changes could have severe consequences on the population's vital rates, but that individuals could tolerate high levels of anthropogenic disturbance. However, this ability depended on where, when and how often disturbance occurred. In scenarios with both environmental change and anthropogenic disturbance, synergistic interactions caused stronger effects than in isolation. In general, larger body size offered a buffer against stochasticity and disturbance, and, consequently, we predicted juveniles to be more susceptible to disturbance. We also predicted that females prioritise their own survival at the expense of the current reproductive attempt, presumably the result of their long lifespan. Our approach provides a general framework to make predictions of the cumulative and synergistic effects of human disturbance and climate change on migratory populations, which can inform effective management and conservation efforts.
Anthropogenic pressures within the breeding range of the Hen Harrier Circus cyaneus in Ireland
(Taylor & Francis Group, 2020-03-27) Caravaggi, Anthony; Irwin, Sandra; Lusby, John; Ruddock, Marc; Mee, Allan; Nagle, Tony; O'Toole, Lorcán; O'Neill, Shane; O'Halloran, John; Department of Agriculture, Food and the Marine, Ireland
Capsule: Patterns in the frequency and co-occurrence of anthropogenic pressures associated with suitable breeding habitat for Hen Harriers Circus cyaneus demonstrates the need for specific, focussed management and policy options aimed at mitigating impacts on this threatened population. Aims: To describe anthropogenic pressures and threats in the upland breeding range of Hen Harriers and to explore their potential impacts on the declining Hen Harrier population. Methods: We used text mining, mixed-effects models, principal component analysis and clustering methods to explore anthropogenic pressures on suitable breeding and foraging habitats for Hen Harriers in Ireland, based on the 2015 national breeding Hen Harrier survey data. Results: Mixed-effects models described a strong influence of agriculture, forestry, predator activity, and recreational activities on survey areas that contained Hen Harrier territories. Cluster analyses described three discrete pressure clusters and showed consistent co-occurrence of independent pressures. Conclusions: Areas of suitable habitat for Hen Harriers in the uplands overlap with areas that experience anthropogenic pressures known to negatively impact on this vulnerable bird species. Combined with clear evidence for the co-occurrence of multiple pressures at a regional scale, this demonstrates a clear need for statutory agencies to consider the potential cumulative impacts of individual pressures when developing conservation strategies for Hen Harriers.
Apatite weathering as a geological driver of high uranium concentrations in groundwater
(Elsevier, 2015-05-09) Banning, Andre; Rüde, Thomas
Uranium is a heavy metal with potential adverse human health effects when consumed via drinking water. Although associated quality regulations have been implemented, geological sources and hydrogeochemical behavior of uranium in groundwater used for drinking water supply remain little understood. This study presents a hydrogeochemical and mineralogical characterization of a Triassic sandstone aquifer on a macro- and micro-scale, and an evaluation of uranium remobilization into groundwater, also considering the paleoenvironment and the distribution of the affected aquifer itself. Syndiagenetic uraniferous carbonate fluorapatite inclusions within the aquifer sandstones (“active arkoses”) were found to show structurally (chemical substitution in the crystal structure) and radiatively (α-recoil damage from uranium decay) enhanced mineral solubility. Extraction experiments indicated that these inclusions release uranium to groundwater during weathering. In conclusion, apatite alteration was identified as the responsible mechanism for widespread groundwater uranium concentrations >10 μg L−1 in the region representing Germany’s most significant problem area in this respect. Therefore, results indicate that the studied sedimentary apatite deposits cause the regional geogenic groundwater uranium problem, and must be considered as potential uranium sources in comparable areas worldwide.
The application of CRISPR-Cas for single species identification from environmental DNA
(John Wiley & Sons, Inc., 2019-06-08) Williams, Molly-Ann; O'Grady, Joyce; Ball, Bernard; Carlsson, Jens; de Eyto, Elvira; McGinnity, Philip; Jennings, Eleanor; Regan, Fiona; Parle-McDermott, Anne; Marine Institute
We report the first application of CRISPR‐Cas technology to single species detection from environmental DNA (eDNA). Organisms shed and excrete DNA into their environment such as in skin cells and faeces, referred to as environmental DNA (eDNA). Utilising eDNA allows non‐invasive monitoring with increased specificity and sensitivity. Current methods primarily employ PCR‐based techniques to detect a given species from eDNA samples, posing a logistical challenge for on‐site monitoring and potential adaptation to biosensor devices. We have developed an alternative method; coupling isothermal amplification to a CRISPR‐Cas12a detection system. This utilises the collateral cleavage activity of Cas12a, a ribonuclease guided by a highly specific single CRISPR RNA. We used the target species Salmo salar as a proof‐of‐concept test of the specificity of the assay among closely related species and to show the assay is successful at a single temperature of 37°C with signal detection at 535 nM. The specific assay, detects at attomolar sensitivity with rapid detection rates (<2.5 h). This approach simplifies the challenge of building a biosensor device for rapid target species detection in the field and can be easily adapted to detect any species from eDNA samples from a variety of sources enhancing the capabilities of eDNA as a tool for monitoring biodiversity.
Application of machine learning techniques for creating urban microbial fingerprints
(Springer Nature, 2019-08-16) Ryan, Feargal J.
Background: Research has found that human associated microbial communities play a role in homeostasis and the disruption of these communities may be important in an array of medical conditions. However outside of the human body many of these communities remain poorly studied. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is characterizing the microbiomes of urban environments with the aim to improve design of mass transit systems. As part of the CAMDA 2018 MetaSUB Forensics Challenge 311 city microbiome samples were provided to create urban microbial fingerprints, as well as a further 3 mystery datasets for validation. Results: MetaSUB samples were clustered using t-SNE in an unsupervised fashion to almost discrete groups, which upon inspection represented city of origin. Based on this clustering, geographically close metropolitan areas appear to display similar microbial profiles such as those of Auckland and Hamilton. Mystery unlabeled samples were provided part of the challenge. A random forest classifier built on the initial dataset of 311 samples was capable of correctly classifying 83.3% of the mystery samples to their city of origin. Random Forest analyses also identified features with the highest discriminatory power, ranking bacterial species such as Campylobacter jejuni and Staphylococcus argenteus as highly predictive of city of origin. The surface from which the sample was collected displayed little detectable impact on the microbial profiles in the data generated here. The proportion of reads classified per sample varied greatly and so de-novo assembly was applied to recover genomic fragments representing organisms not captured in reference databases. Conclusions: Current methods can differentiate urban microbiome profiles from each other with relative ease. De-novo assembly indicated that the MetaSUB metagenomic data contains adequate depth to recover metagenomic assembled genomes and that current databases are not sufficient to fully characterize urban microbiomes. Profiles found here indicate there may be a relationship between geographical distance between areas and the urban microbiome composition although this will need further research. The impact of these different profiles on public health is currently unknown but the MetaSUB consortium is uniquely suited to evaluate these and provide a roadmap for the inclusion of urban microbiome information for city planning and public health policy.
Application of semi-automated strain analysis techniques and anisotropy of magnetic susceptibility in fold and thrust belts
(University College Cork, 2014) McCarthy, Dave J.; Meere, Patrick A.; Mulchrone, Kieran F.; Irish Research Council for Science Engineering and Technology
Quantitative analysis of penetrative deformation in sedimentary rocks of fold and thrust belts has largely been carried out using clast based strain analysis techniques. These methods analyse the geometric deviations from an original state that populations of clasts, or strain markers, have undergone. The characterisation of these geometric changes, or strain, in the early stages of rock deformation is not entirely straight forward. This is in part due to the paucity of information on the original state of the strain markers, but also the uncertainty of the relative rheological properties of the strain markers and their matrix during deformation, as well as the interaction of two competing fabrics, such as bedding and cleavage. Furthermore one of the single largest setbacks for accurate strain analysis has been associated with the methods themselves, they are traditionally time consuming, labour intensive and results can vary between users. A suite of semi-automated techniques have been tested and found to work very well, but in low strain environments the problems discussed above persist. Additionally these techniques have been compared to Anisotropy of Magnetic Susceptibility (AMS) analyses, which is a particularly sensitive tool for the characterisation of low strain in sedimentary lithologies.
Application of signal detection methods to ﬁsheries management
(University College Cork, 2014) Pazhayamadom, Deepak George; Rogan, Emer; Kelly, Ciarán J.; Codling, Edward A.; Marine Institute
The abundance of many commercially important fish stocks are declining and this has led to widespread concern on the performance of traditional approach in fisheries management. Quantitative models are used for obtaining estimates of population abundance and the management advice is based on annual harvest levels (TAC), where only a certain amount of catch is allowed from specific fish stocks. However, these models are data intensive and less useful when stocks have limited historical information. This study examined whether empirical stock indicators can be used to manage fisheries. The relationship between indicators and the underlying stock abundance is not direct and hence can be affected by disturbances that may account for both transient and persistent effects. Methods from Statistical Process Control (SPC) theory such as the Cumulative Sum (CUSUM) control charts are useful in classifying these effects and hence they can be used to trigger management response only when a significant impact occurs to the stock biomass. This thesis explores how empirical indicators along with CUSUM can be used for monitoring, assessment and management of fish stocks. I begin my thesis by exploring various age based catch indicators, to identify those which are potentially useful in tracking the state of fish stocks. The sensitivity and response of these indicators towards changes in Spawning Stock Biomass (SSB) showed that indicators based on age groups that are fully selected to the fishing gear or Large Fish Indicators (LFIs) are most useful and robust across the range of scenarios considered. The Decision-Interval (DI-CUSUM) and Self-Starting (SS-CUSUM) forms are the two types of control charts used in this study. In contrast to the DI-CUSUM, the SS-CUSUM can be initiated without specifying a target reference point (‘control mean’) to detect out-of-control (significant impact) situations. The sensitivity and specificity of SS-CUSUM showed that the performances are robust when LFIs are used. Once an out-of-control situation is detected, the next step is to determine how much shift has occurred in the underlying stock biomass. If an estimate of this shift is available, they can be used to update TAC by incorporation into Harvest Control Rules (HCRs). Various methods from Engineering Process Control (EPC) theory were tested to determine which method can measure the shift size in stock biomass with the highest accuracy. Results showed that methods based on Grubb’s harmonic rule gave reliable shift size estimates. The accuracy of these estimates can be improved by monitoring a combined indicator metric of stock-recruitment and LFI because this may account for impacts independent of fishing. The procedure of integrating both SPC and EPC is known as Statistical Process Adjustment (SPA). A HCR based on SPA was designed for DI-CUSUM and the scheme was successful in bringing out-of-control fish stocks back to its in-control state. The HCR was also tested using SS-CUSUM in the context of data poor fish stocks. Results showed that the scheme will be useful for sustaining the initial in-control state of the fish stock until more observations become available for quantitative assessments.

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