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132
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Introduction
Current institution
Additional affiliations
January 2015 - present
January 2015 - present
Education
January 2003 - March 2007
September 1998 - March 2002
Publications
Publications (132)
Cabled multiparametric observatories are sustaining ecological monitoring by collecting long‐term real‐time biological and environmental data. Here, we investigated fish communities by sampling environmental DNA (eDNA) over 4 days near the multiparametric cabled video‐observatory OBSEA (Northwestern Mediterranean Sea). The multi‐marker eDNA metabar...
Monitoring the health of protected marine mammals is crucial for conservation. Cortisol, a hormone involved in the stress response and metabolism, is a recognised biomarker for physiological states across species. Previous studies assessing blubber cortisol in marine mammals predominantly relied on an extraction methodology using numerous steps wit...
Interest in mesopelagic fish layers is on the rise due to the potential exploitability of their macrofauna; hence, profiling their fish community is crucial to enable the sustainability of future fishing practices. In this context, a dedicated survey was carried out in September 2022 along the Irish shelf break, where fishing (catch) and eDNA metab...
Monitoring the nutritional health of cetaceans has become increasingly important in a changing environment, where multiple stressors impact animals. Particularly for those species that require consumption of energy‐dense prey, such as the common dolphin. Thus far, no uniform measure for monitoring body condition has been recommended across cetacean...
The present study aims at filling genetic structure gaps of grey seals ( Halichoerus grypus ) in the Northeast Atlantic, where effective Management Units (MUs) must be established to fulfil international obligations set by OSPAR and the EU’s MSFD. Mitochondrial and nuclear genetic markers were analysed for seals from the island of Ireland, southwes...
Biomonitoring of marine life has been enhanced in recent years by the integration of innovative DNA‐based approaches, which offer advantages over more laborious techniques (e.g. microscopy). However, trade‐offs between throughput, sensitivity and quantitative measurements must be made when choosing between the prevailing molecular methodologies (i....
The rapid advancement of digital technologies such as digital twins, AI and machine learning has opened up promising avenues for ecological actions, including conservation, research and restoration. These technologies offer improved monitoring capabilities that can enhance our understanding of ecological processes and biodiversity. The EU-funded DI...
Documenting temporal and spatial occurrence trends of Non-Indigenous Species (NIS) is essential to understand vectors and pathways of introduction, and for horizon scanning for future introductions. This study provides an overview of marine NIS found in the Republic of Ireland up to 2020. Taxonomic groups, species origin, and location of first repo...
Photo-identification enables non-invasive identification of individuals from natural markings, with several algorithms developed to recognise individual patterns. ExtractCompare is a key software package for individual semi-automated recognition of harbour seals ( Phoca vitulina ). Its performance, however, may vary with image quality, aspect emplo...
Biomonitoring of marine life has been enhanced in recent years by the integration of innovative DNA-based approaches, which offer advantages over more laborious conventional techniques (e.g. direct capture) and greater taxonomic resolution especially in complex life cycles and early life stages. However, tradeoffs between throughput, sensitivity an...
A model was developed to forecast and compare changes in species presence assessed with either eDNA or traditional observations. We use it to explore how ecosystem conditions could affect the suitability of eDNA for Environmental Impact Assessment. First, a deterministic model simulated the dynamics of the impacted population (called “receptor” in...
https://www.ascobans.org/en/document/impacts-anthropogenic-activities-and-environmental-change-foraging-ecology-and-nutritional
The identification of discrete intraspecific units, such as genetically informed management units (MUs), is important to effectively develop and implement conservation strategies for protected species. Harbour seals ( Phoca vitulina ) occurring in Irish waters are currently viewed as a single nationwide panmictic population (and hence MU), although...
This study evaluates how eDNA information could be used within Environmental Impact Assessment (EIA). We developed an original model to simulate the conditions for which an eDNA signal detects, or does not detect, an impact on a targeted (receptor) species in a given project area. The simulation has four consecutive steps. First, a deterministic mo...
The Norway lobster, Nephrops norvegicus, supports a key European fishery. Stock assessments for this species are mostly based on trawling and UnderWater TeleVision (UWTV) surveys. However, N. norvegicus are burrowing organisms and these survey methods are unable to sample or observe individuals in their burrows. To account for this, UWTV surveys ge...
European North Atlantic ranavirus (ENARV, Iridoviridae), is a ranavirus species recently isolated from lumpfish (Cyclopterus lumpus, L.), which are used as cleaner fish in Atlantic salmon (Salmo salar) farming in Northern Europe. This study aimed to investigate (1) the virulence of ENARV isolates from Ireland, Iceland and the Faroe Islands to lumpf...
Topmouth gudgeon is a freshwater fish species native to East Asia. Nowadays, P. parva is spread throughout Europe which is of concern because besides being considered one of the worst aquatic Invasive Alien Species (IAS) in Europe it is also a known vector of Spherotecum destruens, the rosette-like parasite lethal to other fish species.
The present...
White-clawed crayfish (Austropotamobius pallipes) is a keystone species found in western European freshwater bodies, where it has suffered drastic declines due to pathogens, competition with non-indigenous crayfish species (NICS) and habitat deterioration. In Ireland, populations of (naturalised) A. pallipes have been considered healthy and abundan...
Recent advances in robotic design, autonomy and sensor integration create solutions for the exploration of deep-sea environments, transferable to the oceans of icy moons. Marine platforms do not yet have the mission autonomy capacity of their space counterparts (e.g., the state of the art Mars Perseverance rover mission), although different levels...
Overfishing has massively depleted several target species in European waters, altering marine food webs and impacting populations of top predators. The common dolphin is one of the most abundant cetaceans in the North-east Atlantic, playing a key functional role as a top predator. Large-scale movements in recent years have resulted in increased num...
Deep-sea ecosystems are reservoirs of biodiversity that are largely unexplored, but their exploration and biodiscovery are becoming a reality thanks to biotechnological advances (e.g., omics technologies) and their integration in an expanding network of marine infrastructures for the exploration of the seas, such as cabled observatories. While stil...
White-clawed Crayfish Austropotamobius pallipes surveys were carried out between June and September 2017 in all 15 Special Areas of Conservation (SAC)for which the species is listed as a qualifying interest.
Crayfish were detected in 13 SACs; they were not detected in the two (Lough Bane and Lough Glass SAC and Lough Lene SAC) from which crayfish...
This document provides a series of protocols used to extract eDNA or eRNA from marine environmental samples such as small and large volume (filtered) water, sediment or (fine mesh net) plankton. Specifically, these protocols are recommended for use following sampling as described in Mirmin et al. (2021; Environmental DNA sampling protocols for the...
This document provides a series of protocols used to extract eDNA or eRNA from marine environmental samples such as small and large volume (filtered) water, sediment or (fine mesh net) plankton. Specifically, these protocols are recommended for use following sampling as described in Mirmin et al. (2021; Environmental DNA sampling protocols for the...
Understanding the spread and distribution of Non-Indigenous Species (NIS) is key when implementing legislation to maintain good ecosystem health. Environmental DNA (eDNA) has shown great potential to detect aquatic organisms in a rapid and cost-effective way, however their applicability to new environments must be validated prior to their implement...
This protocol is intended to provide guidelines on the curation and establishment of a specimen/tissue bank and associated DNA sequence data to be used as reference material/data for subsequent environmental DNA (eDNA) analysis, with particular emphasis on marine non-indigenous and invasive species.
Amoebic Gill Disease (AGD), caused by the protozoan extracellular parasite Paramoeba perurans ( P. perurans ) is a disease affecting Atlantic salmon ( Salmo salar ). This study investigated the gill transcriptomic profile of pre-clinical AGD using RNA-sequencing (RNA-seq) technology. RNA-seq libraries generated at 0, 4, 7, 14 and 16 days post infec...
This document describes a series of protocols for the collection of environmental samples intended for the monitoring and surveillance of marine invasive species by means of eDNA metabarcoding analysis, as described in the associated publication (Fernandez et al. 2021: https://doi.org/10.1016/j.marpolbul.2021.112893).
This document describes a series of protocols for the collection of environmental samples intended for the monitoring and surveillance of marine invasive species by means of eDNA metabarcoding analysis, as described in the associated publication (Fernandez et al. 2021: https://doi.org/10.1016/j.marpolbul.2021.112893).
In a recent paper, “Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring,” Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra‐organismal DNA from macro‐organisms. We agree with this...
Invasive Alien Species (IAS) are one of the most contributing constituents of biodiversity loss with the distribution range of an increasing number of IAS being artificially re-shaped by human activities. Rapid and effective tools are therefore needed in order to monitor changes in biodiversity and the dispersal of IAS. Molecular tools such as envi...
Quantitative PCR (qPCR) has been increasingly used for the detection of target organisms in environmental DNA (eDNA) studies, and this is thanks to high sensitivity and ability to quantify DNA targets copy number. However, prior to their implementation, qPCR species-specific assays must be developed and validated and, when implemented, they are lim...
Cabled observatories are marine infrastructures equipped with biogeochemical and oceanographic sensors as well as High-Definition video and audio equipment, hence providing unprecedented opportunities to study marine biotic and abiotic components. Additionally, non-invasive monitoring approaches such as environmental DNA (eDNA) metabarcoding have f...
The discrimination between the several species of the genus Actinia occurring in the Northeastern Atlantic and Mediterranean has been made analyzing morphological characters, with emphasis on external coloration patterns and morphology of cnidom structures. In Iberia, the occurrence of more than two species of Actinia has been suggested, but its va...
Amoebic Gill Disease (AGD), caused by the protozoan extracellular parasite Paramoeba perurans , is a disease affecting Atlantic salmon ( Salmo salar ) aquaculture. Many studies to date have investigated the pathogenesis of ADG focusing on the host immune response in the gill after the appearance of clinical symptoms. This study investigated the gil...
Conservation and management of protected species, particularly of elusive species such as pinnipeds, is hampered by knowledge gaps. In the case of studies using genetic data these are often attributed to a lack of representative samples. Therefore, there is a pressing need for the development of minimally invasive sampling protocols suitable for ge...
In a recent paper, “Environmental DNA: What’s behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring”, Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this...
In a recent paper, “Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring”, Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this...
Cabled video-observatories offer new opportunities to monitor fish species at frequencies and durations never attained before, quantifying the behavioural activities of their individuals, and providing ancillary data to inform stock assessment (in a fishery-independent manner). In this context, our objective was to improve the ecological monitoring...
Populations of Arctic char (Salvelinus alpinus) inhabiting Irish lakes are undergoing a rapid decline. In order to aid monitoring of this species in Irish lakes, a species‐specific qPCR assay was designed and subsequently tested for the detection of Arctic char's environmental DNA (eDNA) in an indoor mesocosm and in natural habitats (six lakes). Sp...
While environmental DNA (eDNA) is becoming increasingly established in biodiversity monitoring of freshwater ecosystems, the use of eDNA surveys in the marine environment is still in its infancy. Here, we use two approaches: targeted quantitative PCR (qPCR) and whole‐genome enrichment capture followed by shotgun sequencing in an effort to amplify k...
Systemic infections with predominantly Exophiala species have emerged as regular and significant pathogens of lumpfish in Ireland and abroad. Exophiala is a genus of melanised fungi in the order Chaetothyriales. They are regularly found as opportunistic pathogens of cold blooded vertebrates and several species have caused high mortalities in aquacu...
Amoebic gill disease (AGD) is one of the main diseases affecting Atlantic salmon (Salmo salar L.) mariculture. Hallmarks of AGD are hyperplasia of the lamellar epithelium and increased production of gill mucus. This study investigated the expression of genes involved in mucus secretion, cell cycle regulation, immunity and oxidative stress in gills...
The functioning of marine protected areas (MPAs) designated for marine megafauna has been criticized due to the high mobility and dispersal potential of these taxa. However, dispersal within a network of small MPAs can be beneficial as connectivity can result in increased effective population size, maintain genetic diversity, and increase robustnes...
Systemic infections with predominantly Exophiala species have emerged as regular and significant pathogens of lumpfish in Ireland and abroad. Exophiala is a genus of melanised fungi in the order Chaetothyriales. They are regularly found as opportunistic pathogens of cold blooded vertebrates and several species have caused high mortalities in aquacu...
The distribution and demographic patterns of marine organisms in the north Atlantic were largely shaped by climatic changes during the Pleistocene, when recurrent glacial maxima forced them to move south or to survive in northern peri-glacial refugia. These patterns were also influenced by biological and ecological factors intrinsic to each species...
An overview of my MRes research project currently being undertaken at GMIT.
The poster provides a general introduction to background, aims and methodology of this project followed by progress and future work under the project.
This study examines the potential of next-generation sequencing based 'genotyping-by-sequencing' (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal prime...
Species identification in sea anemones requires, in most situations, morphological analysis of cnidom structures of preserved individuals. However, in the genus Actinia, several species were described in the last years based on genetic analysis using allozimes. Recently, the sequencing of selected genes allowed the identification of two distinct ge...
Dusky kob, Argyrosomus japonicas, is large finfish indigenous to the south- and east coast of South Africa. Historically, this species supported a lucrative fishery, however declining population numbers in the wild, necessitates the need for alternative sources of supply. Kob aquaculture is in its initial phases, and relies on undomesticated stock...
The ballan wrasse, Labrus bergylta (Labridae), is a protogynous hermaphrodite fish common in the north-eastern Atlantic from Norway to Morocco. It is a commercially important resource for local fisheries and is currently being used as cleaner fish to control sea lice in salmon farms in northern Europe. We analysed the phylogeographic patterns of th...
Morphological identification and molecular data (mtDNA COI) were used to resolve the taxonomic identity of a non-native freshwater shrimp in the Cape Floristic Region (CFR) of South Africa and to evaluate levels of genetic diversity and differentiation in the species' core natural distribution. The species was morphologically and genetically identi...
Overfishing has led to the collapse of many marine fish stocks along the South African coast, particularly species characterised by predictable distribution patterns and vulnerable life-history traits. Dusky kob (Argyrosomus japonicus) is an estuarine-dependent sciaenid fish that has been severely depleted by overfishing and is currently managed by...
This study describes the successful implementation of a modified cetyltrimethyl ammonium bromide (CTAB) protocol to isolate genomic DNA and amplify 14 microsatellite markers from fertilized eggs and larvae of an emerging South African farmed marine fish species, the dusky kob Argyrosomus japonicus. To test and validate the efficiency of this method...
Highly mobile species in the marine environment may be expected to show little differentiation at the population level, but this is often not the case. Instead cryptic population structure is common, and effective conservation will require an understanding of how these patterns evolve. Here we present an assessment from both sides of the North Atla...
Hybridization between fish species can play a significant role in evolutionary processes and can influence management and conservation planning, however, this phenomenon has been widely understudied, especially in marine organisms. The distribution limits of two sciaenid species (silver kob, Argyrosomus inodorus, and dusky kob, A. japonicus) partly...
The next generation sequencing revolution has enabled rapid discovery of genetic markers, however, development of fully functioning new markers still requires a long and costly process of marker validation. This study reports a rapid and economical approach for the validation and deployment of polymorphic microsatellite markers obtained from a 454...
D'Arcy, J., Mirimin, L., and FitzGerald, R. Phylogeographic structure of a protogynous hermaphrodite species, the ballan wrasse Labrus bergylta, in Ireland, Scotland, and Norway, using mitochondrial DNA sequence data. – ICES Journal of Marine Science, 70: 685–693.
The ballan wrasse, Labrus bergylta, is a protogynous hermaphrodite marine fish specie...
The dusky kob (Argyrosomus japonicus) is a large, estuarine-dependent sciaenid fish that has been severely depleted in South African waters and that, in recent years, has received considerable attention from the local fish farming industry. Discovery and application of appropriate molecular markers is necessary to improve the understanding of wild...
By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single-nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non-model teleost, Atlantic cod Gadus morhua from the Celtic Sea, sou...
##Assembly-Data-START## Assembly Method :: MISA v. 1.0 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MISA v. 1.0 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MISA v. 1.0 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MISA v. 1.0 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MISA v. 1.0 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MISA v. 1.0 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MIRA v. 3.0.5 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MIRA v. 3.0.5 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MIRA v. 3.0.5 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MIRA v. 3.0.5 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MIRA v. 3.0.5 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MIRA v. 3.0.5 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MIRA v. 3.0.5 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MIRA v. 3.0.5 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MIRA v. 3.0.5 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: MIRA v. 3.0.5 Sequencing Technology :: 454; Sanger dideoxy sequencing ##Assembly-Data-END##
The present study describes the successful design and testing of a quick, least-invasive, reliable and inexpensive sampling procedure for Atlantic cod Gadus morhua. This protocol can be easily applied to postlarval fish following a simple three-step procedure, without availing of commercial DNA extraction kits, while ensuring survival of sampled in...
The identification of localized discrete populations is particularly important to the management and conservation of animal species, especially in the marine environment, where potential for dispersal is high but barriers to gene flow are often not clear. We investigated population genetic structuring of bottlenose dolphins Tursiops truncatus found...
