Deirdre Brophy

Deirdre Brophy
Galway-Mayo Institute of Technology | GMIT · Marine and Freshwater Research Centre

PhD Marine Ecology, University College Dublin

About

83
Publications
12,730
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,337
Citations
Additional affiliations
January 2003 - present
Galway-Mayo Institute of Technology
Position
  • Centre Leader

Publications

Publications (83)
Article
Stage-based assessment models are a type of fisheries stock assessment model that offer an alternative middle ground between aggregate and compositional models. We compare the capabilities of two theoretically different stage-based assessment approaches: an implementation of a biomass-based delay-difference model first described in a theoretical pa...
Article
Non-invasive methods are needed to enable indirect observation of vulnerable migratory fish populations across their life cycle and spatial distribution. Microchemistry data, such as trace element (TE) concentrations, collected non-invasively from the biomineral in fish scales can be used to characterize fish life history (habitat usage, fish prove...
Article
Full-text available
Almost nothing is known about the historical abundance of the ocean sunfish. Yet as an ecologically and functionally important taxa, understanding changes in abundance may be a useful indicator of how our seas are responding to anthropogenic changes including overfishing and climate change. Within this context, sightings from a coastal bird observa...
Article
Seasonal variation in the incorporation of trace elements into the calcified structures of fish can produce intra annual variation in the microchemistry of those structures. Interpretation of these seasonal signals can provide information about fish age. This approach offers great promise for objectively estimating age and corroborating other metho...
Article
Full-text available
For many environmental indicators, the sustainable status can change because of changes in either the monitored state or the policy goal. Fisheries provide an intensively monitored setting to investigate the relative impacts of such change. Key fisheries sustainability indicators comprise the ratio between fishing pressure or biomass and their resp...
Article
Full-text available
Although gelatinous zooplankton are an important component of marine ecosystems, gelatinous mesozooplankton that are <2 cm are underrepresented in monitoring programmes. Here, the interannual variability of gelatinous mesozooplankton abundance and diversity was estimated from 167 zooplankton net samples that were collected in the Celtic Sea during...
Article
Full-text available
Environmental and habitat change can have profound and complex impacts on fish. We examined an unexploited population of European eel (Anguilla anguilla) from a West of Ireland catchment. The population is long-lived and slow-growing compared to many other European eel populations. Von Bertalanffy growth curves showed decadal changes, with a trend...
Article
Full-text available
Atlantic bluefin tuna (Thunnus thynnus) from the two main spawning populations in the Mediterranean and Gulf of Mexico occur together in the western, central and eastern Atlantic. Stock composition of catches from mixing areas is uncertain, presenting a major challenge to the sustainable management of the fisheries. This study combines genetic and...
Article
Full-text available
Environmental change and fishing activity can produce directional trends in exploited fish populations with consequences for stock productivity. For herring in the Celtic Sea, size at age has been in steady decline since the mid 1980's. In the neighbouring herring stock off the Northwest coast of Ireland, reductions in size at age are noted after 1...
Article
Full-text available
There is debate in the literature as to whether scales of fishes require acidification to remove inorganic carbonates prior to stable isotope analysis. Acid‐treated and untreated scales from 208 Atlantic salmon from nine locations on both sides of the Atlantic were analysed for δ¹³C and δ¹⁵N. Linear mixed effects models determined the effect of aci...
Article
Full-text available
Scales and otoliths (ear stones) from fish are routinely sampled for age estimation and fisheries management purposes. Growth records from scales and otoliths can be used to generate long-term time series data, and in combination with environmental data, can reveal species specific population responses to a changing climate. Additionally, scale and...
Article
Full-text available
Analysis of length frequency distributions from surveys is one well-known method for obtaining growth parameter estimates where direct age estimates are not available. We present a likelihood-based procedure that uses mixture models and the expectation–maximization algorithm to estimate growth parameters from length frequency data (LFEM). A basic L...
Article
Globally, aquaculture products are expected to account for >60% of total seafood produce by 2030. In the European Union, the seafood sector is of considerable economic importance to member states with household spending on seafood produce totalling €54.8 billion in 2016. Within the EU, shellfish aquaculture supports livelihoods and employment in ma...
Article
Fish are adapted to spawn where their larvae will be retained in, or transported to, suitable juvenile habitat. Variability in circulation and behaviour produces variation in larval transport with consequences for recruitment. A biophysical model was used to simulate early larval dispersal of Celtic Sea herring (Clupea harengus) during wintertime i...
Article
Salmo salar post‐smolts were reared in seawater under controlled laboratory conditions for 12 weeks. The fish were exposed to three constant temperature treatments (15°C, 10.5°C and 6°C) and four feeding treatments (constant feeding, food withheld for 7 days, food withheld for 14 days and food withheld intermittently for four periods of 7 days). Sc...
Article
Sprat is a pelagic species of increasing commercial interest in European waters, yet little is known about its biology or the drivers of its population fluctuations. As a result, the species is currently without an analytical assessment or forecast across much of the North East Atlantic. The objectives of this study were to: verify otolith-based ag...
Article
For management purposes, albacore tuna (Thunnus alalunga, Bonnaterre 1788) in the North Atlantic are considered to be from one homogenous stock. However, multiple lines of evidence suggest that there is some degree of stock complexity. In this study, the stock structure of North Atlantic albacore tuna is investigated using otolith shape analysis. J...
Article
Full-text available
Boosted Regression Trees. Excellent for data-poor spatial management but hard to use Marine resource managers and scientists often advocate spatial approaches to manage data-poor species. Existing spatial prediction and management techniques are either insufficiently robust, struggle with sparse input data, or make suboptimal use of multiple explan...
Data
A short document detailing the data sources and their processing techniques. (PDF)
Data
A supplementary document explaining the running of the code in more detail, listing the functions’ arguments and their usage, a guide to running the functions together and separately, as well as additional results outputs, accompanies this manuscript. (PDF)
Data
R functions and packages used. (PDF)
Article
Full-text available
Chronic overfishing has depleted numerous elasmobranch stocks in the North East Atlantic, but addressing this issue has been hampered by management complications and lacking data. Spatial management approaches have thus been advocated. This work presents a novel application and further development of an advanced spatial modeling technique to identi...
Thesis
Full-text available
Traditional catch-limit based management of elasmobranchs such as rays is often confounded by sparse data, among other problems. Spatial management can circumvent such problems using area closures like Marine Protected Areas. However tools to predictively map abundance hotspots often struggle in data-limited situations, produce low-resolution outpu...
Article
It is recommended that demersal elasmobranchs be managed using spatial proxies for Maximum Sustainable Yield. Here we combine escapement biomass—the percentage of the stock which must be retained each year to conserve it—with maps of predicted Catch Per Unit Effort (CPUE) of four ray species [cuckoo (Leucoraja naevus), thornback (Raja clavata), blo...
Article
NOTE: manuscript as accepted by Ecological Modelling 11/05/2015; will be updated to EM format when available, to include typesetting etc.. High resolution figures, and R code, available at simondedman.com Skates and rays represent one of the most vulnerable components of fish communities in temperate demersal fisheries such as the Irish Sea. They...
Article
Full-text available
In this study we use an individual-based coupled physical biological model (ICPBM) to reconstruct the dispersal pathways of 0-group juveniles (young of the year) collected from nursery grounds in Galway Bay and to identify probable spawning ground locations for plaice on the west coast of Ireland. The relative importance of passive transport, behav...
Article
Full-text available
Two stocks of bluefin tuna (Thunnus thynnus) inhabit the north Atlantic; the western and eastern stocks spawn in the Gulf of Mexico and the Mediterranean Sea respectively. TransAtlantic movements occur outside spawning time whereas natal homing maintains stock structure. Commercial fisheries may exploit a mixed assemblage of both stocks. The incorp...
Article
Full-text available
Evidence from morphometric, meristic, oceanographic, genetic and otolith microstructure studies suggest complexity in the structure of the blue whiting (Micromesistius poutassou) population in the Northeast Atlantic. However the boundaries between stock components and the degree to which they overlap on the spawning grounds are uncertain. Blue whit...
Article
The timing of spawning and hatching, larval durations and growth exhibited by juvenile brill Scophthalmus rhombus captured along the Irish west coast were estimated using otolith microstructure analysis. Scophthalmus rhombus were estimated to have hatched between February and May, with fish settling onto nursery grounds between March and June. Fish...
Article
Patterns formed by annual, seasonal, and daily growth marks in the calcified structures of fish are particularly powerful tools in stock identification; they can be used to distinguish between groups of fish with different growth histories, pinpoint the stage in the life cycle at which groups diverge, and enhance the temporal resolution of informat...
Article
Full-text available
Disturbance by towed bottom-fishing gears often kills larger sensitive benthos, leading to changes in the abundance, size, and species composition of benthic communities. Short-term availability of trawl-damaged prey, and longer-term shifts in benthic prey community composition, both have the potential to affect feeding opportunities and realized d...
Article
Otolith elemental composition is a commonly used tool in the classification of fish stocks. Lower detection limits associated with trace element analysis techniques are the source of much debate among fisheries biologists. Using empirical data from herring (Clupea harengus) from two separate origins in the British Isles, we addressed methods of tre...
Article
The ichthyoplankton of Galway Bay was sampled over the spring and summer of 2007 and 2008 to determine what environmental factors influenced the distribution of larval and early juvenile fish. A total of 549 fish representing 27 taxa were caught. Catches decreased throughout each sampling season, and were generally poor in 2007. Catches were numeri...
Article
Full-text available
Transport models for planktonic fish eggs and larvae often use temperature to drive growth because temperature data are readily available. This pragmatic approach can be criticised as too simplistic as it ignores additional factors, such as food availability and growth-rate-dependent mortality. We examined the extent to which temperature could expl...
Technical Report
Full-text available
The Marine Strategy Framework Directive (MSFD, 2008/56/EC) aims to ensure that Europe’s seas achieve Good Environmental Status (GES) by 2020, and “has established itself as the cornerstone of all future EU regulatory measures that are applicable to the marine environment”. The MSFD was transposed into Irish law by the European Community’s (Marine S...
Article
The Atlantic saury Scomberesox saurus saurus (Walbaum) is a widely distributed epipelagic nekton species in the north Atlantic. It is considered one of the most abundant small pelagic species in the north Atlantic and is of increasing interest to commercial fisheries in American and European countries.Ageing of Atlantic saury is difficult, annual m...
Article
Coastal zones are essential nursery habitats for most juvenile flatfish species. Understanding the habitat requirements promoting high abundance and growth of juvenile flatfish is important for evaluating nursery habitat quality. The present study aimed to assess nursery ground quality for the most common flatfish species: dab (Limanda limanda) and...
Conference Paper
Full-text available
When groups of fish inhabit different environments during early life this may produce variation in pre- and post-settlement growth which is recorded in the otolith, providing a useful marker of larval and juvenile origin. In the present study we describe the early growth of Pleuronectes platessa on Irish and Scottish nursery grounds. Plaice were...
Article
Meristic variation within a fish species can arise due to environmental factors and can aid investigation between fish stocks and closely related juvenile fish species. The aim of this study was to investigate the spatial variation in meristic characteristics for juvenile flounder Platichthys flesus from Irish and Welsh coasts. Five meristic fin ra...
Article
Plaice (Pleuronectes platessa) are the most abundant juvenile flatfish present on west of Ireland nursery grounds. 0-group plaice were collected from eleven sandy beach nursery areas along the west coast of Ireland by beach seining (2000–2007). In the majority of years examined, certain beaches were found to support a higher abundance of juvenile p...
Article
This field study showed a lack of a correlation between a morphometric (Fulton’s K) and biochemical (RNA:DNA ratio) condition index in juvenile plaice (Pleuronectes platessa) and dab (Limanda limanda) studied to assess habitat quality in four sandy beach nursery grounds in Galway Bay, Ireland. Based on monthly surveys from June to September in 2008...
Book
Fishing pressure can change the structure of marine foodwebs, which may impair the functioning of these systems. Under the Marine Strategy Framework Directive (MSFD), indicators of the “abundance trends of functionally important selected groups/species” are required in order to track fishing‐induced change in fish community structure. While recent...
Article
Full-text available
Stock heterogeneity was investigated in albacore tuna (Thunnus alalunga, Bonnaterre 1788), a commercially important species in the North Atlantic Ocean and Mediterranean Sea. Twelve polymorphic microsatellite loci were examined in 581 albacore tuna from nine locations, four in the north-east Atlantic Ocean (NEA), three in the Mediterranean Sea (MED...
Article
On sandy beach nursery grounds along the west coast of Ireland, 0 year-group turbot Scophthalmus maximus were found to consume six types of crustaceans, in addition to polychaetes. The 0 year-group brill Scophthalmus rhombus fed almost exclusively on mysids, even though nine taxonomic prey groups were identified in the sediment across the investiga...
Article
This study describes the feeding habits of plaice Pleuronectes platessa and dab Limanda limanda during early juvenile development and relates differences between nursery grounds and sampling years to spatial and temporal variabilities in macrobenthic prey availability. The main prey taxa of both species were copepods, bivalves, amphipods, polychaet...
Conference Paper
Understanding flatfish population structure and dynamics is important to ensure the effective management of the associated fisheries. Stock identification techniques that allow us to discriminate between stocks and trace their recruits back to their nursery grounds, allow us to identify and protect those nursery grounds, which contribute most to th...
Article
Full-text available
Characterization of suitable habitat for settlement of juvenile flatfish is important for the management of nursery areas. Food availability is one important determinant of habitat quality that can affect the condition and growth, and thus survival, of flatfish. Spatial and temporal variation in diet has been widely studied for several species of f...
Article
The early life history of turbot (Psetta maxima Linnaeus) was investigated over a three year period (2007–2009). 0-group turbot were collected in September of each year, from three nursery areas along the Irish west coast. The timing of hatching and settlement and the duration of the larval stage were estimated using otolith microstructure analysis...
Article
The aim of this study was to test the hypothesis that Atlantic saury stocks from the Mediterranean Sea and northeastern Atlantic could be identified by means of saggital otolith shape. Saury is a pelagic fish inhabiting the north Atlantic that undertakes long migrations for feeding and reproduction. A combination of otolith shape indices and ellipt...
Article
Full-text available
Considerable debate surrounds the issue of reproductive exchange between subunits of marine fish populations. Discrete population theories predict that spawning time and location are predetermined during larval life and that spawning season fidelity and natal homing maintain population integrity. Conversely, spawning assemblages may represent inter...
Article
Full-text available
Biomass and production in the marine benthic community typically show rapid declines with bottom trawling. It has been postulated that such incidental reductions in prey abundance with trawling might negatively influence feeding success and hence the body condition of benthivorous fish. Length/weight and density by haul per year for six demersal fi...
Article
Recently settled turbot Psetta maxima and brill Scophthalmus rhombus are difficult to distinguish, as they are almost identical in appearance and lack the diagnostic adult characteristics. Fin ray counts, which can be used as an aid in the identification of flatfish juveniles, are reported to show some overlap between turbot and brill. 0-group flat...
Article
Full-text available
Trace element analysis or “elemental fingerprinting” is widely used in stock structure analyses. Postmortem contamination of bony structures can confound the results of microconstituent studies or introduce an additional source of noise to the data, thus reducing the ability of the technique to detect real variation in trace element concentrations....
Article
Turbot (Psetta maxima Linnaeus) is a high value commercially exploited marine flatfish which occurs in European waters, from the Northeast Atlantic to the Arctic Circle, the Baltic and Mediterranean Sea. In Ireland, turbot are the most valuable commercial non-quota species. Very little is known about their population dynamics in the wild, in partic...
Article
Full-text available
Bottom trawling is associated with reduced biomass and production in the marine benthic community. Abundance of hard-bodied organisms such as bivalves, crustaceans and echinoderms typically declines in favour of soft-bodied opportunists such as polychaetes. Trawling effects vary with habitat; impact and recovery time are typically greater for more...
Article
Full-text available
The study of the morphological and chemical characteristics of otoliths have recently been proposed as complementary tools for fish stock identification. However, their effectiveness remains to be fully assessed, especially in species whose life history is still poorly understood. The relative efficiency of otolith microchemistry and otolith shape...
Article
Full-text available
Cosgrove, R., Arregi, I., Brophy, D., Arrizabalaga, H., Ortiz de Zarate, V., and Griffin, N. 2010. A simulated archival tagging programme for albacore (Thunnus alalunga) in the Northeast Atlantic, including an analysis of factors affecting tag recovery. – ICES Journal of Marine Science, 67: 1216–1221. An archival tagging programme in the Northeast...
Article
Mussel populations on the Irish Atlantic coast comprise an interbreeding mixture of the blue mussel, Mytilus edulis (L.) and the Mediterranean mussel, Mytilus galloprovincialis (Lmk.). The occurrence of hybrid genotypes varies between sites but can be as high 80%. This study compares the reproductive cycle of M. edulis, M. galloprovincialis and the...
Article
Full-text available
Burke, N., Brophy, D., Schön, P-J., and King, P. A. 2009. Temporal trends in stock origin and abundance of juvenile herring (Clupea harengus) in the Irish Sea. – ICES Journal of Marine Science, 66: 1749–1753.Celtic Sea herring (Clupea harengus) larvae partly disperse into the Irish Sea, where they mix with the resident stock during their first year...