23 Works

Data from: Among-sibling differences in the phenotypes of juvenile fish depend on their location within the egg mass and maternal dominance rank

Tim Burton, Mia O. Hoogenboom, Nicholas D. Beevers, John D. Armstrong & Neil B. Metcalfe
We investigated whether among-sibling differences in the phenotypes of juvenile fish were systematically related to the position in the egg mass where each individual developed during oogenesis. We sampled eggs from the front, middle and rear thirds of the egg mass in female brown trout of known dominance rank. In the resulting juveniles, we then measured traits that are related to individual fitness: body size, social status and standard metabolic rate (SMR). When controlling for...

Population and seascape genomics of a critically endangered benthic elasmobranch, the blue skate Dipturus batis

Aurelien Delaval, Michelle Frost, Victoria Bendall, Stuart Hetherington, David Stirling, Galice Hoarau, Catherine Jones & Leslie Noble
The blue skate (Dipturus batis) has a patchy distribution across the North-East Atlantic Ocean, largely restricted to occidental seas around the British Isles following fisheries-induced population declines and extirpations. The viability of remnant populations remains uncertain, and could be impacted by continued fishing and bycatch pressure and the projected impacts of climate change. We genotyped 503 samples of D. batis, obtained opportunistically from the widest available geographic range, across 6,350 single nucleotide polymorphisms (SNPs) using...

Data from: The use of an unsupervised learning approach for characterizing latent behaviors in accelerometer data

Marianna Chimienti, Thomas Cornulier, Ellie Owen, Mark Bolton, Ian M. Davies, Justin M. J. Travis, Beth E. Scott & Justin M.J. Travis
The recent increase in data accuracy from high resolution accelerometers offers substantial potential for improved understanding and prediction of animal movements. However, current approaches used for analysing these multivariable datasets typically require existing knowledge of the behaviors of the animals to inform the behavioral classification process. These methods are thus not well-suited for the many cases where limited knowledge of the different behaviors performed exist. Here, we introduce the use of an unsupervised learning algorithm....

Data from: Spatial variation in the relationship between performance and metabolic rate in wild juvenile Atlantic salmon

Grethe Robertsen, John D. Armstrong, Keith H. Nislow, Ivar Herfindal, Simon McKelvey & Sigurd Einum
1. Maintenance metabolic rate (MR, the energy cost of self-maintenance) is linked to behavioural traits and fitness and varies substantially within populations. Despite having received much attention, the causes and consequences of this variation remain obscure. 2. Theoretically, such within-population variation in fitness-related traits can be maintained by environmental heterogeneity in selection patterns, but for MR this has rarely been tested in nature. 3. Here, we experimentally test if the relationship between MR and performance...

Data from: The Pillars of Hercules as a bathymetric barrier to gene-flow promoting isolation in a global deep-sea shark (Centroscymnus coelolepis)

Diana Catarino, Halvor Knutsen, Ana Veríssimo, Esben Moland Olsen, Per Erik Jorde, Gui Menezes, Hanne Sannæs, David Stanković, Joan Batista Company, Francis Neat, Roberto Danovaro, Antonio Dell'Anno, Bastien Rochowski, Sergio Stefanni, Joan Baptista Company & Hanne Sannaes
Knowledge of the mechanisms limiting connectivity and gene-flow in deep-sea ecosystems is limited, especially for deep-sea sharks. The Portuguese dogfish (Centroscymnus coelolepis) is a globally distributed and Near Threatened deep-sea shark. C. coelolepis population structure was studied using 11 nuclear microsatellite markers and a 497 bp fragment from the mtDNA Control Region. High levels of genetic homogeneity across the Atlantic (ΦST=-0.0091, FST= 0.0024, P > 0.05) were found suggesting one large population unit at this...

Data from: Taking movement data to new depths: Inferring prey availability and patch profitability from seabird foraging behavior

Marianna Chimienti, Thomas Cornulier, Justin M. J. Travis, Beth E. Scott & Ian M. Davies
Detailed information acquired using tracking technology has the potential to provide accurate pictures of the types of movements and behaviors performed by animals. To date, such data have not been widely exploited to provide inferred information about the foraging habitat. We collected data using multiple sensors (GPS, time depth recorders, and accelerometers) from two species of diving seabirds, razorbills (Alca torda, N = 5, from Fair Isle, UK) and common guillemots (Uria aalge, N =...

Volumes, dredged area measurements and estimated contaminants of material disposed at licensed offshore sites around the UK coast from 2000 to 2020

The dataset contains data related to registered offshore sediment disposal sites around the UK coast and includes volumes of disposed material, dredged areas, calculated levels of contaminants in the disposal material and licence details. Data were collated for the years 2000 to 2020. The Centre for Environment, Fisheries and Aquaculture Science (Cefas) on behalf of Department for environment, food and rural affairs (Defra), report these data for the United Kingdom (England, Scotland, Wales, Northern Ireland),...

Data from: Accuracy of assignment of Atlantic salmon (Salmo salar L.) to rivers and regions in Scotland and northeast England based on single nucleotide polymorphism (SNP) markers.

John Gilbey, Eef Cauwelier, Mark W. Coulson, Lee Stradmeyer, James N. Sampayo, Anja Armstrong, Eric Verspoor, Laura Corrigan, Jonathan Shelley & Stuart Middlemas
Understanding the habitat use patterns of migratory fish, such as Atlantic salmon (Salmo salar L.), and the natural and anthropogenic impacts on them, is aided by the ability to identify individuals to their stock of origin. Presented here are the results of an analysis of informative single nucleotide polymorphic (SNP) markers for detecting genetic structuring in Atlantic salmon in Scotland and NE England and their ability to allow accurate genetic stock identification. 3,787 fish from...

Diet, timing of egg laying and breeding success data for Isle of May European shag population 1985-2015

K. Keogan, S. Lewis, R.J. Howells, M.A. Newell, M.P. Harris, S. Burthe, R.A. Phillips, S. Wanless, A.B. Phillimore & F. Daunt
Data on timing of breeding, breeding success and diet of the European shag, sampled from the Isle of May population. The data were collected between 1985 and 2015 by visually checking nests and collecting regurgitated diet samples. These data are part of the Isle of May long-term study to assess population trends of seabirds under environmental change (IMLOTS https://www.ceh.ac.uk/our-science/projects/isle-may-long-term-study).

Data from: Links between parental life histories of wild salmon and the telomere lengths of their offspring

Darryl McLennan, John D. Armstrong, Dave C. Stewart, Simon Mckelvey, Winnie Boner, Pat Monaghan, Neil B. Metcalfe & David C. Stewart
The importance of parental contributions to offspring development and subsequent performance is self-evident at a genomic level; however, parents can also affect offspring fitness by indirect genetic and environmental routes. The life history strategy that an individual adopts will be influenced by both genes and environment; and this may have important consequences for offspring. Recent research has linked telomere dynamics (i.e. telomere length and loss) in early life to future viability and longevity. Moreover, a...

Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

Maria E. Lopez, Laura Benestan, Jean-Sebastien Moore, Charles Perrier, John Gilbey, Alex Di Genova, Alejandro Maass, Diego Díaz, Jean-Paul Lhorente, Katharina Correa, Roberto Neira, Louis Bernatchez & José M. Yáñez
Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In the present study, we aimed to...

Data from: Echolocation detections and digital video surveys provide reliable estimates of the relative density of harbour porpoises

Laura D. Williamson, Kate L. Brookes, Beth E. Scott, Isla M. Graham, Gareth Bradbury, Philip S. Hammond & Paul M. Thompson
1. Robust estimates of the density or abundance of cetaceans are required to support a wide range of ecological studies and inform management decisions. Considerable effort has been put into the development of line-transect sampling techniques to obtain estimates of absolute density from aerial and boat-based visual surveys. Surveys of cetaceans using acoustic loggers or digital cameras provide alternative methods to estimate relative density that have the potential to reduce cost and provide a verifiable...

Data from: Markov switching autoregressive models for interpreting vertical movement data with application to an endangered marine apex predator

Cecilia Pinto & Luigi Spezia
1.Time series of animal movement obtained from bio-loggers are becoming widely used across all taxa. These data are nowadays of high quality, combining high resolution with precision, as the tags are able to collect for longer times and store larger quantities of data. Due to their nature, high-frequency data sequences often pose non-trivial problems in time series analysis: non-linearity, non-Normality, non-stationarity, and long memory. These issues can be tackled by modelling the data sequence as...

Data from: Telomere elongation during early development is independent of environmental temperatures in Atlantic salmon

Darryl McLennan, John D. Armstrong, David C. Stewart, Simon Mckelvey, Winnie Boner, Pat Monaghan & Neil B. Metcalfe
There is increasing evidence from endothermic vertebrates that telomeres, which cap the ends of chromosomes and play an important role in chromosome protection, decline in length during postnatal life and are a useful indicator of physiological state and expected lifespan. However, much less is currently known about telomere dynamics in ectothermic vertebrates, which are likely to differ from that of endotherms, at least in part due to the sensitivity of ectotherm physiology to environmental temperature....

Data from: Simulating nutrient release from parental carcasses increases the growth, biomass and genetic diversity of juvenile Atlantic salmon

Darryl McLennan, Sonya K. Auer, Graeme J. Anderson, Thomas C. Reid, Ronald D. Bassar, David C. Stewart, Eef Cauwelier, James Sampayo, Simon McKelvey, Keith H. Nislow, John D. Armstrong & Neil B. Metcalfe
1. The net transport of nutrients by migratory fish from oceans to inland spawning areas has decreased due to population declines and migration barriers. Restoration of nutrients to increasingly oligotrophic upland streams (that were historically salmon spawning areas) have shown short-term benefits for juvenile salmon, but the longer-term consequences are little known. 2. Here we simulated the deposition of a small number of adult Atlantic salmon Salmo salar carcasses at the end of the spawning...

A baseline for the genetic stock identification of Atlantic herring, Clupea harengus, in ICES Divisions 6.a, 7.b-c

Edward Farrell, Leif Andersson, Dorte Bekkevold, Neil Campbell, Jens Carlsson, Maurice Clarke, Afra Egan, Arild Folkvord, Michael Gras, Susan Mærsk Lusseau, Steven Mackinson, Cormac Nolan, Steven O'Connell, Michael O'Malley, Martin Pastoors, Mats Pettersson & Emma White
Atlantic herring in ICES Divisions 6.a, 7.b-c comprises at least three populations, distinguished by temporal and spatial differences in spawning, which have until recently been managed as two stocks defined by geographic delineators. Outside of spawning the populations form mixed aggregations, which are the subject of acoustic surveys. The inability to distinguish the populations has prevented the development of separate survey indices and separate stock assessments. A panel of 45 SNPs, derived from whole genome...

Data from: Interactions between parental traits, environmental harshness and growth rate in determining telomere length in wild juvenile salmon

Darryl Mclennan, John D. Armstrong, Dave C. Stewart, Simon McKelvey, Winnie Boner, Pat Monaghan & Neil B. Metcalfe
A larger body size confers many benefits, such as increased reproductive success, ability to evade predators and increased competitive ability and social status. However, individuals rarely maximize their growth rates, suggesting that this carries costs. One such cost could be faster attrition of the telomeres that cap the ends of eukaryotic chromosomes and play an important role in chromosome protection. A relatively short telomere length is indicative of poor biological state, including poorer tissue and...

Data for UK OSPAR Common Procedure - Eutrophication Assessment

This dataset contains chlorophyll, nutrients and dissolved oxygen measurements which were used in the 3rd application of the OSPAR Common Procedure for Assessment of Eutrophication and UK Marine Strategy Framework Directive Assessments for descriptor 5. Data for nutrient concentrations, chlorophyll and dissolved oxygen (DO) concentrations and all supporting metadata for coastal and offshore (marine) waters were extracted from the following databases for the period from 1990 to 2014: MERMAN (BODC)1. Discrete samples for chlorophyll (by...

Trends and status of liver neoplasms in flatfish from UK waters collected between 2004 and 2015

These data are the results from histological analysis of liver neoplasms (lesions) found in flatfish taken from UK waters between 2004 and 2015. Data on the length, weight, sex and age of individuals are also included alongside the histological results. The 2016 assessment of the UK's Clean Seas Environment Monitoring Programme described the status and trends of contaminant concentrations and biological effects measurements in biota and sediment at monitoring stations in waters around the UK....

Data from: Shorter juvenile telomere length is associated with higher survival to spawning in migratory Atlantic salmon

Darryl McLennan, John D. Armstrong, David C. Stewart, Simon Mckelvey, Winnie Boner, Pat Monaghan & Neil B. Metcalfe
The risk of mortality associated with a long-distance migration will depend on an animal's physiological state, as well as the prevailing ecological conditions. Here we assess whether juvenile telomere length, which in endotherms has been shown to be a biomarker of physiological state and expected lifespan, predicts whether wild Atlantic salmon Salmo salar successfully complete their marine migration. Over 1800 juvenile fish were trapped, measured, PIT-tagged and a tissue biopsy taken when migrating as juveniles...

Data from: Range wide parallel climate-associated genomic clines in Atlantic salmon

Nicholas W. Jeffery, Ryan R. E. Stanley, Brendan F. Wringe, Javier Guijarro-Sabaniel, Vincent Bourret, Louis Bernatchez, Paul Bentzen, Robert G. Beiko, John Gilbey, Marie Clement & Ian R. Bradbury
Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe respectively, with 12 clinal loci in common between continents. Clinal...

Genetic structuring in Atlantic haddock contrasts with current management regimes

Paul R. Berg, Per E. Jorde, Kevin A. Glover, Geir Dahle, John B. Taggart, Knut Korsbrekke, Gjert E. Dingsør, Jon E. Skjæraasen, Peter J. Wright, Steven X. Cadrin, Halvor Knutsen & Jon-Ivar Westgaard
The advent of novel genetic methods has made it possible to investigate population structure and connectivity in mobile marine fish species: knowledge of which is essential to ensure a sustainable fishery. Haddock (Melanogrammus aeglefinus) is a highly exploited marine teleost distributed along the coast and continental shelf on both sides of the North Atlantic Ocean. However, little is known about its population structure. Here, we present the first study using single nucleotide polymorphism markers to...

Close relatives in population samples: Evaluation of the consequences for genetic stock identification

Johan Östergren, Stefan Palm, John Gilbey & Johan Dannewitz
Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using Genetic Stock Identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are estimated with Mixed Stock Analysis (MSA). In such analyses, allele frequencies in a reference baseline are required. Unknown individuals or mixture proportions are assigned to source populations based on the likelihood...

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Resource Types

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Affiliations

  • Marine Scotland
    22
  • University of Glasgow
    6
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  • Centre for Environment, Fisheries and Aquaculture Science
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  • Northern Research Station
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