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Article ; Online: Benthic animal-borne sensors and citizen science combine to validate ocean modelling.

Lavender, Edward / Aleynik, Dmitry / Dodd, Jane / Illian, Janine / James, Mark / Smout, Sophie / Thorburn, James

2022 Volume 12, Issue 1, Page(s) 16613

Abstract: Developments in animal electronic tagging and tracking have transformed the field of movement ecology, but interest is also growing in the contributions of tagged animals to oceanography. Animal-borne sensors can address data gaps, improve ocean model ... ...

Abstract	Developments in animal electronic tagging and tracking have transformed the field of movement ecology, but interest is also growing in the contributions of tagged animals to oceanography. Animal-borne sensors can address data gaps, improve ocean model skill and support model validation, but previous studies in this area have focused almost exclusively on satellite-telemetered seabirds and seals. Here, for the first time, we develop the use of benthic species as animal oceanographers by combining archival (depth and temperature) data from animal-borne tags, passive acoustic telemetry and citizen-science mark-recapture records from 2016-17 for the Critically Endangered flapper skate (Dipturus intermedius) in Scotland. By comparing temperature observations to predictions from the West Scotland Coastal Ocean Modelling System, we quantify model skill and empirically validate an independent model update. The results from bottom-temperature and temperature-depth profile validation (5,324 observations) fill a key data gap in Scotland. For predictions in 2016, we identified a consistent warm bias (mean = 0.53 °C) but a subsequent model update reduced bias by an estimated 109% and improved model skill. This study uniquely demonstrates the use of benthic animal-borne sensors and citizen-science data for ocean model validation, broadening the range of animal oceanographers in aquatic environments.
MeSH term(s)	Animals ; Citizen Science ; Oceanography ; Oceans and Seas ; Seals, Earless ; Temperature
Language	English
Publishing date	2022-10-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-20254-z
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Article ; Online: Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome.

Wagner, C Isabel / Kopp, Martina E L / Thorburn, James / Jones, Catherine S / Hoarau, Galice / Noble, Leslie R

G3 (Bethesda, Md.)

2023 Volume 13, Issue 9

Abstract: Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here, we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to ... ...

Abstract	Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here, we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to biomedical and conservation efforts, and the first representative of the second largest order of sharks (Squaliformes) with nuclear genome annotations available. Using Pacific Biosciences Continuous Long Read data in combination with Illumina paired-end and Hi-C sequencing, we assembled the genome de novo, followed by RNA-Seq-supported annotation. The final chromosome-level assembly is 3.7 Gb in size, has a BUSCO completeness score of 91.6%, and an error rate of less than 0.02%. Annotation predicted 33,283 gene models in the spiny dogfish's genome, of which 31,979 are functionally annotated.
MeSH term(s)	Animals ; Squalus acanthias/genetics ; Sharks/genetics ; Base Sequence
Language	English
Publishing date	2023-07-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkad146
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Article: Movement patterns of a Critically Endangered elasmobranch (Dipturus intermedius) in a Marine Protected Area

Lavender, Edward / Aleynik, Dmitry / Dodd, Jane / Illian, Janine / James, Mark / Wright, Peter J. / Smout, Sophie / Thorburn, James

Aquatic conservation. 2022 Feb., v. 32, no. 2

2022

Abstract: Marine Protected Areas (MPAs) are widely used in marine management, but for mobile species understanding the spatio‐temporal scale of management measures that is required to deliver conservation benefits depends on a detailed knowledge of species’ ... ...

Abstract	Marine Protected Areas (MPAs) are widely used in marine management, but for mobile species understanding the spatio‐temporal scale of management measures that is required to deliver conservation benefits depends on a detailed knowledge of species’ movements that is often lacking. This is especially the case for species of skate (Rajidae) for which relatively few movement studies have been conducted. In Scotland, the Loch Sunart to the Sound of Jura MPA covering 741 km² has been designated for the conservation of the Critically Endangered flapper skate (Dipturus intermedius), but fine‐scale movements within this area remain poorly understood. A passive acoustic telemetry study which coupled acoustic tagging of 42 individuals and a static array of 58 receivers was conducted from March 2016 to June 2017. Using acoustic detection time series, angler capture–recapture data and depth time series from archival tags, fine‐scale movements of individuals were investigated. Overall, 33 of the 42 tagged individuals were detected. Residency, site fidelity and transiency were documented. Residency around receivers, lasting from 3 to more than 12 months, was documented in 16 acoustically detected individuals (48%) and all life‐history categories, but was most noticeable among females. Acoustic detections were associated with depth, salinity and season, but there was no evidence that individuals formed close‐knit groups in the areas in which they were detected. Taken together with historical occurrence records of flapper skate, the prevalence and scale of residency documented here suggest that the MPA is sufficiently large to benefit a notable percentage (38 [24–52]%) of skate found in the study area over monthly and seasonal timescales. This result strengthens the case for the use of MPAs to support the conservation of flapper skate and other skate species that display similar movement patterns in areas of high local abundance.
Keywords	Rajidae ; acoustics ; life history ; marine protected areas ; mark-recapture studies ; philopatry ; salinity ; telemetry ; time series analysis ; Scotland
Language	English
Dates of publication	2022-02
Size	p. 348-365.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1146285-1
ISSN	1052-7613
ISSN	1052-7613
DOI	10.1002/aqc.3753
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Article: First confirmed complete incubation of a flapper skate (Dipturus intermedius) egg in captivity

Benjamins, Steven / Cole, Georgina / Naylor, Adam / Thorburn, James A. / Dodd, Jane

Journal of fish biology. 2021 Sept., v. 99, no. 3

2021

Abstract: An egg of the critically endangered flapper skate Dipturus intermedius was successfully incubated to hatching in captivity in what is believed to be a first for the species. Water conditions (temperature, salinity, flow rate) were recorded, with mean ... ...

Abstract	An egg of the critically endangered flapper skate Dipturus intermedius was successfully incubated to hatching in captivity in what is believed to be a first for the species. Water conditions (temperature, salinity, flow rate) were recorded, with mean water temperatures ranging from a monthly mean of 8.3 ± 1.2 to 13.2 ± 0.3°C and salinity from a monthly mean of 30.5 ± 1.2 to 36.6 ± 2.3 ppt. Hatching occurred after 534 days, suggesting that flapper skate eggs take c. 5700 growing degree‐days to incubate to hatching. The egg's prolonged embryonic development raises concerns about flapper skate eggs' vulnerability to anthropogenic disturbance.
Keywords	anthropogenic activities ; captive animals ; eggs ; embryogenesis ; fish ; heat sums ; salinity
Language	English
Dates of publication	2021-09
Size	p. 1150-1154.
Publishing place	Blackwell Publishing Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	410564-3
ISSN	1095-8649 ; 0022-1112
ISSN (online)	1095-8649
ISSN	0022-1112
DOI	10.1111/jfb.14816
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Article ; Online: First confirmed complete incubation of a flapper skate (Dipturus intermedius) egg in captivity.

Benjamins, Steven / Cole, Georgina / Naylor, Adam / Thorburn, James A / Dodd, Jane

Journal of fish biology

2021 Volume 99, Issue 3, Page(s) 1150–1154

Abstract	An egg of the critically endangered flapper skate Dipturus intermedius was successfully incubated to hatching in captivity in what is believed to be a first for the species. Water conditions (temperature, salinity, flow rate) were recorded, with mean water temperatures ranging from a monthly mean of 8.3 ± 1.2 to 13.2 ± 0.3°C and salinity from a monthly mean of 30.5 ± 1.2 to 36.6 ± 2.3 ppt. Hatching occurred after 534 days, suggesting that flapper skate eggs take c. 5700 growing degree-days to incubate to hatching. The egg's prolonged embryonic development raises concerns about flapper skate eggs' vulnerability to anthropogenic disturbance.
MeSH term(s)	Animals ; Embryonic Development ; Salinity ; Skates, Fish ; Temperature ; Water
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2021-06-19
Publishing country	England
Document type	Journal Article
ZDB-ID	410564-3
ISSN	1095-8649 ; 0022-1112
ISSN (online)	1095-8649
ISSN	0022-1112
DOI	10.1111/jfb.14816
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Article: Environmental cycles and individual variation in the vertical movements of a benthic elasmobranch

Lavender, Edward / Aleynik, Dmitry / Dodd, Jane / Illian, Janine / James, Mark / Wright, Peter J. / Smout, Sophie / Thorburn, James

Marine biology. 2021 Nov., v. 168, no. 11

2021

Abstract: Trends in depth and vertical activity reflect the behaviour, habitat use and habitat preferences of marine organisms. However, among elasmobranchs, research has focused heavily on pelagic sharks, while the vertical movements of benthic elasmobranchs, ... ...

Abstract	Trends in depth and vertical activity reflect the behaviour, habitat use and habitat preferences of marine organisms. However, among elasmobranchs, research has focused heavily on pelagic sharks, while the vertical movements of benthic elasmobranchs, such as skate (Rajidae), remain understudied. In this study, the vertical movements of the Critically Endangered flapper skate (Dipturus intermedius) were investigated using archival depth data collected at 2 min intervals from 21 individuals off the west coast of Scotland (56.5°N, −5.5°W) in 2016–17. Depth records comprised nearly four million observations and included eight time series longer than 1 year, forming one of the most comprehensive datasets collected on the movement of any skate to date. Additive modelling and functional data analysis were used to investigate vertical movements in relation to environmental cycles and individual characteristics. Vertical movements were dominated by individual variation but included prolonged periods of limited activity and more extensive movements that were associated with tidal, diel, lunar and seasonal cycles. Diel patterns were strongest, with irregular but frequent movements into shallower water at night, especially in autumn and winter. This research strengthens the evidence for vertical movements in relation to environmental cycles in benthic species and demonstrates a widely applicable flexible regression framework for movement research that recognises the importance of both individual-specific and group-level variation.
Keywords	Rajidae ; autumn ; benthic organisms ; coasts ; data collection ; habitat preferences ; habitats ; time series analysis ; winter ; Scotland
Language	English
Dates of publication	2021-11
Size	p. 164.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	1117-4
ISSN	1432-1793 ; 0025-3162
ISSN (online)	1432-1793
ISSN	0025-3162
DOI	10.1007/s00227-021-03973-1
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Extensive oceanic mesopelagic habitat use of a migratory continental shark species.

Schaber, Matthias / Gastauer, Sven / Cisewski, Boris / Hielscher, Nicole / Janke, Michael / Peña, Marian / Sakinan, Serdar / Thorburn, James

Scientific reports

2022 Volume 12, Issue 1, Page(s) 2047

Abstract: The identification of movement and behaviour patterns, as well as inter- and intra-population connectivity is crucial in order to implement effective and functional management and conservation measures for threatened migratory species such as tope ( ... ...

Abstract	The identification of movement and behaviour patterns, as well as inter- and intra-population connectivity is crucial in order to implement effective and functional management and conservation measures for threatened migratory species such as tope (Galeorhinus galeus). Yet, previous studies struggled to elucidate clear and consistent movement and depth usage patterns of adult tope in the Northeast Atlantic, suggesting a high plasticity in the migration and behaviour. We deployed pop-up satellite archival tags on adult tope during their seasonal summer aggregations in the inner German Bight of the south-eastern North Sea and near a presumed mating site in southwest Scotland. Depth distribution and migration pathways were derived from time series data with location processing. Four individuals followed migration trajectories leaving coastal areas and crossed the European shelf slope into oceanic areas of the Northeast Atlantic, remaining fully pelagic for the rest of the deployment duration. These sharks showed far-ranging migration trajectories and undertook regular and frequent diel vertical migrations, reaching daytime depths of over 700 m. Vertical migration patterns closely overlapped with biological mesopelagic habitat structures and closely tracked the diel migration of organisms from deep scattering layers derived from hydroacoustic recordings. It is hypothesized that adult tope regularly utilize oceanic habitats, foraging on mesopelagic layers in an environment generally considered of low prey density.
MeSH term(s)	Animal Migration ; Animals ; Atlantic Ocean ; Behavior, Animal ; Conservation of Natural Resources ; Ecosystem ; Endangered Species ; North Sea ; Oceans and Seas ; Predatory Behavior ; Scotland ; Seasons ; Sharks/physiology
Language	English
Publishing date	2022-02-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-05989-z
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Article ; Online: First report of an egg nursery for the Critically Endangered flapper skate Dipturus intermedius (Rajiformes: Rajidae)

Dodd, Jane / Baxter, John M. / Donnan, David W. / James, Benjamin D. / Lavender, Edward / McSorley, Claire Alice / Mogg, Andrew O.M. / Thorburn, James A.

Aquatic Conservation: Marine and Freshwater Ecosystems. 2022 Oct., v. 32, no. 10 p.1647-1659

2022

Abstract: This study provides the first report of an egg nursery for the Critically Endangered flapper skate Dipturus intermedius and a description of the habitat, thus contributing towards our understanding of essential habitats for the species. In total, 1,395 ... ...

Abstract	This study provides the first report of an egg nursery for the Critically Endangered flapper skate Dipturus intermedius and a description of the habitat, thus contributing towards our understanding of essential habitats for the species. In total, 1,395 flapper skate egg cases were recorded (accounting for overlapping surveys) in two egg case collection dives (n = 67 egg cases), one photogrammetry dive (n = 10 egg cases), 509 drop‐down video (DDV) camera drifts (n = 510 egg cases) and 18 remote operated vehicle (ROV) flights (n = 1,031 egg cases), carried out in the Inner Sound on the west coast of Scotland from 2018 to 2021. All of the egg cases were found on a shallow bedrock plateau between the Isle of Scalpay and a deep (>100 m) water channel between the Isle of Longay and the Crowlin Islands. Egg cases were observed on a cobble/boulder reef between 25 and 58 m depth, with a modelled annual temperature range of 9–12 °C, modelled current speeds up to 0.2 m⁻¹, a rugosity index of 1.7 and low levels of sedimentation. Flapper skate egg cases are large and the incubation period is protracted (18 months), making them potentially vulnerable to anthropogenic disturbance. A description of the habitat where egg cases were observed in this study will help inform the search for egg nurseries for this Critically Endangered species elsewhere. Targeted DDV, ROV and scuba diving surveys will support this search in areas where suitable bathymetric and hydrodynamic conditions are identified. Safeguarding egg nurseries is essential for successful conservation. Protection should involve the designation of egg nurseries as Marine Protected Areas where activities that are likely to damage or alter seabed habitats are managed.
Keywords	Rajidae ; anthropogenic activities ; bedrock ; cameras ; coasts ; eggs ; endangered species ; freshwater ; habitats ; hydrodynamics ; photogrammetry ; temperature ; Scotland
Language	English
Dates of publication	2022-10
Size	p. 1647-1659.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	1146285-1
ISSN	1052-7613
ISSN	1052-7613
DOI	10.1002/aqc.3857
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: MILP for the Multi-objective VM Reassignment Problem

Saber, Takfarinas / Ventresque, Anthony / Marques-Silva, Joao / Thorburn, James / Murphy, Liam

2021

Abstract: Machine Reassignment is a challenging problem for constraint programming (CP) and mixed-integer linear programming (MILP) approaches, especially given the size of data centres. The multi-objective version of the Machine Reassignment Problem is even more ... ...

Abstract	Machine Reassignment is a challenging problem for constraint programming (CP) and mixed-integer linear programming (MILP) approaches, especially given the size of data centres. The multi-objective version of the Machine Reassignment Problem is even more challenging and it seems unlikely for CP or MILP to obtain good results in this context. As a result, the first approaches to address this problem have been based on other optimisation methods, including metaheuristics. In this paper we study under which conditions a mixed-integer optimisation solver, such as IBM ILOG CPLEX, can be used for the Multi-objective Machine Reassignment Problem. We show that it is useful only for small or medium-scale data centres and with some relaxations, such as an optimality tolerance gap and a limited number of directions explored in the search space. Building on this study, we also investigate a hybrid approach, feeding a metaheuristic with the results of CPLEX, and we show that the gains are important in terms of quality of the set of Pareto solutions (+126.9% against the metaheuristic alone and +17.8% against CPLEX alone) and number of solutions (8.9 times more than CPLEX), while the processing time increases only by 6% in comparison to CPLEX for execution times larger than 100 seconds.
Keywords	Computer Science - Artificial Intelligence ; Electrical Engineering and Systems Science - Systems and Control
Subject code	000
Publishing date	2021-03-18
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Evidence of egg‐laying grounds for critically endangered flapper skate (Dipturus intermedius) off Orkney, UK

Phillips, Natasha D. / Garbett, Amy / Wise, Daniel / Loca, Sophie L. / Daly, Olivia / Eagling, Lawrence E. / Houghton, Jonathan D. R. / Verhoog, Peter / Thorburn, James / Collins, Patrick C.

Journal of fish biology. 2021 Oct., v. 99, no. 4

2021

Abstract: Essential fish habitats (EFHs) are critical for fish life‐history events, including spawning, breeding, feeding or growth. This study provides evidence of EFHs for the critically endangered flapper skate (Dipturus intermedius) in the waters around the ... ...

Abstract	Essential fish habitats (EFHs) are critical for fish life‐history events, including spawning, breeding, feeding or growth. This study provides evidence of EFHs for the critically endangered flapper skate (Dipturus intermedius) in the waters around the Orkney Isles, Scotland, based on citizen‐science observation data. The habitats of potential egg‐laying sites were parametrised as >20 m depth, with boulders or exposed bedrock, in moderate current flow (0.3–2.8 knots) with low sedimentation. This information provides a significant contribution to the understanding of EFHs for flapper skate.
Keywords	bedrock ; citizen science ; fish ; life history ; oviposition ; Scotland
Language	English
Dates of publication	2021-10
Size	p. 1492-1496.
Publishing place	Blackwell Publishing Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	410564-3
ISSN	1095-8649 ; 0022-1112
ISSN (online)	1095-8649
ISSN	0022-1112
DOI	10.1111/jfb.14817
Database	NAL-Catalogue (AGRICOLA)

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