ATLAS: A Trans-AtLantic Assessment and deep-water ecosystem-based Spatial management plan for Europe

People: Jeanette Carlsson, Jens Carlsson  •  Funding: Horizon 2020 Life  •   Status: Active, ongoing

ATLAS creates a dynamic new partnership between multinational industries, SMEs, governments and academia to assess the Atlantic's deep-sea ecosystems and Marine Genetic Resources to create the integrated and adaptive planning products needed for sustainable Blue Growth. ATLAS will gather diverse new information on sensitive Atlantic ecosystems (including Vulnerable Marine Ecosystems (VMEs) and Ecologically or Biologically Sensitive Areas (EBSAs)) to produce a step-change in our understanding of their connectivity, functioning and responses to future changes in human use and ocean climate. This is possible because ATLAS takes innovative approaches to its work and interweaves its objectives by placing business, policy and socioeconomic development at the forefront with science. See more at http://www.eu-atlas.org/
Environmental (e)DNA in ecology and evolution: potentials and pitfalls

People: Laura Gargan, Jeanette Carlsson, Jens Carlsson  •  Funding: UCD  •   Status: Active, 2014-2018

Environmental DNA (eDNA) has the potential to become a valuable monitoring tool, particularly where traditional sampling methods are not feasible. This is because the eDNA approach does not involve invasively sampling the species of interest, but utilising the DNA found in its environment as a source of information. This approach has been used so far to detect and quantify a range of taxa in both freshwater and marine environments, and may be applied in a wide number of fields including the early detection of invasive species, fisheries management, population genetics and biodiversity monitoring. While it is clear that analysis of eDNA has the ability to generate data to inform environmental management decisions, its widespread application has been hindered to date as there has been no standardised protocol for its use. For this reason, the project aims to standardise an approach to using eDNA through establishing a best practice workflow, from initial sample collection in the field to sequencing techniques and bioinformatics. Using this method to establish the presence/absence, as well as quantifying the relative abundances, of species in an environmental sample will involve designing species-specific primers and probes for qPCR, as well as employing metagenomic approaches (e.g. species-wide COI barcoding) for identifying species composition. Also, the detection thresholds of eDNA under different conditions are largely unknown, and this will be investigated in controlled laboratory experiments.
Population structure of Dublin Bay Prawn (Nephrops norvegicus ) from the coast of Ireland

People: Jeanne Gallagher, Jens Carlsson  •  Funding: IRC  •   Status: Active, 2015-2018

Nephrops norvegicus is highly valuable commercial species distributed around Ireland, in the northeast Atlantic, and in parts of the Mediterranean Sea. Commonly known as Dublin Bay prawn, langoustine or scampi, it is commercially fished all year round. The study of Nephrops genetic structure is an important tool for the assessment and management of this species as they face ever-increasing fishing pressure. This project will examine population structure and connectivity around the Irish coast using novel molecular markers and next-generation sequencing technologies. Connectivity to Nephrops populations outside Irish waters will also be examined. The genetic structure will be used to provide insight into answering key research questions about demographics, larval dispersal and effective population size. Results may be used to inform fisheries management strategies for this species to ensure its future sustainability.
SalmoSlime - Pilot study to investigate the application of eDNA technology in the assessment of pelagic by-catch of Atlantic salmon

People: Jeanette Carlsson, Bernie Ball, Jens Carlsson  •  Funding: AST  •   Status: Completed,September 2016

This pilot study is focussed on investigating the use of eDNA to detect Atlantic salmon smolt in the commercial catches of Refrigerated Seawater (RSW) fishing vessels. The pilot study involves lab based development and testing of a species specific salmon probe and also the collection and screening of eDNA samples from the tanks of RSW vessels during normal fishing operations in areas where they are likely to encounter the target species. The study was commissioned by the Atlantic Salmon Trust.
Population structure, phlyogeography and stock expansion of the boarfish (Capros aper ) in Atlantic and Mediterranean waters

People: Edward Farrell, Jeanette Carlsson, Jens Carlsson  •  Funding: IRC, KFO  •   Status: Completed, September 2015

The boarfish, Capros aper is a small pelagic shoaling species distributed from Norway to Senegal, including the Mediterranean and oceanic island waters. Boarfish have undergone a recent increase in abundance in the northeast Atlantic and consequently have become the target of a new industrial fishery. Despite the rapid development of the scientific background to the boarfish fishery a number of key research questions remain unanswered: (1) Are long term changes in abundance of boarfish the result of population expansion within the northeast Atlantic or immigration from other stocks? (2) Are the distribution limits of the current stock management unit congruent with the genetic population structure of the stock? (3) Is there fine-scale population structure within the current stock area and how does this relate to recruitment dynamics. This project will answer these questions through molecular genetic analyses of both mitochondrial and nuclear DNA in order to provide a more comprehensive basis for the future sustainable management and exploitation of boarfish.
Horse Mackerel (Trachurus trachurus ) stock genetic Identification pilot study

People: Edward Farrell, Jeanette Carlsson, Jens Carlsson  •  Funding: IMARES, PFA  •   Status: Completed, June 2016

There is a long history of research focussing on attempting to identify and discriminate northeast Atlantic Horse Mackerel stocks. The EU-funded HOMSIR project (2000-2003) suggested that there are three distinct stocks in the region; the southern, western and North Sea. The mixing zones between these putative stocks remain poorly defined and there are no methods for distinguishing horse mackerel from mixed stock fisheries or surveys. The results of a recent preliminary study, which screened a small number of samples from both putative western and North Sea stocks, indicated that there is significant population structure within the western stock and that it may not represent a single population. The degree of separateness of the western and North Sea stocks is also uncertain. It is known that the western stock spawns west of Ireland and the North Sea stock has a separate spawning ground in the North Sea. However it is unclear if these grounds are used interchangeably. The aim of this pilot study is to develop a suite a new species-specific molecular markers and to screen a baseline set of spawning horse mackerel samples from the putative western and North Sea stocks stock to establish a genetic baseline of the spawning stocks.
Pilot study on the genetic stock identification of Atlantic Herring (Clupea harengus ) in ICES areas VIa & VIIbc

People: Edward Farrell, Jeanette Carlsson, Jens Carlsson  •  Funding: KFO  •   Status: Completed, October 2015

There is a longstanding confusion regarding the stock identification of herring in ICES areas VIa & VIIb,c. There are believed to be two herring stocks (VIaN and VIaS & VIIb,c) in these areas which are distinguished by their temporally and spatially discrete spawning seasons. However herring in these areas are known to form mixed aggregations on common feeding grounds. Mixed stock fisheries and mixed stock surveys operate in these areas and the inability to assign herring to their stock of origin prevents accurate assessment and has hampered the development and implementation of effective management strategies. At present ICES is unable to distinguish between the herring stocks in commercial catches or research surveys, which means that ICES has to provide combined management advice for the two stocks, leading to a combined quota and management of the two. Such management can only be precautionary if the two stocks are of similar size and are homogeneously distributed together in commercial catches. If these conditions are not met, the smaller stock will suffer a higher mortality than would be sustainable and will eventually decline. The aim of this pilot study was to utilise new genetic methods to reanalyse spawning herring samples collected during the EU-funded WESTHER project (2003-2006) to determine if there was evidence of population structure between the two putative stocks.
Deep-Links: Ecosystem services of deep-sea biotopes

People: Jens Carlsson  •  Funding: MI  •   Status: Completed, November 2015

The aim of this deep-sea survey onboard the Marine Institute's RV Celtic Explorer was to conduct multidisciplinary characterisation of sponge gardens, cold-water coral reefs, mud volcano associated fauna in the Gulf of Cadiz. Deep-links aimed at assessing the role of geothermal fluids emitted from points of venting (geothermal mud-volcanoes) on cold-water corals and sponge gardens in habitat diversification, biomass accumulation and biodiversity. We related these parameters to benthic-pelagic coupling, carbon sequestration and assess the potential of these biotopes in climate regulation and their importance for fisheries as breeding, nursery, refugia and feeding sites. Ecosystems at hydrothermal vents, geothermal springs and cold-seeps (such as mud-volcanoes), unlike both cold water-corals and sponges gardens, are fuelled primarily by chemosynthetic primary production and may act as ecosystem catalysts for biomass accretion. We will assess dispersal mechanisms of bio-available chemosynthetic derived energy in the wider ecosystem through the identification of biotope linkers such as invertebrates, vertebrates and microorganisms using the unique isotopic signatures found in geothermal chemosynthetic derived primary production. Further, we will investigate whether the proximity of geothermal vents, cold-water corals and sponge gardens result in synergy that leads to further increased biotope complexity, increased capacity for biomass accretion and biodiversity. These enhanced ecosystem services, through synergy effects, have the potential for greater carbon sequestration highlighting a previously unrecognised role of linked deep-sea biotopes in climate regulation. The principal geological question addresses what drives geothermal systems and fluid flow through the seafloor, what controls the composition of those fluids, and what is the history of fluid flow and construction of complex habitats on the seafloor? This knowledge is crucial to understanding the interplay between fluid-flow and tectonics, their effects on geothermal circulation, the transfer of mass and energy from the interior of the earth to the exterior and, ultimately, how this affects the ecosystem services provided by marine biotopes.
Taxonomy and connectivity of animal species at the Moytirra hydrothermal vent field: developing methods for assessing ecological impacts of mineral extraction in the deep-sea

People: Patrick Collins, Jeanette Carlsson, Jens Carlsson  •  Funding: SFI  •   Status: Completed, 2015

Our results indicate that the animal community at the 45N hydrothermal vent site is similar to communities previously described at other North Atlantic hydrothermal vents. While the animals are similar, genetic analyses indicate the possible presence of two previously undescribed species; a crab and a scale worm (with the scale-worm potentially representing a new genus). We are currently working with colleagues at the University of Southampton and the Natural History Museum in London to confirm these new findings. We are developing genetic tools (microsatellite markers) for a hydrothermal vent endemic shrimp and snail to assess how isolated animals at 45N are from other vent sites on the Mid-Atlantic Ridge. To measure how isolated 45N organism are we are working with shrimp and snail samples from other vent sites South of the Azores collected by colleagues at Woods Hole Oceanographic Institute.
Pilot study to develop an eDNA assay for detecting Sea Lamprey Petromyzon marinus and brown trout Salmo trutta in running water

People: Michael Gustavson, Jeanette Carlsson, Jens Carlsson  •  Funding: UCD, IFI  •   Status: Complete, 2013

This pilot study focussed on the development of an environmental DNA (eDNA) assay for sea lamprey (Petromyzon marinus) and brown trout (Salmo trutta), two species of economic and conservation importance in the Republic of Ireland. The assays were deployed on water samples from the Mulcair River and the results demonstrate the effectiveness of eDNA for assessing presence of low-abundance taxa (here, P. marinus) for environmental managers, and they highlight the potential for assessing relative abundance of rare or invasive freshwater species.
Pilot study to develop an eDNA assay for detecting freshwater pearl mussels in running water

People: Jeanette Carlsson, Jens Carlsson  •  Funding: IRD Duhallow Life  •   Status: Complete, 2014

An eDNA qPCR assay for freshwater pearl mussel (Margaritifera margaritifera) eDNA was developed and deployed on water samples from nine locations from the Munster Blackwater river system. Margaritifera margaritifera eDNA was detected in all samples. The developed eDNA assay has the potential to be used to assess concentrations of eDNA which should be related to the biomass of M. margaritifera and could be used for monitoring the status of M. margaritifera in individual locations and river systems. However, utilising the quantifying capabilities of eDNA assays requires careful planning, standardised and coordinated sampling efforts (exact GPS positions, dates, time of day, water levels, weather documentation, details about where in the water body samples were acquired from, etc.) to ensure that samples are of the highest quality. Wide scale deployment of the assay can help detecting cryptic populations in watersheds where M. margaritifera has not previously been reported or where M. margaritifera are considered to have gone extinct.
Characterisation of several rare native Irish cattle populations (Kerry, Dexter, Irish Moiled, DroimFhionn, White Park and Bó Riabhach) at a genome wide level

People: Paul Flynn, Emma Teeling, Jens Carlsson  •  Funding:  •   Status: Active, 2014-2020

This study aims to characterise several rare native Irish cattle populations (Kerry, Dexter, Irish Moiled, DroimFhionn, White Park and Bó Riabhach) at a genome wide level. Utilizing recent SNP microarray technological advancements this project will carry out an in-depth molecular investigation to comparatively assess the levels of genetic diversity, genetic differentiation, population structure and relatedness that exists within and between these populations. Along with assessing population genetics parameters - a "genetic health check" component will screen for a large range of currently known deleterious Bovine molecular mutations within all considered populations. Furthermore genotyping for "trait specific markers" will allow for consideration to be given with regards to targeting breeds towards certain attributes that may be of economic and marketable value to breeders. Establishment of such genetic parameters will go towards facilitating cognisant management strategies, for these valuable genetic resources, to ensure their survival and progression as breeds into the future.
Development of a research and training initiative in Kenya's Galana Wildlife Conservancy

People: John Byrne, Jens Carlsson  •  Funding:  •   Status: Active, ongoing

The Galana Conservancy is one of Kenya's real wildlife treasures. This 60,000 acre wildlife haven for some of the world's most renowned and rarest African wildlife species is situated on the eastern boundary of Tsavo East National Park and on the northern banks of the Galana River. Since 2014 we have been working with John Byrne from the charity 'Friends from Ireland' to develop and establish links between UCD and the Wildlife Conservatory to allow students from UCD to perform research projects in Kenya and at the same time try create opportunities for Kenyan students to be involved in research.
Identification of Mr X

People: John Byrne, Jens Carlsson, Ron Pinhasi  •  Funding:  •   Status: Completed, 2015

Thomas Kent was an Irish rebel who was executed by British forces in the aftermath of the Easter Rising armed insurrection of 1916 and buried in a shallow grave on Cork prison’s grounds. In 2015, ninety-nine years after his death, a state funeral was offered to his living family to honour his role in the struggle for Irish independence. However, inaccuracies in record keeping did not allow the bodily remains that supposedly belonged to Kent to be identified with absolute certainty. Using a novel approach based on homozygous single nucleotide polymorphisms, we identified these remains to be those of Kent by comparing his genetic data to that of two known living relatives. As the DNA degradation found on Kent’s DNA, characteristic of ancient DNA, rendered traditional methods of relatedness estimation unusable, we forced all loci homozygous, in a process we refer to as “forced homozygote approach”. The results were confirmed using simulated data for different relatedness classes. We argue that this method provides a necessary alternative for relatedness estimations, not only in forensic analysis, but also in ancient DNA studies, where reduced amounts of genetic information can limit the application of traditional methods.