How do we quantify biodiversity? All the evidence in one place.

Biodiversity is a multi-dimensional concept that is represented by a large variety of measures. This complexity and lack of consistency limits the development of a coherent scientific understanding of biodiversity and how properties, such as ecosystem services, may depend on it. Here, I demonstrate that the formal discipline of creating a relational database (RDB) for information about biodiversity and its measures, is a useful tool in organising such knowledge into coherent sense. Following steps of the logical database design and data normalization to build a RDB, results in a formal definition of biodiversity within a well defined concept structure; mapping rules between the concepts of biodiversity and entities of RDB and a consistent information structure - all in one place. I show how this is then used to support evidence-based objective statements about biodiversity

Presence of persistent organic pollutants in a breeding common tern (sterna hirundo) population in ireland

Persistent organic pollutants (POPs) are chemical compounds of environmental concern due to their toxic, persistent nature and their ability to bio-accumulate in biological tissue. Seabirds, for often being at the top of the food web, have been used as monitors of environmental pollutants. Adverse effects caused by POPs have been reported in common terns (Sterna hirundo) since the 1970s. Egg shell thinning, embryo and hatchling deformities have been reported for this species. Environmental legislation, such as the Oslo-Paris Convention (OSPAR), has agreed on the monitoring of concentration of POPs in common terns. This study set out to investigate contemporary concentrations of polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), organochlorine pesticides (OCPs) and brominated flame retardants (BFRs) in common terns breeding in Ireland, along with congener profiles. Investigation was conducted in live (n = 15) and dead birds (n = 20) to test for the efficiency of different methodologies using preen oil and feathers versus liver and preen gland. Mean concentrations of POPs followed the order: PCB (36.48 ng/g ww feather) > PAH (30.01 ng/g ww feather) > OCP (13.36 ng/g ww feather) > BFR (1.98 ng/g ww feather) in live birds; and PAH (46.65 ng/g ww preen gland) > PCB (44.11 ng/g ww preen gland) > OCP (15.15 ng/g ww liver) > BFR (5.07 ng/g ww liver) in dead birds. Comparison of contaminant results with toxicity pre-established levels concluded that this population of common terns in Ireland is not at risk of anomalies caused by POPs. However, some levels are higher in comparison to the ones established by OSPAR's EcoQO and must be monitored periodically

Presence of persistent organic pollutants in a breeding common tern (sterna hirundo) population in ireland

Persistent organic pollutants (POPs) are chemical compounds of environmental concern due to their toxic, persistent nature and their ability to bio-accumulate in biological tissue. Seabirds, for often being at the top of the food web, have been used as monitors of environmental pollutants. Adverse effects caused by POPs have been reported in common terns (Sterna hirundo) since the 1970s. Egg shell thinning, embryo and hatchling deformities have been reported for this species. Environmental legislation, such as the Oslo-Paris Convention (OSPAR), has agreed on the monitoring of concentration of POPs in common terns. This study set out to investigate contemporary concentrations of polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), organochlorine pesticides (OCPs) and brominated flame retardants (BFRs) in common terns breeding in Ireland, along with congener profiles. Investigation was conducted in live (n = 15) and dead birds (n = 20) to test for the efficiency of different methodologies using preen oil and feathers versus liver and preen gland. Mean concentrations of POPs followed the order: PCB (36.48 ng/g ww feather) > PAH (30.01 ng/g ww feather) > OCP (13.36 ng/g ww feather) > BFR (1.98 ng/g ww feather) in live birds; and PAH (46.65 ng/g ww preen gland) > PCB (44.11 ng/g ww preen gland) > OCP (15.15 ng/g ww liver) > BFR (5.07 ng/g ww liver) in dead birds. Comparison of contaminant results with toxicity pre-established levels concluded that this population of common terns in Ireland is not at risk of anomalies caused by POPs. However, some levels are higher in comparison to the ones established by OSPAR's EcoQO and must be monitored periodically

Bio-physical models reveal the role of tides, wind and larval behaviour in early transport and retention of Atlantic herring (Clupea harengus L.) in the Celtic Sea

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 bio-physical model was used to simulate early larval dispersal of Celtic Sea herring during wintertime in six years (2002, 2003, 2004, 2005, 2008, 2010). After 30 days, particles occurred in three areas: inshore Celtic Sea, offshore Celtic Sea and south Irish Sea, with the majority (70-78% on average) of particles retained in the Celtic Sea. Inclusion of tidal forcing increased transport to the Irish Sea and decreased transport offshore, as did release during a spring tide. Retention in the Celtic Sea was increased by diel vertical migration and decreased by horizontal diffusion. Strong and frequent west/south-westerly winds increased transport offshore while strong and frequent east/south-southeast winds increased inshore retention in the Celtic Sea and transport into the Irish Sea. The study shows how tides, winds and behaviour influence larval transport and retention and highlights potential impacts of climate change on population persistence.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

The use of beached bird surveys for marine plastic litter monitoring in Ireland

Marine plastic litter has become a major threat to wildlife. Marine animals are highly susceptible to entanglement and ingestion of debris at sea. Governments all around the world are being urged to monitor litter sources and inputs, and to mitigate the impacts of marine litter, which is primarily composed of plastics. European policies, such as Oslo-Paris Convention (OSPAR) and Marine StrategyFramework Directive (MSFD) have adopted the monitoring of a seabird species, the Northern Fulmar (Fulmarus glacialis), as an environmental quality indicator through the analysis of stomach contents of beached Fulmar specimens. The aims of this research were to: firstly set a baseline investigation of multispecies of seabirds in Ireland affected by the ingestion of litter and, secondly to investigate the feasibility of using Fulmar and/or other potential species of seabird as an indicator for marine debris in Ireland through beached bird surveys. Within 30 months, 121 birds comprising 16 different species werecollected and examined for the presence of litter. Of these, 27.3% (n ¼ 33) comprising 12 different species were found to ingest litter, mainly plastics. The average mass of ingested litter was 0.141 g. Among 14 sampled Northern Fulmars, 13 (93%) had ingested plastic litter, all of them over the 0.1 g threshold used in OSPAR and MSFD policy target definitions. Results show that seabirds in Ireland are ingesting marine litter, as in many other countries in the world. Monitoring seabird litter ingestion has the potential to form part of a wider marine litter monitoring programme that can help to inform mitigation andmanagement measures for marine litter

Citation File Format and cffinit

Creating software for research in an academic setting brings a few extra obligations compared to when you work in industry. For example, research software should be FAIR (Findable, Accessible, Interoperable and Reusable) to make research reproducible. Citing software is an important building block in this, but it’s sometimes not easy to find the relevant correct metadata for software. You can support the researchers using your software by making this information available in a CITATION.cff file in the Citation File Format (CFF). This is also good for you to get recognition. CFF is a plain text format based on YAML that provides the relevant fields for enabling the correct citation of software. This session will start off by introducing CFF, and then continue with an interactive session using cffinit. cffinit is the best visual tool to get you started with creating CFF files, or editing existing ones. It helps you automatically validate your CFF file from your browser - you don’t need to install anything on your computer. Beyond cffinit, the Citation File Format is integrated with other existing platforms and tools. At the end of the session, we will demonstrate how your CFF file automatically improves the metadata for publications of your software in the open access repository Zenodo

Evaluation of a marine mammal status and trends contaminants indicator for European waters.

Marine mammals are vulnerable to the bioaccumulation, biomagnification and lactational transfer of specific types of pollutants, such as industrial polychlorinated biphenyls (PCBs), due to their long-life spans, feeding at a high trophic level and unique fat stores that can serve as depots for these lipophilic contaminants. Currently, European countries are developing indicators for monitoring pollutants in the marine environment and assessing the state of biodiversity, requirements under both Regional Seas Conventions and European legislation. As sentinel species for marine ecosystem and human health, marine mammals can be employed to assess bioaccumulated contaminants otherwise below current analytical detection limits in water and lower trophic level marine biota. To aid the development of Regional Seas marine mammal contaminants indicators, as well as Member States obligations under descriptor 8 of the EU Marine Strategy Framework Directive, the current study aims to further develop appropriate methodological standards using data collected by the established UK marine mammal pollutant monitoring programme (1990 to 2017) to assess the trends and status of PCBs in harbour porpoises. Within this case study, temporal trends of PCB blubber concentration in juvenile harbour porpoises were analysed using multiple linear regression models and toxicity thresholds for the onset of physiological (reproductive and immunological) endpoints were applied to all sex-maturity groups. Mean PCB blubber concentrations were observed to decline in all harbour porpoise Assessment Units and OSPAR Assessment Areas in UK waters. However, a high proportion of animals were exposed to concentrations deemed to be a toxicological threat, though the relative proportion declined in most Assessment Units/Areas over the last 10 years of the assessment. Recommendations were made for improving the quality of the assessment going forward, including detailing monitoring requirements for the successful implementation of such an indicator