A. Louise Allcock

University of Galway | NUI Galway · Ryan Institute

As exploration of ocean depths >1000 m is only possible by expensive remotely operated underwater vehicles, deep-sea invertebrates represent a largely untapped source of marine metabolites for potential applications in medicine. Our current study aims to investigate these deep-sea invertebrates in Ireland to discover new biological and chemical div...

Deep-sea corals are rarely identified to species due to a lack of taxonomic expertise and paucity of sampling. Herein we describe a new genus from the family Keratoisididae collected from the Northeast Atlantic. Using both nuclear (2010 conserved element loci) and complete mitogenome phylogenies, we found this genus to be closely related to the gen...

The authors regret that during the proofing process, wherein the authors requested the replacement of the second part of Figure 2, which extends over two pages, the production team inadvertently deleted the first part, leaving an incomplete figure. The complete two-part figure is reproduced herein. The journal would like to apologise for any inconv...

Historically, evolutionary studies have not been able to resolve relationships within Octocorallia but recent advances in genomic techniques have allowed large numbers of Ultra Conserved Elements and exons, collectively referred to as conserved elements, to be extracted from the nuclear genome. Few studies have compared evolutionary histories gener...

The marine-based West Antarctic Ice Sheet (WAIS) is considered vulnerable to irreversible collapse under future climate trajectories, and its tipping point may lie within the mitigated warming scenarios of 1.5° to 2°C of the United Nations Paris Agreement. Knowledge of ice loss during similarly warm past climates could resolve this uncertainty, inc...

Keratoisididae is a globally distributed, and exclusively deep-sea, family of octocorals that contains species and genera that are polyphyletic. An alphanumeric system, based on a three-gene-region phylogeny, is widely used to describe the biodiversity within this family. That phylogeny identified 12 major groups although it did not have enough sig...

Synopsis Cryptic species complexes represent an important challenge for the adequate characterization of Earth’s biodiversity. Oceanic organisms tend to have greater unrecognized cryptic biodiversity since the marine realm was often considered to lack hard barriers to genetic exchange. Here, we tested the effect of several Atlantic and Mediterranea...

The Irish–Scottish margin is geologically and oceanographically heterogeneous. Source waters of subpolar and subtropical origin interact with banks, seamounts, submarine canyon systems, escarpments, and mound provinces resulting in rich and diverse benthic communities that are influenced by local and regional hydrodynamics (e.g., internal waves, ti...

Based on a comprehensive analysis of molecular sequence data, the Sepiidae genera Acanthosepion Rochebrune, 1884; Ascarosepion Rochebrune, 1884; Aurosepina Jothinayagam, 1987; Decorisepia Iredale, 1926; Doratosepion Rochebrune, 1884; Rhombosepion Rochebrune, 1884 and Spathidosepion Rochebrune, 1884 are here re-instated and formally recognised as va...

Keratoisididae is a globally distributed, and exclusively deep-sea, family of octocorals that contains species and genera that are polyphyletic. An alphanumeric system, based on a three-gene-region phylogeny, is widely used to describe the biodiversity within this family. That phylogeny identified 12 major groups although it did not have enough sig...

Despite being landed in commercial cephalopod fisheries, species of Alloteuthis are not yet well defined, with A. subulata and A. media often confused. DNA barcoding combined with morphometric analyses has begun to clarify the distinction between these two morphologically similar species but has been limited in its geographic coverage to date. Here...

WGCEPH worked on six Terms of Reference. These involved reporting on the status of stocks; reviewing advances in stock identification, assessment for fisheries management and for the Marine Strategy Framework Directive (MSFD), including some exploratory stock assessments; reviewing impacts of human activities on cephalopods; developing identificati...

Phylogenies for Octopoda have, until now, been based on morphological characters or a few genes. Here we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes of twenty Octopoda specimens, comprising 18 species of Cirrata and Incirrata, representing 13 genera and all five putative families of Cirrata (Cirroctopodidae, Cirrote...

The marine-based West Antarctic Ice Sheet (WAIS) is considered vulnerable to collapse under future climate trajectories and may even lie within the mitigated warming scenarios of 1.5–2 °C of the United Nations Paris Agreement. Knowledge of ice loss during similarly warm past climates, including the Last Interglacial period, when global sea levels w...

Previous chemical investigation of the Irish deep-sea soft coral Duva florida led to the identification of tuaimenal A (10), a new merosesquiterpene containing a highly substituted chromene core and modest cytotoxicity against cervical cancer. Further MS/MS and NMR-guided investigation of this octocoral has resulted in the isolation and characteriz...

Cephalopod beaks are essential for prey acquisition and fragmentation during feeding. Thus, it is expected that ecological pressures affect cephalopod beak shape. From a practical perspective, these structures are also used to identify gut contents of marine megafauna, such as toothed whales, sharks, seabirds, and large pelagic fishes. Here, we inv...

The term Marine Animal Forest (MAF) was first described by Alfred Russel Wallace in his book “The Malay Archipelago” in 1869. The term was much later re-introduced and various descriptions of MAFs were presented in great detail as part of a book series. The international research and conservation communities have advocated for the future protection...

Deep-sea corals and sponges are known to form associations with other invertebrates, which often use them as a substrate, shelter or as a source of food. Although marine imaging has already proved to be a turning point in deep-sea ecological research, associations are still mainly studied through the analysis of collected specimens. In 2016, 2017...

Four undescribed sesquiterpenoids, crannenols A-D (1-4), have been isolated from CHCl2 and MeOH extracts of the deep-sea bamboo coral Acanella arbuscula. The corals were collected from a submarine canyon on the edge of Ireland's Porcupine Bank via a remotely operated vehicle. The structure elucidation of these (Z,E)-α-farnesene derivatives was achi...

We examine the phylogeny of sea pens using sequences of whole mitochondrial genomes and the nuclear ribosomal cluster generated through low coverage Illumina sequencing. Taxon sampling includes 30 species in 19 genera representing 13 families. Ancestral state reconstruction shows that most sea pen mitochondrial genomes have the ancestral gene order...

Deep-sea corals are important benthic inhabitants that support the biodiversity and function of the wider faunal community; however, their taxonomy is underdeveloped and their accurate identification is often difficult. In our study, we investigated the utility of a superextended (>3000 bp) barcode and explored the effectiveness of various molecula...

The inshore commercial squids, Loligo vulgaris and L. forbesii, co-occur in the ecoregions of Celtic Seas and Greater North Sea but the spatio-temporal structure of their spawning ranges is poorly understood. To help solve the problem, data sets collected during the last 30 years by British, German, French, and Irish scientists, as well as observat...

Cold water benthic environments are a prolific source of structurally diverse molecules with a range of bioactivities against human disease. Specimens of a previously chemically unexplored soft coral, Duva florida, were collected during a deep-sea cruise that sampled marine invertebrates along the Irish continental margin in 2018. Tuaimenal A (1),...

Cold water benthic environments are a prolific source of structurally diverse molecules with a range of bioactivities against human disease. Specimens of a previously chemically unexplored soft coral, Duva florida, were collected during a deep-sea cruise that sampled marine invertebrates along the Irish continental margin in 2018. Tuaimenal A (1),...

A selection of antiviral compounds from the Drug Repurposing Hub were screened as potential inhibitors against SARS-CoV-2 protein targets using CIFDock, a flexible docking method. CIFDock allows for a fully flexible active site of the protein-ligand complex and retaining of explicit water molecules throughout docking simulations. This method provid...

Recent review papers have addressed progress in stock assessment and forecasting for fished cephalopods but there remains a need to develop appropriate management for many European cephalopod fisheries, given that cephalopods are not quota species under the Common Fisheries Policy. Here we briefly review potential barriers to sustainable fishing an...

In past centuries, the impacts on cephalopods from humankind were negligible. The first documented small-scale exploitation of cephalopods occurred in the Mediterranean and Asia. Between 1950-2019, global cephalopod catches increased by about an order of magnitude, from 0.5 million tones to a peak of 4.85 million tons. The human impact on the ocean...

Phylogenies for the Octopodiformes have, until now, been based on morphological characters or several genes. Here we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes of twenty Octopoda specimens, comprising 18 species of Cirrata and Incirrata representing 13 genera and all four families of Cirrata (Cirroctopodidae, Cirro...

The processes that control diversification and speciation in deep-sea species are poorly known. Here, we analyzed data produced by Restriction-Site Associated DNA Sequencing (RAD-Seq) of octocorals in the genus Paramuricea to elucidate diversification patterns and examine the role of environmental gradients in their evolution. The genus Paramuricea...

Members of the family Ommastrephidae Steenstrup, 1857 sustain large and economically important fisheries. As a result, many biological aspects related to fisheries (e.g., reproductive biology, trophism) have been extensively studied. However, knowledge on the taxonomic relationships between ommastrephids remains poor and controversial. Currently, t...

Cephalopod beaks are important chitinous hard structures, used for preying upon and fragmenting prey. Thus, it is expected that ecological pressures drive cephalopod beak shape. These structures, which are used in species identification, may exhibit a certain association with phylogenetic relationships among cephalopod species. Here, we investigate...

Historically, marine oceanic open environments have been considered without barriers to dispersal, and the subsequent speciation of lineages present in distant areas. As a consequence, many marine pelagic invertebrates are considered as monotypic cosmopolitan taxa. However, this view has been consistently challenged in the last decades by the disco...

Knowledge of stock structure is a priority for effective assessment of commercially-fished cephalopods. Loligo forbesii squid are thought to migrate inshore for breeding and offshore for feeding and long-range movements are implied from past studies showing genetic homogeneity in the entire neritic population. Only offshore populations (Faroe and R...

Since the introduction of the online open-source GNPS, molecular networking has quickly become a widely applied tool in the field of natural products chemistry, with applications from dereplication, genome mining, metabolomics, and visualization of chemical space. Studies have shown that data dependent acquisition (DDA) parameters affect molecular...

Cold water benthic environments are a prolific source of structurally diverse molecules with a range of bioactivity against human disease. Specimens of a previously chemically unexplored soft coral, Drifa sp., were collected during a deep-sea cruise that sampled marine invertebrates along the Irish continental margin in 2018. Tuaimenal A ( 1 ), a c...

Sponges are at the forefront of marine natural product research. In the deep sea, extreme conditions have driven secondary metabolite pathway evolution such that we might expect deep-sea sponges to yield a broad range of unique natural products. Here, we investigate the chemodiversity of a deep-sea tetractinellid sponge, Characella pachastrelloides...

Vulnerable marine ecosystems (VMEs) are particularly susceptible to bottom-fishing activity as they are easily disturbed and slow to recover. A data-driven approach was developed to provide management options for the protection of VMEs under the European Union “deep-sea access regulations.” A total of two options within two scenarios were developed...

Bobtail and bottletail squid are small cephalopods with striking anti-predatory defensive mechanisms, bioluminescence, and complex morphology; that inhabit nektobenthic and pelagic environments around the world’s oceans. Yet, the evolution and diversification of these animals remain unclear. Here, we used shallow genome sequencing of thirty-two bob...

European squid, Loligo vulgaris and veined squid, Loligo forbesii have nearly coinciding distributions in the northeast Atlantic, a similar reproductive seasonality, and largely overlapping depth ranges of spawning grounds. There are no unambiguous criteria to distinguish between egg masses of both species. This pioneering study was focused on the...

Fungi populate deep Oceans in extreme habitats characterized by high hydrostatic pressure, low temperature and absence of sunlight. Marine fungi are potential major contributors to biogeochemical events, critical for marine communities and food web equilibrium under climate change conditions and a valuable source of novel extremozymes and small mol...

Historically, marine oceanic open environments have been considered without barriers to dispersal, and the subsequent speciation of lineages from distant areas. As a consequence, many marine pelagic invertebrates are considered as monotypic cosmopolitan taxa, sometimes even including divergent geographic morphotypes. However, this view has been con...

In total, 90 gelatinous spheres, averaging one meter in diameter, have been recorded from ~1985 to 2019 from the NE Atlantic Ocean, including the Mediterranean Sea, using citizen science. More than 50% had a dark streak through center. They were recorded from the surface to ~60-70 m depth, mainly neutrally buoyant, in temperatures between 8-24⁰C....

Here we analyze existing quantitative data available for cephalopod brains based on classical contributions by J.Z. Young and colleagues, to cite some. We relate the relative brain size of selected regions (area and/or lobe), with behavior, life history, ecology and distribution of several cephalopod species here considered. After hierarchical clus...

The United Nations Decade of Ocean Science for Sustainable Development presents an exceptional opportunity to effect positive change in ocean use. We outline what is required of the deep-sea research community to achieve these ambitious objectives.

The ocean plays a crucial role in the functioning of the Earth System and in the provision of vital goods and services. The United Nations (UN) declared 2021–2030 as the UN Decade of Ocean Science for Sustainable Development. The Roadmap for the Ocean Decade aims to achieve six critical societal outcomes (SOs) by 2030, through the pursuit of four o...

Computed tomography (CT) scanning allows for accurate 3D imaging of specimens and their internal structures in a non-invasive, non-destructive manner, which is particularly important for precious specimens, i.e. type specimens or for rare or difficult sample specimens such as cirrate octopods. When successful, micro-CT scans of specimens allow for...

Oceanic squids of the order Oegopsida Orbigny, 1845 have great ecological and evolutionary importance, and some of them also are important economic resources. Despite that, they are among the most mysterious groups of pelagic organisms. There are still many knowledge gaps, such as the actual relationships between the 22 oceanic squid families, and...

Despite the ecological and economic importance of oceanic squids of the order Oegopsida Orbigny 1845, they are among the most mysterious groups of pelagic organisms. Starting in October 2019, the 2-year postdoc project GOIPD/2019/460 “Genome and specific biodiversity of oceanic squids assessed through Next Generation Sequencing”, funded by the Iris...

I'm interested in cephalopod phylogenetics, systematics, taxonomy, natural history, reproductive biology and trophic ecology of cephalopods, especially oceanic squids. Currently, as an Irish Research Council postdoc fellow, my research is focussed on the phylogenetics of oegopsid squids, assessed through shallow whole genome sequencing (Genome Skim...

Black corals (Anthozoa: Antipatharia) are an ecologically and culturally important group of deep-sea cnidarians. However, as the majority of species inhabit depths >50 m, they are relatively understudied. The inaccessibility of well-preserved tissue for species of interest has limited the scope of molecular analysis, and as a result only a small nu...

Many descriptions of paralarval and juvenile cephalopods are poor. By using DNA barcoding, a global bio-identification system for animals, along with morphological investigation, we can confirm species identifications. We have a better chance of eliminating misidentifications and, therefore, documenting the correct abundance and distribution of cep...

Several species of deep-diving odontocetes, including beaked whales, sperm whales and pilot whales, are associated with steep continental slope habitat in the northeast Atlantic, where they feed on cephalopods and meso-bathypelagic fish. Some species such as sperm whales are listed as vulnerable by the IUCN red list, whilst many beaked whale specie...

Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has...

Extensive areas of our Planet are covered by deep sea, constituting the major environment existing on Earth and a valuable reservoir of bioactive compounds. Musculoskeletal diseases such as osteoarthritis and osteoporosis could benefit from the discovery of new drugs to induce tissue regeneration through control of stem cell fate. In the sea, coral...

Interactions in the Marine Benthos - edited by Stephen J. Hawkins August 2019

Deep-sea hydrothermal vents were discovered only 40 years ago. We now know that around 600 of these auditorium-sized oases exist in the vast expanse of the ocean, flourishing with unique life that we are nowhere close to fully understanding. This lack of baseline biodiversity assessments creates an ‘out of sight, out of mind’ conservation dilemma f...

We present the first documented complete mitogenomes of deep-sea Pennatulacea, representing nine genera and eight families. These include one species each of the deep-sea genera Funiculina, Halipteris, Protoptilum and Distichoptilum, four species each of Umbellula and Pennatula, three species of Kophobelemnon and two species of Anthoptilum, as well...

Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has...

Deep sea represents the vast majority of all Oceans and the predominant environment existing on Earth. Beside its unmatched dimension stands its biodiversity, only comparable to barrier reefs or rainforests (1, 2). Despite its scientific relevance the deep sea has never been thoroughly studied in the past because of the difficulty of access, but th...

The original version of this article unfortunately contained a mistake.

This study reinforces and extends the findings of previous molecular studies showing that there is a close relationship between species assigned to the sponge genera Halicnemia, Higginsia, Paratimea and Stelligera and that the family Heteroxyidae is polyphyletic. The present study has led to the description of one new species of Halicnemia and six...

Bathyal octopods of the genus Graneledone Joubin, 1918 in the northeast Pacific differ dramatically in skin texture. To test the hypothesis that these differences are associated with geography, we quantified the skin warts and tubercles of 50 specimens collected between 36°N and 46°N from 1116 to 2850 m depth. Using Principal Component Analysis (PC...