Southern Ocean biodiversity reflects past climate, oceanographic, and tectonic changes. Molecular data from contemporary populations carry signatures of these processes. Here, we review new molecular ...studies on Southern Ocean benthic fauna. Many of these studies focus on species with extensive geographic or bathymetric distributions, and resolve taxonomic questions. Reviewing all available data, we show that, in addition to reflecting life-history characteristics, the molecular signals found in these studies provide an insight into how species survived the last glacial maximum (LGM). We identify molecular signatures that are characteristic of surviving glacial cycles in small refugia on the continental shelf and distinguish them from molecular signatures that are indicative of surviving glacial cycles in the deep sea.
Abstract
Oceanic squids of the order Oegopsida are ecologically and economically important members of the pelagic environment. They are the most diverse group of cephalopods, with 24 families that ...are divergent morphologically. Despite their importance, knowledge of phylogenetic relationships among oegopsids is less than that among neritic cephalopods. Here, we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes for 35 selected oceanic squids, which were generated using genome skimming. We performed maximum likelihood and Bayesian inference analyses that included 21 of the 24 oegopsid families. In our analyses, the architeuthid, chiroteuthid and enoploteuthid family groups, which have been proposed previously based on morphological and natural history characteristics, were retrieved as monophyletic. The morphologically divergent Cranchiidae formed a well-supported clade with families Ommastrephidae and Thysanoteuthidae, with a unique mitochondrial gene order. The family Lycoteuthidae was revealed as paraphyletic and contained Pyroteuthidae. Thus, the two lycoteuthid subfamilies are herein elevated to family level, increasing the number of oegopsid squid families to 25. In order to describe the diversity and evolutionary trends of oegopsid squids accurately, the superfamilies Architeuthoidea, Chiroteuthoidea, Cranchioidea and Enoploteuthoidea are resurrected from the literature, and the superfamilies Cycloteuthoidea, Octopoteuthoidea and Pholidoteuthoidea are proposed. The phylogenetic positions of Gonatidae, Histioteuthidae and Onychoteuthidae were not stable in our phylogenetic analyses and are not assigned to a superfamily. This study supports the utility of genome skimming to solve the phylogenetic relationships of oceanic squids.
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•Mitochondrial and nuclear phylogenies of Pennatulacea conflict.•Gene order A confirmed as ancestral through ancestral state reconstruction.•Mitochondrial gene order rearrangements ...confined to single deep-sea clade of Pennatulacea.•Sliding window analyses show most suitable gene regions for DNA barcoding.
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, and that Pennatulacea with diverse gene orders are found in a single clade. The monophyly of Pennatulidae and Protoptilidae are rejected by both the mitochondrial and nuclear dataset, while the mitochondrial dataset further rejects monophyly of Virgulariidae, and the nuclear dataset rejects monophyly of Kophobelemnidae. We show discordance between nuclear ribosomal gene cluster phylogenies and whole mitochondrial genome phylogenies and highlight key Pennatulacea taxa that could be included in cnidarian genome-wide studies to better resolve the sea pen tree of life. We further illustrate how well frequently sequenced markers capture the overall diversity of the mitochondrial genome and the nuclear ribosomal genes in sea pens.
Microplastics are a ubiquitous pollutant in our seas today and are known to have detrimental effects on a variety of organisms. Over the past decade numerous studies have documented microplastic ...ingestion by marine species with more recent investigations focussing on the secondary impacts of microplastic ingestion on ecosystem processes. However, few studies so far have examined microplastic ingestion by mesopelagic fish which are one of the most abundant pelagic groups in our oceans and through their vertical migrations are known to contribute significantly to the rapid transport of carbon and nutrients to the deep sea. Therefore, any ingestion of microplastics by mesopelagic fish may adversely affect this cycling and may aid in transport of microplastics from surface waters to the deep-sea benthos. In this study microplastics were extracted from mesopelagic fish under forensic conditions and analysed for polymer type utilising micro-Fourier Transform Infrared Spectroscopy (micro-FTIR) analysis. Fish specimens were collected from depth (300 - 600 m) in a warm-core eddy located in the Northwest Atlantic, 1200 km due west of Newfoundland during April and May 2015. In total, 233 fish gut contents from seven different species of mesopelagic fish were examined. An alkaline dissolution of organic materials from extracted stomach contents was performed and the solution filtered over a 0.7 µm borosilicate filter. Filters were examined for microplastics and a subsample originating from 35 fish was further analysed for polymer type through micro-FTIR analysis. 73% of all fish contained plastics in their gut contents with Gonostoma denudatum having the highest ingestion rate (100 %) followed by Serrivomer beanii (93 %) and Lampanyctus macdonaldi (75 %). Overall, we found a much higher occurrence of microplastic fragments, mainly polyethylene fibres, in the gut contents of mesopelagic fish than previously reported. Stomach fullness, species and the depth at which fish were caught at, were found to have no effect on the amount of microplastics found in the gut contents. However, these plastics were similar to those sampled from the surface water. Additionally, using forensic techniques we were able to highlight that fibres are a real concern rather than an artefact of airborne contamination.
Future challenges in cephalopod research Xavier, José C.; Allcock, A. Louise; Cherel, Yves ...
Journal of the Marine Biological Association of the United Kingdom,
08/2015, Volume:
95, Issue:
5
Journal Article
Peer reviewed
Open access
Cephalopods (Mollusca: Cephalopoda) play an important role as keystone invertebrates in various marine ecosystems, as well as being a valuable fisheries resource. At the World Malacological Congress, ...held 21–28 July 2013 in Ponta Delgada, Azores, Portugal, a number of cephalopod experts convened to honour the contribution of the late Malcolm R. Clarke, FRS (1930–2013) to cephalopod research. Endorsed by the Cephalopod International Advisory Council (CIAC), the meeting discussed some of the major challenges that cephalopod research will face in the future. These challenges were identified as follows: (1) to find new ways to ascertain the trophic role and food web links of cephalopods using hard tissues, stable isotopes and novel concepts in theoretical ecology; (2) to explore new approaches to the study of cephalopod morphology; (3) to further develop cephalopod aquaculture research; (4) to find new ways to ascertain cephalopod adaptation and response to environmental change; (5) to strengthen cephalopod genetics research; and (6) to develop new approaches for cephalopod fisheries and conservation. The present paper presents brief reviews on these topics, followed by a discussion of the general challenges that cephalopod research is bound to face in the near future. By contributing to initiatives both within CIAC and independent of CIAC, the principle aim of the paper is to stimulate future cephalopod research.
In order to develop a gripping system or control strategy that improves scientific sampling procedures, knowledge of the process and the consequent definition of requirements is fundamental. ...Nevertheless, factors influencing sampling procedures have not been extensively described, and selected strategies mostly depend on pilots' and researchers' experience. We interviewed 17 researchers and remotely operated vehicle (ROV) technical operators, through a formal questionnaire or in-person interviews, to collect evidence of sampling procedures based on their direct field experience. We methodologically analyzed sampling procedures to extract single basic actions (called atomic manipulations). Available equipment, environment and species-specific features strongly influenced the manipulative choices. We identified a list of functional and technical requirements for the development of novel end-effectors for marine sampling. Our results indicate that the unstructured and highly variable deep-sea environment requires a versatile system, capable of robust interactions with hard surfaces such as pushing or scraping, precise tuning of gripping force for tasks such as pulling delicate organisms away from hard and soft substrates, and rigid holding, as well as a mechanism for rapidly switching among external tools.
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•Spirulida, Bathyteuthoidea and Oegopsida form a monophyletic group.•Sepiidae is the sister taxon to a clade containing all extant Decapodiformes.•A monophyletic clade containing ...Idiosepiidae and Sepiolida is supported by mitochondrial gene order analyses.•Spirulida mitochondrial gene order is identical to that of Octopodiformes.
The phylogenetic position of the only known species within the order Spirulida, the Ram’s Horn Squid, Spirula spirula, may be the key to resolving relationships within Decapodiformes (squids and cuttlefishes). Spirula spirula possesses several unique features including an internal calcareous chambered shell unlike the familiar cuttlebone of Sepiidae (cuttlefishes). The shell is reduced to a gladius or absent in other decapod clades. To resolve decapodiform phylogenetic relationships we sequenced the mitochondrial genome of S. spirula and Sepiadarium austrinum and analysed these along with other mitochondrial genomes. Sequence analyses found that S. spirula and Sepiidae, the only two extant phragmocone bearing groups, were not sister taxa. Rather, in most analyses S. spirula was placed within a clade containing Bathyteuthoidea and Oegopsida either as the sister taxon to Bathyteuthoidea+Oegopsida or the sister taxon to Bathyteuthoidea only, depending upon the analysis method. Sepiidae was the sister taxon to a clade containing all remaining decapods. Spirulid mitochondrial gene order was identical to that of Octopodiformes, which we recognize as close to that of ancestral molluscs. The phylogenetic position of Idiosepiidae differed among analysis methods of molecular sequence data. However, gene order analysis resolved a highly supported monophyletic relationship containing Idiosepiidae and Sepiolida.
Difficulties in elucidating the evolutionary history of the octopods have arisen from problems in identifying informative morphological characters. Recent classifications have divided the largest ...group, the incirrate octopods, into five groups. These include the pelagic superfamily Argonautoidea and three gelatinous pelagic families (Vitreledonellidae, Bolitaenidae, Amphitretidae). All benthic incirrate octopods have been accommodated in the family Octopodidae, itself divided into four subfamilies, Octopodinae, Eledoninae, Bathypolypodinae and Graneledoninae, which are defined by the presence or absence of an ink sac, and uniserial or biserial sucker arrangements on the arms. We used relaxed clock models in a Bayesian framework and maximum likelihood methods to analyse three nuclear and four mitochondrial genes of representatives from each of the previous subfamilies. Strong evidence indicates that the family Octopodidae is paraphyletic and contains the gelatinous pelagic families. The subfamilies of Octopodidae recognised in earlier works do not reflect evolutionary history. The following clades were supported in all analyses: (1) Eledone/Aphrodoctopus, (2) Callistoctopus/Grimpella/Macroctopus/Scaeurgus, (3) Abdopus/Ameloctopus/Amphioctopus/Cistopus/Hapalochlaena/Octopus, (4) Enteroctopus/Muusoctopus/Vulcanoctopus, (5) Vitreledonella/Japetella, (6) Southern Ocean endemic and deep-sea taxa with uniserial suckers. These clades form the basis for a suite of taxa assigned family taxonomic rank: Amphitretidae, Bathypolypodidae, Eledonidae, Enteroctopodidae, Megaleledonidae and Octopodidae sensu nov. They are placed within the superfamily Octopodoidea.
Abstract
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 Rockall Bank) were considered distinct. The present study applied mitchondrial and microsatellite markers (nine loci) to samples from Rockall Bank, north Scotland, North Sea, various shelf locations in Ireland, English Channel, northern Bay of Biscay, north Spain, and Bay of Cadiz. No statistically significant genetic sub-structure was found, although some non-significant trends involving Rockall were seen using microsatellite markers. Differences in L. forbesii statolith shape were apparent at a subset of locations, with most locations showing pairwise differences and statoliths from north Ireland being highly distinct. This suggests that (i) statolith shape is highly sensitive to local conditions and (ii) L. forbesii forms distinguishable groups (based on shape statistics), maintaining these groups over sufficiently long periods for local conditions to affect the shape of the statolith. Overall evidence suggests that L. forbesii forms separable (ecological) groups over short timescales with a semi-isolated breeding group at Rockall whose distinctiveness varies over time.
Submarine canyons are major geomorphic features of continental margins around the world. Several recent multidisciplinary projects focused on the study of canyons have considerably increased our ...understanding of their ecological role, the goods and services they provide to human populations, and the impacts that human activities have on their overall ecological condition. Pressures from human activities include fishing, dumping of land-based mine tailings, and oil and gas extraction. Moreover, hydrodynamic processes of canyons enhance the down-canyon transport of litter. The effects of climate change may modify the intensity of currents. This potential hydrographic change is predicted to impact the structure and functioning of canyon communities as well as affect nutrient supply to the deep-ocean ecosystem. This review not only identifies the ecological status of canyons, and current and future issues for canyon conservation, but also highlights the need for a better understanding of anthropogenic impacts on canyon ecosystems and proposes other research required to inform management measures to protect canyon ecosystems.
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