Hierarchical Fish Species Detection in Real-Time Video Using YOLO

Master's thesis in Information- and communication technology (IKT590)Information gathering of aquatic life is often based on time consuming methods with a foundation in video feeds. It would be beneficial to capture more information in a cost effective manner from video feeds, and video object detection has an opportunity to achieve this. Recent research has shown promising results with the use of YOLO for object detection of fish. As under-water conditions can be difficult and fish species hard to discriminate, we propose the use of a hierarchical structures in both the classification and the dataset to gain valuable information. With the use of hierarchical classification and other techniques we present YOLO Fish. YOLO Fish is a state of the art object detector on nordic fish species, with an mAP of 91.8%. For a more stable video, YOLO Fish can be used with the object tracking algorithm SORT. This results in a complete fish detector for real-time video

Snapshot of macroalgae and fish assemblages in temperate reefs in the Southern European Atlantic Ecoregion

Most of the biodiversity studies in the South European Atlantic Shelf ecoregion are limited to shallow subtidal or intertidal habitats, while deeper reef habitats, also of relevant ecological importance, are particularly understudied. Macroalgal communities, associated fauna, and sea surface temperature were studied in deep reefs (25-30 m) at two locations in this ecoregion: Parcel, North of Portugal (41 degrees N), and Tarifa, Southern Spain (35 degrees N). Specifically, algal assemblages were assessed using biomass collection and associated ichthyofauna was assessed using visual census techniques using scuba. Seawater surface temperature was higher (>3 degrees C) in the southern region-Tarifa, compared to the northern region-Parcel. Our survey revealed 18 fish species and 23 algae species. The highest abundance of cold-water species (both macroalgae and fish species) was recorded in Parcel and warm-water species were dominant in Tarifa. In light of climate global trends, both regions might experience biodiversity shifts towards tropicalization. Current knowledge on their biodiversity is imperative to further evaluate potential shifts.info:eu-repo/semantics/publishedVersio

The feeding ecology of some zooplankters that are important prey items of larval fish

Diets of 76 species of fish larvae from most oceans of the world were inventoried on the basis of information in 40 published studies. Although certaln geographlc, size- and taxon-specific patterns were apparent, certain zooplankton taxa appeared in the diets of larvae of a variety of fish species in numerous localities. Included were six genera of calanoid copepods (Acartia, Calanus, Centropages, Paracalanus, Pseudocaianus, Temora), three genera of cyclopoid copepods (Corycaeus, Oilhona, Oncata), harpacticoid copepods, copepod nauplii, tintinoids, cladocerans of the genera Evadne and Podon, barnacle nauplii, gastropod larvae, pteropods of the genus Limacina, and appendicularians. Literature on feeding habits of these zooplankters reveals that most of the copepods are omnivorous, feeding upon both phytoplankton and other zooplankton. Some taxa, such as Calanus, Paracalanus, Pseudocalanus, and copepod nauplii appear to be primarily herbivorous, while others, such as Acartia, Centropages, Temora, and cyclopoids exhibit broad omnivory or carnivory. The noncopepod zooplankters are primarily filter-feeders upon pbytoplankton and/or bacterioplankton. Despite the importance of zooplankters in larval fish food webs, spectic knowledge of the feeding ecology of many taxa is poor. Further, much present knowledge comes only from laboratory investigations that may not accurately portray feeding habits of zooplankters in nature. Lack of knowledge of the feeding ecology of many abundant zooplankters, which are also important in larval fish food webs, precludes realistic understanding of pelagic ecosystem dynamics. (PDF file contains 34 pages.

Det norske småskalafiskeriet og databidrag til FAO-Duke-WorldFish prosjekt

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Applying length-based assessment methods to fisheries resources of the Bay of Biscay and Atlantic Iberian Waters: stock status and parameters sensitivity

ASLO 2021 Aquatic Sciences Virtual Meeting, 22–27 June 2021Length-based methods have been widely applied to estimate biological parameters and to understand the dynamics of marine resource populations within the category of data-limited stocksProject IMPRESS (RTI2018-099868-B-I00), ERDF, Ministry of Science, Innovation and Universities - State Research Agency, and also of GAIN (Xunta de Galicia), GRC MERVEX (nº IN607-A 2018-4)N

Species Identification And Phylogeny Of Phycinae Hakes And Related Gadoid Fishes

The term hake refers to a number of species belonging to multiple families of fish in the suborder Gadoidei and includes two main groups: Phycinae hakes (family Gadidae) and Merluccius spp. hakes (family Merlucciidae). The use of the common name hake for this diverse group of fish prompts questions such as: how are these species related and how can they be differentiated? Chapter one details the development of the Rapid Gadoid Identification Assay (RaGIA) for molecular identification of 11 gadoid fishes (including six hakes) using Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR-RFLP). RaGIA was used for species identification of fillets of hake, pollock and haddock sold in southern Maine markets. Testing found that market labeling was accurate; however, there were inconsistences in the labels provided by the fish distributors (from whom the markets obtained their fillets). Chapter two explores the development of a phylogeny, based on a mitochondrial DNA gene and a nuclear encoded gene, which includes members of the families Gadidae and Merlucciidae. The resulting phylogeny was used for morphological character mapping and investigation of trait evolution in this group. Consistent with previous studies, the analysis resolved the families Gadidae, as well as several subfamilies, and Merlucciidae with strong support. The putative Lotinae subfamily clade was not resolved in this analysis and suggests that further study is needed to investigate the monophyly of this group. The three dorsal fins and two anal fins morphological states as well as the life history characteristic of the absence of an egg oil globule were all found to be characteristic of the Gadinae, the most derived clade of the Gadoidei

Camera methods for the assessment of coastal biodiversity in low visibility environments

Coastal marine environments are important ecological, economic and social areas providing valuable services such as coastal protection, areas of recreation and tourism, fishing, climate regulation, biotic materials and biofuels. Marine renewable energy developments in the coastal environment are becoming a key objective for many countries globally. Assessing and monitoring the impacts of these developments on features, such as coastal biodiversity, becomes a difficult prospect in these environments due to the complexity of marine process at the locations in which these developments are targeted. This thesis explores the main challenges faced when assessing biodiversity in dynamic coastal environments, in particular those susceptible to high levels of turbidity. Various underwater camera techniques were trialled in reduced visibility environments including baited remote underwater video (BRUV), drop-down video and hydroacoustic methods. This research successfully refined BRUV guidelines in the North-East Atlantic region and identified key methodological and environmental factors influencing data collected BRUV deployments. Key findings included mackerel as the recommended bait type in this region and highlighting the importance of collecting consistent metadata when using these methods. In areas of high turbidity, clear liquid optical chambers (CLOCs) were successfully used to enhance the quality of information gathered using underwater cameras when monitoring benthic fauna and fish assemblages. CLOCs were applied to both conventional BRUV camera systems and benthic drop-down camera systems. Improvements included image quality, species and habitat level identification, and taxonomic richness. Evaluations of the ARIS 3000 imaging sonar and its capability of visualising distinguishing identifying features in low visibility environments for motile fauna showed mixed results with morphologically distinct species such as elasmobranchs much clearer in the footage compared to individuals belonging to finfish families. A combined approach of optical and hydroacoustic camera methods may be most suitable for adequately assessing coastal biodiversity in low visibility environments

Using stable isotopes and a Bayesian mixing model (FRUITS) to investigate diet at the Early Neolithic site of Carding Mill Bay, Scotland

We present δ13C, δ15N, and δ34S measurements on archaeological human and animal bone collagen samples from a shell midden dating to the Neolithic ca. 4000–3500 cal BC, together with measurements on modern fish and shellfish. These data were used in conjunction with the Bayesian mixing model, Food Reconstruction Using Isotopic Transferred Signals (FRUITS), to reconstruct human diet at the site. We demonstrate the importance of using a geographically appropriate faunal baseline in stable isotope paleodietary studies, and suggest that Neolithic individuals at this site consumed up to ca. 21% of dietary protein from marine resources, despite stable isotope ratios that imply a wholly terrestrial diet. This marine resource consumption does not significantly shift the radiocarbon (14C) dates of these individuals, so although we must consider the use of marine resources at the site, the chronology that has previously been established is secure. The δ13C and δ15N measurements from the archaeological herbivore bone collagen indicate that it is unlikely they ate plants enriched with fertilisers such as manure or seaweed. The δ34S values reveal a sea-spray effect; therefore, in this instance, δ34S cannot be used as a dietary indicator but can be used to demonstrate the likely locality of the fauna