Machine learning in marine ecology: an overview of techniques and applications

Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of ∼1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets.Machine learning in marine ecology: an overview of techniques and applicationspublishedVersio

Effect of boat noise on the behaviour of bluefin tuna Thunnus thynnus in the Mediterranean Sea

The effect of boat noise on the behaviour of bluefin tuna Thunnus thynnus was investigated in the Egadi Islands, Sicily, during spring 2005 using a fixed tuna trap set near shipping routes. Tuna behaviour was observed when exposed to both natural ambient sound and sound generated by hydrofoil passenger ferries, small boats and large car ferries. Acoustical and behavioural analyses were conducted with and without extraneous sound to define a list of behavioural categories. Each vessel produced different engine sounds with regard to their composition and bandwidth, and all were distinctly different from ambient sound levels. In the absence of boat noise, tuna assumed a concentrated coordinated school structure with unidirectional swimming and without a precise shape. When a car ferry approached, tuna changed swimming direction and increased their vertical movement toward surface or bottom; the school exhibited an unconcentrated structure and uncoordinated swimming behaviour. Hydrofoils appeared to elicit a similar response, but for shorter periods. Agonistic behaviour was more evident when exposed to sounds from outboard motors of small boats. This study showed that local noise pollution generated by boats produced behavioural deviations in tuna schools. Schooling enhances tuna homing accuracy during their spawning migration, and an alteration in schooling behaviour can affect the accuracy of their migration to spawning and feeding grounds

Hydrodynamic effects on the origin and quality of organic matter for bivalves: an integrated isotopic, biochemical and transplant study

Different hydrodynamic conditions can affect both the origin and the quality of organic matter available to bivalve molluscs. I chose 2 environments with very different hydrodynamics (a Mediterranean lagoon open to flow and a closed pond), but similar with regard to temperature, salinity, depth, wind exposure and algae coverage, to investigate this. The lagoon was characterised by active flow and bivalve molluscs, whereas the pond was closed off from the lagoon’s main flow but characterised by mussel beds of the highest density ever observed in the western Mediterranean. Biochemical features, 13C and 15N contents of particulate and sedimentary organic matter, and isotopic signatures of dominant organisms, were used as descriptors of the trophodynamics in both systems. In the lagoon, intense lateral drifting forces moved organic matter far from production sites, thereby depleting the water column of resuspended sedimentary organic matter. In the pond, winddriven conditions enhanced the coupling between the water column and the sediments, enriching the pond with resuspended sedimentary products. Integrating results, it was deduced that mussels in the pond could exploit, over time, organic matter produced in loco, continually rearranged in loco by means of wind-driven resuspension and consumed in loco with an efficiency able to sustain a massive secondary production. In contrast, under lagoon conditions, the benthic and pelagic habitats were uncoupled, so that each had its own independent status with its own dynamics and production. This reduced the suitability of this habitat for high levels of secondary production

Before and after Jaws: Changing representations of shark attacks

When the film Jaws (1975), about a rogue shark that terrorised a small seaside island community was released, it had an unprecedented paranoia effect on its audience that became entrenched into the psyche of bathers around the world; a fear that media hyperbole exploited. At the same time, the film was also responsible for a surge in scientific interest in sharks and the media responded by giving more attention to the important role of sharks in the marine ecology. In the long term, social perceptions of sharks, changed from fear to conservation, influencing local, national and international government conservation and management policies. Nevertheless, there persists the initial media frenzy after any shark attack and Jaws remains the touchstone for media reporting

The NASA planetary biology internship experience

By providing students from around the world with the opportunity to work with established scientists in the fields of biogeochemistry, remote sensing, and origins of life, among others, the NASA Planetary Biology Internship (PBI) Program has successfully launched many scientific careers. Each year approximately ten interns participate in research related to planetary biology at NASA Centers, NASA-sponsored research in university laboratories, and private institutions. The PBI program also sponsors three students every year in both the Microbiology and Marine Ecology summer courses at the Marine Biological Laboratory. Other information about the PBI Program is presented including application procedure

Using a spatial overlap approach to estimate the risk of collisions between deep diving seabirds and tidal stream turbines : a review of potential methods and approaches

Peer reviewedPublisher PD

The role of sand lances (Ammodytes sp.) in the Northwest Atlantic ecosystem: a synthesis of current knowledge with implications for conservation and management

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Staudinger, M. D., Goyert, H., Suca, J. J., Coleman, K., Welch, L., Llopiz, J. K., Wiley, D., Altman, I., Applegate, A., Auster, P., Baumann, H., Beaty, J., Boelke, D., Kaufman, L., Loring, P., Moxley, J., Paton, S., Powers, K., Richardson, D., Robbins, J., Runge, J., Smith, B., Spiegel, C., & Steinmetz, H. The role of sand lances (Ammodytes sp.) in the Northwest Atlantic ecosystem: a synthesis of current knowledge with implications for conservation and management. Fish and Fisheries, 00, (2020): 1-34, doi:10.1111/faf.12445.The American sand lance (Ammodytes americanus, Ammodytidae) and the Northern sand lance (A. dubius, Ammodytidae) are small forage fishes that play an important functional role in the Northwest Atlantic Ocean (NWA). The NWA is a highly dynamic ecosystem currently facing increased risks from climate change, fishing and energy development. We need a better understanding of the biology, population dynamics and ecosystem role of Ammodytes to inform relevant management, climate adaptation and conservation efforts. To meet this need, we synthesized available data on the (a) life history, behaviour and distribution; (b) trophic ecology; (c) threats and vulnerabilities; and (d) ecosystem services role of Ammodytes in the NWA. Overall, 72 regional predators including 45 species of fishes, two squids, 16 seabirds and nine marine mammals were found to consume Ammodytes. Priority research needs identified during this effort include basic information on the patterns and drivers in abundance and distribution of Ammodytes, improved assessments of reproductive biology schedules and investigations of regional sensitivity and resilience to climate change, fishing and habitat disturbance. Food web studies are also needed to evaluate trophic linkages and to assess the consequences of inconsistent zooplankton prey and predator fields on energy flow within the NWA ecosystem. Synthesis results represent the first comprehensive assessment of Ammodytes in the NWA and are intended to inform new research and support regional ecosystem‐based management approaches.This manuscript is the result of follow‐up work stemming from a working group formed at a two‐day multidisciplinary and international workshop held at the Parker River National Wildlife Refuge, Massachusetts in May 2017, which convened 55 experts scientists, natural resource managers and conservation practitioners from 15 state, federal, academic and non‐governmental organizations with interest and expertise in Ammodytes ecology. Support for this effort was provided by USFWS, NOAA Stellwagen Bank National Marine Sanctuary, U.S. Department of the Interior, U.S. Geological Survey, Northeast Climate Adaptation Science Center (Award # G16AC00237), an NSF Graduate Research Fellowship to J.J.S., a CINAR Fellow Award to J.K.L. under Cooperative Agreement NA14OAR4320158, NSF award OCE‐1325451 to J.K.L., NSF award OCE‐1459087 to J.A.R, a Regional Sea Grant award to H.B. (RNE16‐CTHCE‐l), a National Marine Sanctuary Foundation award to P.J.A. (18‐08‐B‐196) and grants from the Mudge Foundation. The contents of this paper are the responsibility of the authors and do not necessarily represent the views of the National Oceanographic and Atmospheric Administration, U.S. Fish and Wildlife Service, New England Fishery Management Council and Mid‐Atlantic Fishery Management Council. This manuscript is submitted for publication with the understanding that the United States Government is authorized to reproduce and distribute reprints for Governmental purposes. Any use of trade, firm or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government

Ranaviruses: Lethal Pathogens of Ectothermic Vertebrates

Animal Ecology; Environmental Health; Fish & Wildlife Biology & Management; Virology; Freshwater & Marine Ecology; Conservation Biology/Ecolog