Agent‐based models to investigate sound impact on marine animals: bridging the gap between effects on individual behaviour and population level consequences

Cetacean passive acoustic network in the Belgian part of the North sea

In 2016, a design for detecting harbor porpoises (Phocoena phocoena) in the Belgian part of the North Sea (BPNS) was developed in the framework of the LifeWatch project using Passive Acoustic Monitoring (PAM) loggers. In 2018, the network of deployments fully matured, and eight locations across the BPNS are presently housed with a C-POD (Chelonia Ltd., UK), a PAM logger moored on the seafloor using a multi-use platform. The PAM logger continuously listens for harbor porpoise click trains, but only stores the click parameters. This paper presents the generated data series of harbor porpoise click trains at a minute-resolution and the details on the individual click trains. The field recordings, methodology and processing are described, along with its data curation, integration and quality control. The data are annually published online in a standardized format, accompanied with the metadata description, and labelled with a digital object identifier for traceability. Data are published under a CC-BY license, allowing the use of data under the condition of providing reference to the original source.

Fitting individual-based models of spatial population dynamics to long-term monitoring data

Generating spatial predictions of species distribution is a central task for research and policy. Currently, correlative species distribution models (cSDMs) are among the most widely used tools for this purpose. However, a fundamental assumption of cSDMs, that species distributions are in equilibrium with their environment, is rarely fulfilled in real data and limits the applicability of cSDMs for dynamic projections. Process-based, dynamic SDMs (dSDMs) promise to overcome these limitations as they explicitly represent transient dynamics and enhance spatiotemporal transferability. Software tools for implementing dSDMs are becoming increasingly available, but their parameter estimation can be complex. Here, we test the feasibility of calibrating and validating a dSDM using long-term monitoring data of Swiss red kites (Milvus milvus). This population has shown strong increases in abundance and a progressive range expansion over the last decades, indicating a nonequilibrium situation. We construct an individual-based model using the RangeShiftR modeling platform and use Bayesian inference for model calibration. This allows the integration of heterogeneous data sources, such as parameter estimates from published literature and observational data from monitoring schemes, with a coherent assessment of parameter uncertainty. Our monitoring data encompass counts of breeding pairs at 267 sites across Switzerland over 22 years. We validate our model using a spatial-block cross-validation scheme and assess predictive performance with a rank-correlation coefficient. Our model showed very good predictive accuracy of spatial projections and represented well the observed population dynamics over the last two decades. Results suggest that reproductive success was a key factor driving the observed range expansion. According to our model, the Swiss red kite population fills large parts of its current range but has potential for further increases in density. We demonstrate the practicality of data integration and validation for dSDMs using RangeShiftR. This approach can improve predictive performance compared to cSDMs. The workflow presented here can be adopted for any population for which some prior knowledge on demographic and dispersal parameters as well as spatiotemporal observations of abundance or presence/absence are available. The fitted model provides improved quantitative insights into the ecology of a species, which can greatly aid conservation and management efforts.

Ship noise causes tagged harbour porpoises to change direction or dive deeper

Shipping is the most pervasive source of marine noise pollution globally, yet its impact on sensitive fauna remains unclear. We tracked 10 harbour porpoises for 5-10 days to determine exposure and behavioural reactions to modelled broadband noise (10 Hz-20 kHz, VHF-weighted) from individual ships monitored by AIS. Porpoises spent a third of their time experiencing ship noise above ambient, to which they regularly reacted by moving away during daytime and diving deeper during night. However, even ships >2 km away (noise levels of 93 ± 14 dB re 1 μPa2) caused animals to react 5-9 % of the time (∼18.6 ships/day). Ships can thus influence the behaviour and habitat use of cetaceans over long distances, with worrying implications for fitness in coastal areas where anthropogenic noise from dense ship traffic repeatedly disrupt their natural behaviour.

Emergent interactions in the management of multiple threats to the conservation of harbour porpoises

Human activities at sea are intensifying and diversifying. This is leading to more complex interactions of anthropogenic impacts requiring adaptable management interventions to mitigate their cumulative effects on biodiversity conservation and restoration objectives. Bycatch remains the dominant conservation threat for coastal cetaceans. Additionally, the indirect impact of repeated exposure to disturbances, particularly acoustic disturbances, can affect cetacean population growth and therefore conservation objectives. Pingers are used to ensonify nets to provide an effective mitigation of bycatch risk. As those become more prevalent across fisheries at risk to catch for example harbour porpoises, pingers become contributors to the anthropogenic noise landscape which may affect the vital rates of this species as well. Currently, we do not know how to best balance pinger prevalence to minimise both bycatch rate and the population consequences of acoustic disturbance (PCoD). Here we use an agent-based model to determine how pinger prevalence in nets can be adjusted to minimise bycatch rate and noise disturbance propagating to affect population growth for harbour porpoises. We show that counter-intuitively bycatch rate can increase at lower pinger prevalence. When ecological conditions are such that PCOD can emerge, higher prevalence of pingers can lead to indirect effects on population growth. This would result from condition-mediated decreased reproductive potential. Displacing fishing effort, via time-area closure, can be an effective mitigation strategy in these circumstances. These findings have important implications for current management plans which, for practical consideration, may lead to lower overall pinger prevalence at sea. This study also shows that estimating the reproductive potential of the species should be incorporated in bycatch monitoring programmes. We now need to better understand how physiological condition affect reproductive decisions and behavioural responses to noise in cetaceans to better appraise and estimate the cumulative impacts of bycatch and its mitigations.

A decade of underwater noise research in support of the European Marine Strategy Framework Directive

Underwater noise from human activities is now widely recognised as a threat to marine life. Nevertheless, legislation which directly addresses this source of pollution is lacking. The first (and currently only) example globally is Descriptor 11 of the Marine Strategy Framework Directive (MSFD), adopted by the European Union in 2008, which requires that levels of underwater noise pollution do not adversely affect marine ecosystems. The MSFD has stimulated a concerted research effort across Europe to develop noise monitoring programmes and to conduct research towards specifying threshold values which would define 'Good Environmental Status' (GES) for underwater noise. Here, we chart the progress made during the first decade of Descriptor 11's implementation: 2010-2020. Several international joint monitoring programmes have been established for impulsive and continuous noise, enabling ecosystem-scale assessment for the first time. Research into the impact of noise on individual animals has grown exponentially, demonstrating a range of adverse effects at various trophic levels. However, threshold values for GES must be defined for 'populations of marine animals.' Population-level consequences of noise exposure can be modelled, but data to parameterise such models are currently unavailable for most species, suggesting that alternative approaches to defining GES thresholds will be necessary. To date, the application of measures to reduce noise levels (quieting/noise abatement) has been limited. To address this, the EU in 2021 identified an explicit need to reduce underwater noise pollution in its waters. Delivering on this ambition will require further research focused on the development and implementation of quieting measures.

The Gradient-Boosting Method for Tackling High Computing Demand in Underwater Acoustic Propagation Modeling

Agent-based models return spatiotemporal information used to process time series of specific parameters for specific individuals called “agents”. For complex, advanced and detailed models, this typically comes at the expense of high computing times and requires access to important computing resources. This paper provides an example on how machine learning and artificial intelligence can help predict an agent-based model’s output values at regular intervals without having to rely on time-consuming numerical calculations. Gradient-boosting XGBoost under GNU package’s R was used in the social-ecological agent-based model 3MTSim to interpolate, in the time domain, sound pressure levels received at the agents’ positions that were occupied by the endangered St. Lawrence Estuary and Saguenay Fjord belugas and caused by anthropomorphic noise of nearby transiting merchant vessels. A mean error of 3.23 ± 3.76(1σ) dB on received sound pressure levels was predicted when compared to ground truth values that were processed using rigorous, although time-consuming, numerical algorithms. The computing time gain was significant, i.e., it was estimated to be 10-fold higher than the ground truth simulation, whilst maintaining the original temporal resolution.

Recent progress in marine noise pollution: A thorough review

The increase in urbanization and the progressive development of marine industries have led to the appearance of a new kind of pollution called "noise pollution". This pollution exerts an increasing pressure on marine mammals, fish species, and invertebrates, which constitutes a new debate that must be controlled in a sustainable way by environmental and noise approaches with the objective of preserving marine and human life. Despite, noise pollution can travel long distances underwater, cover large areas, and have secondary effects on marine animals; by masking their ability to hear their prey or predators, finding their way, or connecting group members. During the COVID-19 pandemic, except for the transportation of essential goods and emergency services, all the public transport services were suspended including aircraft and ships. This lockdown has impacted positively on the marine environment through reduction of the noise sources. In this article, we are interested in noise pollution in general, its sources, impacts, and the management and future actions to follow. And since this pollution is not studied in Morocco, we focused on the different sources that can generate it on the Moroccan coasts. This is the first review article, which focuses on the impact of the COVID 19 pandemic on this type of pollution in the marine environment; which we aim to identify the impact of this pandemic on underwater noise and marine species. Finally, and given the increase in noise levels, preventive management, both at the national and international level, is required before irreversible damage is caused to biodiversity and the marine ecosystem.

A review of bioenergetic modelling for marine mammal populations

Bioenergetic models describe the processes through which animals acquire energy from resources in the environment and allocate it to different life history functions. They capture some of the fundamental mechanisms regulating individuals, populations and ecosystems and have thus been used in a wide variety of theoretical and applied contexts. Here, I review the development of bioenergetic models for marine mammals and their application to management and conservation. For these long-lived, wide-ranging species, bioenergetic approaches were initially used to assess the energy requirements and prey consumption of individuals and populations. Increasingly, models are developed to describe the dynamics of energy intake and allocation and predict how resulting body reserves, vital rates and population dynamics might change as external conditions vary. The building blocks required to develop such models include estimates of intake rate, maintenance costs, growth patterns, energy storage and the dynamics of gestation and lactation, as well as rules for prioritizing allocation. I describe how these components have been parameterized for marine mammals and highlight critical research gaps. Large variation exists among available analytical approaches, reflecting the large range of life histories, management needs and data availability across studies. Flexibility in modelling strategy has supported tailored applications to specific case studies but has resulted in limited generality. Despite the many empirical and theoretical uncertainties that remain, bioenergetic models can be used to predict individual and population responses to environmental change and other anthropogenic impacts, thus providing powerful tools to inform effective management and conservation.

Offshore wind energy development: Research priorities for sound and vibration effects on fishes and aquatic invertebrates

There are substantial knowledge gaps regarding both the bioacoustics and the responses of animals to sounds associated with pre-construction, construction, and operations of offshore wind (OSW) energy development. A workgroup of the 2020 State of the Science Workshop on Wildlife and Offshore Wind Energy identified studies for the next five years to help stakeholders better understand potential cumulative biological impacts of sound and vibration to fishes and aquatic invertebrates as the OSW industry develops. The workgroup identified seven short-term priorities that include a mix of primary research and coordination efforts. Key research needs include the examination of animal displacement and other behavioral responses to sound, as well as hearing sensitivity studies related to particle motion, substrate vibration, and sound pressure. Other needs include: identification of priority taxa on which to focus research; standardization of methods; development of a long-term highly instrumented field site; and examination of sound mitigation options for fishes and aquatic invertebrates. Effective assessment of potential cumulative impacts of sound and vibration on fishes and aquatic invertebrates is currently precluded by these and other knowledge gaps. However, filling critical gaps in knowledge will improve our understanding of possible sound-related impacts of OSW energy development to populations and ecosystems.