A checklist for maximizing reproducibility of ecological niche models

Nature Ecology & Evolution, Год журнала: 2019, Номер 3(10), С. 1382 - 1395

Опубликована: Сен. 23, 2019

Abstract Reporting specific modelling methods and metadata is essential to the reproducibility of ecological studies, yet guidelines rarely exist regarding what information should be noted. Here, we address this issue for niche or species distribution modelling, a rapidly developing toolset in ecology used across many aspects biodiversity science. Our quantitative review recent literature reveals general lack sufficient fully reproduce work. Over two-thirds examined studies neglected report version access date underlying data, only half reported model parameters. To problem, propose adopting checklist guide reporting at least minimum necessary reproducibility, offering straightforward way balance efficiency accuracy. We encourage community, as well journal reviewers editors, utilize further develop framework facilitate improve future The proposed generalizable other areas ecology, especially those utilizing environmental data statistical could also adopted by broader array disciplines.

Язык: Английский

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A Global Review of Vessel Collisions With Marine Animals

Frontiers in Marine Science, Год журнала: 2020, Номер 7

Опубликована: Май 19, 2020

Concern about the effects of maritime vessel collisions with marine animals is increasing worldwide. To date, most scientific publications on this topic have focused between large vessels and whales. However, our review found that at least 75 species are affected, including smaller whales, dolphins, porpoises, dugongs, manatees, whale sharks, seals, sea otters, turtles, penguins, fish. Collision incidents scarce, likely as a result reporting biases. Some these biases can be addressed through establishment species-specific necropsy protocols to ensure reliable identification collision related injury, particularly blunt force trauma. In addition, creating ship strike database for assist in identifying frequently involved collisions, high-risk areas, determining relationships speed lethal injury. The International Whaling Commission whales provides good example type its potential uses. Prioritising protocol well areas other than would valuable step towards mitigation species.

Язык: Английский

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Marine mammal conservation: over the horizon

Endangered Species Research, Год журнала: 2021, Номер 44, С. 291 - 325

Опубликована: Янв. 28, 2021

Marine mammals can play important ecological roles in aquatic ecosystems, and their presence be key to community structure function. Consequently, marine are often considered indicators of ecosystem health flagship species. Yet, historical population declines caused by exploitation, additional current threats, such as climate change, fisheries bycatch, pollution maritime development, continue impact many mammal species, at least 25% classified threatened (Critically Endangered, Endangered or Vulnerable) on the IUCN Red List. Conversely, some species have experienced increases/recoveries recent decades, reflecting management interventions, heralded conservation successes. To these successes reverse downward trajectories at-risk it is necessary evaluate threats faced mechanisms available address them. Additionally, there a need identify evidence-based priorities both research needs across range settings taxa. that effect we: (1) outline impacts, associated knowledge gaps recommend actions needed; (2) discuss merits downfalls established emerging mechanisms; (3) application monitoring techniques; (4) highlight particular taxa/populations urgent focus.

Язык: Английский

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

ICES Journal of Marine Science, Год журнала: 2023, Номер 80(7), С. 1829 - 1853

Опубликована: Авг. 3, 2023

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

Язык: Английский

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Dynamic ensemble models to predict distributions and anthropogenic risk exposure for highly mobile species

Diversity and Distributions, Год журнала: 2019, Номер 25(8), С. 1182 - 1193

Опубликована: Июнь 4, 2019

Abstract Aim Advances in ecological and environmental modelling offer new opportunities for estimating dynamic habitat suitability highly mobile species supporting management strategies at relevant spatiotemporal scales. We used an ensemble approach to predict daily, year‐round a migratory species, the blue whale ( Balaenoptera musculus ), demonstrate application evaluating dynamics of their exposure ship strike risk. Location The California Current Ecosystem (CCE) Southern Bight (SCB), USA. Methods integrated long‐term (1994–2008) satellite tracking dataset on 104 whales with data‐assimilative ocean model output assess suitability. evaluated relative utility ensembling multiple types compared using single models, selected validated candidate models cross‐validation metrics independent observer data. quantified spatial temporal distribution risk within shipping lanes SCB. Results Multi‐model ensembles outperformed single‐model approaches. final had high predictive skill (AUC = 0.95), resulting predictions CCE that accurately captured behaviour. Risk was variable among years as function conditions (e.g., marine heatwave). Main conclusions Daily information three‐dimensional oceanic habitats daily power indicated could benefit by incorporating information. This is readily transferable other species. Dynamic, high‐resolution are valuable tools assessing targeting needs.

Язык: Английский

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Best practice guidelines for cetacean tagging

IWC Journal of Cetacean Research and Management, Год журнала: 2019, Номер 20(1), С. 27 - 66

Опубликована: Янв. 1, 2019

Animal-borne electronic instruments (tags) are valuable tools for collecting information on cetacean physiology, behaviour and ecology, forenhancing conservation management policies populations. Tags allow researchers to track the movement patterns, habitat use andother aspects of animals that otherwise difficult observe. They can even be used monitor physiology a taggedanimal within its changing environment. Such tags ideal identifying predicting responses anthropogenic threats, thus facilitating thedevelopment robust mitigation measures. With increasing need data best provided by tagging availability tags, suchresearch is becoming more common. Tagging can, however, pose risks health welfare cetaceans personnel involved in taggingoperations. Here we provide ‘best practice’ recommendations tag design, deployment follow-up assessment tagged individuals,compiled biologists veterinarians with significant experience tagging. This paper intended serve as resource assist tagusers, veterinarians, ethics committees regulatory agency staff implementation high standards practice, promote trainingof specialists this area. Standardised terminology describing design illustrations types attachment sites provided, alongwith protocols testing (both remote through capture-release), including training operators. The recommendationsemphasise importance ensuring ethically scientifically justified particular project only toaddress bona fide research or questions addressed tagging, supported an exploration alternative methods.Recommendations minimising effects individual (e.g. careful selection individual, implantsterilisation) improving knowledge increased post-tagging monitoring.

Язык: Английский

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Distribution maps of cetacean and seabird populations in the North‐East Atlantic

Journal of Applied Ecology, Год журнала: 2019, Номер 57(2), С. 253 - 269

Опубликована: Окт. 26, 2019

Abstract Distribution maps of cetaceans and seabirds at basin monthly scales are needed for conservation marine management. These usually created from standardized systematic aerial vessel surveys, with recorded animal densities interpolated across study areas. However, distribution have previously not been possible because individual surveys restricted spatial temporal coverage. This develops an alternative approach consisting of: (a) collating diverse survey data to maximize coverage, (b) using detection functions estimate variation in the surface area covered (km 2 ) among these standardizing measurements effort densities, (c) developing species models (SDM) that overcome issues heterogeneous uneven 2.68 million km North‐East Atlantic between 1980 2018 were collated standardized. SDM Generalized Linear Models General Estimating Equations a hurdle developed. then 12 cetacean seabird 10 resolution. Qualitative quantitative assessment indicated good model performance. Synthesis applications . provides largest ever collation standardization seabirds, most comprehensive taxa Atlantic. numerous including identification important areas needing protection, quantification overlap vulnerable anthropogenic activities. demonstrates how analysis existing can meet management needs.

Язык: Английский

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Human-machine-learning integration and task allocation in citizen science

Humanities and Social Sciences Communications, Год журнала: 2022, Номер 9(1)

Опубликована: Фев. 9, 2022

Abstract The field of citizen science involves the participation citizens across different stages a scientific project; within this there is currently rapid expansion integration humans and AI computational technologies based on machine learning and/or neural networking-based paradigms. distribution tasks between (“the crowd”), experts, type has received relatively little attention. To illustrate current state task allocation in projects that integrate technologies, an integrative literature review 50 peer-reviewed papers was conducted. A framework used for characterizing two main dimensions: (a) nature outsourced to crowd, (b) skills required by crowd perform task. extended include performed experts as well. Most do reported are well-structured, involve interdependence, require prevalent among general population. work typically structured at higher-level interdependence than citizens, requiring expertize specific fields. Unsurprisingly, capable performing mostly well-structured high-level interdependence. It argued results from combination computation may disincentivize certain volunteer groups. Assigning meaningful way scientists alongside unavoidable design challenge.

Язык: Английский

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Performance evaluation of cetacean species distribution models developed using generalized additive models and boosted regression trees

Ecology and Evolution, Год журнала: 2020, Номер 10(12), С. 5759 - 5784

Опубликована: Май 11, 2020

Abstract Species distribution models (SDMs) are important management tools for highly mobile marine species because they provide spatially and temporally explicit information on animal distribution. Two prevalent modeling frameworks used to develop SDMs generalized additive (GAMs) boosted regression trees (BRTs), but comparative studies have rarely been conducted; most rely presence‐only data; few explored how features such as characteristics affect model performance. Since the majority of BRTs predict habitat suitability, we first compared GAMs that presence/absence response variable. We then results from these suitability density (animals per km 2 ) built with a subset data here previously received extensive validation. both explanatory power (i.e., goodness fit) predictive performance novel dataset) taxonomically diverse suite cetacean using robust set systematic survey (1991–2014) within California Current Ecosystem. Both were successful at describing overall patterns throughout study area considered, when predicting data, exhibited substantially greater than BRTs, likely due different variables fitting algorithms. Our an improved understanding some strengths limitations developed two methods. These can be by modelers developing resource managers tasked spatial determine best technique their question interest.

Язык: Английский

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Modelling the spatial distribution of cetaceans in New Zealand waters

Diversity and Distributions, Год журнала: 2020, Номер 26(4), С. 495 - 516

Опубликована: Фев. 3, 2020

Abstract Aim Cetaceans are inherently difficult to study due their elusive, pelagic and often highly migratory nature. New Zealand waters home 50% of the world's cetacean species, but spatial distributions poorly known. Here, we model 30 taxa using an extensive at‐sea sightings dataset ( n > 14,000) high‐resolution (1 km 2 ) environmental data layers. Location Zealand's Exclusive Economic Zone (EEZ). Methods Two models were used predict probability species occurrence based on available records. For with <50 = 15), Relative Environmental Suitability (RES), for ≥50 Boosted Regression Tree (BRT) used. Independently collected presence/absence further evaluation a subset taxa. Results RES rarely sighted showed reasonable fits stranding literature expert knowledge species' autecology. BRT high predictive power commonly (AUC: 0.79–0.99). Important variables predicting temperature residuals, bathymetry, distance 500 m isobath, mixed layer depth water turbidity. Cetacean distribution patterns varied from localised, nearshore (e.g., Hector's dolphin), more ubiquitous common dolphin) primarily offshore blue whale). richness stacked layers illustrated fewer inshore localised hotspots, higher especially in locales Macquarie Ridge, Bounty Trough Chatham Rise. Main conclusions Predicted fill major gap towards informing future assessments conservation planning cetaceans EEZ. While datasets not spatially comprehensive any taxa, these two best approaches allow modelling both common, sighted, limited information.

Язык: Английский

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