June 2025 - MARMAM - devlists.uvic.ca

New publication: Multi-scale habitat modelling reveals contractions of harbour porpoise distribution within the northeast Atlantic
by Tiffany Goh 27 Jun '25

27 Jun '25

Dear MARMAM community, My co-authors and I are delighted to share our latest publication in the journal of Marine Environmental Research: Tiffany Goh, Oriol Giralt Paradell, Mark Jessopp, Emer Rogan, and Enrico Pirotta. 2025. Multi-scale habitat modelling reveals contractions of harbour porpoise distribution within the northeast Atlantic. Marine Environmental Research, 19:107320. Abstract: In the northeast Atlantic, large-scale changes in marine ecosystems are resulting in an ecological regime shift characterised by the degradation and loss of habitats, alterations to the food web, and ultimately, the redistribution and loss of species. Given the complexity and scale of these environmental changes, there is a critical need to reliably detect and monitor changes in species’ distribution. Here, we used a multi-year and multi-season dataset to model harbour porpoise (Phocoena phocoena) summer and winter distribution in the Irish Atlantic, using a multi-scale modelling approach to identify the best spatio-temporal scales of oceanographic variables. Porpoise sightings data were collected during dedicated line-transect aerial surveys from 2015 to 2017 and 2021–2023. Binary generalised additive models were used to assess the relationships between porpoise presence and oceanographic variables at different spatial (5, 20 and 40 km) and temporal (daily, monthly, and average across survey period) scales. Porpoises were present in coastal waters around Ireland across years and seasons. Rising sea surface temperature was negatively associated with porpoise presence, and models predicted a decline in occurrence probability for the summer and winter seasons after 2016, alongside a contraction in distribution to the Irish Sea, which remained a key habitat throughout the study. As their range contracts, porpoises are likely to be exposed to increased human-induced stressors, highlighting the need for targeted conservation measures. This study demonstrates the value of distribution datasets covering multiple years and different seasons for assessing the responses of large vertebrate species to environmental change. Keywords: Phocoena phocoena, Aerial surveys, Species distribution models, Spatio-temporal scale, Environmental change, Ireland The PDF copy can be downloaded at: https://doi.org/10.1016/j.marenvres.2025.107320 <https://doi.org/10.1016/j.marenvres.2025.107320> Please do not hesitate to contact me for any questions. Have a lovely weekend, Tiffany

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JNCC MMO training course, remote delivery, July
by Carolyn Barton 26 Jun '25

26 Jun '25

JNCC-recognised MMO training, by an instructor with over 25 years' experience, is available remotely (by Zoom) on 21st and 22nd July, cost 150GBP (135GBP students/recent graduates). An online distance learning version of the course is also available at any time (same price) for those who prefer to work through the course at their own pace. The course includes comprehensive resources and equips trainees with all the knowledge needed to perform the role of marine mammal observer in the offshore industries: 1) Impacts of noise on marine mammals 2) Introduction to activities that require mitigation 3) Legislation protecting marine mammals and marine licensing 4) Detailed examination of the suite of JNCC mitigation guidelines for different offshore activities 5) Data recording and reporting requirements 6) Visual monitoring and distance estimation 7) Overview of passive acoustic monitoring (PAM) 8) Working as an MMO/PAM operator and life at sea 9) Identification of marine mammals An online PSO course is also available, cost 180GBP (162GBP students/recent graduates). A multi-course discount is available if enrolling on both the JNCC MMO and PSO courses. For further information and for a registration form for any of the courses, see https://carolynbarton.co.uk or email info(a)carolynbarton.co.uk

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Invitation for Collaboration in Long-term Passive Acoustic Monitoring Data on Cetaceans Before and After the COVID-19
by 邱建松 26 Jun '25

26 Jun '25

Dear colleagues, I hope this message finds you well. My name is Jiansong Qiu, a postdoctor reseacher from Wang Ding's lab, Research Group on Conservation Biology of Aquatic Animals at the Institute of Hydrobiology, Chinese Academy of Sciences. My Ph.D. supervisors are Prof. Songhai Li and Zhigang Mei. My research focus on shipping impacts on cetaceans. The theme of this email is: We request your cetacean PAM data collaboration to examine shipping-induced diel rhythm changes in cetaceans before and after the COVID-19. If you are interested, please check detailed information below. We have previously found that daytime shipping has forced the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) to shift diel rhythm (see attached File). Our next study aims to explore the possible universal changes of diel vocalization/feeding/activity rhythms of global cetaceans before and after the pandemic and uncover causal relationships with varying shipping intensities (such as commercial and fishing vessels). To this end, we urgently seek high-quality data* obtained through long-term Passive Acoustic Monitoring, covering both during, pre- and/or post-COVID-19 timeframes**, with a focus on continuous day and night monitoring (intermittent sampling is also acceptable). *The data we required here should be temporal replicates,which means one site was sampled over multiple days. **Specificly, the recommended time range for data collection is from January 2019 to Dec 2021. The minimum time range should include January to June of 2019, 2020 and 2021 (Short periods of data loss throughout the entire monitoring cycle are acceptable). As the strictest confinement of COVID-19 happened during January to June, 2020. Certainly, the implementation timelines of lockdown varied significantly across different countries. Please adjust your data timeframes flexibly according to the specific lockdown period in your study region (see figure below). We sincerely invite you to share your data with us, including but not limited to: 1. Passive acoustic monitoring data on cetaceans (with identified vocalizations) before and after the pandemic, along with information on data collection timelines, locations, methodologies, target species, and equipment used. 2. Any additional information or materials you deem beneficial to our study. All data, once verified, will be incorporated into a dataset, and the corresponding principal investigators will determine whether to make them publicly available. Each data principal investigator will be invited to become a co-author of this publication and will be able to review/comment the manuscript. Those who contribute partial data will be listed in the acknowledgements. Please kindly respond to this email at qiujs(a)ihb.ac.cn if this is of your interesst. We eagerly anticipate establishing a close partnership with you, jointly contributing to the protection of cetaceans worldwide. Furthermore, We kindly request that you disseminate this information to your colleagues who you believe have the potential to join our collaborative research. Thank you very much for your attention and support for this project. Best regards, Jiansong Qiu Postdoctor Reseacher, Institute of Hydrobiology, Chinese Academy of Sciences Wuhan, 430072

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MARMAM - MMO / PSO remote training July
by Zoe Wright 26 Jun '25

26 Jun '25

Seiche Training MMO / PSO remotely via Microsoft Teams. * 14-15 July Remote Learning MMO with (optional) PSO * JNCC MMO £182.40 including vat * BOEM additional modules £78 including vat JNCC MMO/PSO training course will give you a thorough insight into all aspects of life as a marine mammal observer. * Exploring: how noise impacts marine mammals. * The legislative landscape. * Record-keeping. * Reporting requirements. * Mitigation measures. The JNCC accredited Marine Mammal Observer (MMO) course is run over one and a half days to provide comprehensive coverage of the MMO role, delivered by our approved trainers who have many years' of MMO and marine mammal experience. Followed by a half day additional training of BOEM/BSEE Protected Species Observer. Insight to life offshore, the practicalities of the MMO role this training course will ensure a thorough preparation for all future MMOs. Persons from an industry background (and/or working alongside MMOs) will benefit from the full exploration and complexities of mitigation requirements. A scientific background will be an advantage to delegates and a keen interest in marine mammals is key. A certificate for offshore work will be awarded upon successful completion of this course. 5% student discount for one course on proof of full and valid student status. 10% student discount for two full courses (when booking in conjunction with PAM level 1 course) on proof of full and valid student status. This excludes the PSO additional modules course we now offer delegates who are the same day completing JNCC MMO training or have previously completed the JNCC MMO training. To book on the courses or to find out further information email training(a)seiche.com<mailto:training@seiche.com> Zoe Wright Marketing & Training Communications Officer Seiche Ltd E: z.wright(a)seiche.com W: https://www.seiche.com Bradworthy Industrial Estate, Langdon Road, Bradworthy, Holsworthy, Devon, EX22 7SF, United Kingdom Seiche Ltd is registered in England & Wales. Registered number: 03475558. Registered Office: Bradworthy Industrial Estate, Langdon Road, Bradworthy, Holsworthy, Devon, EX22 7SF, United Kingdom The information contained in this e-mail transmission, and any documents, files or previous e-mail messages attached to it, is privileged and confidential, and solely intended for the use of the individual(s) to whom it is addressed. If you are not the intended recipient or a person responsible for delivering it to the intended recipient you should not read, copy, distribute or otherwise use the information, and you are hereby notified that any disclosure, copying, distribution or use of any of the information contained in or attached to this message is strictly prohibited. If you have received this message in error, please notify sender immediately and delete this e-mail and attached documents.

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New publication: Evolution and Organisation of MHC II Genes in Harbour Porpoises: Insights From Long-Read Cetacean Genome Assemblies, Whole Genome Re-Sequencing and Locus-Specific Genotyping
by Enrique Celemin Amaro 26 Jun '25

26 Jun '25

Dear colleagues, On behalf of my co-authors, I’m pleased to share our recently published paper in *Molecular Ecology*, which explores the evolution of the immune-related MHC class II genes in cetaceans. ABSTRACT The Major Histocompatibility Complex (MHC) is a central element in the vertebrate immune system. While MHC genes are a common target of conservation genomic studies, it has been challenging to reliably amplify locus-specific alleles, which is especially problematic when studying endangered lineages, like some harbour porpoise (*Phocoena phocoena*) populations and subspecies. Here, we manually annotated all MHC II genes in the harbour porpoise genome and genotyped every exon 2 in 47 individuals (94 individuals for DRB1 and DQB genes) spanning six geographical regions, including the endangered Black Sea porpoise subspecies (*Phocoena phocoena relicta*) and the critically endangered Baltic proper population of the North Atlantic subspecies (*P. p. phocoena*). We performed gene-wise analyses of diversity and selection and put the results into perspective with 22 available harbour porpoise genomes. Furthermore, we characterised all MHC II genes in 19 available long-read genomes of cetaceans and terrestrial outgroups to study the MHC II evolution across the cetacean diversification. From the 10 MHC II loci annotated in the harbour porpoise genome, two (DRB1 and DQB) exhibited inflated allelic diversity and signatures of positive selection. Interestingly, DRB genes followed different evolutionary trajectories in mysticetes and odontocetes. Our results have significant conservation implications since we identified reduced MHC II diversity in the endangered Black Sea subspecies and provide a case study for reliable MHC II genotyping in other species. Further, our study demonstrates the need for long-read genomes to understand the genomic architecture of MHC and to accurately assess its diversity and evolution. The paper can be found at: https://doi.org/10.1111/mec.70006 With kind regards, Enrique Dr. Enrique Celemin University of Potsdam, Germany

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Online Courses in Occupancy Modeling
by CWS Admin 25 Jun '25

25 Jun '25

Would you like to use occupancy modeling in your studies of marine mammals? Check out these online courses from the Center for Wildlife Studies! Learn at your own pace over a 3-month period. Introduction to Occupancy Modeling <https://www.centerforwildlifestudies.org/courses/p/occupancy-modeling-intro> Species presence/absence is a fundamental concept used in many areas of ecology, including studies of marine mammal species distributions and monitoring efforts. However, imperfect detection can lead to false absences. Unaccounted for false absences can lead to misleading inferences about patterns and dynamics of species occurrence and the factors that influence them. We will learn methods for accounting for imperfect detection with species detection/non-detection data and also discuss important study design considerations. Exercises are completed using Program PRESENCE and RPresence. Advanced Occupancy Modeling <https://www.centerforwildlifestudies.org/courses/p/occupancymodeling-ii> This course is aimed at participants that have completed the introductory-level course, or have suitable practical experience implementing species occurrence models that account for imperfect detection. In this course, learn the underlying theory of multi-scale, multi-state, species co-occurrence, and community level models and then put your new knowledge into practice. All hands-on exercises will be conducted in R, covering data analysis and presentation of results (plotting results, creating maps, etc.). DATES: September 2 - November 23, 2025 PRICE: Starts at $275 students / $375 professionals (early bird ends August 3) LEARN MORE & REGISTER HERE: https://www.centerforwildlifestudies.org/courses [image: Logo] <https://www.centerforwildlifestudies.org/> *Emily J. Uhrig*, PhD Director of Education Center for Wildlife Studies <https://www.centerforwildlifestudies.org/> *Center for Wildlife Studies is a 501(c)(3) nonprofit organization whose **global mission is to provide accessible environmental education and promote wildlife conservation **through science.*

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New publication: Using spatial capture–recapture methods to estimate long-term spatiotemporal variation of a wide-ranging marine species
by Georgina Whittome 25 Jun '25

25 Jun '25

Dear colleagues, My co-authors and I are pleased to share our new paper “Using spatial capture–recapture methods to estimate long-term spatiotemporal variation of a wide-ranging marine species” recently published in Ecography. Authors: Georgina Whittome, John Calambokidis, Philip S Hammond, Sophie Smout, Chris Sutherland https://nsojournals.onlinelibrary.wiley.com/doi/10.1002/ecog.07878 Abstract: Determining population status to inform mitigation of anthropogenic threats requires statistical approaches that investigate spatial and temporal variation. In the face of climate change it is increasingly important to differentiate between changes in population size and redistributions of populations. This is especially true for wide-ranging species such as the blue whale. Abundance of eastern North Pacific blue whales has previously been estimated using (non-spatial) closed capture–recapture and distance sampling methods, but the estimates show opposite and diverging trends over the last 30 years. Evidence that the distribution has been expanding could explain the apparent disparity, due to the confounding effects of spatial variation in sampling and the changing distribution. To investigate this, we apply, for the first time, spatial capture–recapture (SCR) methods to blue whale photo-identification data from small boat surveys to estimate abundance. The study area was defined as the length of the continental USA coastline, extending approximately 100 km offshore. Average annual effort from 1991 to 2023 was 97 days, resulting in 7358 sightings of 1488 unique individuals. We find significant support for non-linear spatiotemporal variation. In all years, there were higher densities at lower latitudes but there were notable decadal cyclical fluctuations in the number of animals using the study area. This large variation in the numbers of animals using these waters motivates further study into the relationship with environmental changes. Our results are an important step in spatially explicit modelling of observational blue whale data, which highlight the value of including spatial and temporal data and are relevant to any marine mammal species monitored using photo-identification. Kind regards, Georgie Georgina Whittome Sea Mammal Research Unit & Centre for Research into Ecological & Environmental Modelling University of St Andrews

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New article: Forest fire smoke as a threat to the health of river dolphins
by Andreas Fahlman 24 Jun '25

24 Jun '25

Dear Marmamers A new study published in Conservation Biology delivers a sobering insight: forest fire smoke in the Amazon is not just a human health crisis-it's now a direct threat to the survival of river dolphins. Endangered species like the Inia (Amazon river dolphin) are being exposed to prolonged smoke from intensifying wildfires. Unlike terrestrial animals, they can't escape the toxic haze. Their lung anatomy-adapted for breath-hold diving-makes them especially vulnerable to smoke inhalation, which can cause pneumonia, impair feeding, and reduce calf survival during the peak fire season. The study documents how dolphins have been observed sneezing and coughing in fire-stricken waters, and it draws troubling parallels to the Deepwater Horizon oil spill's long-term effects on marine cetaceans. With fire seasons growing longer and more intense, in our new paper we urge immediate research and policy action to prevent further declines in these already fragile populations. If you have questions or need help getting a pdf copy of the article, please send an email to Enzo Aliaga-Rossel: ealiagar(a)hotmail.com<mailto:ealiagar@hotmail.com> or Andreas Fahlman: gdrsl16(a)gmail.com<mailto:gdrsl16@gmail.com> Read the full article: Aliaga-Rossel et al. (2025). Forest fire smoke as a threat to the health of river dolphins. https://doi.org/10.1111/cobi.70098 Warm regards, Enzo, David, Miriam, Luis and Andreas

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REMINDER - Call for Proposals: Advancing aquatic eDNA applications for rare species
by Amy Van Cise 24 Jun '25

24 Jun '25

Dear MARMAM, Just a quick reminder that I and my co-editors are accepting proposals for manuscript submissions to a special issue in Methods in Ecology and Evolution under the topic: Advancing aquatic eDNA applications for rare species. Details can be found below and on the MEE website: https://besjournals.onlinelibrary.wiley.com/doi/toc/10.1111/(ISSN)2041-210X… Please feel free to reach out to any of the editors if you have any questions. Warm regards, Amy Van Cise (avancise(a)uw.edu) Kim Parsons (kim.parsons(a)noaa.gov) Julia Clem (julia.sunnarborg(a)maine.edu) Kristina Cammen (kristina.cammen(a)maine.edu) Maggie Hunter (mhunter(a)usgs.gov) <*)))>< <*)))>< <*)))>< <*)))>< <*)))>< <*)))>< <*)))>< <*)))>< Amy M. Van Cise, Ph.D. (she/her/hers) Assistant Professor Whale and Dolphin Ecology Lab <http://amyvancise.com> University of Washington | School of Aquatic and Fisheries Sciences 1122 NE Boat St, Box 355020 Seattle, WA 98105 Office: FSH 216B 206-221-6118 Need to meet with me? Let's find a time <https://calendar.app.google/6S7FAok44L6n2TpF7>. Where is Amy? [Winter 2025 edition]** Monday: hiding (focus day) Tuesday: UW campus Wednesday: UW campus Thursday: UW campus Friday: hiding (focus day) **This is not exact. If you can't find me, shoot me an email and I will get back to you. "My paper was one long gigantic blunder from beginning to end." -Charles Darwin

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Exciting Funded PhD Opportunity – on marine mammal and seabird foraging dynamics
by Ransijn, Janneke 24 Jun '25

24 Jun '25

Dear MARMAM community, Thrilled to share an exciting new PhD position that was advertised a few days ago: PhD: Tide-dependent foraging behaviour of marine mammals and seabirds in relation to anthropogenic and natural discontinuities Host institute: Wageningen University & Research (WUR) Deadline to apply: 21 July 2025 The project focuses on how tidal dynamics influence foraging patterns in marine top predators, and how these behaviours intersect with both natural features (like fronts and tidal mixing zones) and human activities (like offshore wind farms). It’s a great opportunity for someone with a background in marine ecology, strong stats/spatial skills (R/R‑Studio), and interest in offshore fieldwork. Project Focus: * Analyse GPS‑tracking data of seals (grey & harbour seals) and seabirds (sandwich terns) in the North Sea. * Examine how their foraging activities vary with tidal currents, natural habitat boundaries, and human-made structures—particularly offshore wind farms. * Conduct 10–20 days of fieldwork at sea, including vessel‑based and drone‑based surveys. * Integrate empirical data into ecological models to assess broader ecosystem impacts. * Publish results, present at conferences, and mentor BSc/MSc students. Context: This position is part of the NO‑REGRETS project, funded by NWO, in collaboration with institutions like NIOZ, TU Delft, TU Eindhoven, Naturalis, and UvA. The goal: assess and predict how offshore wind farms, fisheries, and other marine uses might transform North Sea ecosystems—from physical dynamics to top predator foraging. 🧑‍🎓 Who Should Apply? Candidates with an MSc in biology, marine biology, ecology, environmental science (or related), strong stats/spatial skills (R), and interest in offshore fieldwork. The position offers full funding, a competitive salary (≈€2,900–3,700 gross/month), excellent benefits. You can find more information here: 👉 https://www.wur.nl/en/vacancy/phd-position-tide-dependent-foraging-behaviou… Cheers, Dr Janneke Ransijn Quantitative marine mammal ecologist Wageningen Marine Research

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