June 2020 - MARMAM - devlists.uvic.ca

New publication on cetacean numbers and trends around Iceland
by Daniel Pike 08 Jun '20

08 Jun '20

We are pleased to announce the publication of our paper: Distribution and abundance of cetaceans in Icelandic waters over 30 years of aerial surveys. The paper is available here: Pike, D. G., Gunnlaugsson, T., Sigurjónsson, J., & Víkingsson, G. A. (2020). Distribution and Abundance of Cetaceans in Icelandic Waters over 30 Years of Aerial Surveys. NAMMCO Scientific Publications 11. https://doi.org/10.7557/3.4805 Best regards, Daniel Pike. ABSTRACT Beginning in 1986, 7 aerial surveys covering the coastal waters of Iceland have been conducted up to and including 2016. In addition, 7 partial surveys covering portions of the same area and at different times of the year have been flown in the same 30-year period. We present previously unpublished abundance estimates, corrected to the extent feasible for known biases, for common minke whales (*Balaenoptera acutorostrata*), humpback whales (*Megaptera novaeangliae*), white-beaked dolphins (*Lagenorhynchus albirostris*) and harbour porpoises (*Phocoena phocoena*) from some or all of the 2007, 2009 and 2016 surveys. We also examine the distribution of these and other species in Icelandic waters over the 30-year timespan of the surveys, and changes observed over the period. The relative abundance of common minke and humpback whales and white-beaked dolphins was comparatively low in the spring and fall, and peaked in June and July when all of the main surveys have been carried out. An analysis of changes in density as an index of relative abundance from all surveys (1986-2016) indicates that common minke whale abundance decreased by up to 75% after 2001 and has remained at a relatively low level since then. This decrease has been particularly apparent in the southwest and southeast of Iceland, areas which previously had very high densities. Relative abundance of humpback whales and white-beaked dolphins has increased over the period 1986-2016, particularly in the northern part of the survey area. Estimating harbour porpoise abundance and trend was considered unfeasible except from the surveys conducted in 2007 and 2016, which provide abundance estimates of similar magnitude. We place these observed changes in context of oceanographic and ecosystem changes documented over the same period.

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New Publication: Modelling pinniped abundance and distribution using counts at terrestrial sites and in-water sightings
by Womble, Jamie N 08 Jun '20

08 Jun '20

Dear MARMAM community, On behalf of my co-authors, I am pleased to announce a recent publication, Modelling pinniped abundance and distribution using counts at terrestrial sites and in-water sightings, that was recently published in the journal Ecological Modelling. Whitlock, S.L., Womble, J.N., Peterson, J.T. (2020) Modelling pinniped abundance and distribution using counts at terrestrial sites and in-water sightings. Ecological Modelling 420, p.108965. https://doi.org/10.1016/j.ecolmodel.2020.108965 Abstract: Pinnipeds are commonly monitored using aerial photographic surveys at land- or ice-based sites, where animals come ashore for resting, pupping, molting, and to avoid predators. Although these counts form the basis for monitoring population change over time, they do not provide information regarding where animals occur in the water, which is often of management and conservation interest. In this study, we developed a hierarchical model that links counts of pinnipeds at terrestrial sites to sightings-at-sea and estimates abundance, spatial distribution, and the proportion of time spent on land (attendance probability). The structure of the model also allows for the inclusion of predictors that may explain variation in ecological and observation processes. We applied the model to Steller sea lions (Eumetopias jubatus) in Glacier Bay, Alaska using counts of sea lions from aerial photographic surveys and opportunistic in-water sightings from vessel surveys. Glacier Bay provided an ideal test and application of the model because data are available on attendance probability based on long-term monitoring. We found that occurrence in the water was positively related to proximity to terrestrial sites, as would be expected for a species that engages in central-place foraging. The proportion of sea lions in attendance at terrestrial sites and overall abundance estimates were consistent with reports from the literature and monitoring programs. The model we describe has benefit and utility for park managers who wish to better understand the overlap between pinnipeds and visitors, and the framework that we present has potential for application across a variety of study systems and taxa. Please contact Steve Whitlock (swhit(a)uw.edu<mailto:swhit@uw.edu>) or Jamie Womble (Jamie_Womble(a)nps.gov<mailto:Jamie_Womble@nps.gov>) to request a PDF of the publication. Thank you, Jamie Jamie N. Womble, Ph.D. Biologist - Marine National Park Service, Glacier Bay Field Station Southeast Alaska Inventory & Monitoring Network Glacier Bay National Park & Preserve 3100 National Park Road Juneau, Alaska 99801 USA 907.364.1577 (phone) 907.957.1563 (mobile) 907.364.2606 (fax) https://www.nps.gov/articles/jamie-womble.htm<https://urldefense.com/v3/__https:/www.nps.gov/articles/jamie-womble.htm__;…> https://www.nps.gov/glba/learn/nature/seal.htm<https://urldefense.com/v3/__https:/www.nps.gov/glba/learn/nature/seal.htm__…> https://www.nps.gov/im/sean/seaotters.htm<https://urldefense.com/v3/__https:/www.nps.gov/im/sean/seaotters.htm__;!!J2…>

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Post-doctoral position in Dolphin ImmunoGenomics, Museum and Institute of Zoology, Poland
by Andre E. Moura 08 Jun '20

08 Jun '20

Dear Marmam subscribers, A postdoctoral research assistant position is available in a project analysing genome wide variation in striped dolphins in relation to Morbillivirus infection. The work will carried out in the cetacean ecology and evolution research group led by Dr Andre E. Moura at the Museum and Institute of Zoology of the Polish Academy of Sciences (MIZ-PAS). We are re-advertising this position, as the previous round got disturbed by the Covid19 lockdowns. It is still a dynamic situation, so if you are interested in applying but worried about time frame, please do get in touch and we will find a workable solution. The position is available for 30 months, and includes a three month probation period. The ideal start date is August 2020, although there is of course flexibility to account for the current pandemic situation. The research group is based at the Research Station of the MIZ-PAS in Gdańsk, and maintains strong links with the main research facilities of the MIZ in Warsaw. Therefore, research visits at the main MIZ facilities in Warsaw may be required as part of the job duties. The Research Station also hosts groups working on canid genomics and avian immunogenetics. The post-doctoral assistant will possess expertise in evolutionary genomics, population genomics or bioinformatics. Candidates can have a background (BSc or MSc degree) in biology, zoology, bioinformatics, computer science, or related fields, and a PhD degree (awarded or to be awarded soon) in a relevant area. The PhD degree should have been awarded no earlier than 7 years before the start of employment. The candidate must be eligible to work in Poland at the time of appointment. A list of required skills can be seen at the end of this message. To apply, the following documents should be sent to Andre Moura at avmoura(a)miiz.waw.pl no later than 28.06.2020: 1. Copy of a PhD certificate 2. Curriculum vitae including a publication list, with the following statement provided at the end and signed: “I give my consent to the processing of personal data provided in my application documents by the Museum and Institute of Zoology PAS for the purpose of the recruitment process, pursuant to the Personal Data Protection Act of 10 May 2018 (Journal of Laws 2018, item 1000) and in agreement with Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing Directive 95/46/EC (General Data Protection Regulation; L 119 from 04.05.2016)”. IMPORTANT: Applications that do not include this statement cannot be processed. 3. Motivation letter (maximum one page) 4. A copy of one research paper to be evaluated in the recruitment process 5. Contact details of two persons who can be contacted for references. The interviews of shortlisted candidates will take place in early July, and will be held by teleconference (Skype, Zoom, etc.). Interviews in person at the Research Station in Gdańsk-Górki Wschodnie are possible, but only if it is logistically feasible and safe to do so. Informal inquiries can also be addressed to Andre Moura. Essential skills: 1. Experience with preparing NGS libraries and processing NGS data 2. Good knowledge of evolutionary theory and/or population genetic theory 3. Experience of Linux/Unix environment; 4. Experience with at least one coding language (e.g. Python, Perl, Unix Shell scripts); 5. Good organisational skills; 6. Experience with large databases; 7. Ability to work independently and to communicate with a multi-disciplinary team; Desirable skills: 8. Experience with analysing whole-genome datasets, aligning to reference genomes, SNP detection; 9. Experience with software for evolutionary genomic analyses; 10. Experience with online genomic databases; 11. Good understanding of natural selection theory; 12. Good understanding of mammalian immune system; 13. Experience of working in an international team. Research environment The research at the MIZ is focused on a broad range of themes in animal biology, including systematics, biogeography, evolutionary biology, ecology and population genetics. Andre Moura research group is part of the Laboratory of the Molecular and Biometric Techniques led by Prof. Wieslaw Bogdanowicz, grouping researchers focused on population genetics, phylogeography and evolutionary genomics of a broad range of animal taxa. MIZ laboratories contain modern equipment for genomic analyses, including Pacific Biosciences RSII long-read sequencer and Illumina MiSeq System. The state-of-the-art ancient DNA laboratory carries out work on mammalian palaeogenetics. The Museum zoological collection is among the largest and most valuable in Europe.

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New publication for spinner dolphins
by Ahmed Shawky 07 Jun '20

07 Jun '20

Dear All, I and my co-authors are very delighted to share our new publication with you. It is entitled " Effects of Swim-with-Dolphins Tourism on the Behaviour of Spinner Dolphins at Samadai Reef, Egyptian Red Sea", that published in Aquatic Conservation: Marine and Freshwater Ecosystems. Abstract: 1. Spinner dolphins, Stenella longirostris, are the primary target for marine mammal tourism in Egypt. The present study investigated the short-term effects of tourist presence on the behaviour of spinner dolphins at Sha'ab Samadai (Samadai Reef), in the southern Egyptian Red Sea. 2. The reef has a large central lagoon where a population of spinner dolphin regularly rest from mid-morning to mid-afternoon; visitors are permitted to snorkel in the southern part of the lagoon, but not in the northern closed zone that the dolphins mainly use. 3. Dolphin behaviour was monitored both on days when tourist boats were present and on days when they were absent. In the presence of tourists the proportion of time that the dolphins spent resting was reduced by two-thirds, whereas the times spent milling, travelling, and showing avoidance behaviour all increased. 4. Furthermore, upon using Markov chain modelling to investigate the effect of tourist presence on the transition probabilities between dolphin activity states, significant changes were found in 10 of the 25 possible behavioural transitions, including increased probabilities of transitioning from resting to milling or travelling, from milling to travelling or avoiding, and from travelling to avoiding. 5. These findings raise concerns that despite the management measures in place, tourist activities affect the dolphins’ behaviour to a greater extent than was previously apparent, with potential long-term negative effects on their energy budget. 6. The study led to proposals for amending the zoning of the site and for strengthening the regulations for tourist vessels. You can access the publication article via this link: http://dx.doi.org/10.1002/aqc.3332 All the best and stay safe. Ahmed Dr Ahmed M. Shawky - Marine Biology - PhD Technical Office of the Minister of Environment Master Instructor PADI No.639747 - EFRI Trainer www.ahmedshawky.net - mobile:(+2)01013854500 [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-anima…]<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…>

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Marine biology on a violated planet: from science to conscience
by Giovanni Bearzi 06 Jun '20

06 Jun '20

Dear colleagues, the article below stems from my experience as a dolphin researcher: Bearzi G. 2020. Marine biology on a violated planet: from science to conscience. Ethics in Science and Environmental Politics 20:1-13. It is open access and freely available at: https://www.int-res.com/abstracts/esep/v20/p1-13/ ABSTRACT - Humanity¹s self-ordained mandate to subdue and dominate nature is part of the cognitive foundation of the modern world--a perspective that remains deeply ingrained in science and technology. Marine biology has not been immune to this anthropocentric bias. But this needs to change, and the gaps between basic scientific disciplines and the global conservation imperatives of our time need to be bridged. In the face of a looming ecological and climate crisis, marine biologists must upgrade their values and professional standards and help foster the radical transformation needed to avert a climate and ecological breakdown. To prevent some of the damage, they must cross the imaginary line that separates science from science-based activism and consciously pursue the health and durability of human and natural communities. To this end, they can (1) develop compelling narratives that engage human society, with emphasis on care for the wild living world; (2) move beyond marine conservation on paper and avoid self-serving complaisance; (3) advocate constructive changes in market and human behaviour, not only by documenting damage but also by clarifying how the extraction, production and consumption system can be steered away from practices that harm nature; (4) push for systemic change in politics through individual and collective efforts, supporting environmental activism and those who demand biosphere-saving policies; and (5) endorse a more ecocentric and holistic world vision, relinquishing contempt for spiritual wisdom and liaising with (or at least not dismissing) spiritual traditions that encourage equality, self-restraint and environmental sustainability. - - - - - - - Giovanni Bearzi <http://www.dolphinbiology.org/people/giovanni_bearzi.htm>

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Virtual Marine Mammal Course Opportunity (June 26-August 6)
by Reny Tyson Moore 04 Jun '20

04 Jun '20

Greetings! The Duke University Marine Lab (DUML) is currently accepting enrollments for our summer Marine Mammals course. This six-week virtual course will cover the biology and conservation of marine mammals. We will introduce you to the basic biology of various taxonomic groups, describe some of the research approaches used to study them, and conclude with a consideration of their conservation. Virtual laboratories and interactive activities will focus on topics including diving physiology, photographic-identification methods, population biology, bio-acoustics, bio-logging, and drones. We will also take advantage of opportunities to interact with marine mammal experts from around the world, including many from DUML, through virtual guest lectures, field trips, and discussion panels, and through the creation of a DUML Marine Mammals podcast. This course is suitable for both undergraduate and graduate students. ENV 376L or BIO 376L (undergraduate) / ENV776L (graduate) 4 Duke credits. Instructor: Reny Tyson Moore (tyson.moore(a)duke.edu) Tuition: $3,200+fees Dates: June 29 - August 6, 2020 Times: Mondays, Wednesdays & Thursdays 9am – 4pm EDT (however, an asynchronous option will be available to accommodate all students) To apply: Visit Duke’s Summer Session website: https://summersession.duke.edu/visiting-college-students and complete the online application:https://duke.qualtrics.com/jfe/form/SV_22XiGjJTUGVB7lb Tuition and fees can be found here: https://summersession.duke.edu/visiting-college-students/u-s-students/tuiti… -- Reny Tyson Moore, PhD Staff Scientist Sarasota Dolphin Research Program Chicago Zoological Society (352) 408-6018 cell rtysonmoore(a)mote.org <rtyson(a)mote.org>

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New publication: Evaluation of two lipid removal methods for stable carbon and nitrogen isotope analysis in whale tissue
by Kerri J. Smith 04 Jun '20

04 Jun '20

Dear all, We are pleased to share our recent publication on lipid extraction methods for stable isotope analysis of beaked whale tissue. Smith, KJ, Trueman, CN, France, CAM, Peterson, MJ. Evaluation of two lipid removal methods for stable carbon and nitrogen isotope analysis in whale tissue. *Rapid Commun Mass Spectrom*. 2020. https://0-doi-org.lib.utep.edu/10.1002/rcm.8851 The presence of lipids in animal tissues can influence the interpretation of stable isotope data, particularly in lipid‐rich tissues such as the skin and muscle of marine mammals. The traditionally employed chloroform:methanol delipidation protocol has the potential to alter δ15N values in proteinaceous tissues. Our objective was to determine whether cyclohexane is an alternative extraction method, effectively removing lipids without altering δ15N values. Kidney, liver, muscle, and skin samples were collected from beach‐cast Sowerby's beaked whales (*Mesoplodon bidens *). Control subsamples were processed without delipidation extraction, and duplicate subsamples were extracted with either chloroform:methanol or cyclohexane. δ13C, δ15N, and C:N values were determined by continuous‐flow elemental analysis isotope ratio mass spectrometry. Paired Wilcoxon tests were used to evaluate the change in isotope ratios after extraction, and unpaired Wilcoxon tests were used to evaluate difference in isotope ratios between extractions. Cyclohexane is an effective delipidation technique for tissues with low and moderate lipid content. Chemical delipidation influenced δ15N values; extracted samples generally showed an increase in δ15N values which varied from 0.0‰ to 1.7‰. Chloroform:methanol extraction resulted in alterations to δ15N values greater than the analytical precision for all analyzed tissues. Changes to δ 15N values after cyclohexane extraction were at or near the analytical precision in liver and muscle but greater than the analytical precision for kidney and skin. We recommend processing duplicate subsamples for stable isotope analysis, one with and one without extraction in order to obtain accurate values for each isotope ratio. Prolonged chemical extractions are not necessary to effectively remove lipids. When samples are limited, we suggest using cyclohexane for tissues with low or moderate lipid content, and chloroform:methanol for lipid‐rich tissues. Cheers, Kerri *--Kerri J. Smith, Ph.D.* Postdoctoral Researcher- Laboratory of Ecological and Adaptational Physiology Research Fellow - Smithsonian Institution Website <https://kerrijsmith.wordpress.com/> “The love for all living creatures is the most noble attribute of man.” -Charles Darwin

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A new publication: Getting to the bottom of bycatch, a GIS-based toolbox to assess thee risk of marine mammal bycatch
by Ellen M Hines 04 Jun '20

04 Jun '20

Greetings all, on behalf of my colleagues, we are happy to share this new open access publication as part of a special issue on Marine Vertebrate Bycatch in Endangered Species Research: https://www.int-res.com/journals/esr/specials/marine-vertebrate-bycatch-pro… Getting to the bottom of bycatch: a GIS-based toolbox to assess the risk of marine mammal bycatch https://www.int-res.com/articles/esr2020/42/n042p037.pdf Ellen Hines, Louisa S. Ponnampalam, Chalatip Junchompoo, Cindy Peter, Long Vu, Thien Huynh, Marjolaine Caillat, Andrew F. Johnson, Gianna Minton, Rebecca L. Lewison, Gregory M. Verutes ABSTRACT: Marine mammal bycatch poses a particular challenge in developing countries, where data to document bycatch and its effects are often lacking. Using the Bycatch Risk Assessment (ByRA) toolkit, based on InVEST open-source models, we chose 4 field sites in Southeast Asia with varying amounts of data on marine mammals and fishing occurrence: Trat province in the eastern Gulf of Thailand, the Sibu-Tinggi Islands and Kuching Bay, Malaysia, and Kien Giang Biosphere Reserve in southwestern Vietnam. These field sites have similar species of coastal marine mammals, small-scale and commercial fisheries, and support for research from universities and/or management. In Thailand and Kuching, results showed changing patterns of fishing and Irrawaddy dolphin Orcaella brevirostris habitat use across seasons, showing how bycatch risk could change throughout the year. Risk maps for dugongs Dugong dugon in peninsular Malaysia highlighted patterns of bycatch risk concentrated around a mainland fishing pier, and revealed high risk in a northern subregion. In Vietnam, first maps of bycatch risk for the Irrawaddy dolphin showed the highest risk driven by intensive use of gillnets and trawling gear. ByRA pinpointed areas of spatial and seasonal bycatch exposure, and estimated the consequence of bycatch on local species, providing managers with critical information on where to focus bycatch mitigation and meet new global standards for US Marine Mammal Protection Act and other international regulation (e.g. Official Journal of the European Union 2019; Regulation 2019/1241) compliance. The toolbox, a transferable open-source tool, can be used to guide fisheries management, marine mammal conservation, spatial planning, and further research. Thanks to funding from the IWC Bycatch Mitigation Initiative, we have manuals for the toolbox in both English and Spanish (Kuit et al 2020). Please email me and I'm glad to send. Be well and be safe, Ellen Ellen Hines, PhD Associate Director and Professor of Geography & Environment Estuary and Ocean Science Center San Francisco State University 3150 Paradise Dr. Tiburon, CA 94920 ehines(a)sfsu.edu<mailto:ehines@sfsu.edu> https://eoscenter.sfsu.edu/content/ellen-hines

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New publication: A standard protocol for reporting species distribution models
by Phil Bouchet 04 Jun '20

04 Jun '20

Dear MARMAMers, My colleagues and are delighted to share our new open access publication in Ecography. The paper presents a standard protocol (called ‘ODMAP’) for building and reporting on species distribution models (SDMs), with direct relevance to marine mammal research. ODMAP was designed as a structured checklist that details the key steps involved in the development and analysis of modern SDMs. With it, we hope to increase the transparency and reproducibility of SDM studies, facilitate peer-review and expert evaluation of model quality, support meta‐analyses, and encourage model users to consider various aspects of the modelling workflow that may sometimes be overlooked. Zurell D, Franklin J, König C, Bouchet PJ, Serra-Diaz JM, Dormann CF, Elith J, Fandos Guzman G, Feng X, Guillera-Arroita G, Guisan A, Leitão PJ, Lahoz-Monfort JJ, Park DS, Peterson AT, Raacciuolo G, Schmatz DR, Schröder B, Thuiller W, Yates KL, Zimmermann NE, Merow C (2020). A standard protocol for reporting species distribution models. Ecography (online early). https://onlinelibrary.wiley.com/doi/full/10.1111/ecog.04960 *Abstract* Species distribution models (SDMs) constitute the most common class of models across ecology, evolution and conservation. The advent of ready‐to‐use software packages and increasing availability of digital geoinformation have considerably assisted the application of SDMs in the past decade, greatly enabling their broader use for informing conservation and management, and for quantifying impacts from global change. However, models must be fit for purpose, with all important aspects of their development and applications properly considered. Despite the widespread use of SDMs, standardisation and documentation of modelling protocols remain limited, which makes it hard to assess whether development steps are appropriate for end use. To address these issues, we propose a standard protocol for reporting SDMs, with an emphasis on describing how a study's objective is achieved through a series of modeling decisions. We call this the ODMAP (Overview, Data, Model, Assessment and Prediction) protocol, as its components reflect the main steps involved in building SDMs and other empirically‐based biodiversity models. The ODMAP protocol serves two main purposes. First, it provides a checklist for authors, detailing key steps for model building and analyses, and thus represents a quick guide and generic workflow for modern SDMs. Second, it introduces a structured format for documenting and communicating the models, ensuring transparency and reproducibility, facilitating peer review and expert evaluation of model quality, as well as meta‐analyses. We detail all elements of ODMAP, and explain how it can be used for different model objectives and applications, and how it complements efforts to store associated metadata and define modelling standards. We illustrate its utility by revisiting nine previously published case studies, and provide an interactive web‐based application to facilitate its use. We plan to advance ODMAP by encouraging its further refinement and adoption by the scientific community. The paper is accompanied by a Shiny app available here at https://odmap.wsl.ch/ Best wishes, Phil Dr. Phil Bouchet | Postdoctoral Research Fellow Centre for Research into Ecological & Environmental Modelling (CREEM) The Observatory, Buchanan Gardens University of St Andrews, St Andrews Fife KY16 9LZ, Scotland (UK) E pjbouchet(a)gmail.com | pb282(a)st-andrews.ac.uk

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DCLDE2020 Kona - Call for participation
by Erin Oleson - NOAA Federal 03 Jun '20

03 Jun '20

Aloha to the marine mammal bioacoustics community. We’re pleased to announce that the calls for abstracts, workshop/tutorial proposals, exhibits, sponsorship, and student travel support for DCLDE 2020 Kona are open! The website has been updated with important dates, updates, and submission forms: http://www.soest.hawaii.edu/ore/dclde/. [DCLDE 2020 Kona = 9th International Workshop on Detection, Classification, Localization and Density Estimation of Marine Mammals using Passive Acoustics, Kailua-Kona Hawaii, 7-11 December 2020]. Re. COVID-19: We know there is a lot of uncertainty in the world and especially as it relates to travel and meetings. For now, we are holding course on scheduling for DCLDE2020 in the hopes of minimal impact to the event. We plan to re-evaluate the situation in mid-summer. Updates will be posted on the DCLDE2020 website as they become available. Best regards, Erin Oleson and Eva-Marie Nosal DLCDE 2020 Kona Co-chairs -- *Erin Oleson, PhD* *Leader*, Cetacean Research Program NOAA Pacific Islands Fisheries Science Center office: (808) 725-5712 Erin.Oleson(a)noaa.gov <erin.oleson(a)noaa.gov> https://www.fisheries.noaa.gov/pacific-islands/about-us/whale-and-dolphin-s… <http://www.pifsc.noaa.gov/cetacean>

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