February 2020 - MARMAM - devlists.uvic.ca

New publication: Visual-only assessment of skin lesions on bottlenose dolphins - Reliability and utility of quantitative tools (Christina Toms)
by Christina Toms 27 Feb '20

27 Feb '20

Dear Colleagues, On behalf of my co-authors, I am pleased to announce that the following article is now available online https://onlinelibrary.wiley.com/doi/10.1111/mms.12670: Toms, C. N., Stone, T., and Och-Adams, T. (2020). Visual-only assessments of skin lesions on free-ranging common bottlenose dolphins (*Tursiops truncatus*); Reliability and utility of quantitative tools. *Marine Mammal Science, *1-30. DOI: 10.1111/mms.12670. ABSTRACT Photo analysis offers a simple, non-invasive approach to characterizing and quantifying skin lesions in cetaceans; however, this process involves methodological considerations that have often gone unaddressed or have varied in approach among investigators. Subjectivity associated with classifying skin lesion types of unknown etiology and quantifying measures of skin lesion prevalence and extent from photo data raises questions about observer bias and agreement (i.e., interrater reliability), which are often ignored. The purpose of the present study was to improve upon data quality control and assessment practices when studying skin lesions using only photo data. Specifically, we tested interrater reliability of a skin lesion classification system, compared methods of quantifying skin lesion extent, and determined the validity of the dorsal fin as a proxy for skin lesions on the entire body. Acceptable levels of interrater reliability were achieved for only 7 of 17 defined lesion types but reliability was high for the two tested measures of lesion extent. Skin lesion extent measured from the dorsal fin alone was not a decent proxy for the whole visible surface; disparities between measures were as high as 43%. We discuss the potential pitfalls discovered and provide recommendations for others attempting similar approaches. Please, do not hesitate to contact me if you have any questions Cheers, Christina Toms PhD, Postdoctoral Scientist Sarasota Dolphin Research Program Chicago Zoological Society Office: 941-388-4441 ext. 375 Cell: 808-990-1931 ctoms(a)mote.org https://www.researchgate.net/profile/Christina_Toms

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New Publication: Harbour porpoise strandings - analysis of UK west coast long-term dataset
by Morris, Ceri 27 Feb '20

27 Feb '20

My colleagues and I are pleased to announce the publication of the following report: ten Doeschate M.T.I., Brownlow A.C., Morris C. W., and Stringell T. B. 2019. UK West Coast Harbour Porpoise (Phocoena phocoena) Strandings. NRW Evidence Report Series, Report No: 358, 66pp, Natural Resources Wales, Bangor Abstract The UK has a statutory obligation under the EU Habitats Directive to report on the conservation status of harbour porpoise (Phocoena phocoena) and to quantify threats and pressures at both an individual and population level. This report summarises strandings data of harbour porpoise collected by the UK Cetacean Strandings Investigation Programme (CSIP) for the west coast of the UK from 1992 to 2017, and highlights the implications for management. Analyses aimed to establish a baseline pattern in strandings, and provide insight into the population structure and potential areas of importance. Spatial variation in cause of death was examined, focussing on direct-anthropogenic (bycatch and ship strike) versus other causes of mortality. The most common direct anthropogenic cause of death (98.5%) was fisheries bycatch, with notable clusters on the south west UK coast consistent with known bycatch hotspots for the inshore fishing fleet. The body condition of harbour porpoise was characterised as a proxy for assessing spatiotemporal variation in population fitness, and indicated that there was no significant change in apparent fitness over this time period. More than a quarter of the strandings on the UK west coast occurred in Cardigan Bay, Wales. GAMM modelling revealed regional differences in seasonality of strandings. A strong seasonal pattern was observed in Wales from May through to October, coinciding with the calving season. This, together with a significantly higher proportion of stranded neonates, possibly indicates that Wales may be an important area for calving. This analysis has provided a baseline against which future monitoring will be measured and demonstrates the value of this globally important, long-term programme of strandings monitoring. It has given us key insights into population structure, mortality and anthropogenic pressures of harbour porpoise in the UK. For a PDF copy of the report please contact: Ceri Wyn Morris ceri.morris(a)naturalresourceswales.gov.uk<mailto:ceri.morris@naturalresourceswales.gov.uk> Mariel ten Doeschate Marielten.Doeschate(a)sac.co.uk<mailto:Marielten.Doeschate@sac.co.uk> Ceri Wyn Morris Cynghorydd Arbenigol Morol: Mamaliaid Môr / Marine Specialist Advisor: Marine Mammals Tîm Cyngor Morol Cymru Gyfan / Marine All Wales Advice Team Cyfoeth Naturiol Cymru / Natural Resources Wales 0300 065 4913 / 07766248402 Maes y Ffynnon, Bangor, Wales, UK

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New publication: Temporal patterns in acoustic presence and foraging activity of oceanic dolphins at seamounts in the Azores
by Irma Cascão 27 Feb '20

27 Feb '20

Dear Colleagues, We are pleased to announce the publication of the following paper in Scientific Reports: Irma Cascão, Marc O. Lammers, Rui Prieto, Ricardo S. Santos & Mónica A. Silva (2020) Temporal patterns in acoustic presence and foraging activity of oceanic dolphins at seamounts in the Azores. Scientific Reports. http://doi.org/10.1038/s41598-020-60441-4 Abstract Several seamounts have been identified as hotspots of marine life in the Azores, acting as feeding stations for top predators, including cetaceans. Passive acoustic monitoring is an efficient tool to study temporal variations in the occurrence and behaviour of vocalizing cetacean species. We deployed bottom-moored Ecological Acoustic Recorders (EARs) to investigate the temporal patterns in acoustic presence and foraging activity of oceanic dolphins at two seamounts (Condor and Gigante) in the Azores. Data were collected in March-May 2008 and April 2010-February 2011. Dolphins were present year round and nearly every day at both seamounts. Foraging signals (buzzes and bray calls) were recorded in >87% of the days dolphin were present. There was a strong diel pattern in dolphin acoustic occurrence and behaviour, with higher detections of foraging and echolocation vocalizations during the night and of social signals during daylight hours. Acoustic data demonstrate that small dolphins consistently use Condor and Gigante seamounts to forage at night. These results suggest that these seamounts likely are important feeding areas for dolphins. This study contributes to a better understanding of the feeding ecology of oceanic dolphins and provides new insights into the role of seamount habitats for top predators. The paper is available at: www.nature.com/articles/s41598-020-60441-4. Or email me irma.cascao(a)gmail.com for a PDF. You can also download two companion papers of this publication, which describe the effect of seamounts on the distribution and dynamics of micronekton scattering layers: I. Cascão, R. Domokos, M.O. Lammers, V. Marques, R. Domínguez, R.S. Santos & M.A. Silva (2017) Persistent Enhancement of Micronekton Backscatter at the Summits of Seamounts in the Azores. Frontiers in Marine Science 4:25. https://doi.org/10.3389/fmars.2017.00025 I. Cascão, R. Domokos, M.O. Lammers, R.S. Santos & M.A. Silva (2019) Seamount effects on the diel vertical migration and spatial structure of micronekton. Progress in Oceanography 175, 1-13. https://doi.org/10.1016/j.pocean.2019.03.008 Best regards, Irma Cascão ............................................................................................................................................................ Irma Cascão PhD MARE - Marine and Environmental Sciences Centre IMAR - Institute of Marine Research DOP - Department of Oceanography and Fisheries University of the Azores Rua Professor Dr. Frederico Machado 4 9901-862 Horta Portugal ResearchGate: https://www.researchgate.net/profile/Irma_Cascao2 Azores Whale Lab: http://whales.scienceontheweb.net

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New methods paper: An autonomous hydrophone array to study the acoustic ecology of deep-water toothed whales (Chloe Malinka)
by Chloe Malinka 26 Feb '20

26 Feb '20

Dear colleagues, We are pleased to share our new publication: Malinka C, Atkins J, Johnson M, Pernille Tønnesen P, Dunn C, Claridge D, Aguilar de Soto N, & PT Madsen (2020) "*An autonomous hydrophone array to study the acoustic ecology of deep-water toothed whales*." *Deep Sea Research I*. https://doi.org/10.1016/j.dsr.2020.103233 *Abstract of abstract:* - We developed an autonomous deep-water, large-aperture vertical hydrophone array using off-the-shelf components to address challenge of recording time-synchronised, high sample rate acoustic data at depth. - Array recordings can be used to quantify source parameters of toothed whale clicks. - We report on the design and performance of the portable and lightweight array. - Step-by-step directions on how to construct the array, as well as an analysis library for time synchronisation, are provided. *Abstract*: For vocal animals with distinctive calls, passive acoustic monitoring can be used to infer presence, distribution, and abundance provided that the calls and calling behaviour are known. Key to enabling quantitative acoustic surveys are calibrated recordings of identified species from which the source parameters of the sounds can be estimated. Obtaining such information from free-ranging aquatic animals such as toothed whales requires multi-element hydrophone arrays, the use of which is often constrained by cost, the logistical challenge of long cables, and the necessity for attachment to a boat or mooring in order to digitise and store multiple channels of high-sample rate audio data. Such challenges are compounded when collecting recordings or tracking the diving behaviour of deep-diving animals for which the array must be deployed at depth. Here we report the development of an autonomous drifting deep-water vertical passive acoustic array that uses readily available off-the-shelf components. This lightweight portable array can be deployed quickly and repeatedly to depths of up to 1000 m from a small boat. The array comprises seven ST-300 HF SoundTrap autonomous recorders equally spaced on an 84 m electrical-mechanical cable. The single-channel digital sound recordings were configured to allow for synchronisation in post-processing using an RS-485 timing signal logged by all channels every second. We outline how to assemble the array, and provide software for time-synchronising the acoustic recorders. To demonstrate the utility of the array, we present an example of short-finned pilot whale clicks localised on the deep-water (700 m) array configuration. This array method has broad applicability for the cost-effective study of source parameters, acoustic ecology, and diving behaviour of deep diving toothed whales, which are valuable not only to understand the sensory ecology of deep-diving cetaceans, but also to improve passive acoustic monitoring for conservation and management. Please get in touch for a PDF. Cheers, *Chloe Malinka* PhD Fellow Marine Bioacoustics Lab <https://marinebioacoustics.wordpress.com/> Dept. Biology, Aarhus University, Denmark. twitter: @c_malinka <https://twitter.com/c_malinka> email: chloe.e.malinka(a)gmail.com

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New publication: implementation of seal exclusion devices_squid bottom trawl fishery_Southwest Atlantic
by Verónica Iriarte (Seabirds & Marine Mammals Scientif ic Officer) 26 Feb '20

26 Feb '20

Dear marmamers, On behalf of my co-authors, I am very proud to announce the publication of our work: "Implementation of exclusion devices to mitigate seal (Arctocephalus australis, Otaria flavescens) incidental mortalities during bottom-trawling in the Falkland Islands (Southwest Atlantic)". The paper and supplemental videos can be downloaded from: https://authors.elsevier.com/a/1aeAlbiU1p2xy ABSTRACT: In the Falkland Islands, the South American fur seal and South American sea lion spatially overlap and interact with bottom-trawling fisheries. Until 2015, interactions of these species with the Patagonian bottom trawl squid fishery were uncommon. During the second fishing season 2017 a dramatic increase in seal interactions was observed, with a corresponding increase in incidental mortalities. Various mitigation measures were applied, seal exclusion devices (SEDs) fitted inside a net extension inserted between the trawl net and cod-end being the most efficient. The SEDs became mandatory in the fishery in September 2017. Since then, the number of seal mortalities remains negligible. SED efficiency is monitored by 100% observer coverage. To the best of our knowledge, the Falkland Islands Patagonian squid fishery is currently the only trawl fishery in the Southwest Atlantic with full observer coverage and SED usage. It is hoped in the near future similar mitigation measures extend to other coastal countries whose fisheries also interact with these otariids. Verónica Iriarte, MSc. Scientific Officer (Seabirds & Marine Mammals) Falkland Islands Fisheries Department Bypass Road, Stanley, FIQQ 1ZZ, Falkland Islands Tel: +500 27260 ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Second Call For A New Training Course - An Introduction To Integrating QGIS/GIS And R For Spatial Analysis
by Colin D. MacLeod 26 Feb '20

26 Feb '20

This is the second call for a brand new training course from GIS In Ecology. It's called 'An Introduction To Integrating QGIS.GIS and R For Spatial Analysis' and will be held in Glasgow, Scotland, between the 7th and 9th of April 2020. This course is aimed at those who wish to learn how to use and integrate QGIS (the leading freely available GIS software package) and R (the leading freely available data analysis software package) for spatial analysis. It will be taught by Dr. Colin D. MacLeod, the author of ‘An Introduction To Integrating QGIS And R for Spatial Analysis’ (Pictish Beast Publications) and a renowned expert in using GIS in biological and ecological research. He is also a co-author of the upcoming ‘An Introduction To Basic Statistics For Biologists Using R’, which is a practical guide to carrying out the analysis of biological data in R. The course assumes no prior knowledge of either QGIS/GIS or R, and so is open to complete beginners as well as those how know how to use one of these software packages, and wish to learn how to integrate it with the other. Attendance will be limited to a maximum of 16 people. The course for this three day course will cost GBP 395 per person (with a discounted rate of GBP 300 for students, the unwaged and those working for registered charities). To book a place, or for more information, visit http://gisinecology.com/an-introduction-to-integrating-qgis-gis-and-r-for-s… or email info(a)GISinEcology.com. GIS and statistical analysis are two of the most fundamental software tools for marine mammalogists wishing to conduct spatial analyses, which is, itself, a cornerstone for the management and conservation of marine mammal species. However, GIS and statistical analyses have their own sets of software packages, and sometimes it can be difficult to know how to integrate the two. This course will provide an introduction to the integration of QGIS (the leading freely available GIS software package) and R (the leading data analysis software packages used by biologists) to create a combined tool set that makes the most of the strengths of each of these individual software packages. It will consist of a series of background sessions on using GIS and R for spatial analysis, mixed in with practical sessions where you will learn how to use QGIS, how to use R, and how to integrate two to complete a spatial analysis project. This last part will include working through an example project, starting with creating a high quality map for publication through creating raster data layers of environmental variables, joining data together based on their spatial relationships and analysing the combined data set using R (including creating summary statistics, conducting linear regressions and conducting generalised additive modelling - GAMs). While it will primarily be based around QGIS, this course is taught using software-independent approach, and it is also open to those who wish to learn how to use ArcGIS to do biological GIS. When you attend this course you will receive a free copy of An Introduction To Integrating QGIS And R for Spatial Analysis (GIS For Biologists Workbooks) as the practical exercises in that course are based on the ones contained in that book. NOTE: If you wish to use ArcGIS software for this course, alternative materials will be provided for the practical sessions. ================================================================================== GIS IN ECOLOGY - Providing Training, Advice And Consultancy On The Use Of GIS In Ecology Web: www.GISinEcology.com Email: info(a)GISinEcology.com Need to ask a question about using GIS? Try the GIS In Ecology Forum: www.GISinEcology.com/GIS_in_Ecology_forum.htm Books From GIS In Ecology Staff: GIS For Biologists: A Practical Introduction For Undergraduates; RRP: £24.99 An Introduction To Using GIS In Marine Biology; RRP: £44.99 An Introduction To Using GIS In Marine Biology: Supplementary Workbook One - Creating Maps Of Species Distribution; RRP: £19:99 If you wish to purchase these books, visit: http://www.gisinecology.com/Book_Shop.htm To help the environment, please do not print out this email unless it is unavoidable. ==================================================================================

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New publication: Blubber cortisol levels in humpback whales
by Mr Fletcher Mingramm 25 Feb '20

25 Feb '20

Dear MARMAM colleagues, We are pleased to announce that the following paper is now available online: Fletcher M.J. Mingramm, Tamara Keeley, Deanne J. Whitworth, Rebecca A. Dunlop, Blubber cortisol levels in humpback whales (Megaptera novaeangliae): A measure of physiological stress without effects from sampling, General and Comparative Endocrinology, Volume 291, 2020, 113436, Abstract: Baleen whales are vulnerable to environmental impacts due to low fecundity, capital breeding strategies, and their reliance on a large amount of prey resources over large spatial scales. There has been growing interest in monitoring health and physiological stress in these species but, to date, few measures have been validated. The purpose of this study was to examine whether blubber cortisol could be used as a measure of physiological stress in humpback whales. Cortisol concentrations were initially compared between live, presumably ‘healthy’ whales (n = 187) and deceased whales (n = 35), which had died after stranding or entanglement, or washed ashore as a carcass. Deceased whales were found to have significantly higher cortisol levels (mean ± SD; 5.47 ± 4.52 ng/ g) than live whales (0.51 ± 0.14 ng/g; p < 0.001), particularly for those animals that had experienced prolonged trauma (e.g. stranding) prior to death. Blubber cortisol levels in live whales were then examined for evidence of life history-related, seasonal, or sampling-related effects. Life history group and sampling-related factors, such as encounter time and the number of biopsy sampling attempts per animal, were found to be poor predictors of blubber cortisol levels in live whales. In contrast, blubber cortisol levels varied seasonally, with whales migrating north towards the breeding grounds in winter having significantly higher levels (0.54 ± 0.21 ng/g, p = 0.016) than those migrating south towards the feeding grounds in spring (0.48 ± 1.23 ng/g). These differences could be due to additional socio-physiological stress experienced by whales during peaks in breeding activity. Overall, blubber cortisol appears to be a suitable measure of chronic physiological stress in humpback whales. An open access copy can currently be downloaded from: https://authors.elsevier.com/a/1abQm3oGhHjxk Kind regards, Fletcher Get Outlook for Android<https://aka.ms/ghei36>

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Large NATO sonar exercise in the Ionian Sea - Local Ziphius population unit may be at risk
by Alexandros Frantzis 25 Feb '20

25 Feb '20

Dear all, We have just been informed from the NavalNews website that NATO exercise Dynamic Manta (DYMA20) began yesterday Feb. 24 2020. https://navalnews.net/natos-advanced-asw-exercise-dynamic-manta-2020-kicks-… According to the above article, 9 Allied nations are converging in the Central Mediterranean Sea (almost the entire Ionian Sea) for advance anti-submarine warfare (ASW) and anti-surface warfare (ASuW) training. That means that military sonar will be used, in areas inhabited by Cuvier's beaked whales, and very close to areas where several previous atypical mass strandings have occurred. Four atypical mass strandings (1996, 1997, 2011, 2014) and one live stradning (2000) have occurred in the past during the use of military sonar along the Hellenic Trench (Greek coasts), and some more along the Italian coasts. Most of the participating nations (France, Greece, Italy, Spain and Turkey) are members of ACCOBAMS. ACCOBAMS has repeatedly urged for avoiding habitats of Cuviers beaked whales while designing such exercises and has mapped critical areas for the species in the Mediterranean Sea. The Hellenic Trench is probably the most important hotspot for this species according to this maps, it is a proposed MPA by ACCOBAMS and more recently was the first area to be listed as IMMA (Important Marine Mammal Area) at the global scale for both its sperm whale and Cuvier's beaked whale population units. Although the published map (Notice to airmen) of the current military activity does not include the Hellenic Trench (Italy is the hosting country and no precise geographical info is available about the military sonar use), previous military sonar use in the Ionian Italian coasts provoked a mass stranding in both the Italian and the Greek coasts (mainly in Corfu and western Greece in 2011). We cannot know how important the damage will be this time and if the way that sonar will be used will send impacted whales to the Ionian coasts or make them sink and disappear in deep waters. With this message we wish: 1) To inform the cetological community 2) To alert local stranding networks in the Ionian coasts, so that they are ready to respond in case of stranding events 3) To let all the concerned parties, national and international, know that a major old environmental problem remains still unresolved and keeps impacting critical areas of threaten cetacean species. All the best, Alexandros -- ___________________________________________ Dr. Alexandros Frantzis Scientific director Pelagos Cetacean Research Institute Terpsichoris 21 16671 Vouliagmeni, GREECE Tel.: +30-210-8960108 e-mail: afrantzis(a)otenet.gr website: http://www.pelagosinstitute.gr ___________________________________________

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State of the Science Workshop on Wildlife and Offshore Wind
by Julia Gulka 25 Feb '20

25 Feb '20

Registration and call for poster abstracts are now open for the State of the Science on Offshore Wind Energy: Workshop on Cumulative Impacts to Wildlife. The New York State Energy Research and Development Authority (NYSERDA) is hosting its second State of the Science Workshop <http://www.nyetwg.com/2020-workshop> on Wildlife and Offshore Wind Energy on May 5-6, 2020 in Rye Brook, New York. The first day of the workshop will consist of plenary presentations to summarize the current state of knowledge on cumulative impacts to wildlife from offshore wind energy development, including a review of major stressors to marine mammals, discussions of population consequences of disturbance (PCOD) modeling, and cumulative noise impacts to marine mammals from pile driving and other sources. The second day of the workshop will primarily consist of smaller workshops focused on developing research plans to improve our understanding of cumulative impacts, with one of the breakout groups focused on marine mammals. To register for the workshop, reserve a discounted room at the conference hotel, or submit a poster abstract, visit the workshop webpage: www.nyetwg.com/2020-workshop. The deadline for registration and abstract submission is April 13, 2020. -- Julia Gulka Marine Biologist Biodiversity Research Institute 276 Canco Rd., Portland, Maine 04103 (207) 839-7600 x303 www.briloon.org

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New publication: Unmanned surface vehicles for remote focal follows
by Carey Kuhn - NOAA Federal 24 Feb '20

24 Feb '20

Dear MARMAM colleagues, My coauthors and I are pleased to share our new open access publication: https://www.int-res.com/abstracts/meps/v635/p1-7/ Test of unmanned surface vehicles to conduct remote focal follow studies of a marine predator Carey E. Kuhn1, Alex De Robertis2, Jeremy Sterling1, Calvin W. Mordy3,4, Christian Meinig4, Noah Lawrence-Slavas4, Edward Cokelet4, Mike Levine2, Heather Tabisola3,4, Richard Jenkins5, David Peacock5, Danny Vo6 1Marine Mammal Laboratory, Alaska Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), Seattle, Washington, USA 2 Resource Assessment and Conservation Engineering Division, Alaska Fisheries Science Center, NOAA, Seattle, Washington, USA 3Joint Institute for the Study of the Atmosphere and Ocean, University of Washington, Seattle, Washington, USA 4Pacific Marine Environmental Laboratory, NOAA, Seattle, Washington, USA 5Saildrone Inc., Alameda, California, USA 6Wildlife Computers Inc., Redmond, Washington, USA Abstract: We tested the feasibility of using Saildrone unmanned wind- and solar-powered surface vehicles to conduct remote focal follow studies of northern fur seals Callorhinus ursinus. Using Argos satellite and transmitted GPS locations, the Saildrones followed a fur seal while recording oceanographic conditions and mapping prey abundance and depth distribution using a scientific echosounder. The Saildrones successfully followed 6 fur seals over 2.4 ± 0.2 d and 149.7 ± 16.3 km of the foraging path. Median separation distance between the Saildrone and fur seal path was 0.65 ± 0.1 km and average time separation was 9.9 ± 1.4 h, with minimum time separations ranging from 1.9 to 4.9 h. Time and distance separation were a function of both animal behavior and study design. Our results show that Saildrones can approach satellite tracked marine predators from long distances and follow them over extended periods while collecting oceanographic and prey data. These successful focal follows demonstrate that unmanned surface vehicles are a valuable tool for collecting data on fine-scale relationships between marine predators, their prey, and the environment. Please, do not hesitate to contact me if you have any questions. Cheers, Carey Kuhn Ecologist Marine Mammal Laboratory / NOAA Fisheries Alaska Fisheries Science Center, Seattle, WA

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