December 2018 - MARMAM - devlists.uvic.ca

new publication: Applying deep learning to right whale photo identification
by Christin Khan - NOAA Federal 06 Dec '18

06 Dec '18

Bogucki, R. , Cygan, M. , Khan, C. B., Klimek, M. , Milczek, J. K. and Mucha, M. (2018), Applying deep learning to right whale photo identification. Conservation Biology. . DOI: 10.1111/cobi.13226 <https://onlinelibrary.wiley.com/doi/epdf/10.1111/cobi.13226> *Abstract:* Photo identification is an important tool for estimating abundance and monitoring population trends over time. However, manually matching photographs to known individuals is time-consuming. Motivated by recent developments in image recognition, we hosted a data science challenge on the crowdsourcing platform Kaggle to automate the identification of endangered North Atlantic rightwhales (Eubalaena glacialis).The winning solution automatically identified individual whales with 87% accuracy with a series of convolutional neural networks to identify the region of interest on an image, rotate, crop, and create standardized photographs of uniform size and orientation and then identify the correct individual whale from these passport-like photographs. Recent advances in deeplearning coupled with this fully automated workflow have yielded impressive results and have the potential to revolutionize traditional methods for the collection of data on the abundance and distribution of wild populations. Presenting these results to a broad audience should further bridge the gap between the data science and conservation science communities. *Keywords: *algorithm, automated image recognition, computer vision, convolutional neural networks, Kaggle competition, machine learning, photo identification - Christin *Christin B. KhanFishery Biologist, Right Whale AerialsNOAA Northeast Fisheries Science Centerchristin.khan(a)noaa.gov <christin.khan(a)noaa.gov> * *www.cbkhan.com <http://www.cbkhan.com>617.256.4452* *psb websitewww.nefsc.noaa.gov/psb/ <http://www.nefsc.noaa.gov/psb/>noaa facebookwww.facebook.com/NOAAFisheries <https://www.facebook.com/NOAAFisheries>personal websitewww.cbkhan.com <http://www.cbkhan.com>photo gallerywww.nefsc.noaa.gov/rcb/photogallery/scenic-khan.html <http://nefsc.noaa.gov/rcb/photogallery/scenic-khan.html>*

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NEW PUBLICATION: Alopecia in Gray Seals
by Katie Pugliares 06 Dec '18

06 Dec '18

Dear MARMAM, My co-authors and I are pleased to announce that the following paper has been published and is available via open-access: Pugliares-Bonner, K., McKenna, K., Sette, L., Niemeyer, M., & Tlusty, M. (2018). Prevalence of alopecia in gray seals Halichoerus grypus atlantica in Massachusetts, USA, 2004-2013. Diseases of aquatic organisms, 131(3), 167-176. Abstract: There has been an increase in the presence of alopecia among gray seals Halichoerus grypus atlantica in Massachusetts, USA. To understand the prevalence and describe the presentation of this condition, data records and photographs of 10070 gray seals from 2004-2013 were reviewed; there were sufficient data to confidently assess the presence or absence of alopecia in 2134 seals. Mild hair loss presented in multifocal patches with minimal to no skin lesions or erythema. In severe cases, alopecia was concentrated over the dorsal head, neck, and shoulders and extended down the ventrum, affecting >50% of the body. Associated skin lesions and erythema were often present. Alopecia was documented in 7.1% of the surveyed seals, and was centered in Nantucket. Alopecia was more prevalent in stranded/sighted animals in spring and summer, with 81% of cases documented from April to July. There was no sex bias, and weanlings were the most affected age class (38%). The etiology for alopecia in Massachusetts gray seals is unknown. Possible causes of alopecia in wildlife are infectious disease, nutritional deficiencies, endocrinopathies, or chronic physiologic stress. High population density around Nantucket may escalate intraspecific competition for resources, which may indirectly lead to stress-induced immunosuppression or nutritional deficiencies. Crowded haul-out sites increase the opportunity for disease transmission. The weanling age class may be prone to alopecia due to naïve immune systems and inexperienced foraging capabilities. Diagnostic sample collection from gray seals will be required to characterize the etiology, pathogenesis, and significance of alopecia in this population. https://www.int-res.com/abstracts/dao/v131/n3/p167-176/ Thank you. Katie Pugliares-Bonner Senior Biologist - Necropsy Coordinator Rescue & Rehabilitation New England Aquarium Office: 617.226.2263 kpugliares(a)neaq.org<mailto:kpugliares@neaq.org>

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New publication on mammal-eating killer whales in the Salish Sea
by Monika Wieland 06 Dec '18

06 Dec '18

Dear Colleagues, On behalf of the Orca Behavior Institute, I'm pleased to announce our latest publication in PeerJ: Shields MW, Hysong-Shimazu S, Shields JC, Woodruff J. 2018. Increased presence of mammal-eating killer whales in the Salish Sea with implications for predator-prey dynamics. PeerJ 6:e6062 https://doi.org/10.7717/peerj.6062 Abstract: The inland waters of Washington State and southern British Columbia, collectively known as the Salish Sea, comprise key habitat for two regional populations of killer whales (/Orcinus orca/): the mammal-eating West Coast Transients and the endangered fish-eating Southern Residents. These two populations are genetically distinct and may avoid each other. Transient killer whale usage of the Salish Sea has been previously assessed over two seven-year time periods, showing an increase from 1987 to 2010. We documented a continued significant increase in mammal-eating killer whale presence in the Salish Sea from 2011 to 2017, with intra- and inter-annual variability and with record sightings in 2017. This continued increase, likely in response to abundant marine mammal prey, is related to both a growing population and an increase in the number of West Coast Transients visiting the area. Additionally, a negative binomial regression shows that absence of Southern Residents is correlated to transient presence. Finally, both populations of killer whales have been linked to regional harbor seal populations; harbor seals are salmonid-eating competitors of the Southern Residents and are prey for the mammal-eating transients. With Southern Residents listed as endangered, culling harbor seals has been proposed as a measure to help in their recovery. With this in mind, we developed an energetic model to assess the minimum number of harbor seals consumed by transient killer whales. Using the actual number of whales present in each age-sex class for each day of the year, we estimate that, at a minimum, transients in the Salish Sea consumed 1090 seals in 2017. This is more than 2% of the 2014 estimated harbor seal population the Salish Sea. The population controlling effects of transient killer whale predation on harbor seals should be considered when evaluating any pinniped management actions in the Salish Sea. Full paper available open access here: https://peerj.com/articles/6062/ Best regards, Monika Wieland Shields Orca Behavior Institute

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New review paper
by Vanessa Pirotta (HDR) 05 Dec '18

05 Dec '18

Dear MARMAM colleagues, My co-authors and I are pleased to announce the publication of the following manuscript available online: Consequences of global shipping traffic for marine giants Vanessa Pirotta, Alana Grech, Ian D Jonsen, William F Laurance, Robert G Harcourt Front Ecol Environ 2018; doi: 10.1002/fee.1987 Abstract Shipping routes in the ocean are analogous to terrestrial roads, in that they are regularly used thoroughfares that concentrate the movement of vessels between multiple locations. We applied a terrestrial road ecology framework to examine the ecological impacts of increased global shipping on “marine giants” (ie great whales, basking sharks [Cetorhinus maximus], and whale sharks [Rhincodon typus]). This framework aided in identifying where such “marine roads” and marine giants are likely to interact and the consequences of those interactions. We also reviewed known impacts of shipping routes on these species, and then applied the road ecology framework to detect unknown and potentially threatening processes. In the marine environment, such a framework can be used to incorporate knowledge of existing shipping impacts into management practices, thereby reducing the detrimental effects of future expansion of shipping routes on marine giants. Publication available here: https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/fee.1987 Best regards, Vanessa Pirotta Twitter: @vanessapirotta

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Living Seas Volunteer Positions 2019, Cardigan Bay Marine Wildlife Centre, New Quay, west Wales
by CBMWC 05 Dec '18

05 Dec '18

The Cardigan Bay Marine Wildlife Centre (CBMWC) <https://www.welshwildlife.org/visitor-centres/cardigan-bay-marine-wildlife- centre/> is looking for dedicated and enthusiastic volunteers to join our Living Seas Team for the 2019 field season, to help with our marine mammal research and awareness raising work. The Cardigan Bay Marine Wildlife Centre is the Living Seas wing of the Wildlife Trust of South and West Wales. Since 1996 we have been dedicated to raising awareness of the local marine environment through research and education. Using land and boat based surveys, photo-identification and acoustic studies we collect data on marine megafauna, focusing on bottlenose dolphins, harbour porpoises and Atlantic grey seals in the Cardigan Bay Special Area of Conservation (SAC) and the wider Irish Sea. We operate a busy visitor centre and also provide marine educational activities for families, school and groups. Volunteering with CBMWC is a unique opportunity for you to carry out marine mammal research and to help inspire the public through our visitor centre and community engagement events. You'll learn about the marine species of Cardigan Bay and gain experience in field work, processing data, environmental education, community engagement and much more! The volunteer programme at CBMWC has received national recognition after achieving the Investing in Volunteers Award (IiV), the UK's quality standard for volunteer management. We provide a fantastic volunteer experience! We have a number of volunteering roles available - Living Seas Volunteers <https://www.welshwildlife.org/visitor-centres/cardigan-bay-marine-wildlife- centre/volunteer/livingseas-volunteers/> -tasks include land and boat based surveys, data entry, running our visitor centre, assisting with community engagement events and beach cleans. Volunteer dates - * Block A - 25th March - 29th April (5 weeks) * Block B - 29th April - 3rd June (5 weeks) * Block C - 3rd June - 8th July - (8 weeks) * Block D - 8th July - 2nd September (8 weeks) * Block E - 2nd September - 4th November (9 weeks) ShoreFin Volunteers <https://www.welshwildlife.org/visitor-centres/cardigan-bay-marine-wildlife- centre/volunteer/shorefin-volunteers/> - tasks include photographing bottlenose dolphins from land, photo-ID, analysing data and writing the annual ShoreFin report. We are looking for two ShoreFin volunteers for the period of 25th March - 5th July 2019 and another two volunteers for the period 1st July - 4th November 2019. SeaSeal Volunteer <https://www.welshwildlife.org/visitor-centres/cardigan-bay-marine-wildlife- centre/volunteer/seal-photo-id/> - tasks include land based seal surveys, photographing seals, photo-ID, analysing data and writing the annual SeaSeal report. We are looking for one SeaSeal volunteer for the period of 25th March - 5th July 2019 and another volunteer for the period 1st July - 4th November 2019. Visit https://www.welshwildlife.org/visitor-centres/cardigan-bay-marine-wildlife-c entre/volunteer/seasonal-volunteer-positions/ for further information on the roles and how to apply. Deadline for applications is 23:59pm on Sunday 6th January. Contact - Laura Evans at volunteer(a)cbmwc.org or 01545 560224 for more information.

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Interp/Remote Video Monitoring Steller Sea Lions Internship-Alaska SeaLife Center
by Anna Pullins 04 Dec '18

04 Dec '18

The Alaska SeaLife Center is now recruiting for: *Interpretation/Remote Video Monitoring of Steller Sea Lions Intern* Intern will team with the interpretive staff for 20 hours a week and with the Chiswell staff for 20 hours a week. Interns will assist with the day-to-day support of animal-related research activities involving Steller sea lions. Candidates should exhibit a strong interest in field-based and animal-related research work and associated support. Applicants should possess the ability to work for extended periods of time while staying focused on the task at hand. Under the guidance of Chiswell and Interpretation staff, the Intern will be trained and expected to perform the following duties: - Interpret all of the Alaska SeaLife Center’s static and live animal exhibits housing marine mammals, birds, fish, and invertebrates. Help maintain the physical appearance of manned exhibits and deliver announcements over the public address system. - Present briefings, lectures, presentations, multi-media shows, structured and impromptu talks, and guided tours by learning to employ appropriate interpretive techniques and devices geared to the characteristics and interest of particular audiences. - Operate remotely controlled cameras from a desktop computer. - Make behavioral observations of Steller sea lions and demonstrate learned skills through video recording, data entry, and management. - Follow a regimented schedule of observations and be prompt with daily duties. Apply at http://www.alaskasealife.org/employment_opportunities Application deadline is 1/7/19 -- <https://www.facebook.com/AlaskaSeaLifeCenter> <https://twitter.com/alaskasealife> <http://instagram.com/alaskasealifecenter> <https://www.youtube.com/user/AKSeaLifeCenter> <https://www.linkedin.com/company/alaska-sealife-center> *Anna Pullins* *Human Resources Coordinator*Alaska SeaLife Center P.O. Box 1329 • 301 Railway Ave • Seward, AK 99664 <https://maps.google.com/?q=1329%C2%A0%E2%80%A2+301+Railway+Ave%C2%A0%E2%80%…> Direct: 907-224-6327 Mobile: 907-362-7773 Fax: 907-224-6320 www.alaskasealife.org

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Veterinary Lab Internship-Alaska SeaLife Center
by Anna Pullins 04 Dec '18

04 Dec '18

The Alaska SeaLife Center is now recruiting for: *Marine Wildlife Veterinary Laboratory Intern-Summer 2019* Intern will learn about the diagnostics and instruments commonly used in a veterinary laboratory specializing in Alaskan marine mammals, birds and fish. Intern will be exposed to the methods used to maintain a clean and efficient laboratory. Skills and procedures learned will include: blood analysis, urine and fecal analysis, fecal coliform water quality analysis, sample collection during animal exams or necropsy, and maintaining veterinary records and sample inventory. Under guidance of Laboratory staff, the Intern will be trained and expected to perform the following duties: - Assist with set up and processing routine blood samples. Work with laboratory technicians to perform plasma/serum separations, prepare blood slides, and assist with performing serum chemistries and cell counts using an automated analyzer. - Assist with maintaining laboratory and veterinary clinic cleanliness and routine maintenance of equipment. - Assist with weekly water quality testing. - Assist with maintaining sample inventory - Assist with shipping samples to outside researchers - Assist with maintaining medical and laboratory records and logs. - Assist with organizing and inventorying consumable supplies for the laboratories. - Assist with other duties relating to the Center’s goals and mission statement as required. Applicants should be agile with a good sense of balance in order to maneuver around the exhibits and holding areas. Applicants must be comfortable working with database computer programs and sensitive equipment. Must be willing to work with frozen samples and in walk-in freezers and able to lift 50 pounds. Job duties will vary from day to day. *Although tasks will be in direct support of animal welfare, there is very little direct contact with animals in this position.* Apply at http://www.alaskasealife.org/employment_opportunities Application deadline is 1/7/19 -- <https://www.facebook.com/AlaskaSeaLifeCenter> <https://twitter.com/alaskasealife> <http://instagram.com/alaskasealifecenter> <https://www.youtube.com/user/AKSeaLifeCenter> <https://www.linkedin.com/company/alaska-sealife-center> *Anna Pullins* *Human Resources Coordinator*Alaska SeaLife Center P.O. Box 1329 • 301 Railway Ave • Seward, AK 99664 <https://maps.google.com/?q=1329%C2%A0%E2%80%A2+301+Railway+Ave%C2%A0%E2%80%…> Direct: 907-224-6327 Mobile: 907-362-7773 Fax: 907-224-6320 www.alaskasealife.org

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New publication on baleen whale biomechanics and morphology
by Alex Werth 04 Dec '18

04 Dec '18

Dear MARMAM colleagues, On behalf of my coauthors I am pleased to announce the publication of our new paper in the Journal of Experimental Biology on the flexibility and histology of baleen: Alexander J. Werth, Diego Rita Espada, Michael V. Rosario, Michael J. Moore, and Todd L. Sformo. 2018. How do baleen whales stow their filter? A comparative biomechanical analysis of baleen bending. Journal of Experimental Biology, jeb189233. doi:10.1242/jeb.189233. Abstract: Bowhead and right whale (balaenid) baleen filtering plates, longer in vertical dimension (≥3-4 m) than the closed mouth, presumably bend during gape closure. This has not been observed in live whales, even with scrutiny of video-recorded feeding sequences. To determine what happens to the baleen during gape closure, we conducted an integrative, multifactorial study including materials testing, functional (flow tank and kinematic) testing, and histological examination. We measured baleen bending properties along the dorsoventral length of plates and anteroposterior location within a rack of plates via mechanical (axial bending, composite flexure, compression and tension) tests of hydrated and air-dried tissue samples from balaenid and other whale baleen. Balaenid baleen is remarkably strong yet pliable, with ductile fringes, and low stiffness and high elasticity when wet; it likely bends in the closed mouth when not used for filtration. Calculation of flexural modulus from stress/strain experiments shows that the balaenid baleen is slightly more flexible where it emerges from the gums and at its ventral terminus, but kinematic analysis indicates plates bend evenly along their whole length. Fin and humpback whale baleen has similar material properties but less flexibility, with no dorsoventral variation. The internal horn tubes have greater external and hollow luminal diameter but lower density in the lateral relative to medial baleen of bowhead and fin whales, suggesting a greater capacity for lateral bending. Baleen bending has major consequences not only for feeding morphology and energetics but also for conservation given that entanglement in fishing gear is a leading cause of whale mortality. If you are interested please contact me for a pre-print pdf. Alex Werth _______________________________ Alexander J. Werth, Ph.D. Trinkle Professor of Biology Hampden-Sydney College Box 162, Hampden-Sydney, VA 23943 434-223-6326, fax 434-223-6374 http://www.hsc.edu/alex-werth

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Job Announcement: Two (2) MMPA/ESA Positions in NOAA Fisheries' Office of Protected Resources
by Trevor Spradlin - NOAA Federal 04 Dec '18

04 Dec '18

NOAA Fisheries’ Office of Protected Resources (OPR) is pleased to announce two (2) full-time employee (FTE) positions focused on marine mammal conservation issues under the Marine Mammal Protection Act and Endangered Species Act. Both positions are at the Pay Band IV level (GS 13/14 equivalent) and based at NOAA Fisheries’ headquarters in Silver Spring, MD in OPR’s Marine Mammal and Sea Turtle Conservation Division. The two positions are distinct but complementary: one will focus primarily on large cetacean conservation and recovery efforts with an emphasis on North Atlantic right whales, while the other will focus on a broader suite of marine mammal species (large cetaceans, small cetaceans, and pinnipeds). Successful candidates will be assigned to either one of the portfolios based on their expertise. The announcement can be found on USAJobs at: https://www.usajobs.gov/GetJob/ViewDetails/518353800 (for applicants already in the Federal government) https://www.usajobs.gov/GetJob/ViewDetails/518353900 (for applicants outside the Federal government) Successful candidates should have strong backgrounds in marine mammal science and policy issues. Please note these positions are only open to U.S. citizens and relocation expenses are not included. *Applications are currently being accepted until 11:59pm ET on Monday, December 17, 2018. * Interested applicants who have questions about the position should first contact the Human Resources specialist listed in the job announcement. -- ******************** Trevor R. Spradlin, M.Res. Deputy Chief Marine Mammal and Sea Turtle Conservation Division (F/PR2) Office of Protected Resources NOAA/National Marine Fisheries Service Tel: 301-427-8479 E-mail: Trevor.Spradlin(a)noaa.gov

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Video Archive: 2018 Webinar Series on Underwater Acoustics for the International Regulatory Community
by Holly Morin 04 Dec '18

04 Dec '18

***apologies for cross postings*** The Discovery of Sound in the Sea (DOSITS) <http://www.dosits.org/> Team is pleased to announce that video recordings for all webinars from the 2018 webinar series on underwater acoustics for the international regulatory community are now available online <https://dosits.org/decision-makers/webinar-series/webinars-2018/>. Webinar topics included foundational science on sound reception and potential effects in marine mammals and fishes and was comprised of the following presentations: Dr. Darlene Ketten, Sound Reception in Marine Mammals Dr. Brandon Southall, Potential Effects of Sound on Marine Mammals Dr. Craig Radford, Sound Production and Reception in Teleost Fishes Dr. Arthur Popper, Potential Effects of Sound on Marine Fishes The 2018 Webinar Series Archive can be found here: https://dosits.org/decision-makers/webinar-series/webinars-2018/. In addition to the video recordings, outlines for each webinar with links to background content on DOSITS are also available. Associated webinar recordings and their resources from the 2015 and 2016 webinar series have been archived here <https://dosits.org/decision-makers/webinar-series/webinar-archive-2015-16/>. A 2019 webinar series on underwater sound sources is currently being planned. These webinars will provide overviews of various anthropogenic sound sources and review existing and upcoming noise attenuation measures, their effectiveness, and logistical issues. Further details and webinar dates will be announced after January 2019. Questions? Please contact Holly Morin (holly_morin(a)uri.edu <mailto:holly_morin@uri.edu>). *********************************** Holly Morin Marine Research Associate III URI/GSO/ISC (401) 874-6414 holly_morin(a)uri.edu

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