Exciting news for the GEMM Lab: SMM conference and a twitter feed!

By Amanda Holdman (M.S Student)

At the end of the week, the GEMM Lab will be pilling into our fuel efficient Subaru’s and start heading south to San Francisco! The 21st Biennial Conference on the Biology of Marine Mammals, hosted by the Society of Marine Mammalogy, kicks off this weekend and the GEMM Lab is all prepped and ready!

Workshops start on Saturday prior to the conference, and I will be attending the Harbor Porpoise Workshop, where I get to collaborate with several other researchers worldwide who study my favorite cryptic species. After morning introductions, we will have a series of talks, a lunch break, and then head to the Golden Gate Bridge to see the recently returned San Francisco harbor porpoise. Sounds fun right?!? But that’s just day one. A whole week of scientific fun is to be had! So let’s begin with Society’s mission:

smm-2015-logo

‘To promote the global advancement of marine mammal science and contribute to its relevance and impact in education, conservation and management’ 

And the GEMM Lab is all set to do just that! The conference will bring together approximately 2200 top marine mammal scientists and managers to investigate the theme of Marine Mammal Conservation in a Changing World. All GEMM Lab members will be presenting at this year’s conference, accompanied by other researchers from the Marine Mammal Institute, to total 34 researchers representing Oregon State University!

Here is our Lab line-up:

Our leader, Leigh will be starting us off strong with a speed talk on Moving from documentation to protection of a blue whale foraging ground in an industrial area of New Zealand

Tuesday morning I will be presenting a poster on the Spatio-temporal patterns and ecological drivers of harbor porpoises off of the central Oregon coast

Solène follows directly after me on Tuesday to give an oral presentation on the Environmental correlates of nearshore habitat distribution by the critically endangered Maui dolphin.

Florence helps us reconvene Thursday morning with a poster presentation on her work, Assessment of vessel response to foraging gray whales along the Oregon coast to promote sustainable ecotourism. 

And finally, Courtney, the most recent Master of Science, and the first graduate of the GEMM Lab will give an oral presentation to round us out on Citizen Science: Benefits and limitations for marine mammal research and education

However, while I am full of excitement and anticipation for the conference, I do regret to report that you will not be seeing a blog post from us next week. That’s because the GEMM Lab recently created a twitter feed and we will be “live tweeting” our conference experience with all of you! You can follow along the conference by searching #Marman15 and follow our Lab at @GemmLabOSU

Twitter is a great way to communicate our research, exchange ideas and network, and can be a great resource for scientific inspiration.

If you are new to twitter, like the GEMM Lab, or are considering pursuing graduate school, take some time to explore the scientific world of tweeting and following. I did and as it turns out there are tons of resources that are aimed for grad students to help other grad students.

For example:

Tweets by the thesis wisperer team (@thesiswisperer) offer advice and useful tips on writing and other grad related stuff. If you are having problems with statistics, there are lots of specialist groups such as R-package related hashtags like #rstats, or you could follow @Rbloggers and @statsforbios to name a few.

As always, thanks for following along, make sure to find us on twitter so you can follow along with the GEMM Labs scientific endeavors.

 

 

Successfully a Master, or at Least a Bit More Enlightened

By Courtney Hann (M.S. Marine Resource Management)

A week ago, I successfully defended my Masters of Science thesis on “Citizen Science Research: A Focus on Historical Whaling Data and a Current Citizen Science Project, Whale mAPP”, which included a 60 minute presentation to my committee, colleagues, friends, and family. Although a bit nervous at the start, my two weeks of revisions and practice prepared me to enjoy the experience once it started, and be thankful for all of the guidance and knowledge I have gained while at Oregon State University and with the Geospatial Ecology of Marine Megafauna Lab.

PresentationM.S. pic

My thesis focused on the value of collaboration and creativity in developing new methods for gathering and analyzing marine mammal data; and was driven by the overall question of

How do we study marine mammals over vast spatial and temporal scales without breaking the bank, while still being scientifically rigorous?

This is important because marine mammal data collected over large spatial and temporal scales is relatively rare, and requires extensive collaboration and funding (Calambokidis et al. 2008; Dahlheim et al. 2009). A majority of marine mammal research is conducted over limited time frames (weeks to months) and on local spatial scales, requiring the data to be extrapolated out in order to understand regional patterns (Baker et al. 1985; Rosa et al. 2012). As a result, ecological modeling and other analyses are limited by geographic and temporal scale (Hamazaki 2002; Redfern et al. 2006).

I presented two potential approaches to the use of citizen science data to cost-effectively study marine mammal distributions across vast spatial and temporal scales. The first method is described below:

(1) Use the oldest form of large cetacean citizen science data, historical whaling records, to analyze species trends across extensive spatial and temporal scales. Amazingly, these 200-year-old records provide some of the most informative data for highlighting regional and global marine mammal distributions and abundance estimates (Gregr and Trites 2001; Torres et al. 2013). This information is vital for adapting management strategies as populations recover, change their distribution due to climate changes, or undergo various interactions with humans (net entanglements, ship strikes, competition for commercially important fish and invertebrate species, etc.).

Replicating such datasets today is not fiscally feasible with traditional research methods, but distribution data is still vital for understanding how populations have changed over time and how they are responding to large-scale climate and anthropogenic changes. Modern day citizen science research may be the solution to collecting such baseline data. Therefore, the following second method was evaluated:

(2) Data collected by 39 volunteers using the marine mammal citizen science app, Whale mAPP (www.whalemapp.org), over the summer of 2014 was examined to interpret various spatial, users, and species biases present in the dataset. In addition, the educational benefits, user motivations, and suggestions for revisions to the citizen science project were investigated with two user surveys. Results were used to revise Whale mAPP and highlight both the potential and limitations of citizen science data collected with Whale mAPP.

While I believe in the power of citizen science research for expanding our knowledge of large-scale marine mammal distributions, it is important to continue to interpret the biases in the dataset and truly examine how we can use the results for research. For, although collecting an abundance of data may be fun and exciting, careful examination of the methods and analyses techniques are vital if we hope to one day use the data to inform management and conservation decisions. I hope that my research contributes not only to this knowledge, but also to opening our eyes to the value of embracing a new method of data collection. Such a method relies on collaboration across various disciplines including biologists, managers, educators, app developers, volunteers, and statisticians. Maybe someday a current citizen science project, such as Whale mAPP, will provide a dataset as vast, abundant, and valuable as historical whaling records. Even the possibility of accomplishing such a goal is worth fighting for.

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Literature Cited

Baker, C. S., L.M. Herman, A. Perry, et al. 1985. Population characteristics and migration of summer and late-season humpback whales (Megaptera novaengliae) in Southeastern Alaska. Marine Mammal Science 1:304–323.

Calambokidis, J., E.A. Falcone, T.J. Quinn, et al. 2008. SPLASH: Structure of Populations, Levels of Abundance and Status of Hump- back Whales in the North Pacific. Final Report for Contract AB133F-03-RP- 00078 prepared by Cascadia Research for U.S. Department of Commerce.

Dahlheim, M. E., P.A. White and J.M. Waite. 2009. Cetaceans of Southeast Alaska: distribution and seasonal occurrence. J. Biogeogr 36:410–426

Gregr, E.J., A.W. Trites. 2001. Predictions of critical habitat for five whale species in the waters of coastal British Columbia. Canadian Journal of Fisheries and Aquatic Sciences 58:1265–1285

Hamazaki, T. 2002. Spatiotemporal prediction models of cetacean habitats in the mid-western North Atlantic Ocean (from Cape Hatteras, North Carolina, USA to Nova Scotia, Canada). Marine Mammal Science 18:920–939.

Redfern, J.V., M.C. Ferguson, E.A. Becker, et al. 2006. Techniques for cetacean-habitat modeling. Marine Ecology Progress Series 310: 271–295.

Rosa, L. D., J.K. Ford and A.W. Trites. 2012. Distribution and relative abundance of humpback whales in relation to environmental variables in coastal British Columbia and adjacent waters. Cont. Shelf Res. 36:89–104.

Torres, L. G., T. D. Smith, P. Sutton, A. MacDiarmid, J. Bannister, and T. Miyashita. 2013. From exploitation to conservation: habitat models using whaling data predict distribution patterns and threat exposure of an endangered whale. Diversity and Distributions 19:1138-1152.

Recap: 2nd World Seabird Conference

By Rachael Orben, post-doc

I have just returned home from attending the 2nd World Seabird Conference held in Cape Town, South Africa. My bags are still only half unpacked as I roll back into the work world of emails, planning field-work, report writing and data analysis. I am still very jet-lagged and the cool crisp Oregon air feels strange after so recently being in the dry heat of Africa. And here comes the rain! (Oh, and should I mention that bit of sickness that always seems to creep up behind you when you travel?)

The conference was a 4-day affair that filled my days from 8:30 am until sometime after 8:30 pm. Talks, poster sessions, and a really great Early Career Scientist evening – the organizers did an excellent job squeezing so much in. Of course a conference also involves visiting with colleagues and networking….and with roughly 600 conference participants from 53 countries, I had my work cut out trying to catch up with friends and colleagues! It was amazing to have so many seabird researchers and so much seabird science in one place.

So with all the science going on, what did I learn? Well, seabird scientists have certainly embraced the use of small electronic devices in the form of GPS loggers and GLS loggers (geolocation loggers that use light levels to calculate approximate locations – think sailors and celestial navigation). To give you a taste, follow this link to a short article on BirdLife’s Global Seabird Tracking Database.

BirdLife International: 5 million data points for the world's seabirds provided by 120 research institutes (www.seabirdtracking.org)
BirdLife International: 5 million data points for the world’s seabirds provided by 120 research institutes (www.seabirdtracking.org)

This is really just the beginning, and the exciting thing is seabird scientists are getting into the more nuanced questions of seabird spatial ecology. How do birds navigate at sea? Where do non-breeding birds forage? Where do fledglings go? Do birds return to the same places to forage (spatial fidelity), both when they constrained to their breeding colonies and while on migrations? How does this change through an individual’s lifetime? Why do some individuals in a population return to the same foraging locations while others don’t? As it turns out, though the ocean might appear featureless to us, seabirds know where they are at-sea and are able to return to the same places to forage – which they do depending on all sorts of things including what species they are, predictability of prey, individual personality, and likely a few more things.

Seabird conservation was also a large and pervasive theme. However, I can’t really do the entire conference justice here. So check out #WSC2 on twitter for the posts. You can go back in time and get a flavor for many of the talks as there are 1000s of tweets!

You might ask – what is the value of traveling half way around the world to talk about seabirds? And indeed there is much discussion about the carbon cost of scientific conferences. I am not saying the WSC is the perfect model, but it does have one thing in its favour as a newly established conference: It’s infrequent occurrence. The first World Seabird Conference was held in Victoria, Canada in 2010 and the next one will happen in 2020. I wonder how seabird science will change over the next five years?!

To stay globally connected in the meantime Seabirders are experimenting with on-line conferences. I participated in the first one, held on Twitter, and I really enjoyed it and learned a lot. You too can check it out at #WSTC1 and stay tuned for #WSTC2.

After the conference I took a break from seabirds and went to explore the terrestrial world of South Africa with my parents. It was a wonderful trip and I am so glad my parents came and joined me!

IMG_5818 copy IMG_6020 copy notaseabird Lions IMG_5136 copy

Looking back on a busy field season

Solène Derville, EnTroPie Lab, Institute of Research for Development, Nouméa, New Caledonia (Ph.D. student under the co-supervision of Dr. Leigh Torres)

After one month and a half in the field, I am now comfortably sitting at my desk in the Institute of Research for Development (IRD) in Nouméa and I am finally finding the time to look back on my first marine mammal field experience.

The New Caledonian South Lagoon is certainly not the worst place on earth to study whales. While some people spend hours trying to spot extremely rare and shy species living in freezing cold polar waters, I have to endure a 25°C temperature, turquoise waters and a study species desperate for attention (series of a dozen breaches are not uncommon). As with all field work, there were ups and downs but following humpback whales during the 2015 breeding season was by far the most exhilarating field experience I’ve ever had.

During the austral winter, humpback whales are thought to travel and stay in different areas of the New Caledonian Economic Exclusive Zone. Using satellite telemetry, several seamounts (e.g. Antigonia), banks (e.g. Torche bank) and shallow areas have been shown to play an important role for breeding and migrating humpback whales (Garrigue et al. In Press). However, as much as we would like to study whales in these areas, offshore field missions are logistically and financially hard to conduct. This is why most of the data on humpback whales in New Caledonian waters have been collected in coastal waters, and more specifically in the South Lagoon. Opération Cétacés, a local NGO, has been studying whales in this area for about two decades and I was lucky to participate in this year’s field season with their experienced team.

The South Lagoon of New Caledonia
The South Lagoon of New Caledonia

The usual day in Prony (the village that we live in during the whale season) usually starts early. We get up at about 5:30, and start by engulfing a bowl of porridge (nicknamed “globi” and considered as a highly exotic dish). By 6:30 everyone is standing in our rigid-hulled inflatable boat, listening to the weather forecast on the radio. After a 15 minute trip across the bay of Prony, two people disembark and climb to a land-based lookout, the N’Doua Cape, where they will spend the day trying to spot humpback whales and guiding the boat towards their location via VHF radio communication. The vessel-based team slowly approaches the whale groups to do photo-identification (using the unique marks on the ventral surface of the tail flukes), biopsy collection, and behavioral activity monitoring. The particular coastal geography of this study area (see previous post: Crossing Latitudes) allows us to uniquely combine land-based and boat-based surveying. These methods increase our encounter rate and allow us to collect more individual-based data. Yet, compared to a standardized boat-based surveys, our survey effort is much more complex to estimate and account for in a spatial distribution model.

This season, the number of whale encounters was particularly high. We spent 31 days at sea and observed a total of 99 groups. Using photo-identification, we documented 113 different individuals, some of which were first observed more than 15 years ago! Biopsy samples were collected from 139 different individuals and we managed to record 4h of songs performed by six different whales. Given that the size of the New Caledonian population is currently thought to be less than 1000 individuals, our sampling is not too bad!

A calf breaching out of the water on a late afternoon. No wonder humpback whales are favored by whale-watching companies, they can be very active at the surface!
A calf breaching out of the water on a late afternoon. No wonder humpback whales are favored by whale-watching companies, they can be very active at the surface!
These two adult whales were part of a very active competitive group of eight individuals and displayed a peculiar behavior that included gently rolling and rubbing themselves against each other.
These two adult whales were part of a very active competitive group of eight individuals and displayed a peculiar behavior that included gently rolling and rubbing themselves against each other.

Another great achievement of this season was the tagging of two adult humpback whales with ARGOS satellite-tracking devices. It was a thrilling experience to be part of this procedure and witness the level of concentration and experience required to place a tag on a whale. Our two individuals, one a presumed male and the other a female with calf, were respectively baptized Lutèce (the name Romans gave to Paris) and Ovalie (an old fashioned way to call rugby in France). Their tags transmitted for 15 and 20 days respectively, which was not long enough to follow their migration south towards Antarctica. Yet, both whales spent time on seamounts that are known to play an important role for humpback whales in the region. We were very interested in Ovalie’s track (map given below), as she travelled along the Loyalty ridge, a seafloor structure of great interest to us. We suspect that whales could be using this ridge as a navigational aid and/or using shallow areas (seamounts and banks) along the ridge as resting or breeding habitats. The amount of humpback whales present in this area and the eventual role played by oceanic features along the Loyalty ridge will be the subject of my future research.

Raw ARGOS track: Ovalie visiting seamounts south of New Caledonia and then travelling towards the Loyalty ridge (Don’t worry whales didn’t start walking on land since you saw your last National Geographic documentary; the accuracy of the satellite transmitter is to blame. For some of these points accuracy simply can’t be estimated –classes A and B- and unrealistic locations will have to be removed before performing analysis. In general, accuracy of ARGOS locations ranges between 250 and 1500m).
Raw ARGOS track: Ovalie visiting seamounts south of New Caledonia and then travelling towards the Loyalty ridge (Don’t worry whales didn’t start walking on land since you saw your last National Geographic documentary; the accuracy of the satellite transmitter is to blame. For some of these points accuracy simply can’t be estimated –classes A and B- and unrealistic locations will have to be removed before performing analysis. In general, accuracy of ARGOS locations ranges between 250 and 1500m).

 

But now that we have all this data, let’s get back to work! As much as I love being in the field, there comes a time when you have to sit in front of your computer and try to make sense of all this information you collected.

And that is where my collaboration with the GEMM Lab comes in! I am looking forward to visiting Newport once again in December and to start shedding a light on the ‘How’s and ‘Why’s of New Caledonian humpback whales’ space use.

Literature cited:

Garrigue, C., Clapham, P. J., Geyer, Y., Kennedy, A. S., & Zerbini, A. N. (In Press). Satellite tracking reveals novel migratory patterns and the importance of seamounts for endangered South Pacific Humpback Whales. Royal Society Open Science.

 

“[We] have only one month to survey an inhospitable Antarctic wilderness, the size of Oklahoma, moving at the speed of a bicycle”

– Oscar Schofield, Professor Bio-Optical Oceanography

By: Erin Pickett

There is nothing like a feature film about an upcoming field research project to get you pumped. I’m talking about Antarctic Edge: 70˚ South (now available on DVD, iTunes and Netflix!). In two months a few of us from the Biotelemetry and Behavioral Ecology Laboratory (BTBEL) will be headed down south to participate in the research project that is documented in this film.

The project is called the Palmer Station Antarctica LTER. LTER stands for long term ecological research. The Palmer site is located along the Western Antarctic Peninsula (WAP) and is part of a network of LTER sites around the world that have been established over the last three decades or so for the purpose of long term ecological monitoring. The WAP is a particularly unique place to monitor the effects of climate change because it is one of the most rapidly warming areas in the world. Temperature increases in this region are six times greater than the global average. As a result of increasing temperatures, the peninsula has experience a decline in the extent, concentration and duration of winter sea ice.

After my first viewing of Antarctic Edge with its graphic scenes of calving glaciers I thought, well, that’s a little dramatic. If you watch the preview you’ll get a taste of what I’m talking about. However, in an ecosystem dependent on sea ice, the loss of three months-worth of ice a year is dramatic! The scientists leading the Palmer LTER project have watched the marine ecosystem at Palmer Station transform radically over the course of their careers. Coastal areas along the peninsula more closely resemble the warmer and moister sub-Antarctic rather than a traditionally cold and arid Antarctic climate. The most visible effect of this southward climate shift has been an expansion of sub-Antarctic, or ice-intolerant species, into areas where ice-dependent species are disappearing. Antarctic Edge attempts to convey the urgency and importance of understanding ecological changes like these.

In January, a team of researchers from all over the country will board the R/V Lawrence M. Gould (LMG) and depart Punta Arenas, Chile. From Chile we’ll cross the Drake Passage and continue south to Anvers Island, where our research station is located. Personnel and research gear will be exchanged and then the LMG will transit south along a pre-established sampling grid. This grid covers the entire Western Antarctic Peninsula, an area the size of Oklahoma (69, 498 square miles). Over the course of a month we will collect samples and data on nearly every possible component of the marine ecosystem, including everything from microbes and zooplankton to cetaceans.

I will be working with folks from OSU’s BTBEL lab and collaborators at Duke University to study the region’s whale populations. We will be focusing our efforts on humpback whales and we will be using methods such as photo identification, tagging and biopsy sampling to understand more about this species in this area and to learn more about the ecological roles that these large baleen whales play in this fragile marine ecosystem.  We are especially interested in learning more about the foraging ecology of this species and how their behavior is influenced by their primary prey, Antarctic krill. Many of the region’s top predators share this prey resource, which is declining as a result of sea ice loss. A central objective of our research is to understand how climate induced changes in this polar marine environment are affecting these top predators.

Over the next few months I’ll be keeping you updated on our preparations and journey south. Until then, I encourage you to watch Antarctic Edge: 70˚ South and get pumped!

 

Fishing with dolphins

By Leila Lemos, Ph.D. Student, Department of Fisheries and Wildlife, OSU

Hello everybody! I am Leila Lemos, a new member of the GEMM Lab. I am from Rio de Janeiro, Brazil, and moved to Corvallis just 2 months ago where I am now taking classes at OSU. Although I have not yet travelled around Oregon to see my surroundings I am loving the fall colors! We don’t have all of this yellow/orange/red in our Brazilian trees; it’s amazing! The green of the pines also enchanted me. What a beautiful place! However, I confess that I do miss being close to the ocean, so I am looking forward to being based in Newport next year. So, since I cannot see the ocean for now, let’s talk a bit about it and the dynamic cetaceans that live there.

My thesis will explore the impact of ocean noise on the physiology of gray whales, but I have not started my fieldwork yet. So for my first blog post I will discuss a unique interaction between bottlenose dolphins (Tursiops truncatus) and fisherman that occurs in the cities of Laguna, in the state of Santa Catarina, and Tramandaí and Imbé, in the state of Rio Grande so Sul, in southern Brazil. Unlike most relationships between fishermen and marine mammals, this interaction is mutually beneficial and both species appear to seek each other out. There are only three other places in the world where a similar interaction occurs: Mauritania, in the west coast of Africa; Myanmar, in the south coast of Asia; and in the east coast of Australia.

In the southern Brazil, dolphins and artisanal mullet fishermen have adapted their hunting strategies to perform a cooperative foraging strategy. Cast net fisherman wait for the dolphins to arrive and then observe their behavior. Only when a specific aggressive behavior pattern is observed do the fishermen enter the water with their nets. The dolphins move closer to the fishermen and begin rolling movements that trap fish close to the margin. The fishermen wait to throw their cast nets into the water until the dolphins perform specific and vigorous behaviors described by Simões-Lopes et al. (1998):

  • the dolphin shows an arched back;
  • the dolphin exposes its head and hits the surface with the throat;
  • the dolphin moves rapidly, showing just the dorsal fin, producing a whirl;
  • the dolphin slaps its tail against the surface.

 

Fishermen waiting for a signal to throw the cast net in Laguna, Santa Catarina, Brazil. Source: Diário Catarinense, 2013.
Fishermen waiting for a signal to throw the cast net in Laguna, Santa Catarina, Brazil. Source: Notícias UFSC, 2009.
Another shots of fishermen waiting to throw the cast net in Laguna, Santa Catarina, Brazil. Source: Notícias UFSC, 2009.

 

This partnership is mutually beneficial. Dolphins use the disturbance caused by the net to separate the mullet school and trap individual prey. This method allows the dolphins to reduce escapees, capture more prey, and ultimately increase their net energy gain.

For fishermen, this cooperative association leads to greatly increased captures of mullet. The water in the southern coast of Brazil is too murky for the fishermen to see the schools and therefore know where to throw their net. By watching the behavior of the dolphins, the fisherman is able to throw his net at the exact time and location of the passing mullet shoal.

While this symbiotic relationship is remarkable, it is also hereditary in both humans and dolphins. The calves follow their mothers during the foraging events and learn the movements used in this cooperative behavior. Likewise, the fishermen learn their techniques from their relatives through observation. This cross-species interaction has created cultural ties of great socioeconomic value for both humans and dolphins. Furthermore, this unique relationship demonstrates how clever and adaptive both taxa are when it comes to capturing prey. Wouldn’t it be great if more teamwork like this were possible?

 

Here is a video that captures this amazing relationship:

Until next time and thanks for reading!

 

 

Bibliographic References:

Diário Catarinense, 2013. Interação entre golfinhos e pescadores em Laguna chama a atenção de produtores da BBC. Retrieved from http://diariocatarinense.clicrbs.com.br/sc/geral/noticia/2013/05/interacao-entre-golfinhos-e-pescadores-em-laguna-chama-a-atencao-de-produtores-da-bbc-4151948.html

Notícias UFSC, 2009. Especial pesquisa: UFSC estuda pesca cooperativa entre golfinhos e pescadores em Laguna. Retrieved from http://noticias.ufsc.br/2009/08/especial-pesquisa-ufsc-estuda-pesca-cooperativa-entre-golfinhos-e-pescadores-em-laguna/

Simões-Lopes, P.C., Fabián, M.E., Menegheti, J.O., 1998. Dolphin Interactions with the mullet artisanal fishing on southern Brazil: a qualitative and quantitative approach. Revta bras. Zool. 15(3), 709-726.

 

 

On learning to Code…

By Amanda Holdman, MSc student, Dept. Fisheries and Wildlife, OSU

I’ve never sworn so much in my life. I stared at a computer screen for hours trying to fix a bug in my script. The cause of the error escaped me, pushing me into a cycle of tension, self-loathing, and keyboard smashing.

The cause of the error? A typo in the filename.

When I finally fixed the error in my filename and my code ran perfectly – my mood quickly changed. I felt invincible; like I had just won the World Cup. I did a quick victory dance in my kitchen and high-fived my roommate, and then sat down and moved on the next task that needed to be conquered with code. Just like that, programming has quickly become a drug that makes me come back for more despite the initial pain I endure.

I had never opened a computer programming software until my first year of graduate school. Before then Matlab was just the subject of a muttered complaint by my college engineering roommate. As a biology major, I blew it off as something (thank goodness!) I would never need to use. Needless to say, that set me up for a rude awakening just one year later.

The time has finally come for me to, *gulp*, learn how to code. I honestly think I went through all 5 stages of grief before I realized I was at the point where I could no longer put it off.

By now you are familiar with the GEMM Lab updating you with photos of our charismatic study species in our beautiful study areas. However, summer is over. My field work is complete, and I’m enrolled in my last course of my master’s career. So what does this mean? Winter. And with winter comes data analysis. So, instead of spending my days out on a boat in calm seas, watching humpbacks breach, or tagging along with Florence to watch gray whales forage along the Oregon coast, I’ve reached the point of my graduate career that we don’t often tell you about: Figuring out what story our data is telling us. This stage requires lots of coffee and patience.

However, in just two short weeks of learning how to code, I feel like I’ve climbed mountains. I tackle task after task, each allowing me to learn new things, revise old knowledge, and make it just a little bit closer to my goals. One of the most striking things about learning how to code is that it teaches you how to problem solve. It forces you to think in a strategic and conceptual way, and to be honest, I think I like it.

For example, this week I mapped the percent of my harbor porpoise detections over tidal cycles. One of the most important factors explaining the distribution and behavior of coastal marine mammals are tides. Tidal forces drive a number of preliminary and secondary oceanographic processes like changes in water depth, salinity, temperature, and the speed and direction of currents. It’s often difficult to unravel which part of the tidal process is most influential to a species due to the several covariates related to the change in tides , how inter-related those covariates are, and the elusive nature of the species (like the cryptic harbor porpoise). However, while the analysis is preliminary, if we map the acoustic detections of harbor porpoise over the tidal cycle, we can already start to see some interesting trends between the number of porpoise detections and the phases of the tide. Check it out!

reef3_clicks

Now, I won’t promise that I’ll be an excellent coder by the end of the winter, but I think I might have a good chance at being able to mark the “proficient” box next to Matlab and R on my first job application. Yet, whatever your reason for learning code – whether you are an undergraduate hoping to get ahead for graduate school, a graduate student hoping to escape the inevitable (like me), or just someone who thinks getting a code to work properly is a fun game – my advice to you is this:

Google first. If that fails, take mental breaks. Revisit the problem later. Think through all possible sources of error. Ask around for help. Then, when you finally fix the bug or get the code to work the way you would like it to, throw a mini-party. After it’s all over, take a deep breath and go again. Remember, you are not alone!

Happy coding this winter GEMM Lab readers – and I wish you lots of celebratory dancing!

New Zealand’s mega-fauna come to Newport, Oregon.

By Olivia Hamilton, PhD Candidate, University of Auckland, New Zealand.

The week leading up to my departure from New Zealand was an emotional rollercoaster. Excited, nervous, eager, reluctant… I did not feel like the fearless adventurer that I thought I was. D-day arrived and I said my final goodbyes to my boyfriend and mother at the departure gate. Off I went on my three-month research stint at the Hatfield Marine Science Center.

Some thirty hours later I touched down in Portland. I collected my bags and headed towards the public transport area at the airport. A young man greeted me, “Would you like to catch a taxi or a shuttle, ma’am?” “A taxi please! I have no idea where I am”, I responded. He nodded and smiled. I could see the confusion all over his face… My thick kiwi accent was going to make for some challenging conversations.

After a few days in Portland acclimatizing to the different way of life in Oregon, it was time to push on to Newport. I hit a stroke of luck and was able take the scenic route with one of the girls in the GEMM lab, Rachael Orben. With only one wrong turn we made it to the Oregon coast. I was instantly hit with a sense of familiarity. The rugged coastline and temperate coastal forest resembled that of the west coast of New Zealand. However, America was not shy in reminding me of where I was with its big cars, drive-through everything, and RVs larger than some small kiwi houses.

The Oregon Coast. Photo by Olivia Hamilton.
The Oregon Coast. Photo by Olivia Hamilton.

We arrived at Hatfield Marine Science Center: the place I was to call home for the next quarter of a year.

So, what am I doing here?

In short, I have come to do computer work on the other side of the world.

Dr. Leigh Torres is on my PhD committee and I am lucky enough to have been given the opportunity to come to Newport and analyze my data under her guidance.

My PhD has a broad interest in the spatial ecology of mega-fauna in the Hauraki Gulf, New Zealand. For my study, megafauna includes whales, dolphins, sharks, rays, and seabirds. The Hauraki Gulf is adjacent to Auckland, New Zealand’s most populated city and home to one of our largest commercial ports. The Hauraki Gulf is a highly productive area, providing an ideal habitat for a number of fish species, thus supporting a number of top marine predators. As with many coastal areas, anthropogenic activities have degraded the health of the Gulf’s ecosystem. Commercial and recreational fishing, run-off from surrounding urban and rural land, boat traffic, pollution, dredging, and aquaculture are some of the main activities that threaten the Gulf and the species that inhabit it. For instance, the Nationally Endangered Bryde’s whale is a year-round resident in the Hauraki Gulf and these whales spend much of their time close to the surface, making them highly vulnerable to injury or death from ship-strikes. In spite of these threats, the Gulf supports a number of top marine predators.  Therefore it is important that we uncover how these top predators are using the Gulf, in both space and time, to identify ecologically important parts of their habitat. Moreover, this study presents a unique opportunity to look at the relationships between top marine predators and their prey inhabiting a common area.

The Hauraki Gulf, New Zealand. The purple lines represent the track lines that aerial surveys were conducted along.

 

Common dolphins in the Hauraki Gulf. Photo by Olivia Hamilton
Common dolphins in the Hauraki Gulf. Photo by Olivia Hamilton

 

A Bryde’s whale, common dolphins, and some opportunistic seabirds foraging in the Hauraki Gulf. Photo by Isabella Tortora Brayda di Belvedere.
A Bryde’s whale, common dolphins, and some opportunistic seabirds foraging in the Hauraki Gulf. Photo by Isabella Tortora Brayda di Belvedere.

 

Australisian Gannets and shearwaters foraging on a bait ball in the Hauraki Gulf. Photo by Olivia Hamilton.
Australisian Gannets and shearwaters foraging on a bait ball in the Hauraki Gulf. Photo by Olivia Hamilton.

To collect the data needed to understand the spatial ecology of these megafauna, we conducted 22 aerial surveys over a year-long period along pre-determined track lines within the Hauraki Gulf. On each flight we had four observers that collected sightings data for cetaceans, sharks, predatory fish, prey balls, plankton, and other rare species such as manta ray. An experienced seabird observer joined us approximately once a month to identify seabirds. We collected environmental data for each sighting including Beaufort Sea State, glare, and water color.

The summary of our sightings show that common dolphins were indeed common, being the most frequent species we observed. The most frequently encountered sharks were bronze whalers, smooth hammerhead sharks, and blue sharks. Sightings of Bryde’s whales were lower than we had hoped, most likely an artifact of our survey design relative to their distribution patterns. In addition, we counted a cumulative total of 11,172 individual seabirds representing 16 species.

Summary of sightings of megafauna in the Hauraki Gulf.

Summary of sightings of megafauna in the Hauraki Gulf.My goal while here at OSU is to develop habitat models for the megafauna species to compare the drivers of their distribution patterns. But, at the moment I am in the less glamorous, but highly important, data processing and decision-making stage. I am grappling with questions like: What environmental variables affected our ability to detect which species on surveys? How do we account for this? Can we clump species that are functionally similar to increase our sample size? These questions are important to address in order to produce reliable results that reflect the megafauna species true distribution patterns.

Once these questions are addressed, we can get on to the fun stuff – the habitat modeling and interpretation of the results. I will hopefully be able to start addressing these questions soon: What environmental and biological variables are important predictors of habitat use for different taxa? Are there interactions (attraction or repulsion) between these top predators? What is driving these patterns? Predator avoidance? Competition? So many questions to ask! I am looking forward to answering these questions and reporting back.

Gray whale field work wrap-up; sea you later

Hello everyone,

Florence here with an update about the final numbers from this summer’s gray whale field season.

For folks just hearing about the project, my team of interns and I spent the summer alternating between study sites at Depoe Bay and Port Orford to conduct fine-scale focal follows of gray whales foraging in near-shore Oregon waters using a theodolite.  That is to say, we gathered 10,186 ‘marks’ or ‘locations’ where whales came to the surface, and by connecting the dots, we are able to create tracklines and analyze their movement patterns.  The idea is to document and describe gray whale foraging behavior in order to answer the questions: Are there patterns in how the whales use the space? Is there a relationship between foraging success and proximity to kelp beds? Do behaviors vary between individuals, location, or over time during the season?

All these tracklines are from one whale, Keyboard, visiting the same area multiple times over the course of a month. I'll break this figure down a little later in the post. Notice how the whale consistently returns to the bay just west of the port jetty
All these tracklines are from one whale, Keyboard, visiting the same area multiple times over the course of a month. I’ll break this figure down a little later in the post. Notice how the whale consistently returns to the bay just west of the port jetty

While at our study sites, we often received questions about vessel disturbance on the whale’s behavior. Over the course of the summer, we saw whales completely ignore boats, approach boats, and actively avoid boats. Therefore, we documented these vessel interactions in order to ask questions such as: Does vessel disturbance alter behavior? How close is too close? Does the potential for vessel disturbance vary depending on (1) size of motor, (2) speed of approach, (3) type of vessel, i.e. kayak, fishing boat, tour boat, (4) the number of vessels already in the area, (5) amount of time a vessel has been following a whale, (6) time of season, (7) the presence of a calf or other whales? The end goal, once the data have been analyzed, is to bring our results to local vessel operators (commercial and recreational) and work together to write reasonable, effective, and scientifically informed guidelines for vessel operations in the presence of gray whales.

And now, the numbers you’ve all been waiting for, here is the tally of our data collection this summer:

 

Boiler Bay Graveyard Point Humbug Mountain
Whales total 80 73 28
Boats total 307 105 7
Total survey time (HH:MM:SS) 122:22:41 72:49:17 50:22:35
Total survey time with whales (HH:MM:SS) 64:47:54 80:39:57 22:59:00
Total Marks 4744 4334 1108

Table 1. Summary of survey effort for gray whale foraging ecology field season summer 2015

Whale named "Keyboard" visits graveyard head multiple times. Green track: 7.21.15, Pink track: 7.21.15, Teal track: 7.30.15. The orange polygons are approximate locations of kelp patches.
Whale named “Keyboard” visits graveyard head multiple times. Green track: 7.21.15, Pink track: 7.21.15, Teal track: 7.30.15. The orange polygons are approximate locations of kelp patches.
"Keyboard" continues to visit. Red trackline: 8.27.15, white trackline: 8.28.15, purple trackline: 8.28.15
“Keyboard” continues to visit. Red trackline: 8.27.15, white trackline: 8.28.15, purple trackline: 8.28.15

 

Whale 130 foraged near Boiler Bay for 5.5 hours on Aug 12. Trying to look at the whole trackline in one go is a little complicated, so let’s break it down by hour.
Whale 130 foraged near Boiler Bay for 5.5 hours on Aug 12. Trying to look at the whole trackline in one go is a little complicated, so let’s break it down by hour.
This panel shows hours 4-6 of the track. Things get more complex as various vessels use the same area. Whale 130 is always in red.
This panel shows hours 4-6 of the track. Things get more complex as various vessels use the same area. Whale 130 is always in red.

So, what does this all mean?  Well, the unsatisfying answer is of course: we don’t know yet. However, it is my job to find out!  I will spend the fall and winter processing data, writing and running behavioral models, communicating my successes and frustrations, and finally presenting my results to the community.

The human eye is well adapted to pick out patterns. Test yourself – what trends can you see in these images?  Are there areas that the whales seem to prefer over other areas?  In the Port Orford images with Keyboard & our kelp patches, does our theory of a relationship between whale presence and kelp patches seem valid?

This field season would not have been possible without the help of some truly excellent people.  Thank you Cricket and Justin and Sarah for making up the core of Team Ro”buff”stus. It was a pleasure working with you this summer.  Thank you to guest observers and photographers Era, Steven, Diana, Cory, Kelly, Shea and Brittany for filling in when we needed extra help! Thank you to our support network down in Port Orford: Tom, Tyson and the team at the Port Orford Field Station – we appreciate the housing and warm welcome, and to Jim and Karen Auborn and the Port of Port Orford for allowing us access to such a fantastic viewing location. Thank you to Oregon State Parks for allowing us access to the field sites at Boiler Bay and Humbug. Finally, thank you to Depoe Bay Pirate Coffee Company for keeping us warm and caffeinated on many foggy, cold early mornings. This work was funded by the William and Francis McNeil Fellowship Award, the Wild Rivers Coast Alliance, and the American Cetacean Society: Oregon Chapter.

Fair winds,

Florence

Whale mAPP Goes Global!

By Courtney Hann

The Whale mAPP team of Lei Lani Stelle, Melo King of Smallmelo Geographic Information Services, and me (Courtney Hann) has been busy recruiting ocean enthusiasts and applying for grants to fund volunteer-suggested Whale mAPP revisions. As a refresher, Whale mAPP is an Android-based mobile application that can be used by anyone to record marine mammal (whale, dolphins, porpoises, pinniped) sightings around the world. It is easy to sign up as a beta tester on the Whale mAPP website, www.whalemapp.org, and use the mobile app on your personal device to help scientists and conservationists learn more about marine mammals.

What is most spectacular is that the app has truly gone global! We now have over 100 users and are getting a couple new user requests each week! These volunteers have been busy at work this summer, recording thousands of marine mammal sightings during the summer months. Sightings have streamed in from the U.S. West Coast, Hawaiian, Japanese, and Russian waters, the Caribbean, the middle of the Southern Ocean, and the Greenland Sea. You can click on any sighting on the web map to see details about what species were recorded, how many were seen, what their behavior was like, the weather conditions that day, and other notes.

This map shows global marine mammal sightings recorded by Whale mAPP volunteers. The blue whale tale icons represent whale sightings, the pink dolphin icons represent dolphin or porpoise sightings, and the orange seal icon represents a seal, sea lion, or sea otter sighting. Data recorded during each sighting include the location (automatic), the species, the weather and sea conditions, the number of individuals, and a five-star confidence rating (http://www.whalemapp.org/map/#/, CEBCO, DeLorme | Melodi King, MS GIS Program – Cohort 21, University of Redlands).
This map shows global marine mammal sightings recorded by Whale mAPP volunteers. The blue whale tale icons represent whale sightings, the pink dolphin icons represent dolphin or porpoise sightings, and the orange seal icon represents a seal, sea lion, or sea otter sighting. Data recorded during each sighting include the location (automatic), the species, the weather and sea conditions, the number of individuals, and a five-star confidence rating (http://www.whalemapp.org/map/#/, CEBCO, DeLorme | Melodi King, MS GIS Program – Cohort 21, University of Redlands).

If we zoom into my particular study area of Southeast Alaska, we see that volunteers are still doing a superb job at recording the abundant number of marine mammals in the area.

Zoomed in image of the northeast Pacific, showing marine mammal sightings recorded this summer in Alaska, Southeast Alaska, British Columbia, and Washington (http://www.whalemapp.org/map/#/, CEBCO, DeLorme | Melodi King, MS GIS Program – Cohort 21, University of Redlands).
Zoomed in image of the northeast Pacific, showing marine mammal sightings recorded this summer in Alaska, Southeast Alaska, British Columbia, and Washington (http://www.whalemapp.org/map/#/, CEBCO, DeLorme | Melodi King, MS GIS Program – Cohort 21, University of Redlands).

Initial funding through the California Coastal Commission Whale Tail grant facilitated the creation of the Whale mAPP project, while current funding from the Hatfield Marine Science Center’s Mamie Markham Research Award that I received this Spring 2015 is funding the top two revisions requested by our users:
(1) Enable the user to edit observations during a trip and after a trip has ended. This revision is huge, was requested by almost every user I spoke to in Southeast Alaska, and was shown very evidently in our survey results.
(2) Add site-specific animal behavior and descriptions to Whale mAPP. For Southeast Alaska, this means adding the famous bubble-net feeding behavior to our list, as well as important descriptions of how to identify, recognize, and understand marine mammal behaviors.
In addition to the above two revisions, a few other revisions will be completed by Smallmelo Geographic Information Services this winter. These revisions include improving world-wide coverage of region-specific species lists, creating tools for validating the quality of the data, enabling data downloads directly from the website (www.whalemapp.org), and including the beta-tested “marine mammal fun facts” into the global application.

All of these incredible accomplishments and progress toward a successful, educational, fun, and data-generating marine mammal citizen science project could not have happened without Dr. Lei Lani’s open mind toward incorporating more people, including me, into her Whale mAPP project. Whale mAPP represents a new age of scientists, one of collaboration across disciplines (ecology, statistics, coding, education, and more!), and one that over-steps previous boundaries to re-define science. I hope that my participation with Whale mAPP and future citizen science projects will inspire individuals to know and feel that they can be scientists and that we can inspire the world to work together for the common good of our oceans.