Tag: collaboration

Reflecting on a solitary journey surrounded by an incredible team

Clara Bird, PhD Candidate, OSU Department of Fisheries, Wildlife, and Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

Graduate school is an odd phase of life, at least in my experience. You spend years hyperfocused on a project, learning countless new skills – and the journey is completely unique to you. Unlike high school or undergrad, you are on your own timeline. While you may have peers on similar timelines, at the end of day your major deadlines and milestone dates are your own. This has struck me throughout my time in grad school, and I’ve been thinking about it a lot lately as I approach my biggest, and final milestone – defending my PhD! 

I defend in just about two months, and to be honest, it’s very odd approaching a milestone like this alone. In high school and college, you count down to the end together. The feelings of anticipation, stress, excitement, and anticipatory grief that can accompany the lead-up to graduation are typically shared. This time, as I’m in an intense final push to the end while processing these emotions, most of the people around me are on their own unique timeline. At times grad school can feel quite lonely, but this journey would have been impossible without an incredible community of people.

A central contradiction of being a grad student is that your research is your own, but you need a variety of communities to successfully complete it. Your community of formal advisors, including your advisor and committee members, guide you along the way and provide feedback. Professors help you fill specific knowledge and skill gaps, while lab mates provide invaluable peer mentorship. Finally, fellow grad students share the experience and can celebrate and commiserate with you. I’ve also had the incredible fortune of having the community of the GRANITE team, and I’ve recently been reflecting on how special the experience has been.

To briefly recap, GRANITE stands for Gray whale Response to Ambient Noise Informed by Technology and Ecology (read this blog to learn more). This project is one of the GEMM lab’s long-running gray whale projects focused on studying gray whale behavior, physiology, and health to understand how whales respond to ocean noise. Given the many questions under this project, it takes a team of researchers to accomplish our goals. I have learned so much from being on the team. While we spend most of the year working on our own components, we have annual meetings that are always a highlight of the year. Our team is made up of ecologists, physiologists, and statisticians with backgrounds across a range of taxa and methodologies. These meetings are an incredible time to watch, and participate in, scientific collaboration in action. I have learned so much from watching experts critically think about questions and draw inspiration from their knowledge bases. It’s been a multi-year masterclass and a critically important piece of my PhD. 

The GRANITE team during our first in person meeting

These annual meetings have also served as markers of the passage of time. It’s been fascinating to observe how our discussions, questions, and ideas have evolved as the project progressed. In the early years, our presentations shared proposed research and our conversations focused on working out how on earth we were going to tackle the big questions we were posing. In parallel, it was so helpful to work out how I was going to accomplish my proposed PhD questions as part of this larger group effort. During the middle years, it was fun to hear progress updates and to learn from watching others go through their process too. In grad school, it’s easy to feel like your setbacks and stumbles are failures that reflect your own incompetence, but working alongside and learning from these scientists has helped remind me that setbacks and stumbles are just part of the process. Now, in the final phase, as results abound, it feels extra exciting to celebrate with this team that has watched the work, and me grow, from the beginning. 

The GRANITE team taking a beach walk after our second in person meeting.

We just wrapped up our last team meeting of the GRANITE project, and this year provided a learning experience in a phase of science that isn’t often emphasized in grad school. For graduate students, our work tends to end when we graduate. While we certainly think about follow-up questions to our studies, we rarely get the opportunity to follow through. In our final exams, we are often asked to think of next steps outside the constraints of funding or practicality, as a critical thinking exercise. But it’s a different skillset to dream up follow-up questions, and to then assess which of those questions are feasible and could come together to form a proposal. This last meeting felt like a cool full-story moment. From our earliest meetings determining how to answer our new questions, to now deciding what the next new questions are, I have learned countless lessons from watching this team operate. 

The GRANITE team after our third in person meeting.

There are a few overarching lessons I’ll take with me. First and foremost, the value of patience and kindness. As a young scientist stumbling up the learning curve of many skills all at once, I am so grateful for the patience and kindness I’ve been shown. Second, to keep an open mind and to draw inspiration from anything and everything. Studying whales is hard, and we often need to take ideas from studies on other animals. Which brings me to my third takeaway, to collaborate with scientists from a wide range of backgrounds who can combine their knowledges bases with yours, to generate better research questions and approaches to answering them.

I am so grateful to have worked with this team during my final sprint to the finish. Despite the pressure of the end nearing, I’m enjoying moments to reflect and be grateful. I am grateful for my teachers and peers and friends. And I can’t wait to share this project with everyone.

P.S. Interested in tuning into my defense seminar? Keep an eye on the GEMM lab Instagram (@gemm_lab) for the details and zoom link.

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Hope lies in cooperation: the story of a happy whale!

By Solène Derville, Postdoc, OSU Department of Fisheries, Wildlife, and Conservation Science, Geospatial Ecology of Marine Megafauna Lab

I wrote my last blogpost in the midst of winter and feeling overwhelmed as I was trying to fly to the US at the peak of the omicron pandemic… Since then, morale has improved exponentially. I have spent two months in the company of my delightful GEMM lab friends, nerding over statistics, sharing scientific conversations, drinking (good!) beer and enjoying the company of this great group of people. During that stay, I was able to focus on my OPAL project more than I have ever been able to, as I set myself the goal of not getting distracted by anything else during my stay in Newport.

The only one distraction that I do not regret is a post I read one morning on the Cetal Fauna Facebook page, a group of cetacean experts and lovers who share news, opinions, photos… anything cetacean related! Someone was posting a photo of a humpback whale stranded in the 1990s’ on Coolum beach, on the east coast of Australia, which is known as a major humpback whale migratory corridor. The story said that (probably with considerable effort) the whale was refloated by many different individuals and organizations present at the beach on that day, specifically Sea World Research, Rescue & Conservation.

I felt very touched by this story and the photo that illustrated it (Figure 1). Seeing all these people come together in this risky operation to save this sea giant is quite something. And the fact that they succeeded was even more impressive! Indeed, baleen whales strand less commonly than toothed whales but their chances of survival when they do so are minimal. In addition to the actual potential damages that might have caused the whale to strand in the first place (entanglements, collisions, diseases etc.), the beaching itself is likely to hurt the animal in a permanent way as their body collapses under their own weight usually causing a cardiovascular failure (e.g., Fernández et al., 2005)⁠. The rescue of baleen whales is also simply impaired by the sheer size and weight of these animals. Compared to smaller toothed whales such as pilot whales and false killer whales that happen to strand quite frequently over some coastlines, baleen whales are almost impossible to move off the beach and getting close to them when beached can be very dangerous for responders. For these reasons, I found very few reports and publications mentioning successful rescues of beached baleen whales (e.g., Priddel and Wheeler, 1997; Neves et al., 2020).⁠

Figure 1: Stranded humpback whale on Coolum Beach, East Australia, in 1996. Look at the size of the fluke compared to the men who are trying to rescue her! Luckily, that risky operation ended well. This image won Australian Time Magazine Cover of the year. Credit: Sea World Research, Rescue and Conservation. Photo posted by P. Garbett on https://www.facebook.com/groups/CetalFauna – February 26, 2022)

Now the story gets even better… the following day I received an email from Ted Cheeseman, director and co-founder of Happywhale, a collaborative citizen science tool to share and match photographes of cetaceans (initially only humpback whales but has extended to other species) to recognize individuals based on the unique patterns of the their fluke or dorsal fin. The fluke of the whale stranded in Australia in 1991 had one and only match within the Happywhale immense dataset… and that match was to a whale seen in New Caledonia (Figure 2). “HNC338” was the one!

Figure 2: Happy whale page showing the match of HNC338 between East Australia and New Caledonia. https://happywhale.com/individual/78069;enc=284364?fbclid=IwAR1QEG_6JkpH_k2UrF-qp-9qrOboHYakKjlTj0lLbDFygjN5JugkkKVeMQw

Since I conducted my PhD on humpback whale spatial ecology in New Caledonia, I have continued working on a number of topics along with my former PhD supervisor, Dr Claire Garrigue, in New Caledonia. Although I do not remember each and every whale from her catalogue (composed of more than 1600 humpback whales as of today), I do love a good “whale tale” and I was eager to know who this HNC338 was. I quickly looked into Claire’s humpback whale database and sure enough I found it there: encountered at the end of the 2006 breeding season on September 12th, at a position of 22°26.283’S and 167°01.991’E and followed for an hour. Field notes reported a shy animal that kept the boat at a distance. But most of all, HNC338 was genetically identified as a female and was accompanied by a calf during that season! The calf was particularly big, as expected at this time of the season. What an inspiring thing to think that this whale, stranded in 1996, was resighted 10 years later in a neighboring breeding ground, apparently healthy and raising a calf of her own.

As genetic paternity analysis have been conducted on many New Caledonia calf biopsy samples as part of the Sexy Singing project conducted with our colleagues from St Andrews University in Scotland, we might be able to identify the calf’s father in this breeding stock. Thanks to the great amount of data shared and collected through Happywhale, we are discovering more and more about whale migratory patterns and behavior. It might as well be that this calf’s father was one of those whales that seem to roam over several different breeding grounds (New Caledonia and East Australia). This story is far from finished…

Figure 3: A (pretty bad!) photo of HNC338’s fluke. Luckily the Happywhale matching algorithm is very efficient and was able to detect the similarities of the fluke’s trailing edge compared to figure 1 (Cheeseman et al., 2021)⁠. Also of note, see that small dorsal fin popping out of the waters behind big mama’s fluke? That’s her calf!

From the people who pulled this whale back into the water in 1996, to the scientists and cetacean enthusiasts who shared their data and whale photos online, this story once again shows us that hope lies in cooperation! Happywhale was only created in 2015 but since then it has brought together the general public and the scientists to contribute over 465,000 photos allowing the identification of 75,000 different individuals around the globe. In New Caledonia, in Oregon and elsewhere, I hope that these collective initiatives grow more and more in the future, to the benefit of biodiversity and people.

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References

Cheeseman, T., Southerland, K., Park, J., Olio, M., Flynn, K., Calambokidis, J., et al. (2021). Advanced image recognition: a fully automated, high-accuracy photo-identification matching system for humpback whales. Mamm. Biol. doi:10.1007/s42991-021-00180-9.

Fernández, A., Edwards, J. F., Rodríguez, F., Espinosa De Los Monteros, A., Herráez, P., Castro, P., et al. (2005). “Gas and fat embolic syndrome” involving a mass stranding of beaked whales (Family Ziphiidae) exposed to anthropogenic sonar signals. Vet. Pathol. 42, 446–457. doi:10.1354/vp.42-4-446.

Neves, M. C., Neto, H. G., Cypriano-Souza, A. L., da Silva, B. M. G., de Souza, S. P., Marcondes, M. C. C., et al. (2020). Humpback whale (megaptera novaeangliae) resighted eight years after stranding. Aquat. Mamm. 46, 483–487. doi:10.1578/AM.46.5.2020.483.

Priddel, D., and Wheeler, R. (1997). Rescue of a Bryde’s whale Balaenoptera edeni entrapped in the Manning River, New South Wales: Unmitigated success or unwarranted intervention? Aust. Zool. 30, 261–271. doi:10.7882/AZ.1997.002.

It Takes a Village to Raise a PhD Student

By Rachel Kaplan, PhD student, Oregon State University College of Earth, Ocean, and Atmospheric Sciences and Department of Fisheries, Wildlife, and Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

This year in late February is the 2022 Ocean Sciences Meeting, an interdisciplinary bonanza of ocean scientists from all over the world. The conference will be held online this year as a precaution against Covid-19, and a week of virtual talks and poster sessions will cover new research in diverse topics from microbial ecology to ocean technology to whale vocalizations.

The meeting will also include my first poster presentation at a major conference, and so I have the typical grad student jitters that accompany each new thing I do (read more about the common experience of “imposter syndrome” here). This poster is the first time since starting graduate school and joining Project OPAL that I’m trying to craft a full science story that connects whales, their prey, and oceanographic conditions.

Learning how to do the analyses to assess and quantify these connections has involved plenty of head-scratching and periodic frustration on my part, but it has also offered a surprisingly joyful and even moving experience. In my efforts to troubleshoot a problem with my prey analysis, I’ve reached out to nearly everyone who works with krill acoustic data on the West Coast. Every single person has been incredibly welcoming and ready to help me, and excited to learn about my work in return. This experience has made me realize how many people I have on my team, and that even strangers are willing to support me on the whacky journey that is a PhD.

Through these collaborations, I am learning to analyze the acoustic signal of krill, small animals that are important food for whales foraging off the coast of Oregon and beyond. As part of Project OPAL, we plan to compare krill swarms with whale survey data to learn about the types of aggregations that whales are drawn to. From the perspective of a hungry whale, not all krill are created equal.

Analysis of a layer of krill in the upper ocean. The blue color in the top panel indicates scattering of acoustic signal by the krill, and the outline in the bottom panel shows the results of an algorithm programmed to detect krill aggregations.

In addition to developing great remote relationships through this work, the ability to meet in person as we continue adapting to life during the pandemic has absolutely not lost its thrill. After over a year of meetings and collaborating on Zoom, I was delighted to meet GEMM Lab postdoc Solène Derville this January, after she journeyed from her home in New Caledonia to Oregon. It was so exciting to see her in real life (we’re more similar in height than I knew!) and a few minutes into our first lunch together she was already helping me refine my analysis plans and think of new approaches.

Our interaction also made me think about how impressive the GEMM Lab is. The first two people Solène saw upon her arrival in Oregon were me and fellow GEMM Lab student Allison Dawn, two newer members who joined the lab after her last trip to Oregon. Without a moment of hesitation, Allison stepped up to give Solène a ride to Newport from Corvallis to finish her long journey. The connection our lab has developed and maintained during a pandemic, across borders and time zones, is special.

Hiking on gorgeous days is just one of the many benefits of being in the same place! This adventure included spotting a whale blow off the coast and a lot of GEMM excitement.

As I look out at the next few weeks until the Ocean Sciences meeting, and out towards the rest of my PhD, I inevitably feel worried about all I need to accomplish. But, I know that the dynamics in our lab and the other collaborative relationships I’m forming are what will carry me through. Every meeting and new connection reminds me that I’m not doing this alone. I’m grateful that there’s a team of people who are ready and willing to help me muddle my way through my first Principal Components Analysis, puzzle over algorithm errors, and celebrate with me as we make progress.

The teamwork of conservation science

Dr. Leigh Torres
PI, Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute
Assistant Professor, Oregon Sea Grant, Department of Fisheries and Wildlife, Oregon State University

I have played on sports teams all my life – since I was four until present day. Mostly soccer teams, but a fair bit of Ultimate too. Teams are an interesting beast. They can be frustrating when communication breaks down, irritating when everyone is not on the same timeline, and disastrous if individuals do not complete their designated job. Yet, without the whole team we would never win. So, on top of the fun of competition, skill development, and exercise, playing on teams has always been part of the challenging and fulfilling process for me: everyone working toward the same goal – to win – by making the team fluid, complimentary, integrated, and ultimately successful.

I have come to learn that it is the same with conservation science.

A few of my teams through the ages, as player and coach. Some of my favorite people are on these teams, from 1981 to 2018.

Conservation efforts are often so complex, that it is practically impossible to achieve success alone. Forces driving the need for conservation typically include monetary needs/desires, social values, ecological processes, animal physiology, multi-jurisdictional policies, and human behavior. Each one of these forces alone is challenging to understand and takes expertise to comprehend the situation. Hence, building a well-functioning team is essential. Here’s a recent example from the GEMM Lab:

Since 2014 entanglements of blue, humpback and gray whales in fishing gear along the west coast of the USA have dramatically increased, particularly in Dungeness crab fishing gear. Many forces likely led to this increase, including increased whale population abundance, potential shifts in whale distributions, and changes in fishing fleet dynamics. While we cannot point a finger at one cause, many people and groups recognize that we cannot continue to let whales become entangled and killed at such high rates: whale populations would decline, fisheries would look bad in the public eye and potentially lose profits, whales have an intrinsic right to live in the ocean without being bycaught, and whales are an important part of the ecosystem that would deteriorate without them. In 2017, the Oregon Whale Entanglement Working Group was formed to bring stakeholders together that were concerned about this problem to discuss possible solutions and paths forward. I was lucky to be a part of this group, which also included members of the Dungeness crab fishery and commission, the Oregon Department of Fish and Wildlife (ODFW), other marine mammal scientists, and representatives of the American Cetacean Society, The Nature Conservancy, and a local marine gear supplier.

We met regularly over 2.5 years, and despite some hesitation at first about walking into a room of potentially disgruntled fishermen (I would be lying if I did not admit to this), after the first meeting I looked forward to every gathering. I learned an immense amount about the Dungeness crab fishery and how it operates, how ODFW manages the fishery and why, and what people do, don’t and need to know about whales in Oregon. Everyone agreed that reducing whale entanglements is needed, and a frequent approach discussed was to reduce risk by not setting gear where and when we expect whales to be. Yet, this idea flagged a very critical knowledge gap: We do not have a good understanding of whale distribution patterns in Oregon. Thus leading to the development of a highly collaborative research effort to describe whale distribution patterns in Oregon and identify areas of co-occurrence between whales and fishing effort to reduce the risk of entanglements. Sounds great, but a tough task to accomplish in a few short years. So, let me introduce the great team I am working with to make it all happen.

While I may know a few things about whales and spatial ecology, I don’t know too much about fisheries in Oregon. My collaboration with folks at ODFW, particularly Kelly Corbett and Troy Buell, has enabled this project to develop and go forward, and ultimately will lead to success. These partners provide feedback about how and where the fishery operates so I know where and when to collect data, and importantly they will provide the information on fishing effort in Oregon waters to relate to our generated maps of whale distribution. This spatial comparison will produce what is needed by managers and fishermen to make informed and effective decisions about where to fish, and not to fish, so that we reduce whale entanglement risk while still harvesting successfully to ensure the health and sustainability of our coastal economies.

So, how can we collect standardized data on whale distribution in Oregon waters without breaking the bank? I tossed this question around for a long time, and then I looked up to the sky and wondered what that US Coast Guard (USCG) helicopter was flying around for all the time. I reached out to the USCG to enquire, and proposed that we have an observer fly in the helicopter with them along a set trackline during their training flights. Turns out the USCG Sector North Bend and Columbia River were eager to work with us and support our research. They have turned out to be truly excellent partners in this work. We had some kinks to work out at the beginning – lots of acronyms, protocols, and logistics for both sides to figure out – but everyone has been supportive and pleasant to work with. The pilots and crew are interested in our work and it is a joy to hear their questions and see them learn about the marine ecosystem. And our knowledge of helicopter navigation and USCG duties has grown astronomically.

On the left is a plot of the four tracklines we survey for whales each month for two years aboard a US Coast Guard helicopter. On the right are some photos of us in action with our Coast Guard partners.

Despite significant cost savings to the project through our partnership with the USCG, we still need funds to support time, gear and more. And full credit to the Oregon Dungeness Crab Commission for recognizing the value and need for this project to support their industry, and stepping up to fund the first year of this project. Without their trust and support the project may not have got off the ground. With this support in our back pocket and proof of our capability, ODFW and I teamed up to approach the National Oceanographic and Atmospheric and Administration (NOAA) for funds to support the remaining years of the project. We found success through the NOAA Fisheries Endangered Species Act Section 6 Program, and we are now working toward providing the information needed to protect endangered and threatened whales in Oregon waters.

Despite our cost-effective and solid approach to data collection on whale occurrence, we cannot be everywhere all the time looking for whales. So we have also teamed up with Amanda Gladics at Oregon Sea Grant to help us with an important outreach and citizen science component of the project. With Amanda we have developed brochures and videos to inform mariners of all kinds about the project, objectives, and need for them to play a part. We are encouraging everyone to use the Whale Alert app to record their opportunistic sightings of whales in Oregon waters. These data will help us build and test our predictive models of whale distribution. Through this partnership we continue important conversations with fishermen from many fisheries about their concerns, where they are seeing whales, and what needs to be done to solve this complex conservation challenge.  

Of course I cannot collect, process, analyze, and interpret all this data on my own. I do not have the skills or capacity for that. My partner in the sky is Craig Hayslip, a Faculty Research Assistant in the Marine Mammal Institute. Craig has immense field experience collecting data on whales and is the primary observer on the survey flights. Together we have navigated the USCG world and developed methods to collect our data effectively and efficiently (all within a tiny space flying over the ocean). In a few months we will be ¾ of the way through our data collection phase, which means data analysis will take over. For this phase I am bringing back a GEMM Lab star, Solene Derville, who recently completed her PhD. As the post-doc on the project, Solene will take the lead on the species distribution modeling and fisheries overlap analysis. I am looking forward to partnering with Solene again to compile multiple data sources on whales and oceanography in Oregon to produce reliable and accurate predictions of whale occurrence and entanglement risk. Finally I want to acknowledge our great partners at the Cascadia Research Collective (Olympia, WA) and the Cetacean Conservation and Genomics Lab (OSU, Marine Mammal Institute) who help facilitate our data collection, and conduct the whale photo-identification or genetic analyses to determine population assignment.  

As you can see, even this one, smallish, conservation research project takes a diverse team of partners to proceed and ensure success. On this team, my position is sometimes a player, coach, or manager, but I am always grateful for these amazing collaborations and opportunities to learn. I am confident in our success and will report back on our accomplishments as we wrap up this important and exciting conservation science project.   

A fin whale observed off the Oregon coast during one of our surveys aboard a US Coast Guard helicopter.

Data Wrangling to Assess Data Availability: A Data Detective at Work

By Alexa Kownacki, Ph.D. Student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

Data wrangling, in my own loose definition, is the necessary combination of both data selection and data collection. Wrangling your data requires accessing then assessing your data. Data collection is just what it sounds like: gathering all data points necessary for your project. Data selection is the process of cleaning and trimming data for final analyses; it is a whole new bag of worms that requires decision-making and critical thinking. During this process of data wrangling, I discovered there are two major avenues to obtain data: 1) you collect it, which frequently requires an exorbitant amount of time in the field, in the lab, and/or behind a computer, or 2) other people have already collected it, and through collaboration you put it to a good use (often a different use then its initial intent). The latter approach may result in the collection of so much data that you must decide which data should be included to answer your hypotheses. This process of data wrangling is the hurdle I am facing at this moment. I feel like I am a data detective.

Data wrangling illustrated by members of the R-programming community. (Image source: R-bloggers.com)

My project focuses on assessing the health conditions of the two ecotypes of bottlenose dolphins between the waters off of Ensenada, Baja California, Mexico to San Francisco, California, USA between 1981-2015. During the government shutdown, much of my data was inaccessible, seeing as it was in possession of my collaborators at federal agencies. However, now that the shutdown is over, my data is flowing in, and my questions are piling up. I can now begin to look at where these animals have been sighted over the past decades, which ecotypes have higher contaminant levels in their blubber, which animals have higher stress levels and if these are related to geospatial location, where animals are more susceptible to human disturbance, if sex plays a role in stress or contaminant load levels, which environmental variables influence stress levels and contaminant levels, and more!

Alexa, alongside collaborators, photographing transiting bottlenose dolphins along the coastline near Santa Barbara, CA in 2015 as part of the data collection process. (Image source: Nick Kellar).

Over the last two weeks, I was emailed three separate Excel spreadsheets representing three datasets, that contain partially overlapping data. If Microsoft Access is foreign to you, I would compare this dilemma to a very confusing exam question of “matching the word with the definition”, except with the words being in different languages from the definitions. If you have used Microsoft Access databases, you probably know the system of querying and matching data in different databases. Well, imagine trying to do this with Excel spreadsheets because the databases are not linked. Now you can see why I need to take a data management course and start using platforms other than Excel to manage my data.

A visual interpretation of trying to combine datasets being like matching the English definition to the Spanish translation. (Image source: Enchanted Learning)

In the first dataset, there are 6,136 sightings of Common bottlenose dolphins (Tursiops truncatus) documented in my study area. Some years have no sightings, some years have fewer than 100 sightings, and other years have over 500 sightings. In another dataset, there are 398 bottlenose dolphin biopsy samples collected between the years of 1992-2016 in a genetics database that can provide the sex of the animal. The final dataset contains records of 774 bottlenose dolphin biopsy samples collected between 1993-2018 that could be tested for hormone and/or contaminant levels. Some of these samples have identification numbers that can be matched to the other dataset. Within these cross-reference matches there are conflicting data in terms of amount of tissue remaining for analyses. Sorting these conflicts out will involve more digging from my end and additional communication with collaborators: data wrangling at its best. Circling back to what I mentioned in the beginning of this post, this data was collected by other people over decades and the collection methods were not standardized for my project. I benefit from years of data collection by other scientists and I am grateful for all of their hard work. However, now my hard work begins.

The cutest part of data wrangling: finding adorable images of bottlenose dolphins, photographed during a coastal survey. (Image source: Alexa Kownacki).

There is also a large amount of data that I downloaded from federally-maintained websites. For example, dolphin sighting data from research cruises are available for public access from the OBIS (Ocean Biogeographic Information System) Sea Map website. It boasts 5,927,551 records from 1,096 data sets containing information on 711 species with the help of 410 collaborators. This website is incredible as it allows you to search through different data criteria and then download the data in a variety of formats and contains an interactive map of the data. You can explore this at your leisure, but I want to point out the sheer amount of data. In my case, the OBIS Sea Map website is only one major platform that contains many sources of data that has already been collected, not specifically for me or my project, but will be utilized. As a follow-up to using data collected by other scientists, it is critical to give credit where credit is due. One of the benefits of using this website, is there is information about how to properly credit the collaborators when downloading data. See below for an example:

Example citation for a dataset (Dataset ID: 1201):

Lockhart, G.G., DiGiovanni Jr., R.A., DePerte, A.M. 2014. Virginia and Maryland Sea Turtle Research and Conservation Initiative Aerial Survey Sightings, May 2011 through July 2013. Downloaded from OBIS-SEAMAP (http://seamap.env.duke.edu/dataset/1201) on xxxx-xx-xx.

Citation for OBIS-SEAMAP:

Halpin, P.N., A.J. Read, E. Fujioka, B.D. Best, B. Donnelly, L.J. Hazen, C. Kot, K. Urian, E. LaBrecque, A. Dimatteo, J. Cleary, C. Good, L.B. Crowder, and K.D. Hyrenbach. 2009. OBIS-SEAMAP: The world data center for marine mammal, sea bird, and sea turtle distributions. Oceanography 22(2):104-115

Another federally-maintained data source that boasts more data than I can quantify is the well-known ERDDAP website. After a few Google searches, I finally discovered that the acronym stands for Environmental Research Division’s Data Access Program. Essentially, this the holy grail of environmental data for marine scientists. I have downloaded so much data from this website that Excel cannot open the csv files. Here is yet another reason why young scientists, like myself, need to transition out of using Excel and into data management systems that are developed to handle large-scale datasets. Everything from daily sea surface temperatures collected on every, one-degree of latitude and longitude line from 1981-2015 over my entire study site to Ekman transport levels taken every six hours on every longitudinal degree line over my study area. I will add some environmental variables in species distribution models to see which account for the largest amount of variability in my data. The next step in data selection begins with statistics. It is important to find if there are highly correlated environmental factors prior to modeling data. Learn more about fitting cetacean data to models here.

The ERDAPP website combined all of the average Sea Surface Temperatures collected daily from 1981-2018 over my study site into a graphical display of monthly composites. (Image Source: ERDDAP)

As you can imagine, this amount of data from many sources and collaborators is equal parts daunting and exhilarating. Before I even begin the process of determining the spatial and temporal spread of dolphin sightings data, I have to identify which data points have sex identified from either hormone levels or genetics, which data points have contaminants levels already quantified, which samples still have tissue available for additional testing, and so on. Once I have cleaned up the datasets, I will import the data into the R programming package. Then I can visualize my data in plots, charts, and graphs; this will help me identify outliers and potential challenges with my data, and, hopefully, start to see answers to my focal questions. Only then, can I dive into the deep and exciting waters of species distribution modeling and more advanced statistical analyses. This is data wrangling and I am the data detective.

What people may think a ‘data detective’ looks like, when, in reality, it is a person sitting at a computer. (Image source: Elder Research)

Like the well-known phrase, “With great power comes great responsibility”, I believe that with great data, comes great responsibility, because data is power. It is up to me as the scientist to decide which data is most powerful at answering my questions.

Data is information. Information is knowledge. Knowledge is power. (Image source: thedatachick.com)

 

“The joy of paper acceptance” or “The GEMM Lab’s recent scientific contributions”

Dr. Leigh Torres, Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute, Oregon State University

The GEMM Lab is always active – running field projects, leading outreach events, giving seminars, hosting conferences, analyzing data, mentoring young scientists, oh the list goes on! (Yes, I am a proud lab PI). And, recently we have had a flurry of scientific papers either published or accepted for publication that I want to highlight. These are all great pieces of work that demonstrate our quality work, poignant and applied science, and strong collaborations. For each paper listed below I provide a short explanation of the study and implications. (Those names underlined are GEMM Lab members, and I provided a weblink where available.)

 

Sullivan, F.A. & Torres, L.G. Assessment of vessel disturbance to gray whales to inform sustainable ecotourism. The Journal of Wildlife Management, doi:10.1002/jwmg.21462.

This project integrated research and outreach regarding gray whale behavioral response to vessels. We simultaneously tracked whales and vessels, and data analysis showed significant differences in gray whale activity budgets when vessels were nearby. Working with stakeholders, we translated these results into community-developed vessel operation guidelines and an informational brochure to help mitigate impacts on whales.

 

Hann, C., Stelle, L., Szabo, A. & Torres, L. (2018) Obstacles and Opportunities of Using a Mobile App for Marine Mammal Research. ISPRS International Journal of Geo-Information, 7, 169. http://www.mdpi.com/2220-9964/7/5/169

This study demonstrates the strengths (fast and cheap data collection) and weaknesses (spatially biased data) of marine mammal data collected using the mobile app Whale mAPP. We emphasize the need for increased citizen science participation to overcome obstacles, which will enable this data collection method to achieve its great potential.

 

Barlow, D.R., Torres, L.G., Hodge, K., Steel, D., Baker, C.S., Chandler, T.E., Bott, N., Constantine, R., Double, M.C., Gill, P.C., Glasgow, D., Hamner, R.M., Lilley, C., Ogle, M., Olson, P.A., Peters, C., Stockin, K.A., Tessaglia-Hymes, C.T. & Klinck, H. (in press) Documentation of a New Zealand blue whale population based on multiple lines of evidence. Endangered Species Research. https://doi.org/10.3354/esr00891.

This study used genetics, acoustics, and photo-id to document a new population of blue whales around New Zealand that is genetically isolated, has high year-round residence, and shows limited connectivity to other blue whale populations. This discovery has important implication for population management, especially in the South Taranaki Bight region of New Zealand where the whales forage among industrial activity.

 

Burnett, J.D., Lemos, L., Barlow, D.R., Wing, M.G., Chandler, T.E. & Torres, L.G. (in press) Estimating morphometric attributes of baleen whales with photogrammetry from small UAS: A case study with blue and gray whales. Marine Mammal Science.

Here we developed methods to measure whale body morphometrics using images captured via Unmanned Aerial Systems (UAS; ‘drones’). The paper presents three freely available analysis programs and a protocol to help the community standardize methods, assess and minimize error, and compare data between studies.

 

Holdman, A.K., Haxel, J.H., Klinck, H. & Torres, L.G. (in press) Acoustic monitoring reveals the times and tides of harbor porpoise distribution off central Oregon, USA. Marine Mammal Science.

Right off the Newport, Oregon harbor entrance we listened for harbor porpoises at two locations using hydrophones. We found that porpoise presence at the shallow rocky reef site corresponds with the ebb tidal phase, while harbor porpoise presence at the deeper site with sandy bottom was associated with night-time foraging. It appears that harbor porpoise change their spatial and temporal patterns of habitat use to increase their foraging efficiency.

 

Derville, S., Torres, L.G., Iovan, C. & Garrigue, C. (in press) Finding the right fit: Comparative cetacean distribution models using multiple data sources. Diversity and Distributions.

Species distribution models (SDM) are used widely to understand the drivers of cetacean distribution patterns, and to predict their space-use patterns too. Using humpback whale sighting datasets in New Caledonia, this study explores the performance of different SDM algorithms (GAM, BRT, MAXENT,  GLM, SVM) and methods of modeling presence-only data. We highlight the importance of controlling for model overfitting and thorough model validation.

 

Bishop, A.M., Brown, C., Rehberg, M., Torres, L.G. & Horning, M. (in press) Juvenile Steller sea lion (Eumetopias jubatus) utilization distributions in the Gulf of Alaska. Movement Ecology.

This study examines the distribution patterns of juvenile Steller sea lions in the Gulf of Alaska to gain a better understanding of the habitat needs of this vulnerable demographic group within a threatened population. Utilization distributions were derived for 84 tagged sea lions, which showed sex, seasonal and spatial differences. This information will support the development of a species recovery plan.

This comic seemed appropriate here. Thanks for everyone’s hard work!

Coastal oceanography takes patience

Joe Haxel, Acoustician, Assistant Professor, CIMRS/OSU

Greetings GEMM Lab blog readers. My name is Joe Haxel and I’m a close collaborator with Leigh and other GEMM lab members on the gray whale ecology, physiology and noise project off the Oregon coast. Leigh invited me for a guest blog appearance to share some of the acoustics work we’ve been up to and as you’ve probably guessed by now, my specialty is in ocean acoustics. I’m a PI in NOAA’s Pacific Marine Environmental Laboratory’s Acoustics Program and OSU’s Cooperative Institute for Marine Resources Studies where I use underwater sound to study a variety of earth and ocean processes.

As a component of the gray whale noise project, during the field seasons of 2016 and 2017 we recorded some of the first measurements of ambient sound in the shallow coastal waters off Oregon between 7 and 20 meters depth. In the passive ocean acoustics world this is really shallow, and with that comes all kinds of instrument and logistical challenges, which is probably one of the main reasons there is little or no acoustic baseline information in this environment.

For instance, one of the significant challenges is rooted in the hydrodynamics surrounding mobile recording systems like the drifting hydrophone we used during the summer field season in 2016 (Fig 1). Decoupling motion of the surface buoy (e.g., caused by swell and waves) from the submerged hydrophone sensor is critical, and here’s why. Hydrophones convert pressure fluctuations at the sensor/ water interface to a calibrated voltage recorded by a logging system. Turbulence resulting from moving the sensor up and down in the water column with surface waves introduces non-acoustic pressure changes that severely contaminate the data for noise level measurements. Vertical and horizontal wave motions are constantly acting on the float, so we needed to engineer compliance between the surface float and the suspended hydrophone sensor to decouple these accelerations. To overcome this, we employed a couple of concepts in our drifting hydrophone design. 1) A 10 cm diameter by 3 m long spar buoy provided floatation for the system. Spar buoys are less affected by wave motion accelerations compared to most other types of surface floatation with larger horizontal profiles and drag. 2) A dynamic shock cord that could stretch up to double its resting length to accommodate vertical motion of the spar buoy; 3) a heave plate that significantly reduced any vertical motion of the hydrophone suspended below it. This was a very effective design, and although somewhat cumbersome in transport with the RHIB between deployment sites, the acoustic data we collected over 40 different drifts around Newport and Port Orford in 2016 was clean, high quality and devoid of system induced contamination.

Figure 1. The drifting hydrophone system used for 40 different drifts recording ambient noise levels in 7-20 m depths in the Newport and Port Orford, OR coastal areas.

 

 

 

 

 

 

 

 

 

 

 

 

Spatial information from the project’s first year acoustic recordings using the drifting hydrophone system helped us choose sites for the fixed hydrophone stations in 2017. Now that we had some basic information on the spatial variability of noise within the study areas we could focus on the temporal objectives of characterizing the range of acoustic conditions experienced by gray whales over the course of the entire foraging season at these sites in Oregon. In 2017 we deployed “lander” style instrument frames, each equipped with a single, omni-directional hydrophone custom built by Haru Matsumoto at our NOAA/OSU Acoustics lab (Fig. 2). The four hydrophone stations were positioned near each of the ports (Yaquina Bay and Port Orford) and in partnership with the Oregon Department of Fish and Wildlife Marine Reserves program in the Otter Rock Marine Reserve and the Redfish Rocks Marine Reserve. The hydrophones were programmed on a 20% duty cycle, recording 12 minutes of every hour at 32 kHz sample rate, providing spectral information in the frequency band from 10 Hz up to a 13 kHz.

Figure 2. The hydrophone (black cylinder) on its lander frame ready for deployment.

Here’s where the story gets interesting. In my experience so far putting out gear off the Oregon coast, anything that has a surface expression and is left out for more than a couple of weeks is going to have issues. Due to funding constraints, I had to challenge that theory this year and deploy 2 of the units with a surface buoy. This is not typically what we do with our equipment since it usually stays out for up to 2 years at a time, is sensitive, and expensive. The 2 frames with a surface float were going to be deployed in Marine Reserves far enough from the traffic lanes of the ports and in areas with significantly less traffic and presumably no fishing pressure.  The surface buoy consisted of an 18 inch diameter hard plastic float connected to an anchor that was offset from the instrument frame by a 150 foot weighted groundline. The gear was deployed off Newport in June and Port Orford in July. What could go wrong?

After monthly buoy checks by the project team, including GPS positions, and buoy cleanings my hopes were pretty high that the surface buoy systems might actually make it through the season with recoveries scheduled in mid-October. Had I gambled and won? Nope. The call came in September from Leigh that one of the whale watching outfits in Depoe Bay recovered a free floating buoy matching ours. Bummer. Alternative recovery plans initiated and this is where things began to get hairy. Fortunately, we had an ace in our back pocket. We have collaborators at the Oregon Coast Aquarium (OCA) who have a top-notch research diving team led by Jim Burke. In the last week of October, they performed a successful search dive on the missing unit near Gull Rock and attached a new set of floats directly to the instrument frame. The divers were in the water for a short 20 minutes thanks to the good series of marks recorded during the buoy checks throughout the summer (Fig. 3).

Figure 3. OCA divers, Jenna and Doug, heading out for a search dive to locate and mark the Gull Rock hydrophone lander.

 

 

 

 

 

We had surface marker floats on the frame, but there was a new problem. Video taken by Jenna and Doug from the OCA dive team revealed the landers were pretty sanded in from a couple of recent October storms (Fig. 4). Ugghhh!

Figure 4. Sanded in lander at Gull Rock. Notice the sand dollars and bull kelp wrapped on the frame.

Alternative recovery plan adjustment: we’re gonna need a diver assisted recovery with 2 boats. One to bring a dive team to air jet the sand out away from the legs of the frame and another larger vessel with pulling power to recover the freed lander. Enter the R/V Pacific Surveyor and Capt. Al Pazar. Al, Jim and I came up with a new recovery plan and only needed a decent weather window of a few hours to get the job done. Piece of cake in November off the Oregon coast, right?

The weather finally cooperated in early December in-line with the OCA dive team and R/V Pacific Surveyor’s availability. The 2 vessels and crew headed up to Gull Rock for the first recovery operation of the day. At first we couldn’t locate the surface floats. Oh no. It seemed the rough fall/ winter weather and high seas since late October were too much for the crab floats? As it turns out, we eventually found the floats eastward about 200 m but couldn’t initially see them in the glare and whitecapping conditions that morning. The lander frame had broken loose from its weakened anchor legs in the heavy weather (as it was designed to do through an Aluminum/ Stainless Steel galvanic reaction over time) and rolled or hopped eastward by about 200 m (Fig. 5). Oh dear!

Figure 5. A hydrophone lander after recovery. Notice all but 1 of the concrete anchor legs missing from the recovered lander and the amount of bio-fouling on the hydrophone (compared to Figure 2).

 

 

 

 

 

 

Thankfully, the hydrophone was well protected, and no air jetting was required. With OCA divers out of the water and clear, the Pacific Surveyor headed over to the floats and easily pulled the lander frame and hydrophone on board (Fig. 6). Yipee!

On to the next hydrophone station. This station, deployed ~ 800 m west of the south reef off of South Beach near the Yaquina Bay port entrance. It was deployed entirely subsurface and was outfitted with an acoustic release transponder that I could communicate with from the surface and command to release a pop-up messenger float and line for eventual recovery of the instrument frame. Once on station, communication with the release was established easily (a good start) and we began ranging and moving the OCA vessel Gracie Lynn in to a position within about 2 water depths of the unit (~40 m). I gave the command to the transponder and the submerged release confirmed it was free of its anchor and heading for the surface, but it never made it. Uh oh. Turns out this lander had also broke free of its anchored legs and rolled/ hopped 800 m eastward until it was pinned up against the boulder structure of the south reef. Amazingly, OCA divers Jenna and Doug located the messenger float ~ 5 m below the surface and the messenger line had been fouled by the rolling frame so it could not reach the surface. They dove down the messenger line and attached a new recovery line to the lander frame and the Pacific Surveyor hauled up the frame and hydrophone in-tact (Fig. 6). Double recovery success!

Figure 6. R/V Pacific Surveyor recovering hydrophone landers off Gull Rock and South Beach.

The hydrophone data from both systems looks outstanding and analysis is underway. This recovery effort took a huge amount of patience and the coordination of 3 busy groups (NOAA/OSU, OCA, Capt. Al). Thanks to these incredible collaborations and some heroic diving from Jim Burke and his OCA dive team, we now have a unique and unprecedented shallow water passive acoustic data set from the energetic waters off the Oregon coast.

So that’s some of the story from the 2016 and 2017 field season acoustic point of view. I’ll save the less exciting, but equally successful instrument recoveries from Port Orford for another time.