Experiencing the Oregon Coast

By Dominique Kone, Masters Student in Marine Resource Management

An ecologist’s research may involve some combination of fieldwork and lab work. Yet, with modern advances in quantitative tools, such as models, computer-based research is becoming more popular. Furthermore, as the predictive capacity of models improve, they are becoming valuable to decision-makers to forecast how marine environments may respond to management decisions or phenomenon like climate change. While this type of research is important to society, I’ve often wondered if and how researchers may benefit by stepping away from their computer, every now and then, to observe the very subjects they’re studying.

For my thesis, I’m conducting an ecological assessment of a potential sea otter reintroduction to the Oregon coast. Through this work, I spend most of my time working at a desktop, analyzing spatial layers, and researching and synthesizing the literature. While I’ve learned a great deal about sea otters and the Oregon Coast, I felt that I needed to gain a better contextual understanding of this area, especially as someone from outside the region. Luckily, this summer, I had the perfect opportunity to explore this great state. Here, I share just some of the places I visited this past summer, what I’ve learned from my travels, and how these explorations have given me a deeper appreciation for the Oregon Coast and the implications of my research.

Source: Beachcombers NW.

For those of you unfamiliar with Oregon geography, the Oregon Coast is an expansive area stretching from Warrenton, which borders the Columbia River, in the north to the Oregon-California border just south of Brookings (approximately 362 miles). However, if we divide this area into three geographic regions – northern, central, and southern – some noticeable regional differences become apparent, both in terms of local topography and human use and visitation.

Relative to the northern and central coastlines, the geology of southern coastline (approximately Coos Bay to Brookings) is much more complex – comprising of rocky shorelines, sheltered coves and inlets, islands, and calm estuaries (overall, less sandy beaches). The region also appears to support a relatively higher biomass of macroalgae, including kelp. Taken altogether, the presence of these physical features appears to make the southern coast potentially suitable sea otter habitat, an important prerequisite of reintroduction efforts.

Pictured: Southern coastlines. Left: Samuel H. Boardman State Park near Brookings, OR. Right: Port Orford Heads State Park in Port Orford, OR. Source: Dominique Kone.

In contrast, the northern and central coastlines are predominantly comprised of sandy shorelines. However, these stretches of beaches are sometimes disrupted by complex and rocky habitat and have some of the largest estuaries and bays found along the entire Oregon Coast – such as Yaquina Bay, Tillamook Bay, and the Columbia River – all of which could also be potentially suitable habitat for sea otters. Furthermore, while you can find some kelp in these regions (i.e. Yaquina Head Lighthouse), these beds appear to be more dispersed and less dense than along the southern coast. By observing these features in person this summer, I came away with a much greater sense of just how biogeographically unique each of these regions is, as well as what it truly means for habitat to be “suitable”.

Pictured: Central coastlines. Left: Yaquina Head Marine Garden. Right: Agate Beach, OR. In this photo, Yaquina Head can be seen in the distance, demonstrating how quickly shorelines can change from sandy to rocky habitat in the northern and central regions. Source: Dominique Kone.

Aside from these physical characteristics, I also came away with a greater sense of the type of people who live and visit these regions. Along the Oregon Coast, dozens of towns, cities, unincorporated communities, and census-designated places are called home by some 653,112 people (State of Oregon. 2012). Yet, the southern coast is much less populated than the rest of the Oregon Coast. In fact, only 13% (people in Coos and Curry County) of the Oregon Coast population lives along the southern coast (State of Oregon. 2012). During my visit to the southern region, I noticed the typical beach-goers and overnight campers at various state parks, but there were not nearly as many in the northern and central regions. This demographic disparity is not surprising, given each region’s location in the state. The northern and central coasts are much closer to highly-populated cities such as Portland, Salem, Corvallis, and Eugene, potentially making them more accessible to weekend or seasonal visitors. In southern Oregon, the nearest in-land cities include Roseburg, Grants Pass, and Medford, but these populations pale in comparison to those in the central and northern regions.

Pictured: Beach-goers enjoying a pleasant stroll on Cannon Beach, OR. Source: Roger’s Inn.

After spending some time on the Oregon Coast, I wonder how these communities may be impacted by sea otters if they were to be reintroduced. Tourism and recreation are a huge part of the Oregon Coast lifestyle and economy. If managers were to bring sea otters back to Oregon, we could potential see an increase in visitation – as sea otters are an iconic and charismatic species – particularly to communities on the southern coast where sea otters may be more likely to establish. This increased tourism may come in the form of tourist redistribution from the northern and central coast to the southern region, an increase in overall tourists from all over the state, or even an influx from outside the state. Although these predictions are premature and based only on my recent observations, it is important to consider the societal impacts of sea otter reintroduction to our local communities.

To brings things back full circle, my coastal adventures provided me with a much deeper understanding of the uniqueness of the Oregon coast, as well as the people who call it home. Having this sound understanding is not only important for me as I conduct my research, but it is also vitally important for managers who are considering a sea otter reintroduction as this action could have coast-wide or localized impacts on these communities. If managers decide to move forward with a reintroduction effort, they could look at other regions along the U.S. west coast that currently have sea otters to assess how wildlife tourism is managed in these communities. For me, I’m glad I decided to step way from the computer to experience this beautiful area because it has provided me with a perspective I could not get from my data and models.

 

References:

State of Oregon. 2012. Natural Hazards Mitigation Plan: Region 1: Oregon Coast. Accessed here < https://www.oregon.gov/LCD/HAZ/docs/2.A.ORNHMP12-Reg1Profile.pdf >

A Summer of “Firsts” for Team Whale Storm

By Lisa Hildebrand, MSc student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

To many people, six weeks may seem like a long time. Counting down six weeks until your favourite TV show airs can feel like time dragging on slowly (did anyone else feel that way waiting for Blue Planet II to be released?). Or crossing off the days on your calendar toward that much-needed holiday that is still six weeks away can feel like an eternity. It makes sense that six weeks should feel like a long time. After all, six weeks are approximately a ninth of an entire year. Yet, I can assure you that if you asked anyone on my research team this summer whether six weeks was a long time, they would all say no.

As I watched each of my interns present our research to a room of 50 engaged community members (Fig. 1) after our six week research effort, I couldn’t help but feel an overwhelming sense of pride for all of them at how far they had come during the course of the field season.

Figure 1. Our audience at the community presentation on August 31. Photo by Leigh Torres.

On the very first day of our two-week training back in July, I gave my team an introductory presentation covering gray whales, their ecology, what the next six weeks would look like, how this project had developed and its results to date (Quick side-note here: I want to give a huge shout out to Florence and Leigh as this project would not be what it is today without their hard work and dedication as they laid the groundwork for it three years ago and have continued to improve and expand it). I remember the looks on my interns’ faces and the phrase that comes to mind is ‘deer in headlights’. It isn’t surprising that this was the case as this internship was the first time any of them had done marine mammal field work, or any kind of field work for that matter. It makes me think back to my first taste of field work. I was a fresh high school graduate and volunteering with a bottlenose dolphin research group. I remember feeling out of place and unsure of myself, both in terms of data collection skills but also having to live with the same people I had worked with all day. But as the first few days turned into the first few weeks, I grew into my role and by the end of my time there, I felt like an expert in what I was doing. Based on the confidence with which my interns presented our gray whale foraging ecology research to an audience just over a week ago, I know that they too had become experts in these short six weeks. Experts in levelling a theodolite, in sighting a blow several kilometres out from our cliff site, in kayaking in foggy conditions, in communicating effectively in high stress situations – the list goes on and on.

While you may have read the previous blog posts written by each of my interns in the last four weeks and thus have a sense of who they are, I want to tell you a little more about each of these hardworking undergraduates that played a large role in making this year’s Port Orford gray whale season so effective. Although we did not have any local high school interns this year, the whole team hails from Oregon, specifically from Florence, Sweet Home and Portland.

Figure 2. Haley on the cliff equipped with the camera waiting for a whale to surface. Photo by Cynthia Leonard.

Haley Kent (Fig. 2), my co-captain and Marine Studies Initiative (MSI) intern, an Environmental Science major, is going into her senior year at OSU this fall. She is focused and driven, which I know will enable her to pursue her dream of becoming a shark researcher (I can’t even begin to describe her excitement when we saw the thresher shark on our GoPro video). I couldn’t have asked for a better right hand person for my first year taking over this project and I am excited to see what results she will reveal through her project of individual gray whale foraging preferences. Also, Haley has a big obsession for board games and provided the team with many evenings of entertainment thanks to Munchkin and King of Tokyo.

Figure 3. Dylan in the stern of the kayak on a foggy day reeling down the GoPro stick on the downrigger. Photo by Haley Kent.

Dylan Gregory (Fig. 3) is transferring from Portland Community College and is going to be an OSU junior this fall. Not only was Dylan always extremely helpful in working with me to come up with ways to troubleshoot or fix gear, but his portable speaker and long list of eclectic podcasts always made him a very good cliff team partner. He was also Team Whale Storm’s main chef in the kitchen, and while some of his dishes caused tears & sweat among some team members (Dylan is a big fan of spices), there were never any leftovers, indicating how delicious the food was.

Figure 4. Robyn on one of our day’s off visiting the gigantic Redwoods in California. Photo by Haley Kent.

Robyn Norman (Fig. 4) will be a sophomore at OSU this fall and her commitment to zooplankton identification has been invaluable to the project. Last year when she was a freshman, Robyn was given our zooplankton samples from 2017, a few identification guides and instructions on how to use the dissecting microscope, before she was left to her own devices. Her level of independence and dedication as a freshman was incredible and I am very grateful for the time and skills she has given to this work. Besides this though, Robyn always brought an element of happiness to the room and I can speak on behalf of the rest of the team, that when she was gone for a week on a dive trip, the house did not feel the same without her.

Figure 5. Hayleigh Middleton at the community presentation. Her dry humour and quips earned her a lot of laughter from the audience keeping them entertained. Photo by Tom Calvanese.

Hayleigh Middleton (Fig. 5), a fresh high school graduate and freshly turned 18 during the project, is starting as a freshman at OSU this fall. She is extremely perceptive and would (thankfully) often remind others of tasks that they had forgotten to do (like take the batteries out of the theodolite or to mention the Secchi depth on the GoPro videos). I was very impressed by Hayleigh’s determination to continue working on the kayak despite her propensity for sea sickness (though after a few days we did remedy this by giving her raw ginger to chew on – not her favourite flavour or texture but definitely very, very effective!). She is inquisitive about almost everything and I know she will do very well in her first year at OSU.

Thank you, Team Whale Storm (Fig. 6), for giving me six weeks of your summer and for making my first year as project leader as seamless as it could have been! Without each and every one of you, I would not have been able to survey for 149.2 hours on the cliff, collect over 300 zooplankton samples, identify 31 gray whales, or launch a tandem kayak at 6:30 am every morning.

Figure 6. Team Whale Storm. Back row, from left to right: Haley Kent, Robyn Norman, Hayleigh Middleton, Dylan Gregory. Front row, from left to right: Tom Calvanese, Dr. Leigh Torres, Lisa Hildebrand. Photo by Mike Baran.

My interns were not the only ones to experience many “firsts” during this field season. I learned many new things for the first time right alongside them. While taking leadership is not a foreign concept to me, these six weeks were my first real experience of leading a project and a team for a sustained period of time. Managing teams, delegating tasks and compiling data felt gratifying because I felt like I was exactly where I should be (Fig. 7).

Figure 7. From left to right: Tom, myself, Hayleigh & Dylan on the cliff site looking for whales. Photo by Leigh Torres.
Figure 8. Haley & I on a cold evening out on the water but very excited to have gotten back the GoPro stick retrieved by divers after it had been stuck in a crevice for over 5 days. Photo by Lisa Hildebrand.

I dealt with many daunting tasks, yet thanks to the support of my interns, as well as Tom (Port Orford field station’s incredible station manager), Florence and Leigh, I learned how to resolve my problems: I fixed and replaced broken or lost gear (I am not a very mechanically inclined person; Fig. 8), budgeted food for five hungry people doing tiring field work (I’ve only ever budgeted for one person previously), and taught people how to use gear that I had not often used before (I can say now that the theodolite and I are friends, but this wasn’t the case for the first few weeks…).

 

Figure 9. Me with all the gear packed into the truck ready to leave Port Orford after the end of the field season. Photo by Haley Kent.

In the lead up to the summer field season this year, Leigh said to me, in one of the many emails we exchanged, that leading the project was a big task but that it was just six weeks long. She suggested that I rest up and get organised as much as I could ahead of time because, after all, the data collected this summer was going to be my thesis data, so I would want it to be as good as possible. Looking back, she couldn’t have been more right – the six weeks simply flew by, I did need the rest she had advised, and it definitely was a big task. I can’t wait for it to happen all over again next summer.

Looking through the scope: A world of small marine bugs

By Robyn Norman, GEMM Lab summer 2018 intern, OSU undergraduate

Although the average human may think all zooplankton are the same, to a whale, not all zooplankton are created equal. Just like us, different whales tend to favor different types of food over others. Thus, creating a meal perfect for each individual preference. Using a plankton net off the side of our kayak, each day we take different samples, hoping to figure out more about prey and what species the whales, we see, like best. These samples are then transported back to the lab for analysis and identification. After almost a year of identifying zooplankton and countless hours of looking through the microscope you would think I would have seen everything these tiny organisms have to offer.  Identifying mysid shrimp and other zooplankton to species level can be extremely difficult and time consuming, but equally rewarding. Many zooplankton studies often stop counting at 300 or 400 organisms, however in one very long day in July, I counted over 2,000 individuals. Zooplankton tend to be more difficult to work with due to their small size, fragility, and large quantity.

Figure 1. A sample fresh off the kayak in the beginning stages of identification. Photo by Robyn Norman.

A sample that looks quick and easy can turn into a never-ending search for the smallest of mysids. Most of the mysids that I have sorted can be as small as 5 mm in length. Being difficult to identify is an understatement. Figure 1 shows a sample in the beginning stages of analysis, with a wide range of mysids and other zooplankton. Different species of mysid shrimp generally have the same body shape, structure, size, eyes and everything else you can think of. The only way to easily tell them apart is by their telson, which is a unique structure of their tail. Their telsons cannot be seen with the naked eye and it can also be hard to find with a microscope if you do not know exactly what you are looking for.

 

Throughout my time identifying these tiny creatures I have found 9 different species of mysid from this gray whale foraging ecology project in Port Orford from the 2017 summer. But in 2018 three mysid species have been particularly abundant, Holmesimysis sculpta, Neomysis rayii, and Neomysis mercedis.

Figure 2. Picture taken with microscope of a Holmesimysis sculpta telson. Photo by Robyn Norman.

H. sculpta has a unique telson with about 18 lateral spines that stop as they reach the end of the telson (Figure 2). The end of the telson has 4 large spines that slightly curve to make a fork or scoop-like shape. From my own observations I have also noticed that H. sculpta has darker coloring throughout their bodies and are often heavily pregnant (or at least during the month of August). Neomysis rayii and Neomysis mercedis have been extremely difficult to identify and work with. While N. rayii can grow up to 65 mm, they can also often be the same small size as N. mercedis. The telsons of these two species are very similar, making them too similar to compare and differentiate. However, N. rayii can grow substantially bigger than N. mercedis, making the bigger shrimp easier to identify. Unfortunately, the small N. rayii still give birth to even smaller mysid babies, which can be confused as large N. mercedis. Identifying them in a timely manner is almost impossible. After a long discussion, we decided it would be easier to group these two species of Neomysis together and then sub-group by size. Our three categories were 1-10 mm, 11-15 mm, 16+ mm. According to the literature, N. mercedis are typically 11-15 mm meaning that anything over this size should be a N. rayii (McLaughlin 1980).

Figure 3. Microscopic photo of a gammarid. Photo source: WikiMedia.
Figure 4. Caprellidae found in sample with unique coloration. Photo by Robyn Norman.

While mysids comprise the majority of our samples, they are not the only zooplankton that I see. Amphipods are often caught along with the shrimp. Gammarids look like the terrestrial potato bug and can grow larger than some species of mysid (Fig. 3).

As well as, Caprellidae (Fig. 4) that remind me of little tiny aliens as they have large claws compared to their body size, making it hard to get them out of our plankton net. These impressive creatures are surprisingly hardy and can withstand long times in the freezer or being poked with tweezers under a microscope without dying.

In 2017, there was a high abundance of amphipods found in both of our study sites, Mill Rocks and Tichenor Cove. Mill Rocks surprisingly had 4 times the number of amphipods than Tichenor Cove. This result could be one of the possible reasons gray whales were observed more in Mill Rocks last year. Mill Rocks also has a substantial amount of kelp, a popular place for mysid swarms and amphipods. The occurrence of mysids at each of these sites was almost equal, whereas amphipods were almost exclusively found at Mill Rocks. Mill Rocks also had a higher average number of organisms than Tichenor Cove per samples, potentially creating better feeding grounds for gray whales here in Port Orford.

Analyzing the 2018 data I can already see some differences between the two years. In 2018 the main species of mysid that we are finding in both sites are Neomysis sp. and Holmesimysis sculpta, whereas in 2017 Alienacanthomysis macropsis, a species of mysid identified by their long eye stalks and blunt telson, made up the majority of samples from Tichenor Cove. There has also been a large decrease in amphipods from both locations compared to last year. Two samples from Mill Rocks in 2017 had over 300 amphipods, however this year less than 100 have been counted in total. All these differences in zooplankton prey availability may influence whale behavior and movement patterns. Further data analysis aims to uncover this possibility.

Figure 5. 2017 zooplankton community analysis from Tichenor Cove. There was a higher percentage and abundance of Neomysis rayii (yellow) and Alienacanthomysis macropsis (orange) than in Mill Rocks.
Figure 6. 2017 zooplankton community analysis from Mill Rocks. There was a higher abundance and percentage of amphipods (blue) and Holmesimysis sculpta (brown) than in Tichenor cove. Caprellidae (red) increased during the middle of the season, and decreased substantially towards the end.

The past 6 weeks working as part of the 2018 gray whale foraging ecology research team in Port Orford have been nothing short of amazing. We have seen over 50 whales, identified hundreds of zooplankton, and have spent almost every morning on the water in the kayak. An experience like this is a once in a lifetime opportunity that we were fortunate to be a part of. For the past few years, I have been creating videos to document important and exciting times in my life. I have put together a short video that highlights the amazing things we did every day in Port Orford, as well as the creatures that live just below the surface. I hope you enjoy our Gray Whale Foraging Ecology 2018 video with music by Myd – The Sun. 

[B]reaching New Discoveries about Gray Whales in Oregon

By Haley Kent, Marine Studies Initiative (MSI) & summer GEMM Lab intern, OSU senior

“BLOW!”, yells a team “Whale Storm” member, as mist remains above the water from an exhaling gray whale (Eschrichtius robustus). While based at the Port Orford Field Station for 6 weeks of my final summer as an undergrad at Oregon State University my heart has only grown fonder for marine wildlife. I am still in awe of this amazing opportunity of researching the foraging ecology of gray whales as a Marine Studies Initiative and GEMM Lab intern. From this field work I have already learned so much about gray whales and their zooplankton prey, and now it’s time to analyze the data we have collected and see what ecological stories we can uncover.

Figure 1. Robyn and Haley enjoy their time in the research kayak. Photo by Lisa Hildebrand.

WORK IN THE FIELD

This internship is my first field work experience and I have learned many skills and demands needed to study marine wildlife: waking up before the sun (every day begins with screaming alarms), being engulfed by nature (Port Orford is a jaw-dropping location with rich biodiversity), packing up damp gear and equipment to only get my feet wet in the morning ocean waves again, and of course waiting on the weather to cooperate (fog, wind, swell). I wouldn’t want it any other way.

Figure 2. Smokey sunrise from the research kayak. Photo by Haley Kent.

Whether it is standing above the ocean on the ‘Cliff Site’ or sitting in our two-man kayak, every day of this internship has been full of new learning experiences. Using various field work techniques, such as using a theodolite (surveying equipment to track whale location and behavior), Secchi disks (to measure water clarity), GoPro data collection, taking photos of wildlife, and many more tools, have given me a new bank of valuable skills that will stick with me into my future career.

Figure 3. Haley drops Secchi disk from the research kayak. Photo by Dylan Gregory.

Data Analysis

To maximize my amazing internship experience, I am conducting a small data analysis project using the data we have collected these past weeks and in previous summers.  There are so many questions that can be asked of these data, but I am particularly interested in how many times individual gray whales return to our study area to forage seasonally or annually, and if these individual whales forage preferentially where certain zooplankton prey are available.

Photo Identification

After many hours of data collection in the field either in the kayak or on the cliff, we get to take a breather in the lab to work on various projects we are each assigned. Some job tasks include processing data, identifying zooplankton, and looking through the photos taken that day to potentially identify a known whale. Once photos are processed and saved onto the rugged laptop, they are ready for some serious one on one. Looking through each of the 300 photos captured each day can be very tedious, but it is worthwhile when a match is found. Within the photos of each individual whale I first determine whether it is the left or right side of the whale – if we are lucky we get both! – and maybe even a fluke (tail) photo!

Figure 4. Buttons’ left side. Photo taken by Gray Whale Team of 2018.
Figure 5. Buttons’ left side. Photo taken by Gray Whale Team of 2017.

The angles of these photos (Fig. 4 & 5) are very different, so it could be difficult to tell these are the same whale. But, have a closer look at the pigmentation patterns on this whale. Focus on a single spot or area of spots, and see how patterns line up. Does that match in the same area in the next photo? If yes, you could have yourself a match!

Buttons, one of the identified gray whales (Fig. 4 & 5), was seen in 2016, 17, and 18. I was so excited to identify Buttons for the 3rd year in a row as this result demonstrates this whale’s preference for foraging in Port Orford.

Zooplankton and whale foraging behavior

By using the theodolite we track the whale’s position from the cliff location. I have plugged these coordinates into Google Earth, and compared the coordinates to our zooplankton sample stations from that same day. These methods allow me to assess where the whale spent time, and where it did not, which I can then relate to the zooplankton species and abundance we caught in our sample tows (we use a net from the research kayak to collect samples throughout the water column).

Figure 6. Holmesimysis sculpta. This species can range between 4-12mm. The size of this zooplankton relative to the large gray whales foraging on it shows the whale’s incredible senses for prey preference. Photo source: Scripps Institute of Oceanography.

Results (preliminary)

‘Eyeball’ is one of our resident whales that we have identified regularly throughout this season here in Port Orford. I have compared the amount of time Eyeball has spent near zooplankton stations to the prey community we captured at each station.

There is a positive trend in the amount of time the whale spent in an area with the percent abundance of Holmesimysis sculpta (Fig. 7: blue trend line).

Figure 7. Comparative plot between the amount of time the whale “Eyeball” spent within 50m of each zooplankton sampling station and the relative amount of zooplankton species caught at each station. Note the positive trend between time and Holmesimysis sculpta, and the negative trend relative to Neomysis sp. or Caprellidae.

Conversely, there is an inverse trend with two other zooplankton species:  Neomysis sp. (grey trend line) and Caprellidae (orange trend line). These results suggest that Eyeball has a foraging preference for areas where Holmesimysis sculpta (Fig. 6) is more abundant. Who would have known a whale could be so picky? Once the season comes to an end, I plan to use more of our data to continue to make discoveries about the foraging preferences of gray whales in Oregon.

Where the Wild Things Are

By Dylan Gregory, GEMM Lab summer 2018 intern, OSU undergraduate transfer

In ecology, biodiversity is a term often touted for its key importance in stable ecosystems. Every organism plays its role in the constant struggle of nature, competing and cooperating with each other for survival. The sun provides the initial energy to primary producers, herbivores eat those producers, and predators then eat the consumers. The food chain is a simplistic way to look at how ecosystems work, and of course, it is more like an intricate web of interactions. Fungus and plants work together to trade nutrients and create a vast network of fertile soils; kelp forests provide habitats and food for a variety of prey that marine predators feed on. There are checks and balances between all these organisms that give breath into the beauty and color we see in ecosystems around the world. And, here in Port Orford is no exception. Coming to the project I expected to see some whales, of course. However only three weeks in and I’ve been absolutely astounded with the amount of marine biodiversity we’ve experienced. These past three weeks have been nothing if, well, wild.

Eschrichtius robustus, The Gray Whale

There was no doubt we would see gray whales, that is what we are here for after all, and studying them in the field has been an incredibly enlightening experience. Watching an animal every day for weeks really gets you into their head. You start to connect with them and think about their behaviors in different ways. You begin to realize that the individuals have unique quirks, habits and tendencies. For example, one whale would feed quickly for a time, and then seem to run out of energy and “log” itself, floating on the surface, taking multiple breaths in succession to recover before diving back down. Many whales come from the south, to feed in Mill Rocks before moving to Tichenor Cove, and then leave our study region through “Hell’s Gate” to the North, often resting a moment, taking multiple breaths and then launching into the open sea. Still, when you think you know these whales, they surprise you with an alarming unpredictability, making tracking them a new experience every day.

Figure 1 A gray whale surprised us by surfacing right next to our kayak during a routine zooplankton sampling. The site has shown to have a significant amount of zooplankton and it must have been very interested in the prey available, completely ignoring our presence. Photo by Haley Kent.

The whale in Fig. 1 surprised us, and honestly, being so close to it was as humbling as it was awesome. I expected to see whales, but never expected such a close encounter. These gentle giants are one of our not so distant relatives in the ocean. Many of us do this kind of research for more than just the science and the data. Many of us do it for the connection we feel to our mammal family.

Phoca vitulina richardii, The Pacific Harbor Seal

I absolutely adore these harbor seals! They’re well known for their friendliness towards humans as their dopey little heads pop up out of the water to greet you with a curious look in their eyes. They like to bob in the surf and stare at us while we’re out sampling in the kayak. At first, we got quite excited seeing one, often startling them as we’d squeal “seal!” to each other and they’d dip back under and scurry away. Now though, they seem more comfortable being around our kayak (Fig. 2).

Figure 2 This harbor seal surfaced next to Haley and me shortly before the whale in Fig 1. We named him Courage, as he stuck around and kept us company during the whole encounter. Photo by Haley Kent.

One day a seal followed Lisa and Hayleigh around the jetty on their way back from sampling, swimming around the kayak and investigating them. Out in Mill Rocks, we often see them stretching on top of the rocks, seemingly doing a little yoga session while basking in the morning sun. Despite their cute and cuddly appearance, they are still predators. With plenty of fish to eat and make them happy, these harbor seals are quite plentiful themselves, and I’d like to think we’ve become quite good friends with the little guys.

Tursiops truncatus, The Bottlenose Dolphin

Figure 3 A shot of the dorsal fin seen on August 9th in Mill Rocks. Photo by Dylan Gregory.

One morning we were in Mill Rocks and a large cloud of fog moved in, so we decided to wait it out before making our passage to Tichenor Cove. While sitting there, enjoying a snack, we noticed some dorsal fins popping up about 100 meters from us. Caught by surprise, Haley and I scrambled for our cameras and lo and behold, we noticed they were a small pod of dolphins! Two adults and a calf. Unfortunately, as you can see from our pictures, it is difficult to identify what species they were exactly.

Figure 4 The head and rostrum of the dolphin seen in Mill Rocks on August 9th. Photo by Dylan Gregory.

After communicating with Lisa and Leigh, we have decided that their dorsal fins were far too big and curved to be harbor porpoises (Fig. 3), and the intersection of the head and rostrum seem to have the classic look of a bottlenose dolphin (Fig. 4).

If these were in fact bottlenose dolphins, why are they here in Port Orford, Oregon? It’s uncommon for them to be so far north in our colder waters. Were they foraging for food? Finding refuge from predators? Is it because our waters are becoming warmer? A sighting like this gives more weight to how climate change is affecting our oceans and how marine animals are responding by adapting their migratory and feeding behaviors.

Pisaster and Pycnopodia, The Common Sea Star and the Sunflower Star

Figure 5 Pisaster sea stars and anemones on a rock in Mill Rocks. No Pycnopodia (often called sunflower stars for their many legs) have been spotted in our study zone. Photo by Haley Kent.

One of the coolest aspects of living at the Port Orford Field Station is the fact that we have access to a lot of engagement with other scientists. For instance, we were able to attend a webinar about Sea Star Wasting Disease (SSWD) research currently happening at OSU by Post Doc Sarah Gravem. In a nutshell, a bacterial disease has been infecting sea stars along the west coast, causing a rapid plummet in their populations. Pisaster and Pycnopodia (Fig. 5) have been particularly affected. They are keystone predators, and as such, hold an important role in intertidal ecosystems. Feeding on snails, urchins, other sea stars and various mollusks, these sea stars maintain species populations and allow for a diverse and stable intertidal zone, which then supports many other near shore marine species. While SSWD’s cause is relatively unknown, Pisaster seems to be recovering while Pycnopodia is still struggling. I’ve even heard some anecdotal reports that fishermen here in Port Orford have noticed the lack of Pycnopodia as well, but they are rather pleased that these “ragmops” have stopped mucking up their lines and crab pots.

Below the Surface

There is a charm to the deep, a mystery and wonder that has captured the imagination of humans ad nauseam. Stories, movies, music and masterpieces of art have been inspired by The Abyss. Below the surface lies a diverse world teeming with life, full of questions and answers to be found. While marine mammals are why we’re here, there’s an entirely different environment under the water that is unseen from the safety of our dry, oxygen rich air. Our research doesn’t involve any diving, and so our eyes under the water are a GoPro camera attached to a downrigger on our kayak. Although designed to measure zooplankton community density, we’ve seen quite a bit more than itty bitty sea bugs in the depths of our little harbor here in Port Orford.

Strongylocentrotus purpuratus, The Purple Sea Urchin

Urchins are known for their bright colors and spiny ball like exterior. Close relatives to the sea stars, urchins inhabit the intertidal zones and also take residence within kelp beds. During our kayak training, we passed by some rocks near the cliffs and it was an awesome sight seeing the diversity of intertidal critters such as anemones, sea stars and sea urchins. However, a week into data collection, we have noticed something startling: a large quantity of the urchins cover the seafloor and the kelp, or at least what was left of the kelp (Fig. 6).

Figure 6 Sea Urchins decimating a kelp bed in Tichenor Cove. Photo captured from GoPro footage.

Sea urchins are important members in their communities. They graze on algae and control it from overwhelming the waters, but when left unchecked urchins can completely decimate kelp beds. This pattern is often referred to as “urchin barrens”. Sea otters and sea stars are the urchin’s main predator, and due to the absence of otters and the emergence of SSWD, the occurrence of urchin barrens has risen. An assessment of the reintroduction of the sea otters to Oregon by Dominique Kone, a GEMM Lab graduate student, is underway, and there is a lot of new research on SSWD, both of which could support the ‘ecosystem control’ of urchin populations. We’ve already spotted the urchins wreaking their havoc on the kelp in two separate sites in Tichenor Cove. Since gray whales primarily feed within these kelp beds, this increase in urchin populations is something that we are monitoring. An urchin barren can happen quickly and causes significant ecosystem damage, so this is not something to ignore. If we lose the kelp, it’s easy to imagine that we may lose the whales.

Alopias vulpinus, The Thresher Shark

Figure 7 A thresher shark spotted in Tichenor Cove in Port Orford, OR. Photo captured by GoPro footage.

By far, the most exciting thing I’ve seen so far has been this lovely creature (Fig. 7). The thresher shark usually inhabits the oceanic and coastal zones in tropical and temperate waters. They feed on pelagic schooling fish, squid and sometimes even shorebirds. They attack by whipping their tails (which grow to be the size of their body!) at their prey to stun them. Threshers are on the IUCN Red List of Threatened Species as “Vulnerable” due to their declining populations. They are often hunted for shark fin soup, or by trophy hunters due to their elegant and unique tails.

Haley, our resident shark enthusiast, was able to tell that this shark was a female by the lack of claspers (male appendages) on her pelvic fin. Why was she here though? During the summer, threshers will migrate to colder yet productive northern waters to feed, and on some rare occasions, such as this one, they will come closer to shore. Perhaps she was chasing prey into the harbor and found it to be full of yummy food, or she is a juvenile, which often stay near the continental shelf.

Either way, we were all surprised and excited to see such an exotic and beautiful species of shark caught on camera in our study zone. She even does a little strut in front of the GoPro camera, showing off her beautiful caudal fin!

Protecting our Wilds      

These are only a few examples of the many different animals at work in Port Orford’s ecosystem. Perhaps the biodiversity here is why this is such a hot spot for our whale friends. The productive and lively waters have shown us so many critters, and likely many more we have yet to see. But alas, we have three more weeks of data collection and new discoveries, and I couldn’t be more excited.

“It is a curious situation that the sea, from which life first arose should now be threatened by the activities of one form of that life. But the sea, though changed in a sinister way, will continue to exist; the threat is rather to life itself.”

– Rachel Carson, The Sea Around Us

This experience only drives me further into my pursuit of ecological research. I believe it’s incredibly important to understand the world and how it functions, and to do so before it’s too late. All too often we have breakthrough discoveries in science because something has already fallen apart. Ecosystems are fragile, and climate change, pollution, and other anthropogenic disturbances all have an impact which damage and alter ecosystems and the services they provide. However, it’s an impact we can control with a fundamental understanding of how nature works. With a little hope, some integrity, and a whole lot of passion, I believe we have the power to truly make a difference.

Cold Fingers and Carabiners

By Hayleigh Middleton, GEMM Lab summer 2018 intern, entering OSU undergrad 

Cold Fingers and Carabiners: that’s what most of the past three weeks have been about. We’ve progressively been getting up earlier—with many thanks to the coffee pot and multiple alarms— in order to be on the water collecting data before the wind and fog decide to kick in. Working on the ocean at 7 am with wet hands, metal equipment, a tight suit, and a “refreshing” breeze while trying to keep an eight-foot sit-on-top kayak from tipping over is challenging to say the least. Making sure the Theodolite is perfectly level on its tripod resting on sand-covered ground at the top of a cliff? Not much easier. The air is cold, the wind is cold, the equipment is cold, I’m cold, and now, everything is wet.

Rugged laptop on the cliff site. Photo by Hayleigh Middleton.

I absolutely love it.

Of all the ways I could have chosen to spend my summer before starting college at OSU, I’m so glad I took a chance and asked to spend it here. The official goals of our research project are to monitor and record the foraging habits of the Pacific Coast Feeding Group of gray whales, attempt to find out if specific individuals tend to have site fidelity and forage here year after year, and why or how they choose certain spots to feed over others. What does that mean for me? I get to kayak and take pictures of whales for six weeks! Of course, there’s a bunch of technical stuff and expensive equipment that took us two weeks to learn, but now we’re off to a great start and ready to learn more about these amazing creatures.

We have such a short amount of time to collect all this data to try and fill in the puzzle that is gray whale behavior, and we’re only a few weeks in, but I feel like I’ve already connected with this group of 60,000-pound mammals. That, in essence, is really what we’re doing here. We’re on top of a 33-meter-high cliff watching empty water for hours on the chance that we’ll be able to see a whale, identify it through photo-ID, track it with the theodolite to figure out its behavior, and use our kayak data to figure out its diet and feeding choices. Even though the whales forage up to two kilometers away from our tracking spot, it feels like they know we’re watching them. Sometimes it feels like they’re teasing us—we’ll see one, and once we get the sights fixed on it, it dives down and doesn’t come back up until we’ve turned our attention. One whale got into a very predictable pattern: three blows and then a deep dive, forage for five minutes, pop up half a viewfinder away, three more blows. We set our sights on the third blow and waited for her to resurface.

…and waited.

…and waited.

She swam away and didn’t show herself again.

Other times it’s like they conspire against us. Earlier this week, we spent most of the morning tracking the same whale. A couple hours into the track, another whale popped up right next to the first. Since we use a computerized tracking program, each whale is assigned a group number. That way, we can track each individual’s path and later match it to the photo identification database and sometimes a nickname. The two whales surfaced at just the right frequency and distance apart that deciding which number was currently up was guesswork for a good 15 minutes, but we gave them new track numbers and were able to sort it out later after reviewing our photos.

Searching for whales. Photo by Haley Kent.

On another day, we surveyed for whales until quitting time, which is 3:00 pm. About 2:30 pm, one was finally spotted. I named her Princess because she couldn’t be bothered to bring her body out of the water enough so we could mark her location or take a picture except for when her pectoral fin, the tip of which was “gloved” in white, came out and made a motion like a princess in a parade. When there are whales around, we can’t just say “oh look, 3:00 pm time to go” because this is important data to collect. So, we decided to wait until 3:30 pm to see if she surfaced again within visual range. 3:30 pm came and still no sign of her, so I packed up the theodolite and tripod. As soon as the box was closed, she blew, and another whale surfaced right in front of the cliff. We got some pictures of the closer one for a bit and decided that was enough. As the camera was being lowered into its case, another whale surfaced in the cove. It felt like the first went and told all the whales heading south “hey, these guys want to leave at 3, so show up right around then.” That day we got back to the lab around 5. Even though this meant being on the cliff for almost 10 hours that day, it was thrilling to have seen so many whales in one day.

Then there are times when the whales seem to beg for attention. On our third day on the cliff, we saw what we believe to be a juvenile come swimming into view. We assume that he was a juvenile because he was “small” and quite blank in terms of pigmentation and scarring. He was adorable. He stayed over at Mill Rocks for a while foraging, all of which we “fixed” into the tracking program via the Theodolite, and then he came toward us into the little kelp patch just in front of our cliff site. He would dive down, scoop up some zooplankton to eat, and resurface right in the middle of the kelp. The cutest part is that he would then proceed to roll around in the kelp and further drape himself in it.

Kelp whale. Photo by Lisa Hildebrand.

Having such a young whale come and forage made us wonder if mothers who have site fidelity then teach their young “hey, you don’t have to go all the way north, there’s a ton of good food here in Port Orford.”  Hopefully that’s one of the things we’ll be able to figure out with the data collected with this longterm study. But in the meantime, I still have three weeks of data to collect and a bunch more whales to meet. 

Are bacteria important? What do we get by analyzing microbiomes?

By Leila Lemos, PhD candidate, Fisheries and Wildlife Department, OSU

As previously mentioned in one of Florence’s blog posts, the GEMM Lab holds monthly lab meetings, where we share updates about our research and discuss articles and advances in our field, among other activities.

In a past lab meeting we were asked to bring an article to discuss that had inspired us in the past to conduct research in the marine field or in our current position. I brought to the meeting a literature review regarding methodologies to overcome the challenges of studying conservation physiology in large whales [1]. This article discusses different non-invasive or minimally invasive matrices (e.g., feces, blow, skin/blubber) that can be gathered from whales, and what types of analyses could be carried out, as well as their pros and cons.

One of the possible analyses that can be performed with fecal samples that was discussed in the article is the gut microflora (i.e., bacterial gut community) via genetic analysis. Since my PhD project analyzes fecal samples to determine/quantify stress responses in gray whales, we have since discussed the possibility of integrating this extra parameter to our analysis.

But… what is the importance of analyzing the gut microflora of a whale? What is the relationship between microflora and stress responses? Should we really use our limited sample size, time and money to work on this extra analysis? In order to be able to answer all of these questions, I began reading some articles of the field to better understand its importance and what kind of research questions this analysis can answer.

The gut of a mammal comprises a natural habitat for a large and dynamic community of bacteria [2] that is first developed in early life. Colonization of facultative bacteria (i.e., aerobic bacteria) begins at birth [3], and later, anaerobic bacteria also colonizes the gut. In humans, at the age of 1 year old, the microbiome should have a stable adult-like signature (Fig. 1).

Figure 01: Development of the microbiome in early life.
Source: [3]

The gut bacterial community is important for the physiology and pathology of its host and plays an important role in mammal digestion and health [2], responsible for many metabolic activities, including:

  • fermentation of non-digestible dietary residue and endogenous mucus [2];
  • recovery of energy [2];
  • recovery of absorbable nutrients [2];
  • cellulose digestion [4];
  • vitamin K synthesis [4];
  • important trophic effects on intestinal epithelia (cell proliferation and differentiation) [2];
  • angiogenesis promotion [4];
  • enteric nerve function [4];
  • immune structure [2];
  • immune function [2];
  • protection of the colonized host against invasion by alien microbes (barrier effect) [2];

Despite all the benefits, the bacterial community might also be potentially harmful when changes in the community composition (i.e., dysbiosis) occur due to the use of antibiotics, illness, stress, aging, lifestyle, bad dietary habits [4], and prolonged food and water deprivation [5]. Thus, potential pathological disorders might emerge when the microbiome community changes, such as allergy, obesity, diabetes, autism, multisystem organ failure, gastrointestinal and prostate cancers, inflammatory bowel diseases (IBD), and cardiovascular diseases [2, 4].

Changes in gut bacterial composition may also alter the brain-gut axis and the central nervous system (CNS) signaling [3]. More specifically, the core pathway affected is the hypothalamic-pituitary-adrenal (HPA) axis, which is activated by physical/psychological stressors. According to a previous study [6], the microbial community in the gut is critical for the development of an appropriate stress response. In addition, the microbial colonization in early life should occur within a certain time window, otherwise an abnormal development of the HPA axis might happen.

However, the gut microbiome can not only affect the HPA axis, but the opposite can also occur [3]. Signaling molecules released by the axis can alter the gastrointestinal (GIT) environment (i.e., motility, secretion, and permeability) [7]. Stress responses, as well as diseases, may also alter the gut permeability, causing the bacteria to cross the epithelial barrier (reducing the overall numbers of bacteria in the gut), activating immune responses that also alter the composition of the bacterial community in the gut [8, 9].

Figure 02: Communication between the brain, gut and microbiome in a healthily and in a stressed or diseased (mucosal inflammation) mammal.
Source: [3]

Thus, when thinking about whales, monitoring of the gut microflora might allow us to detect changes caused by factors such as aging, illness, prolonged food deprivation, and stressful events [2, 5]. However, since these are two-way factors, it is important to find an association between bacterial composition alterations and stressful events, such as the presence of predators (e.g., killer whales), illness (e.g., bad body condition), prolonged food deprivation (e.g., low prey availability and high competition), noise (e.g., noisy vessel traffic, fisheries opening and seismic surveys), and stressful reproductive status (e.g., pregnancy and lactating period). Examination of possible shifts in the gut microflora may be able to detect and be linked to many of these events, and also forecast possible chronic events within the population. In addition, the bacterial community monitoring study could aid in validating the hormone data (i.e., cortisol) we have been working with.

Therefore, the main research questions that arise in this context that can aid in elucidating the stress physiology in gray whales are:

  1. What is the microflora community content in guts of gray whales along the Oregon coast?
  2. Is it possible to detect shifts in the gut microflora from our gray fecal samples over time?
  3. How do gut microflora and cortisol levels correlate?
  4. Am I able to correlate shifts in gut microflora with any of the stressful events listed above?

We can answer so many other questions by analyzing the microbiome of baleen whales. Microbiomes are mainly correlated with host diet [10], so the composition of a microbiome can be associated with specific diets and functional gut capacity, and consequently, be linked to other animal populations, which helps to decode evolutionary questions. Results of a previous study on baleen whale microbiomes [10] point out that whales harbor unique gut microbiomes that are actually similar to those of terrestrial herbivores. Baleen whales and terrestrial herbivores have a shared physical structure of the GIT tract itself (i.e., multichambered foregut) and a shared hole for fermentative metabolisms. The multichambered foregut of baleen whales fosters the maintenance of the gut microbiome that is capable of extracting relatively unavailable nutrients from zooplankton (i.e., chitin, “sea cellulose”).

Figure 03: The similarities between whale and other terrestrial herbivore gut microbiomes: sea and land ruminants.
Source: [11]

Thus, the importance of studying the gut microbiome of a baleen whale is clear. Monitoring of the bacterial community and possible shifts can help us elucidate many questions regarding diet, overall health, stress physiology and evolution. Thinking about my PhD project, it may also help in validating our cortisol level results. I am confident that a microbiome analysis would significantly enhance my studies on the health and ecology of gray whales.

 

References

  1. Hunt, K.E., et al., Overcoming the challenges of studying conservation physiology in large whales: a review of available methods.Conservation Physiology, 2013. 1: p. 1-24.
  2. Guarner, F. and J.-R. Malagelada, Gut flora in health and disease.The Lancet, 2003. 360: p. 512–519.
  3. Grenham, S., et al., Brain–gut–microbe communication in health and disease.Frontiers in Physiology, 2011. 2: p. 1-15.
  4. Zhang, Y., et al., Impacts of Gut Bacteria on Human Health and Diseases.International Journal of Molecular Sciences, 2015. 16: p. 7493-7519.
  5. Bailey, M.T., et al., Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium.Infection and Immunity, 2010. 78: p. 1509–1519.
  6. Sudo, N., et al., Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice.The Journal of Physiology, 2004. 558: p. 263–275.
  7. Rhee, S.H., C. Pothoulakis, and E.A. Mayer, Principles and clinical implications of the brain–gut–enteric microbiota axis Nature Reviews Gastroenterology & Hepatology, 2009. 6: p. 306–314.
  8. Kiliaan, A.J., et al., Stress stimulates transepithelial macromolecular uptake in rat jejunum.American Journal of Physiology, 1998. 275: p. G1037–G1044.
  9. Dinan, T.G. and J.F. Cryan, Regulation of the stress response by the gut microbiota: Implications for psychoneuroendocrinology.Psychoneuroendocrinology 2012. 37: p. 1369—1378.
  10. Sanders, J.G., et al., Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores.Nature Communications, 2015. 6(8285): p. 1-8.
  11. El Gamal, A. Of whales and cows: the baleen whale microbiome revealed. Oceanbites 2016[cited 2018 07/31/2018]; Available from: https://oceanbites.org/of-whales-and-cows-the-baleen-whale-microbiome-revealed/.

 

Big Data: Big possibilities with bigger challenges

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

Did you know that Excel has a maximum number of rows? I do. During Winter Term for my GIS project, I was using Excel to merge oceanographic data, from a publicly-available data source website, and Excel continuously quit. Naturally, I assumed I had caused some sort of computer error. [As an aside, I’ve concluded that most problems related to technology are human error-based.] Therefore, I tried reformatting the data, restarting my computer, the program, etc. Nothing. Then, thanks to the magic of Google, I discovered that Excel allows no more than 1,048,576 rows by 16,384 columns. ONLY 1.05 million rows?! The oceanography data was more than 3 million rows—and that’s with me eliminating data points. This is what happens when we’re dealing with big data.

According to Merriam-Webster dictionary, big data is an accumulation of data that is too large and complex for processing by traditional database management tools (www.merriam-webster.com). However, there are journal articles, like this one from Forbes, that discuss the ongoing debate of how to define “big data”. According to the article, there are 12 major definitions; so, I’ll let you decide what you qualify as “big data”. Either way, I think that when Excel reaches its maximum row capacity, I’m working with big data.

Collecting oceanography data aboard the R/V Shimada. Photo source: Alexa K.

Here’s the thing: the oceanography data that I referred to was just a snippet of my data. Technically, it’s not even MY data; it’s data I accessed from NOAA’s ERDDAP website that had been consistently observed for the time frame of my dolphin data points. You may recall my blog about maps and geospatial analysis that highlights some of the reasons these variables, such as temperature and salinity, are important. However, what I didn’t previously mention was that I spent weeks working on editing this NOAA data. My project on common bottlenose dolphins overlays environmental variables to better understand dolphin population health off of California. These variables should have similar spatiotemporal attributes as the dolphin data I’m working with, which has a time series beginning in the 1980s. Without taking out a calculator, I still know that equates to a lot of data. Great data: data that will let me answer interesting, pertinent questions. But, big data nonetheless.

This is a screenshot of what the oceanography data looked like when I downloaded it to Excel. This format repeats for nearly 3 million rows.

Excel Screen Shot. Image source: Alexa K.

I showed this Excel spreadsheet to my GIS professor, and his response was something akin to “holy smokes”, with a few more expletives and a look of horror. It was not the sheer number of rows that shocked him; it was the data format. Nowadays, nearly everyone works with big data. It’s par for the course. However, the way data are formatted is the major split between what I’ll call “easy” data and “hard” data. The oceanography data could have been “easy” data. It could have had many variables listed in columns. Instead, this data  alternated between rows with variable headings and columns with variable headings, for millions of cells. And, as described earlier, this is only one example of big data and its challenges.

Data does not always come in a form with text and numbers; sometimes it appears as media such as photographs, videos, and audio files. Big data just got a whole lot bigger. While working as a scientist at NOAA’s Southwest Fisheries Science Center, one project brought in over 80 terabytes of raw data per year. The project centered on the eastern north pacific gray whale population, and, more specifically, its migration. Scientists have observed the gray whale migration annually since 1994 from Piedras Blancas Light Station for the Northbound migration, and 2 out of every 5 years from Granite Canyon Field Station (GCFS) for the Southbound migration. One of my roles was to ground-truth software that would help transition from humans as observers to computer as observers. One avenue we assessed was to compare how well a computer “counted” whales compared to people. For this question, three infrared cameras at the GCFS recorded during the same time span that human observers were counting the migratory whales. Next, scientists, such as myself, would transfer those video files, upwards of 80 TB, from the hard drives to Synology boxes and to a different facility–miles away. Synology boxes store arrays of hard drives and that can be accessed remotely. To review, three locations with 80 TB of the same raw data. Once the data is saved in triplet, then I could run a computer program, to detect whale. In summary, three months of recorded infrared video files requires upwards of 240 TB before processing. This is big data.

Scientists on an observation shift at Granite Canyon Field Station in Northern California. Photo source: Alexa K.
Alexa and another NOAA scientist watching for gray whales at Piedras Blancas Light Station. Photo source: Alexa K.

In the GEMM Laboratory, we have so many sources of data that I did not bother trying to count. I’m entering my second year of the Ph.D. program and I already have a hard drive of data that I’ve backed up three different locations. It’s no longer a matter of “if” you work with big data, it’s “how”. How will you format the data? How will you store the data? How will you maintain back-ups of the data? How will you share this data with collaborators/funders/the public?

The wonderful aspect to big data is in the name: big and data. The scientific community can answer more, in-depth, challenging questions because of access to data and more of it. Data is often the limiting factor in what researchers can do because increased sample size allows more questions to be asked and greater confidence in results. That, and funding of course. It’s the reason why when you see GEMM Lab members in the field, we’re not only using drones to capture aerial images of whales, we’re taking fecal, biopsy, and phytoplankton samples. We’re recording the location, temperature, water conditions, wind conditions, cloud cover, date/time, water depth, and so much more. Because all of this data will help us and help other scientists answer critical questions. Thus, to my fellow scientists, I feel your pain and I applaud you, because I too know that the challenges that come with big data are worth it. And, to the non-scientists out there, hopefully this gives you some insight as to why we scientists ask for external hard drives as gifts.

Leila launching the drone to collect aerial images of gray whales to measure body condition. Photo source: Alexa K.
Using the theodolite to collect tracking data on the Pacific Coast Feeding Group in Port Orford, OR. Photo source: Alexa K.

References:

https://support.office.com/en-us/article/excel-specifications-and-limits-1672b34d-7043-467e-8e27-269d656771c3

https://www.merriam-webster.com/dictionary/big%20data

Cloudy with a chance of blue whales

By Dawn Barlow, PhD student, Department of Fisheries & Wildlife, Geospatial Ecology of Marine Megafauna Lab

As a PhD student studying the ecology of blue whales in New Zealand, my time is occupied by questions such as: When and where are the blue whales? Can we predict where they will be based on environmental conditions? How does their distribution overlap with human activity such as oil and gas exploration?

Leigh and I have just returned from New Zealand, where I gave an oral presentation at the Society for Conservation Biology Oceania Congress entitled “Cloudy with a chance of whales: Forecasting blue whale presence to mitigate industrial impacts based on tiered, bottom-up models”. While the findings I presented are preliminary, an exciting ecological story is emerging, and one with clear management implications.

The South Taranaki Bight (STB) region of New Zealand is an important area for a population of blue whales which are unique to New Zealand. A wind-driven upwelling system brings cold, productive waters into the bight [1], which sustains high densities of krill [2], blue whale prey. The region is also frequented by busy shipping traffic, oil and gas drilling and extraction platforms as well as seismic survey effort for subsurface oil and gas reserves, and is the site of a recently-permitted seabed mine for iron sands (Fig. 1). However, a lack of knowledge on blue whale distribution and habitat use patterns has impeded effective management of these potential anthropogenic threats.

Figure 1. A blue whale surfaces in front of a floating production storage and offloading vessel servicing the oil rigs in the South Taranaki Bight. Photo by D. Barlow.

Three surveys were conducted in the STB region in the summer months of 2014, 2016, and 2017. During that time, we not only looked for blue whales, we also collected oceanographic data and hydroacoustic backscatter data to map and measure aspects of the krill in the region. These data streams will help us understand the functional, ecological relationships between the environment (oceanography), prey (krill), and predators (blue whales) in the ecosystem (Fig. 2). But in practice these data are costly and time-consuming to collect, while other data sources such as satellite imagery are readily accessible to managers at a variety of spatial and temporal scales. Therefore, another one of my aims is to link the data we collected in the field to satellite imagery, so that managers can have a practical tool to predict when and where the blue whales are most likely to be found in the region.

Figure 2. Data streams collected during surveys of the South Taranaki Bight Region in 2014, 2016, and 2017. 

So what did I find? Here are the highlights from my preliminary analyses:

  • The majority of the patterns in blue whale distribution can be explained by the density, depth, and thickness of the krill patches.
  • Patterns in the krill are driven by oceanography.
  • Those same oceanographic parameters that drive the krill can be used to explain blue whale distribution.
  • There are tight relationships between the important oceanographic variables and satellite images of sea surface temperature.
  • Blue whale distribution can, to some degree, be explained using just satellite imagery.

We were able to identify a sea surface temperature range in the satellite imagery of approximately 18°C where the likelihood of finding a blue whale is the highest. Is this because blue whales really like 18° water? Well, more likely this relationship exists because the satellite imagery is reflective of the oceanography, and the oceanography drives patterns in the krill distribution, and the krill drives the distribution of blue whales (Fig. 3). We were able to make each of these functional linkages through our series of models, which is quite exciting.

Figure 3. The tiered modeling approach we took to investigate the ecological relationships between blue whales, krill, oceanography, and satellite imagery. Because of the ecological linkages we made, we are able to say that any relationship between whale distribution and satellite imagery most likely reflects a relationship between the blue whales and their prey. 

That’s all well and good, but we were interested in testing these relationships to see if our identified habitat associations hold up even when we do not have field data (oceanographic, krill, and whale data). This past austral summer, we did not have a field season to collect data, but there was a large seismic airgun survey of the STB region. Seismic survey vessels are required to have trained marine mammal observers on board, and we were given access to the blue whale sightings data they recorded during the survey. In December, when the water was right around the preferred temperature identified by our models (18°C), the observers made 52 blue whale sightings (Fig. 4). In January and February, the waters warmed and only two sightings were made in each month. This is not only reassuring because it supports our model results, it also implies that there is the potential to balance industrial use of the area with protection of blue whale habitat, based on our understanding of the ecology. In January and February, very few blue whales were likely disturbed by the industrial activity in the STB, as conditions were not favorable for foraging at the location of the seismic survey. In contrast, the blue whales that were in the STB region in December may have experienced physiological consequences of sustained exposure to airgun noise since the conditions were favorable for foraging in the STB. In other words, the whales may have tolerated the noise exposure to gain access to good food, but this could have significant biological repercussions such as increased stress [3].

Figure 4. Monthly sea surface temperature (MODIS Aqua) overlaid with blue whale sightings from marine mammal observers aboard seismic survey vessel R/V Amazon Warrior. Black rectangles represent areas of seismic survey effort. Blue whale sighting location data were provided by RPS Energy Pty Ltd & Schlumberger, and Todd Energy.

In the first two weeks of July, we presented these latest findings to managers at the New Zealand Department of Conservation, the Minister of Conservation, the CEO and Policy Advisor of a major oil and gas conglomerate, NGOs, advocacy groups, and scientific colleagues. It was valuable to gather feedback from many different stakeholders, and satisfying to see such a clear interest in, and management application of, our work.

Dr. Leigh Torres and Dawn Barlow in front of Parliament in Wellington, New Zealand, following the presentation of their recent findings.

What’s next? We’re back in Oregon, and diving back into analysis. We intend to take the modeling work a step further to make the models predictive—for example, can we forecast where the blue whales will be based on the temperature, productivity, and winds two weeks prior? I am excited to see where these next steps lead!

References:

  1. Shirtcliffe TGL, Moore MI, Cole AG, Viner AB, Baldwin R, Chapman B. 1990 Dynamics of the Cape Farewell upwelling plume, New Zealand. New Zeal. J. Mar. Freshw. Res. 24, 555–568. (doi:10.1080/00288330.1990.9516446)
  2. Bradford-Grieve JM, Murdoch RC, Chapman BE. 1993 Composition of macrozooplankton assemblages associated with the formation and decay of pulses within an upwelling plume in greater cook strait, New Zealand. New Zeal. J. Mar. Freshw. Res. 27, 1–22. (doi:10.1080/00288330.1993.9516541)
  3. Rolland RM, Parks SE, Hunt KE, Castellote M, Corkeron PJ, Nowacek DP, Wasser SK, Kraus SD. 2012 Evidence that ship noise increases stress in right whales. Proc. Biol. Sci. 279, 2363–8. (doi:10.1098/rspb.2011.2429)

Searching for seabirds on the Garden Island

By Erin Pickett, M.Sc. (GEMM Lab member 2014-2016)

Field Assistant, Kaua’i Endangered Seabird Recovery Project

I heaved my body up with both arms, swung one leg up and attempted to muster any remaining energy I had into standing on the ridgeline of the valley that I had just crawled out of. Soaked from the rain, face covered with bits of dirt and with ferns sticking out of my hair I probably resembled a creature crawling out of a swamp. I smiled at this thought knowing that my dramatic emergence from the swamp might have been captured on a nearby motion-sensing trail camera.

I surveyed my surroundings to gain my bearings. I was searching for seabird burrows in a densely vegetated valley called Upper Limahuli Preserve in the mountains of Kaua’i, Hawaii. I was looking for the nests of the endangered Hawaiian Petrel (or ‘Ua’u in Hawaiian) and the threated Newell’s Shearwater (A’o), Hawaii’s only two endemic (found nowhere else in the world) Procellarid species. I registered the trail, the nearby fence line and the two valleys on either side of the ridge I was standing on. If a drone had photographed me from above, the scene of lush green mountains, waterfalls and rugged cliffs would not only look like the views from the helicopter arrival scene in the movie Jurassic Park, but indeed was the same Nā Pali coastline.

Northeastern facing view from the trail at Upper Limahuli Preserve looking toward the author’s hometown of Kīlauea and the site of the Nihokū predator-fence at Kīlauea National Wildlife Refuge

When I finished my graduate program at Oregon State University in 2017, I began working for a project called the Kaua’i Endangered Seabird Recovery Project (KESRP). Our work at KESRP focuses on monitoring Kauai’s populations of breeding a’o and ‘ua’u, mitigating on-land threats through recovery activities and conducting research (e.g. habitat modeling & at-sea tracking) to learn more about the two species.

An estimated 90% of the Newell’s Shearwater population breeds on the island of Kaua’i, as does a large portion of the Hawaiian Petrel population. Both populations have declined rapidly on Kaua’i over the past two decades, where radar surveys found a 78% decrease of Hawaiian Petrels and a 94% decrease in overall numbers of Newell’s Shearwaters (Raine et al., 2017). Light pollution, collision with electrical power lines, and invasive vertebrate predators represent primary threats to both the a’o and ‘ua’u while on land during the breeding season. As with all seabirds that nest on islands, the a’o and ‘ua’u are easy prey for invasive species such as feral cats and black rats, thus, there is a large effort within our study area to alleviate the threat of these predators.

A ‘ua’u adult incubating an egg at Upper Limahuli Preserve, 2018

The purpose of my burrow search effort on this day was to find suitable candidate burrows for a translocation project that KESRP has undertaken since 2015. This fall, we will attempt to relocate via helicopter up to 20 a’o and ‘ua’u chicks from the mountains of Kaua’i, where they are vulnerable to invasive predators, to a predator-proof fenced area located within nearby Kīlauea National Wildlife Refuge. The ultimate aim of our translocation project, a critical component of the Nihokū Ecosystem Restoration Project, is to establish successful breeding colonies of a’o and ‘ua’u within the protected boundaries of a fence that is impermeable to rats, cats, and pigs.

On Kaua’i, the imperiled a’o and ‘ua’u nest on verdant cliffs amid native Hawaiian uluhe ferns and ‘ohi‘a lehua trees. Both species raise their chicks in burrows that can only be located by humans after an extensive search effort that involves scanning the densely vegetated forest floor for tiny feathers and guano trails, and following the musty scent of seabirds until an underground tunnel is found, sometimes with a bird nestled inside.

The author with an a’o chick that was relocated to the Nihokū Ecosystem Restoration Site in 2017

My afternoon of burrow searching had been strenuous, and being day three it had already been a long week in the field so I sighed and started heading in the direction that would lead me back to our field camp. Though, after a few steps I caught the musty smell of seabird in the air and immediately stopped walking. Like an animal, I followed my nose and turned my head over my right shoulder and sniffed the air. I climbed over the fence that separated the trail I was hiking on from the 3,000 foot drop into the valley below, carefully positioned my feet on the fragile cliff side and lifted a large tuft of grass to find a freshly dug hole that smelled unmistakably like a seabird.

A triumphant selfie by the author after finding a particularly difficult to locate a’o burrow

Either a prospecting Hawaiian Petrel or Newell’s Shearwater had broken ground on this new burrow the night before. The birds had been busy digging into the cliff side while I had been conducting an auditory survey a few hundred meters away. The auditory survey had begun at sunset and over the course of the next two hours I listened for and recorded the locations of seabirds transiting overhead, heading from the sea to the mountains and calling from their burrows nearby. Ideally, this auditory survey would help me pinpoint locations of ‘ground callers’ who’s raucous would lead me to their burrows the next day.

Finding a burrow is not often as easy as pinpointing the location of a ground caller, catching a whiff of seabird near that location and immediately locating a hole in the ground. Yet, finding a burrow that is ‘reachable’ and that is reasonably close to a helicopter landing zone, is even more difficult. And this task is one of our objectives throughout the field season this year.

If you’re interested in keeping up with our progress you can follow KESRP on Facebook: https://www.facebook.com/kauaiseabirdproject/

Reference(s):

Raine, A. F., Holmes, N. D., Travers, M., Cooper, B. A., & Day, R. H. (2017). Declining population trends of Hawaiian Petrel and Newell’s Shearwater on the island of Kaua‘i, Hawaii, USA. The Condor119(3), 405-415.