October 2016 - Geospatial Ecology of Marine Megafauna Laboratory

Assembling a Toolbox

By Dawn Barlow, MSc student, Oregon State University

The season has shifted since the post I wrote this summer about diving into the world of New Zealand blue whales and the beginnings of my masters research. My fieldwork will take place during the upcoming austral summer, which will require me to miss the winter term here on campus. This quarter, I have put my research on the back burner for the time being in favor of a full load of coursework. But my project is still there, simmering subtly and persistently, and giving relevance to the coursework that I’m focusing my energy on this fall term.

As an undergraduate student, I acquired a broad scientific background and had the opportunity to dabble in the areas of biology that piqued my interest. I arrived here with a basic understanding of chemistry, physics, cell biology, anatomy, marine ecology and conservation biology. I gained experience working in the field with intertidal sea stars, snails, mussels, crabs and barnacles, with bottlenose dolphins and with humpback whales. But now my focus has narrowed as I’ve honed in on the specific questions that I will pursue over the next two years. My passion lies in marine ecology and conservation. Now, as a graduate student studying the ecology of a little-known population in a highly industrial area, this passion can come to fruition. For my masters, I hope to do the following:

A) Use photo-identification analysis to obtain a population abundance estimate for blue whales in New Zealand

B) Investigate blue whale residency and distribution patterns in New Zealand waters

C) Develop a comprehensive blue whale habitat use model for the South Taranaki Bight region of New Zealand, which incorporates physical and biological data

Down the road I hope to have implemented a capture-recapture abundance estimate model that best fits the dynamics of this population of blue whales, to have mapped where sightings have occurred and where the highest densities of blue whales are found in both space and time, and to have paired blue whale presence and absence with prey distribution, remote-sensed environmental data, and in situ oceanographic data. But how does one accomplish these things? I need a toolbox to draw from. And so this fall, I am assembling my toolbox, learning programs and analytical skills. I am taking methods courses—statistics, data management in R, analysis in GIS, methods in physiology and behavior of marine megafauna—that are no longer explorations into the world of natural science, but rather tools for exploring, identifying, and interpreting specific phenomena in ecology. While each comes with its own hiccups and headaches (see Florence’s post about this…), they are powerful tools.

Aside from coursework, the research I’m conducting has gained weight and relevance beyond being an investigation in ecology. My study area lies in the South Taranaki Bight of New Zealand, which is a contentious proposed seabed mining site for iron sands. As an undergraduate student I read case studies and wrote papers on the environmental impacts of industry, and I decided to go graduate school because I want to do research that has direct conservation applications. Last week I compiled all the data I’ve processed on blue whale sightings, seasonal residency, and photo identification for the South Taranaki Bight, which will be included as evidence submitted in environmental court in New Zealand by my advisor, Dr. Leigh Torres. “Applied conservation science” has been an abstract idea that has excited and motivated me for a long time, and now I am partaking in this process, experiencing applied conservation science firsthand.

And so my toolbox is growing, and the scope of my work is simultaneously narrowing in focus and expanding in relevance. The more tools I acquire, the more excited I am to apply them to my research. As I build my toolbox this fall, this process is something I look forward to enhancing while I’m in the field, when I dig deeper into data analysis, and as I grow as a conservation scientist.

A blue whale dives in the South Taranaki Bight, New Zealand. Photo by Leigh Torres.

The seamounts are calling and I must go: a humpback’s landscape

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

The deep ocean is awe-inspiring: vast, mysterious, and complex… I can find many adjectives to describe it, yet the immensity of it prevents me from picturing it in my mind. Landscapes are easy to imagine because we see them all the time, but their hidden ocean counterparts of seascapes with several kilometer-high seamounts and abyssal trenches are hard to visualize.

When I started a PhD on the spatial ecology of humpback whales, a species typically known for its coastal distributions, I never imagined my research would lead me to seamounts. Lesson of the day: you never know where research will lead you… So here is how it happened.

About twenty years ago when my supervisor, Dr Claire Garrigue, started working on humpback whales in New Caledonia, she was told by fishermen that humpbacks were often observed in prime fishing locations, about 170 km south of the mainland. After a little more investigation into this claim, it was discovered that these fishing spots corresponded with two seafloor topographic features: the Antigonia seamount and Torch Bank (Fig. 1), These features rise from the seafloor to depths of 30 m and 60 m respectively and are surrounded by waters about 1500 m deep. This led Dr. Garrigue to implement an ARGOS-satellite tagging program to follow the movements of humpbacks leaving the South Lagoon (one of the main breeding area in New Caledonia, Fig. 1). Sure enough, most of the tagged whales (61%) visited the Antigonia seamount (Fig. 2; Garrigue et al. 2015)⁠.

Map of New Caledonia and our study areas: the South Lagoon and the Southern Seamounts. Light grey lines represent 200m isobaths. Land is shown in black and reefs in grey. — Figure 1: Map of New Caledonia and our study areas: the South Lagoon and the “Southern Seamounts”. Light grey lines represent 200m isobaths. Land is shown in black and reefs in grey.

Figure 2: ARGOS tracking of 34 humpback whales tagged between 2007 and 2012 in the South Lagoon. The Antigonia seamount and Torch Bank are completely covered by tracklines.

Seamounts are defined as “undersea mountains rising at least 100m from the ocean seafloor” (Staudigel et al. 2010). Most of them have a volcanic origin and the majority of them are located in the Pacific Ocean (Wessel 2001). But what is the link between these structures and marine life? The physical and biological mechanisms by which seamounts attract marine wildlife are diverse (for a review see: Pitcher et al. 2008)⁠. In a nutshell, topography of the ocean floor influences water circulation and isolated seabed features such as seamounts affect vertical mixing and create turbulences, consequently resulting in higher productivity.

For instance, have you ever heard of internal waves? Contrary to the surface waves people play in at the beach, internal waves propagate in three dimensions within the water column and can reach heights superior to a 100m! When these waves encounter steep topography, they break, similar to what a “normal” wave would do when reaching shore. This creates complex turbulence, which in turn may attract megafauna such as cetaceans (see com. by Hans van Haren).

The importance of seamounts for cetaceans is often referenced in the literature, however, few studies have tried to quantify this preference (one of which was recently published by our labmate Courtney Hann, see Hann et al. 2016 for details). So what importance do these seamounts serve for humpback whales in New Caledonia? Are they breeding grounds, do they serve as a navigation cue, a resting area, or even a foraging spot (the latter being the less likely hypothesis given that humpback whales have never been observed feeding in tropical waters)?

To answer this question, an expedition to Antigonia was organized in 2008 and about 40 groups of whales were observed in only 7 days! The density of this aggregation, the high occurrence of groups with calves and the consistent singing of males suggested that this area may be associated with breeding or calving behavior. Several other missions followed, confirming the importance of this offshore habitat for humpbacks.

Looking through all this data I was struck by two things: 1) whales were densely aggregated on top of these seamounts but were rarely found in the surrounding area (Fig. 3), and 2) other seamounts with similar characteristics are only a few kilometers from Antigonia, but seem to be rarely visited by tagged whales.

What is so special about these seamounts? Why would energetically depleted females with calves choose to aggregate in these off-shore, densely occupied and unsheltered waters?

Figure 3: 3D surface plot of the seabed in the Southern seamount area. Humpback whale groups observed in-situ during the boat-based surveys conducted between 2001 and 2011 are projected at the surface of the seabed: blue points represent groups without calf and white points represent groups with calf. Antigonia and Torch Bank have a clear flat-top shaped which classifies them in the “guyot” seamount type. Most whale groups aggregated on top of these guyots. — Figure 3: 3D surface plot of the seabed in the Southern Seamounts area. Humpback whale groups observed during the boat-based surveys (2001-2011) are projected at the surface of the seabed: blue points represent groups without calf and white points represent groups with calf. Antigonia and Torch Bank have a clear flat-top shaped and are called “guyots” seamounts. Most whale groups aggregated on top of these guyots. For 3D interactive plot: click here.

I will spend the next two months at the GEMM lab in Newport, OR, trying to answer these questions using ocean models developed by New Caledonian local research teams (at IRD and Ifremer). I will be comparing maps of local currents and topography of several seabed features located south of the New Caledonia main island. The oceanographic model used for this study will allow me to analyze a great number of environmental variables (temperature, salinity, vertical mixing, vorticity etc.) through the water column (one layer every 10m, from 0 to 500m deep) and at a very fine spatio-temporal scale (1km and 1day, even 1 hour at specific discrete locations) to better understand humpback whale habitat preferences.

Figure 4: Modeled Sea Surface Temperature for July 15th 2013 (model in progress, based on MARS3D, development by Romain Legendre). A temperature front occurs in the middle of the study area, along the Norfolk ridge. On this image, a cold eddy is forming right on top of the Antigonia seamount. — Figure 4: Modeled Sea Surface Temperature for July 15th 2013 (model in progress, based on MARS3D, development by Romain Le Gendre). A temperature front occurs in the middle of the study area, along the Norfolk ridge. On this image, a cold eddy is forming right on top of the Antigonia seamount.

Looking forward to uncovering the mysteries of seamounts and sharing the results in December!

Literature Cited

Garrigue C, Clapham PJ, Geyer Y, Kennedy AS, Zerbini AN (2015) Satellite tracking reveals novel migratory patterns and the importance of seamounts for endangered South Pacific Humpback Whales. R Soc Open Sci

Hann CH, Smith TD, Torres LG (2016) A sperm whale’s perspective: The importance of seasonality and seamount depth. Mar Mammal Sci:1–12

Pitcher TJ, Morato T, Hart PJ, Clark MR, Haggan N, Santos RS (2008) Seamounts: ecology, fisheries & conservation. Oxford, UK: Blackwell Publishing Ltd.

Wessel P (2001) Global distribution of seamounts inferred from gridded Geosat/ERS-1 altimetry. J Geophys Res 106:19431–19441

Staudigel H, Koppers AP, Lavelle JW, Pitcer TJ, Shank TM (2010) Defining the word ‘seamount’. Oceanography 23,20–21.

The five senses of fieldwork

By Leila Lemos, PhD student

This summer was full of emotions for me: I finally started my first fieldwork season after almost a year of classes and saw my first gray whale (love at first sight!).

During the fieldwork we use a small research vessel (we call it “Red Rocket”) along the Oregon coast to collect data for my PhD project. We are collecting gray whale fecal samples to analyze hormone variations; acoustic data to assess ambient noise changes at different locations and also variations before, during and after events like the “Halibut opener”; GoPro recordings to evaluate prey availability; photographs in order to identify each individual whale and assess body and skin condition; and video recordings through UAS (aka “drone”) flights, so we can measure the whales and classify them as skinny/fat, calf/juvenile/adult and pregnant/non-pregnant.

However, in order to collect all of these data, we need to first find the whales. This is when we use our first sense: vision. We are always looking at the horizon searching for a blow to come up and once we see it, we safely approach the animal and start watching the individual’s behavior and taking photographs.

If the animal is surfacing regularly to allow a successful drone overflight, we stay with the whale and launch the UAS in order to collect photogrammetry and behavior data.

Each team member performs different functions on the boat, as seen in the figure below.

Figure 1: UAS image showing each team members’ functions in the boat at the moment just after the UAS launch.

While one member pilots the boat, another operates the UAS. Another team member is responsible for taking photos of the whales so we can match individuals with the UAS videos. And the last team member puts the calibration board of known length in the water, so that we can later calculate the exact size of each pixel at various UAS altitudes, which allows us to accurately measure whale lengths. Team members also alternate between these and other functions.

Sometimes we put the UAS in the air and no whales are at the surface, or we can’t find any. These animals only stay at the surface for a short period of time, so working with whales can be really challenging. UAS batteries only last for 15-20 minutes and we need to make the most of that time as we can. All of the members need to help the UAS pilot in finding whales, and that is when, besides vision, we need to use hearing too. The sound of the whale’s respiration (blow) can be very loud, especially when whales are closer. Once we find the whale, we give the location to the UAS pilot: “whale at 2 o’clock at 30 meters from the boat!” and the pilot finds the whale for an overflight.

The opposite – too many whales around – can also happen. While we are observing one individual or searching for it in one direction, we may hear a blow from another whale right behind us, and that’s the signal for us to look for other individuals too.

But now you might be asking yourself: “ok, I agree with vision and hearing, but what about the other three senses? Smell? Taste? Touch?” Believe it or not, this happens. Sometimes whales surface pretty close to the boat and blow. If the wind is in our direction – ARGHHHH – we smell it and even taste it (after the first time you learn to close your mouth!). Not a smell I recommend.

Fecal samples are responsible for the 5^th sense: touch!

Once we identify that the whale pooped, we approach the fecal plume in order to collect as much fecal matter as possible (Fig.2).

Figure 2: A: the poop is identified; B: the boat approaches the feces that are floating at the surface (~30 seconds); C: one of the team members remains at the bow of the boat to indicate where the feces are; D: another team member collects it with a fine-mesh net. Filmed under NOAA/NMFS permit #16111 to John Calambokidis).

After collecting the poop we transfer all of it from the net to a small jar that we then keep cool in an ice chest until we arrive back at the lab and put it in the freezer. So, how do we transfer the poop to the jar? By touching it! We put the jar inside the net and transfer each poop spot to the jar with the help of water pressure from a squeeze bottle full of ambient salt water.

Figure 3: Two gray whale individuals swimming around kelp forests. Filmed under NOAA/NMFS permit #16111 to John Calambokidis).

That’s how we use our senses to study the whales, and we also use an underwater sensory system (a GoPro) to see what the whales were feeding on.

GoPro video of mysid swarms that we recorded near feeding gray whales in Port Orford in August 2016:

Our fieldwork is wrapping up this week, and I can already say that it has been a success. The challenging Oregon weather allowed us to work on 25 days: 6 days in Port Orford and 19 days in the Newport and Depoe Bay region, totaling 141 hours and 50 minutes of effort. We saw 195 whales during 97 different sightings and collected 49 fecal samples. We also performed 67 UAS flights, 34 drifter deployments (to collect acoustic data), and 34 GoPro deployments.

It is incredible to see how much data we obtained! Now starts the second part of the challenge: how to put all of this data together and find the results. My next steps are:

– photo-identification analysis;

– body and skin condition scoring of individuals;

– photogrammetry analysis;

– analysis of the GoPro videos to characterize prey;

– hormone analysis laboratory training in November at the Seattle Aquarium

For now, enjoy some pictures and a video we collected during the fieldwork this summer. It was hard to choose my favorite pictures from 11,061 photos and a video from 13 hours and 29 minutes of recording, but I finally did! Enjoy!

Figure 4: Gray whale breaching in Port Orford on August 27th. (Photo by Leila Lemos; Taken under NOAA/NMFS permit #16111 to John Calambokidis).

Figure 5: Rainbow formation through sunlight refraction on the water droplets of a gray whale individual's blow in Newport on September 15th. (Photo by Leila Lemos; Taken under NOAA/NMFS permit #16111 to John Calambokidis). — Figure 5: Rainbow formation through sunlight refraction on the water droplets of a gray whale individual’s blow in Newport on September 15th. (Photo by Leila Lemos; Taken under NOAA/NMFS permit #16111 to John Calambokidis).

Likely gray whale nursing behavior (Taken under NOAA/NMFS permit #16111 to John Calambokidis):

A few things I’ve learned while writing a thesis

By: Amanda Holdman, MS student, Geospatial Ecology and Marine Megafauna Lab & Oregon State Research Collective for Applied Acoustics, MMI

“Never use the passive where you can use the active.” I recently received this comment in a draft of my thesis. While this pertained to a particular edit, it has since become my motto for writing in general – to stay active in writing. I knew before beginning this process, from my peers, that it takes time to write a thesis or dissertation, and usually much longer than anticipated, resulting in late caffeinated hours. My roommates have recently moved out, making it a perfect opportunity to convert my home into a great evening office. I needed fewer distractions so I unplugged the TV and set up a desk with ideal conditions for writing. I’m in a race against time with my defense set for only a month away, and getting into good writing habits has helped me smooth out a lot of the writing stress, so I figured I could share those tips.

Write sooner

The writing process can be daunting due to its size and importance. In the beginning I tended to wait until I thought I had researched enough about the topic. But, I have now learned not to wait until all the data is in and the results are clear to start writing. Some researchers might argue that results are needed before one can put the proper spin on the introduction, but spin isn’t quite needed for a first draft. Most of the writing can be actually be done before all the data have arrived. For example, I didn’t need to know the results of my observations before writing the manuscript about them; the rationale for having done the research doesn’t change with the results, so a draft of the introduction can be written without knowing the results. The methodology also doesn’t depend on the results, nor does the analysis that will be performed on the data, so a good framework for the results section can be written before all of the statistical tests are run. And before I know it, I have almost a full draft, just with quite a few gaps.

Write Continually

Productivity begets productivity, so don’t stop writing. It keeps my mind working and my project moving. I try to write a little every day or set a goal word limit. (500 words a day is easily obtainable and you feel proud at the end of the day). Writing as frequently as possible for me has helped to reveal gaps in my knowledge or understanding. Vague and disoriented writing tends to reflect a vague and disorganized thought, leading me to dig through the literature for more clarity.

Figure out how you write and edit

Some people are better writers when they first put their thoughts on paper and plan to go back and fix awkward sentences, poor word choices, or illogical sentences later. My perfection has always plagued me, so I always edit as a write, with one goal only: to make sure I’ve expressed the idea in my head clearly on the page. I don’t move on until the sentence (or thought) makes sense with no ambiguity in the meaning. Clarity of thought is always the aim in writing a manuscript, yet it is very difficult to come back to a section of writing days or weeks later and sort out a mess of thought if I don’t clarify my writing while the thought is still fresh in your head. This means I am constantly re-reading and revising what I’ve written, but also hopefully means that when I submit something to my advisor or committee it only needs simple revisions, thereby saving time by getting as “close to right” as I could the first time around.

Develop a routine

It’s important to learn when and what makes us productive. For me, writing in several short bursts is more efficient than writing in a few, long extended periods. When I try to write for long hours, I notice my concentration diminishing around the hour mark, so I try to take frequent 15 minute breaks. For me, the most productive parts of the day are the beginning the end. It’s important to build momentum early, and have a routine for ending the day too. At the end of each day, I always leave myself something easy to get started with the next day, so I wake up knowing exactly where I am going to start.

Find a template

Usually, when we decide on a date and deadlines for the final draft of our thesis due, we’re so frantic and pressed for time trying to get all the content, that we forget about the time it takes to make a draft pretty. My last HUGE time-saving tip is to find a colleague who has recently turned in their thesis or dissertation and still has their final word document. You can save time by reusing their document as a template for margins, page number position and other formatting guidelines. Everything you’ve written can easily be pasted into a formatted template.

Keep your motivation near

Finally, always try to keep the end result in mind. Whether it be holding a beautifully bound version of your thesis or a first author publication, keeping motivated is important. Publishing is not a requirement for completing a thesis but it is an ultimate goal for me. I know I owe it to myself, the people who I have worked with along the way, those who have supported me in some way (e.g., my committee), and to the funders that have helped pay for the research. Plus, to have a competitive edge in the next job I apply for, and to get the most leverage possible from my masters training, it is important for me to finish strong with a publication or two. Visualizing the end result helps me to take action to finish my thesis and advance my career.

Now, I think it’s about time to stop writing about writing a thesis and get back to actually writing my thesis.

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