Data Analysis – Page 3 – Geospatial Ecology of Marine Megafauna Laboratory

GEMM Lab 2017: A Year in the Life

By Dawn Barlow, MSc Student, Department of Fisheries and Wildlife

The days are growing shorter, and 2017 is drawing to a close. What a full year it has been for the GEMM Lab! Here is a recap, filled with photos, links to previous blogs, and personal highlights, best enjoyed over a cup of hot cocoa. Happy Holidays from all of us!

Things started off with a bang in January as the New Zealand blue whale team headed to the other side of the world for another field season. Leigh, Todd and I joined forces with collaborators from Cornell University and the New Zealand Department of Conservation aboard the R/V Star Keys for the duration of the survey. What a fruitful season it was! We recorded sightings of 68 blue whales, collected biopsy and fecal samples, as well as prey and oceanographic data. The highlight came on our very last day when we were able to capture a blue whale surface lunge feeding on krill from an aerial perspective via the drone. This footage received considerable attention around the world, and now has over 3 million views!

A blue whale surfaces just off the bow of R/V Star Keys. Photo by D. Barlow.

In the spring Rachael made her way to the remote Pribilof Islands of Alaska to study the foraging ecology of red-legged kittiwakes. Her objectives included comparing the birds that reproduce successfully and those that don’t, however she was thrown a major curveball: none of the birds in the colony were able to successfully reproduce. In fact, they didn’t even build nests. Further analyses may elucidate some of the reasons for the reproductive failure of this sentinel species of the Bering Sea… stay tuned.

The 2017 Port Orford field team. Photo by A. Kownacki.

Florence is a newly-minted MSc! In June, Florence successfully defended her Masters research on gray whale foraging and the impacts of vessel disturbance. She gracefully answered questions from the room packed with people, and we all couldn’t have been prouder to say “that’s my labmate!” during the post-defense celebrations. But she couldn’t leave us just yet! Florence stayed on for another season of field work on the gray whale foraging ecology project in Port Orford, this time mentoring local high school students as part of the project. Florence’s M.Sc. defense!

Upon the gray whales’ return to the Oregon Coast for the summer, Leila, Leigh, and Todd launched right back into the stress physiology and noise project. This year, the work included prey sampling and fixed hydrophones that recorded the soundscape throughout the season. The use of drones continues to offer a unique perspective and insight into whale behavior.

Video captured under NOAA/NMFS permit #16111.

Solene with a humpback whale biopsy sample. Photo by N. Job.

Solene spent the austral winter looking for humpback whales in the Coral Sea, as she participated in several research cruises to remote seamounts and reefs around New Caledonia. This field season was full of new experiences (using moored hydrophones on Antigonia seamount, recording dive depths with SPLASH10 satellite tags) and surprises. For the first time, whales were tracked all the way from New Caledonia to the east coast of Australian. As her PhD draws to a close in the coming year, she will seek to understand the movement patterns and habitat preferences of humpback whales in the region.

A humpback whale observed during the 2017 coral sea research cruise. Photo by S. Derville.

This summer we were joined by two new lab members! Dom Kone will be studying the potential reintroduction of sea otters to the Oregon Coast as a MSc student in the Marine Resource Management program, and Alexa Kownacki will be studying population health of bottlenose dolphins in California as a PhD student in the Department of Fisheries and Wildlife. We are thrilled to have them on the GEMM Lab team, and look forward to seeing their projects develop. Speaking of new projects from this year, Leigh and Rachael have launched into some exciting research on interactions between albatrosses and fishing vessels in the North Pacific, funded by the NOAA Bycatch Reduction Engineering Program.

During the austral wintertime when most of us were all in Oregon, the New Zealand blue whale project received more and more political and media attention. Leigh was called to testify in court as part of a contentious permit application case for a seabed mine in the South Taranaki Bight. As austral winter turned to austral spring, a shift in the New Zealand government led to an initiative to designate a marine mammal sanctuary in the South Taranaki Bight, and awareness has risen about the potential impacts of seismic exploration for oil and gas reserves. These tangible applications of our research to management decisions is very gratifying and empowers us to continue our efforts.

In the fall, many of us traveled to Halifax, Nova Scotia to present our latest and greatest findings at the 22^nd Biennial Conference on the Biology of Marine Mammals. The strength of the lab shone through at the meeting during each presentation, and we all beamed with pride when we said our affiliation was with the GEMM Lab at OSU. In other conference news, Rachael was awarded the runner-up for her presentation at the World Seabird Twitter Conference!

GEMM Lab members present their research. From left to right, top to bottom: Amanda Holdman, Leila Lemos, Solène Derville, Dawn Barlow, Sharon Nieukirk, and Florence Sullivan.

Leigh had a big year in many ways. Along with numerous scientific accomplishments—new publications, new students, successful fieldwork, successful defenses—she had a tremendous personal accomplishment as well. In the spring she was diagnosed with breast cancer, and after a hard fight she was pronounced cancer-free this November. We are all astounded with how gracefully and fearlessly she navigated these times. Look out world, this lab’s Principle Investigator can accomplish anything!

This austral summer we will not be making our way south to join the blue whales. However, we are keenly watching from afar as a seismic survey utilizing the largest seismic survey vessel in the world has launched in the South Taranaki Bight. This survey has been met with considerable resistance, culminating in a rally led by Greenpeace that featured a giant inflatable blue whale in front of Parliament in Wellington. We are eagerly planning our return to continue this study, but that will hopefully be the subject of a future blog.

New publications for the GEMM Lab in 2017 include six for Leigh, three for Rachael, and two for Alexa. Highlights include Classification of Animal Movement Behavior through Residence in Space and Time and A sense of scale: Foraging cetaceans’ use of scale-dependent multimodal sensory systems. Next year is bound to be a big one for GEMM Lab publications, as Amanda, Florence, Solene, Leila, Leigh, and I all have multiple papers currently in review or revision, and more in the works from all of us. How exciting!

In our final lab meeting of the year, we went around the table to share what we’ve learned this year. The responses ranged from really grasping the mechanisms of upwelling in the California Current to gaining proficiency in coding and computing, to the importance of having a supportive community in graduate school to trust that the right thing will happen. If you are reading this, thank you for your interest in our work. We are looking forward to a successful 2018. Happy holidays from the GEMM Lab!

GEMM Lab members, friends, and families gather for a holiday celebration.

The passion of a researcher

By Quince Nye, GEMM Lab Summer Intern, Pacific High School Junior

I have spent a lot of my life surrounded by nature. I like to backpack, bike, dive, and kayak in these natural environments. I also have the luck of having parents who are always planning to take me on another adventure where I get to see nature and its inhabitants in ways most people don’t get to enjoy.

Through my backyard explorations, I have begun to realize that Port Orford has an amazing ecosystem in the coves and rivers that are very tied into our community. I’ve fished and swam in these rivers, gone on kayaking tours in these coves (with a great kayak company called South Coast Tours that we partner with), and I’ve seen the life that dwells in them.

Nathan and Maggie paddle out to Mill Rocks for early morning sample collection

Growing up in a school of less than 100 kids I have learned to never reject an opportunity to be a part of something bigger and learn from that experience. So when one of my close friends told me about an OSU project (a college I’m interested in attending) that needed interns to help collect data on gray whales, and kayak almost every day, I signed up without a doubt in my mind.

The team gets some good practice tracking Buttons (Whale #3). Left to right; Quince, Nathan, Maggie, Florence.

Fast forward a month, and I wake up at 5:20 am. I eat breakfast and get to the Port Orford Field Station. We make a plan for the operations of both the kayak team and cliff team. Today, I’m part of the cliff team, so I head up above the station to Fort Point. Florence and I set up the theodolite and computer at the lookout point and start taking half hour watch shifts searching the horizon for the spout of a gray whale. Sometimes you see one right away, but other times it feels like the whales are actively hiding from you. These are the times I wish Maggie was here with her endless supply of Disney soundtracks to help pass the hours.

Imitating a ship’s captain, Quince points toward our whale while shouting “Mark”.

A whale spouts out at Mill Rocks and starts heading across to the jetty. Hurray, its data collection time! I try to quickly move the cross-hairs of the theodolite onto the position of the whale using a set of knobs like those on an etch-a-sketch. As you may understand, it’s not an easy task at first but I manage to do it because I’ve been practicing for three weeks. I say “Mark!” cueing Florence to click a button in the program Pythagoras on the computer to record the whale’s position.

The left hand side of Buttons – notice the scatter of white markings on the upper back.

Meanwhile, Florence sees that the whale has two white spots where the fluke meets the knuckles. Those are identifying marks of the beloved whale, Buttons. This whale has been seen here since 2016 and is a fan favorite for our on-going research program. Florence gets just as excited every time and texts her eagerly awaiting interns of previous years all about the sighting. Of course Buttons is not the only whale to have identifying marks such as scars and pigmentation marks. This is why we make sure to get photos of the whales we spot, allowing us to do photo-ID analysis on them through comparison to our database of pictures from previous years.

Quince practices CPR protocol on a training mannequin on his first day.

So far I have gained skill after skill in this internship. I got CPR certified, took a kayak training class, learned how to use a theodolite, and have spent many educational (and frustrating) hours entering data in Excel. I joined the program because I was interested in all of these things. It surprised me that I was developing a relationship with the whales I’m researching. By the end of August I’m now sure that I will also know many of the whales by name. I will probably be much better at using an etch-a-sketch, and I will have had my first taste at what being a scientist is like. What I strive for, however, is to have the same look in my eyes that appears in Florence’s whenever a familiar whale decides to browse our kelp beds.

Finding the edge: Preliminary insights into blue whale habitat selection in New Zealand

By Dawn Barlow, MSc student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

I was fortunate enough to spend the Austral summer in the field, and so while the winter rain poured down on Oregon I found myself on the water with the sun and wind on my face, looking for blue whales in New Zealand. This spring I switched gears and spent time taking courses to build my analytical toolbox. In a course on technical writing and communication, I was challenged to present my research using only pictures and words with no written text, and to succinctly summarize the importance of my research in an introduction to a technical paper. I attended weekly seminars to learn about the diverse array of marine science being conducted at Oregon State University and beyond. I also took a course entitled “Advanced Spatial Statistics and Geographic Information Science”. In this skill-building course, we were given the opportunity to work with our own data. Even though my primary objective was to expand the tools in my toolbox, I was excited to explore preliminary results and possible insight into blue whale habitat selection in my study area, the South Taranaki Bight region (STB) of New Zealand (Figure 1).

Figure 1. A map of New Zealand, with the South Taranaki Bight (STB) region delineated by the black box. Farewell Spit is denoted by a star, and Kahurangi point is denoted by an X.

Despite the recent documentation of a foraging ground in the STB, blue whale distribution remains poorly understood in New Zealand. The STB is New Zealand’s most industrially active marine region, and the site of active oil and gas extraction and exploration, busy shipping traffic, and proposed seabed mining. This potential space-use conflict between endangered whales and industry warrants further investigation into the spatial and temporal extent of blue whale habitat in the region. One of my research objectives is to investigate the relationship between blue whales and their environment, and ultimately to build a model that can predict blue whale presence based on physical and biological oceanographic features. For this spring term, the question I asked was:

Is the number of blue whales present in an area correlated with remotely-sensed sea surface temperature and chlorophyll-a concentration?

For the purposes of this exploration, I used data from our 2017 survey of the STB. This meant importing our ship’s track and our blue whale sighting locations into ArcGIS, so that the data went from looking like this:

… to this:

The next step was to get remote-sensed images for sea surface temperature (SST) and chlorophyll-a (chl-a) concentration. I downloaded monthly averages from the NASA Moderate Resolution Imaging Spectrometer (MODIS aqua) website for the month of February 2017 at 4 km² resolution, when our survey took place. Now, my images looked something more like this:

But, I can’t say anything reliable about the relationships between blue whales and their environment in the places we did not survey. So next I extracted just the portions of my remote-sensed images where we conducted survey effort. Now my maps looked more like this one:

The above map shows SST along our ship’s track, and the locations where we found whales. Just looking at this plot, it seems like the blue whales were observed in both warmer and colder waters, not exclusively in one or the other. There is a productive plume of cold, upwelled water in the STB that is generated off of Kahurangi point and curves around Farewell Spit and into the bight (Figure 1). Most of the whales we saw appear to be near that plume. But how can I find the edges of this upwelled plume? Well, I can look at the amount of change in SST and chl-a across a spatial area. The places where warm and cold water meet can be found by assessing the amount of variability—the standard deviation—in the temperature of the water. In ArcGIS, I calculated the deviation in SST and chl-a concentration across the surrounding 20 km² for each 4 km²cell.

Now, how do I tie all of these qualitative visual assessments together to produce a quantitative result? With a statistical model! This next step gives me the opportunity to flex some other analytical muscles, and practice using another computational tool: R. I used a generalized additive model (GAM) to investigate the relationships between the number of blue whales observed in each 4 km²cell our ship surveyed and the remote-sensed variables. The model can be written like this:

Number of blue whales ~ SST + chl-a + sd(SST) + sd(chl-a)

In other words, are SST, chl-a concentration, deviation in SST, and deviation in chl-a concentration correlated with the number of blue whales observed within each 4 km²cell on my map?

This model found that the most important predictor was the deviation in SST. In other words, these New Zealand blue whales may be seeking the edges of the upwelling plume, honing in on places where warm and cold water meet. Thinking back on the time I spent in the field, we often saw feeding blue whales diving along lines of mixing water masses where the water column was filled with aggregations of krill, blue whale prey. Studies of marine mammals in other parts of the world have also found that eddies and oceanic fronts—edges between warm and cold water masses—are important habitat features where productivity is increased due to mixing of water masses. The same may be true for these New Zealand blue whales.

These preliminary findings emphasize the benefit of having both presence and absence data. The analysis I have presented here is certainly strengthened by having environmental measurements for locations where we did not see whales. This is comforting, considering the feelings of impatience generated by days on the water spent like this with no whales to be seen:

Moving forward, I will include the blue whale sighting data from our 2014 and 2016 surveys as well. As I think about what would make this model more robust, it would be interesting to see if the patterns become clearer when I incorporate behavior into the model—if I look at whales that are foraging and traveling separately, are the results different? I hope to explore the importance of the upwelling plume in more detail—does the distance from the edge of the upwelling plume matter? And finally, I want to adjust the spatial and temporal scales of my analysis—do patterns shift or become clearer if I don’t use monthly averages, or if I change the grid cell sizes on my maps?

I feel more confident in my growing toolbox, and look forward to improving this model in the coming months! Stay tuned.

GEMM Lab 2016: A Year in the Life

By Dawn Barlow, MSc Student, Department of Fisheries and Wildlife, Oregon State University

The year is rapidly coming to a close, and what a busy year it has been in the Geospatial Ecology of Marine Megafauna Lab! In 2016, our members have traveled to six continents for work (all seven if we can carry Rachael’s South African conference over from the end of 2015…), led field seasons in polar, temperate, and tropical waters, presented at international conferences, processed and analyzed data, and published results. Now winter finds us holed up in our offices in Newport, and various projects are ramping up and winding down. With all of the recent turmoil 2016 has brought, it is a nice to reflect on the good work that was accomplished over the last 12 months. In writing this, I am reminded of how grateful I am to work with this talented group of people!

The year started with a flurry of field activity from our southern hemisphere projects! Erin spent her second season on the Antarctic peninsula, where she contributed to the Palmer Station Long Term Ecological Research Project.

Erin collecting a crabeater seal scat sample. — Erin in action collecting a crabeater seal scat sample along the West Antarctic Peninsula.

Aerial image of the research vessel and a pair of blue whales during the 2016 New Zealand survey.

The New Zealand blue whale project launched a comprehensive field effort in January and February, and it was a fruitful season to say the least. The team deployed hydrophones, collected tissue biopsy and fecal samples, and observed whales feeding, racing and nursing. The data collected by the blue whale team is currently being analyzed to aid in conservation efforts of these endangered animals living in the constant presence of the oil and gas industry.

Midway atoll is home to one of the largest albatross colony in the world, and Rachael visited during the winter breeding season. In addition to deploying tracking devices to study flight heights and potential conflict with wind energy development, she became acutely aware of the hazards facing these birds, including egg predation by mice and the consumption of plastic debris.

Laysan albatross equipped with a GPS data logger.

Fledgling from last year with a stomach full of plastic.

Early summertime brought red-legged kittiwakes to the remote Pribilof Islands in Alaska to nest, and Rachael met them there to study their physiology and behavior.

Rachael with a noosepole on St. George Island, Alaska

Solene with Dr. Claire Garrigue during fieldwork at the Chesterfield Reefs, New Caledonia.

As the weather warmed for us in the northern hemisphere, Solene spent the austral winter with the humpback whales on their breeding grounds in New Caledonia. Her team traveled to the Chesterfield Reefs, where they collected tissue biopsy samples and photo-IDs, and recorded the whale’s songs. But Solene studies far more than just these whales! She is thoroughly examining every piece of environmental, physical, and oceanographic data she can get her hands on in an effort to build a thorough model of humpback whale distribution and habitat use.

A humpback whale in New Caledonia's South Lagoon. — A humpback whale in New Caledonia’s South Lagoon.

Summertime came to Oregon, and the gray whales returned to these coastal waters. Leigh, Leila, and Todd launched into fieldwork on the gray whale stress physiology project. The poop-scooping, drone-flying team has gotten a fair bit of press recently, follow this link to listen to more!

The overhead drone captures a pair of gray whales surfacing between kelp beds off Cape Blanco, Oregon, with the research vessel nearby. Take under NOAA/NMFS permit #16111 given to John Calambokidis.

And while Leigh, Leila, and Todd followed the grays from the water, Florence and her team watched them from shore in Port Orford, tracking their movement and behavior. In an effort to gain a better understanding of the foraging ecology of these whales, Florence and crew also sampled their mysid prey from a trusty research kayak.

Florence and the summer 2016 gray whale field team.

DSCF0758 — Kelli Iddings sampling mysid near Port Orford.

With the influx of gray whales came an influx of new and visiting GEMM Lab members, as Florence’s team of interns joined for the summer season. I was lucky enough to join this group as the lab’s newest graduate student!

All summer 2016 GEMM Lab members. — All of the summer 2016 GEMM Lab members.

Our members have presented their work to audiences far and wide. This summer Leigh, Amanda, and Florence attended the International Marine Conservation Congress, and Amanda was awarded runner-up for the best student presentation award! Erin traveled to Malaysia for the Scientific Convention on Antarctic Research, and Rachael and Leigh presented at the International Albatross and Petrel Conference in Barcelona. With assistance from Florence and Amanda, Leigh led an offshore expedition on OSU’s research vessel R/V Oceanus to teach high school students and teachers about the marine environment.

Science Party musters in the dry lab for safety debrief aboard R/V Oceanus. — Science Party musters in the dry lab for safety debrief aboard *R/V Oceanus*.

Courtney fledged from the GEMM Lab nest before 2016 began, but the work she did while here was published in Marine Mammal Science this year. Congrats Courtney! And speaking of publications, additional congratulations to Solene for her publication in Marine Ecology Progress Series, Rachael for her four publications this year in PLOS ONE, Marine Ecology Progress Series, Marine Ornithology, and the Journal of Experimental Biology, and Leigh for her five publications this year in Polar Biology, Diversity and Distributions, Marine Ecology Progress Series, and Marine Mammal Science!

Wintertime in Newport has us tucked away indoors with our computers, cranking through analyses and writing, and dreaming about boats, islands, seabirds, and whales… Solene visited from the South Pacific this fall, and graced us with her presence and her coding expertise. It is a wonderful thing to have labmates to share ideas, frustrations, and accomplishments with.

No heat in the lab can't stop us from solving a coding problem together on a wintery evening! — Solving a coding problem together on a wintery evening.

As the year comes to a close, we have two newly-minted Masters of Science! Congratulations to Amanda and Erin on successfully defending their theses, and stay tuned for their upcoming publications!

Amanda's post-defense celebration! — Amanda’s post-defense celebration!

Erin's post-defense celebration! — Erin’s post-defense celebration!

We are looking forward to what 2017 brings for this team of marine megafauna enthusiasts. Happy holidays from the GEMM Lab!

Happy GEMM Lab members. — Happy GEMM Lab members, enjoying one another’s company and playing Evolution.

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.

Grad School Headaches

By Florence Sullivan, MSc student GEMM lab

Over the past few months I have been slowly (and I do mean SLOWLY – I don’t believe I’ve struggled this much with learning a new skill in a long, long time) learning how to work in “R”. For those unfamiliar with why a simple letter might cause me so much trouble, R is a programming language and free software environment suitable for statistical computing and graphing.

My goal lately has been to interpolate my whale tracklines (i.e. smooth out the gaps where we missed a whale’s surfacing by inserting artificial locations). In order to do this I needed to know (1) How long does a gap between fixes need to be to identify a missed surfacing? (2) How many artificial points should be used to fill a given gap?

The best way to answer these queries was to look at a distribution of all of the time steps between fixes. I started by importing my dataset – the latitude and longitude, date, time, and unique whale identifier for each point (over 5000 of them) we recorded last summer. I converted the locations into x & y coordinates, adjusted the date and time stamp into the proper format, and used the package adehabitatLT to calculate the difference in times between each fix. A package known as ggplot2 was useful for creating exploratory histograms – but my data was incredibly skewed (Fig 1)! It appeared that the majority of our fixes happened less than a minute apart from each other. When you recall that gray whales typically take 3-4 short breathes at the surface between dives, this starts to make a lot of sense, but we had anticipated a bimodal distribution with two peaks: one for the quick surfacings, and one for the surfacings between 4-5 minutes dives. Where was this second peak?

Histogram of the difference in time (in seconds) between whale fixes. — Fig. 1. Histogram of the difference in time (in seconds on x-axis) between whale fixes.

Sometimes, calculating the logarithm of one of your axes can help tease out more patterns in your data – particularly in a heavily skewed distribution like Fig. 1. When I logged the time interval data, our expected bimodal distribution pattern became evident (Fig. 2). And, when I back-calculate from the center of the two peaks we see that the first peak occurs at less than 20 seconds (e^2.5 = 18 secs) representing the short, shallow blow intervals, or interventilation dives, and that the second peak of dives spans ~2.5 minutes to ~5 minutes (e^4.9 = 134 secs, e^5.7 = 298 secs). Reassuringly, these dive intervals are in agreement with the findings of Stelle et al. (2008) who described the mean interval between blows as 15.4 ± 4.73 seconds, and overall dives ranging from 8 seconds to 11 minutes.

Fig. 2. Histogram of the log of time difference between whale fixes.

So, now that we know what the typical dive patterns in this dataset are, the trick was to write a code that would look through each trackline, and identify gaps of greater than 5 minutes. Then, the code calculates how many artificial points to create to fill the gap, and where to put them.

Fig. 3. A check in my code to make sure the artificial points are being plotted correctly. The blue points are the originals, and the red ones are new.

One of the most frustrating parts of this adventure for me has been understanding the syntax of the R language. I know what calculations or comparisons I want to make with my dataset, but translating my thoughts into syntax for the computer to understand has not been easy. With error messages such as:

Error in match.names(clabs, names(xi)) :

names do not match previous names

Solution: I had to go line by line and verify that every single variable name matched, but turned out it was a capital letter in the wrong place throwing the error!

Error in as.POSIXct.default(time1) :

do not know how to convert ‘time1’ to class “POSIXct”

Solution: a weird case where the data was in the correct time format, but not being recognized, so I had to re-import the dataset as a different file format.

Error in data.frame(Whale.ID = Whale.ID, Site = Site, Latitude = Latitude, : arguments imply differing number of rows: 0, 2, 1

Solution: HELP! Yet to be solved….

Is it any wonder that when a friend asks how I am doing, my answer is “R is kicking my butt!”?

Science is a collaborative effort, where we build on the work of researchers who came before us. Rachael, a wonderful post-doc in the GEMM Lab, had already tackled this time-based interpolation problem earlier in the year working with albatross tracks. She graciously allowed me to build on her previous R code and tweak it for my own purposes. Two weeks ago, I was proud because I thought I had the code working – all that I needed to do was adjust the time interval we were looking for, and I could be off to the rest of my analysis! However, this weekend, the code has decided it doesn’t work with any interval except 6 minutes, and I am lost.

Many of the difficulties encountered when coding can be fixed by judicious use of google, stackoverflow, and the CRAN repository.

But sometimes, when you’ve been staring at the problem for hours, what you really need is a little praise for trying your best. So, if you are an R user, go download this package: praise, load the library, and type praise() into your console. You won’t regret it (See Fig. 4).

Screenshot (74) — Fig. 4. A little compliment goes a long way to solving a headache.

Thank you to Rachael who created the code in the first place, thanks to Solene who helped me trouble shoot, thanks to Amanda for moral support. Go GEMM Lab!

Why do pirates have a hard time learning the alphabet? It’s not because they love aaaR so much, it’s because they get stuck at “c”!

Stelle, L. L., W. M. Megill, and M. R. Kinzel. 2008. Activity budget and diving behavior of gray whales (Eschrichtius robustus) in feeding grounds off coastal British Columbia. Marine mammal science 24:462-478.

Smile! You’re on Camera!

By Florence Sullivan, MSc. Student, GEMM Lab

Happy Spring everyone! You may be wondering where the gray whale updates have been all winter – and while I haven’t migrated south to Baja California with them, I have spent many hours in the GEMM Lab processing data, and categorizing photos.

You may recall that one of my base questions for this project is:

Do individual whales have different foraging strategies?

In order to answer this question, we must be able to tell individual gray whales apart. Scientists have many methods for recognizing individuals of different species using tags and bands, taking biopsy samples for DNA analysis, and more. But the method we’re using for this project is perhaps the simplest: Photo-Identification, which relies on the unique markings on individual animals, like fingerprints. All you need is a camera and rather a lot of patience.

Bottlenose dolphins were some of the first cetaceans to be documented by photo-identification. Individuals are identified by knicks and notches in their fins. Humpback whales are comparatively easy to identify – the bold black and white patterns on the underside of their frequently displayed flukes are compared. Orcas, one of the most beloved species of cetaceans, are recognized thanks to their saddle patches – again, unique to each individual. Did you know that the coloration and shape of those patches is actually indicative of the different ecotypes of Orca around the world? Check out this beautiful poster by Uko Gorter to see!

Gray whale photo identification is a bit more subtle since these whales don’t have dorsal fins and do not show the undersides of their fluke regularly. Because gray whales can have very different patterns on either side of their body, it is also important to get photos of both their right and left sides, as well as the fluke, to be sure of recognizing an individual if it comes around again. When taking photos of a gray whale, it’s a good idea to include the dorsal hump, where the knuckles start as it dives, as an easy indicator of which side of the body you are looking at when you’re trying to match photos. Some clues that I often use when identifying an individual include the placement of barnacles, and patterns of pigmentation and scars. You can see that patience and a talent for pattern recognition come in handy for this sort of work.

While we were in the field, it was important for my team to quickly find reference features to make sure we were always tracking the same whale. If you stopped by to visit our field station, you may have heard use saying things like “68 has white on both fluke-tips”, “70 has a propeller scar on the left side”, “the barnacles on 54’s head looks like a polyp”, or “27 has a smiley face in front of the first knuckle left side.” Sometimes, if a trait was particularly obvious, and the whale visited our field station more than once, we would give them a name to help us remember them. These notes were often (but to my frustration, not always!) recorded in our field notebook, and have come in handy this winter as I have systematically gone through the 8000+ photos we took last summer, identifying each individual, and noting whenever one was a repeat visitor. With these individuals labeled, I can now assess their level of behavioral and distribution consistency within and between study sites, and over the course of the summer.

Why don’t you try your luck? How many individuals are in this photoset? How many repeats? If I tell you that my team named some of these whales Mitosis, Smiley, Ninja and Keyboard can you figure out which ones they are?

Keep scrolling for the answer key ( I don’t want to spoil it too easily!)

Answers:

There are 7 whales in this photoset. Smiley and Keyboard both have repeat shots for you to find, and Smiley even shows off both left and right sides.

Whale 18 – Mitosis
Whale 70 -Keyboard
Whale 23 -Smiley
Whale 68 – Keyboard
Whale 27 -Smiley
Whale 67
Whale 36 -Ninja
Whale 60 – “60”
Whale 38 – has no nickname even if we’ve seen it 8 times! Have any suggestions? leave it in the comments!
Whale 55 – Smiley

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

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

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

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

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

The Oregon Coast. Photo by Olivia Hamilton.

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

So, what am I doing here?

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

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

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

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

Common dolphins in the Hauraki Gulf. Photo by Olivia Hamilton

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

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

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

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

Summary of sightings of megafauna in the Hauraki Gulf.

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

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

Gray Whale Goofs

Hello there! Florence here, signing in from Newport. We had a fantastic trip south to Port Orford, and tracked another 53 whales bringing our season total up to 117 so far! This morning, we were back out at Boiler Bay and spent 5 hours staring at empty water – in keeping with the theme of this post, field work does not always go as planned.

Our two study areas couldn’t be more different. At the Boiler Bay State Wayside, we are approximately 18 meters off the water. In Port Orford, we are perched on the side of a 63 meter tall cliff. This extra height greatly increases our range and accuracy as well as changing the angle of our photography and the type of photo analysis we can do. We’re quite excited to have a top down view of our whales, because the photos we are capturing will allow us to use certain photogrammetry techniques to measure the length and girth of the individuals. With luck, when we compare the photos from the beginning of the season (now) to the end of our study (September) we may be able to see a change in the height of the post-cranial fat deposit, which would indicate a successful foraging season. Gray whales do not eat from the beginning of their southward migration, through the breeding and calving season, until they reach productive foraging grounds at the end of their northward migration. This means that all their sustenance for 6+ months is derived from their summer foraging success. Did you know that they even generate their own water through an oxidation reaction which creates ‘metabolic water’ from their blubber stores? So it will be rather fantastic if we manage to measure the change in whale body condition over the course of the summer – particularly if we are able to spot any mother-calf pairs who will have had an especially grueling journey north.

Sharking: A foraging behavior where the whale turns on its side in shallow water. The triangle of the fluke resembles a shark fin

So, while our photo database is advancing nicely, technical difficulties are to be expected when you’re in the field, and sometimes, troubleshooting takes longer than you would like it to. This evening, let me introduce you to the elusive species known as ‘the Chinese land whale.’ It is a very rare breed which spontaneously generates itself from misaligned computer files.

When the theodolite beeps as we ‘mark’ a whale, a pair of horizontal and vertical angles are getting sent from the machine to a program called ‘Pythagoras’ on the laptop. Given our starting coordinates and a few other variables, the program auto-calculates for us the latitude and longitude of that whale. While we hoped it would be a simple matter to upload these coordinates to Google Earth to visualize the tracklines, it turns out that Pythagoras stores the East/West hemisphere information in a separate column, so if we just plot the raw numbers, our whale tracks end up in the middle of a field in rural China! Hence, the rare ‘Chinese land whale’. Now that we know the trick, it is not so difficult to fix, but we were quite surprised the first time it happened!

If you dont have your hemisphere correctly labeled, you end up in China instead of Oregon. — If you don’t have your hemisphere correctly labeled, you end up in China instead of Oregon.

Of course, that is not the only thing that has gone wrong with visualizing the tracklines. When we first got to Graveyard Point survey site, it turns out that we had set our azimuth (our reference angle) the wrong direction from true north, so all our whales seemed to be foraging near the fish and chips restaurant in the middle of town.

If the azimuth is incorrectly referenced, you might end up on land instead of in the water.

After discovering that in order to rotate something 180degrees, you simply need to alter the azimuth angle by 90degrees, (we’re still not sure why this is working), the whales left the fish and chips to us and returned to the harbor. Anyways, now that we’ve figured out these glitches, we can focus on identifying individual whales, and figuring out which track-lines might be repeat visitors.

Once all the kinks got worked out - the real trackline! Dont worry, whale 60 did not go through the jetty, thats an artifact of the program wanting to draw straight lines from point a to b. more likely we simply missed a surface as it transited around the point of the jetty. — Once all the kinks got worked out – the real trackline! Dont worry, whale 60 did not go through the jetty, thats an artifact of the program wanting to draw straight lines from point a to b. more likely we simply missed a surface as it transited around the point of the jetty.

In other outreach news, the OSU media department came out to the field and interviewed us a few weeks ago (on a day that the theodolite and computer were refusing to talk to each other due to a faulty connector cable – which is always delightful when one is trying to showcase research in progress). The resulting article has been posted should you wish to take a look:

http://oregonstate.edu/ua/ncs/archives/2015/aug/researchers-studying-oregon%E2%80%99s-%E2%80%9Cresident-population%E2%80%9D-gray-whales

Well known for having the shortest, toughest baleen of any of the great whales, here you can see the plates in its mouth!

Until next time,

Team Ro”buff”stus

Southern Sunshine Meets Oregon Wind: Interning with the GEMM Lab!

**GUEST POST**written by Cheyenne Coleman of Savannah State University

My first journey to the west coast, was spent on a six hour flight to Portland, Oregon in anticipation of my upcoming summer internship with the Geospatial Ecology and Marine Megafuana lab (GEMM Lab) at the Hatfield Marine Science Center (HMSC). I had never before been to the west coast, but luckily for me I did not have to make this long journey alone; my friend, Kamiliya Daniels, was also doing an internship at HMSC. After a long bus ride to Corvallis, Kamiliya and I, were warmly greeted by one of my GEMM lab members, Amanda Holdman. With her, was honorary GEMM lab member and Amanda’s dog, Boiler, who spent the greater part of the drive to Newport sleeping on my lap while I spent the drive asking Amanda several series of questions,

“Are there bears in these woods?”

“What do the dorms look like? How do I get around town? I hear it’s a small town, is there at least a Walmart?”

But without any answer to my curiosity, all of these questions were left with one reply:

“I’ll let you see for yourself.”

And then just as Amanda proposed, I did exactly that.

My name is Cheyenne and I am from Savannah State University in Georgia interning with LMRCSC (Living Marine Resources Cooperative Science Center) in Newport, Oregon. My expectations of the Oregon coast and the reality was vastly different than what I had pictured. I imagined the entire West Coast would match a California summer; Sunny and hot.

But on the contrary, upon arrival to Newport, I learned, it doesn’t. It is windy and chilly and hardly ever above 70 degrees. Thinking an Oregon summer would match a California summer, in my suitcase I possessed only three small sweaters and an abundant supply of shorts and tank tops. Needless, to say I was quickly off to buy an Oregon Coast sweatshirt that would double as warmth and a souvenir. Upon first entering Newport, I was mostly shocked at how small the town felt, and I noticed every structure was made of wood, and coming from Georgia this was strange to me. In Georgia, everything is made of bricks and cement. The dorms on first glance reminded me of summer camp for adults: slightly dated with bunk bed sleeping arrangements. Yikes!

However, my worries that come along with moving to a new place, were quickly diminished when I was welcomed to the GEMM lab; Florence greeted with a warm cup of tea, I was introduced to everyone who worked at HMSC, and even given my very own desk in the GEMM lab. After a day of transitions, and a much needed good night’s rest, I was introduced to my project on California Sea Lions (Zalophus californianus).

If you’ve been following along with all of the latest posts from GEMM lab students, you might think the lives of spatial ecologists revolve around glamorous fieldwork. We’ve got Amanda eavesdropping on porpoises, Florence surveying for foraging gray whales, and Leigh playing hide and seek with seabirds down in Yachats. I, however, am admittedly not spending my summer in the field this year and am learning that there is more to being a scientist than picturesque moments with charismatic study species in beautiful locations.

Prior to entering the GEMM lab, I had limited experience in computing and data analysis and spent my prior summer’s doing fieldwork on invertebrates, usually bagging sediment and collecting water samples. This internship was a new and unique opportunity for me to learn the next step of the scientific process. While I had always wondered, “What happens after data collection?” I was not given the experience to find out. I quickly learned, that this includes a lot of sorting, categorizing, and modeling, all of which are very time consuming.

By using satellite tracking information of California sea lions collected by the Oregon Department of Fish and Wildlife (ODFW) from 2005 and 2007, I am able to measure movements and habitat use of California sea lions. By analyzing their routes between their initial and final locations, we can study their distributions patterns.

To some people, sitting at a computer doing analysis may not seem as glamorous as working in the field. Some people might question why someone would chose to spend their career in front of a computer screen. But my internship this summer, really showed me the value of having experience working at all stages of the scientific process. Seeing all of my efforts in processing, sorting, and categorizing come together to create an end result really enhanced my love for science. By connecting the questions to the answers, and making contributions to the scientific community, I feel rewarded for my hard work.

My internship has come to an end, and given my initial hesitations, I’ve grown accustomed to Newport and the GEMM lab. I enjoy sitting at my desk running through a wild assortment of data and hearing the wonderful ding of the teapot. In the last days of my internship, I was able to escape my computer screen to assist Florence in data collection on beautiful gray whale surveys. Last Thursday, a lab meeting was held and my lab mates and I were able to update each other on our research. We shared ideas on how to enhance everyone’s project, and who might be able to answer questions we were struggling with in our own data sets. As my internship comes to a close, I have gained more knowledge and real life skill then I would ever hope to gain just through courses at Savannah State. I learned new software programs like R Statistical Package and sharpened my own skills in ArcGIS. I gained the experience of collaborating with a lab, and understanding how powerful working with your peers and colleagues can be. Gaining this much experience has, without a doubt, given me an edge in the competitive field I will enter after graduation. I have made connections, hopefully life long, with the nicest people; I know that in the future, which ever path I may choose, I’ll always be a part of the GEMM lab.

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