Visiting Researcher Archives - Page 2 of 2 - Geospatial Ecology of Marine Megafauna Laboratory

Feed from the scientific network: the digital library of a millennial student

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

If you are a follower of our blog, you may have noticed that bioinformatics and statistics hold a very important role in the everyday life of the GEMM Lab. As good-old field observations remain essential to the study of animal behaviour and ecosystems, the ecology field has greatly benefited from advances in information technologies. In fact, data analysis is now a discipline in itself, as innovative solutions must continuously be developed to cope with the challenges of ever increasing dataset size and complexity.

Artist’s impression of a complex network. ©iStock.com/Vertigo3d

So how does a poor biology student find her/his way in this digital and mathematical world? Most ecology departments will provide classes to learn the basics of statistical modelling and data analysis, but there is only so much you can learn through formal education. In practice, we ultimately always run into a problem, an exception that we have never heard of, and we have to figure it out on our own. As my initial training was in fundamental biology, self-teaching of other disciplines (statistics and bioinformatics) has taken a lot of my time as a Master’s student and now as a PhD student. This has made me feel lonely and a bit lost at times when I run into challenges that always seemed too big for me. But in the end, there is nothing more rewarding then solving problems by yourself after long hours of mind-scrambling.

Oh, sorry, did I say by myself? Nothing could be more wrong and more true at the same time! Because the place where I find all the answers to my questions, is in fact born from the contribution of thousands of scientists, which, despite not actually knowing each other, all work together to develop innovative solutions to modern world scientific challenges. The internet scientific network has been my best colleague over these past years and here I would like to share my enthusiasm for some of its best features that have helped me in my research.

If you look at my Firefox toolbar you will find two types of websites: let’s call them the “practical” and the “reflectional”.

The practical websites:

These are the websites I consult if I have a specific and practical question. Many forums exist where people exchange their experiences solving a great variety of problems. But sometimes conversations get lost in never-ending exchanges of opinions, some of which are not always scientifically well-founded. On the contrary, the StackExchange platform launched in 2009 has a strict policy on how questions should be asked (as precise and focused as possible) and should be answered (in an objective, opinion-free way). This makes it a very powerful tool to find quick and practical solutions to your everyday problems. This platform includes 136 different websites, each dedicated to a different topic. In my field, I mostly use: CrossValidated for statistical issues (e.g., Why does including latitude and longitude in a GAM account for spatial autocorrelation?) and StackOverflow for programming (e.g., plotting pie graphs on map in ggplot).

The latter will usually provide you with codes in the programming language of your choice (R, python, java, sql, etc.). Interestingly, even with more queries regarding Python to StackOverflow in 2015, R was the fastest-growing language between 2013 and 2015 on this same platform. If you haven’t decided on the language you want to “speak” yet, check out this fun infographic. But always remember that these tools keep evolving…

Academia can also be useful for questions regarding publications. For instance: How to reference multiple authors of a chapter from a book [APA]? Why might a journal editor reject a submission, but suggest submission to a sister journal? Or, h ow to best kill a manuscript as a peer reviewer?

And finally, if you’ve always wondered, “W hy don’t we remove door handles and let doors open both ways (inwards, outwards)?”, you’ll be pleased to know that other out-of-the-box-thinking people are sharing their opinion on the web…

Coming back to serious matters, it is important to recognize that you need the right key-word to access this gold-mine of website knowledge and sharing. The accuracy of your search answer will only be proportional to the quality of your question. In R for instance, if you keep googling “table” instead of “dataframe”, “list” instead of “vector”, or “size” instead of “dimensions”, you will likely get quickly drowned in the google-limbo. One way to be more efficient at your search strategy is to make sure you know your basics. Most of the programming languages used in ecology (e.g., R, Python, Matlab) share a similar vocabulary and structure, but before you start to run all sorts of crazy statistical analysis it is important to know what types of objects you are working with and how you want to format them. In R, I have found Hadley Wickham’s book, Advanced R, particularly useful to understand what happens back-stage.

Another good reference in the spatial ecology field is ZevRoss “Technical Tidbits From Spatial Analysis & Data Science”. This website is a particularly up-to-date blog for data processing and visualization in R.

More generally, I regularly check R-bloggers or simply the Comprehensive R Archive Network. A note on the latter: I know it doesn’t look pretty and the reference manuals for R packages are rather intimidating but it is still the number one reference to check when encountering a problem with a given function. Some authors make a special effort to write more user-friendly tutorials to their packages. Check for those by looking at the CRAN page of a given package, in the “downloads” section, “vignettes” subsection (e.g., for the adehabitatLT package vignette).

The reflectional websites:

The web is also an amazing media to reflect on our scientific practices, learn about current ecological theories, and acquire general knowledge across disciplines. In the scientific network, many blogs and forums exist where scientists can converse and debate ideas without the pressure of publication requirements. As a student trying to find my way in the great world of statistical modelling, I find these discussions and blogposts most useful to put my methodological choices in perspective and progressively build myself an opinion (still rather vague I’ll admit). Some of my most recent findings are: Dynamic Ecology Multa novit vulpes and From the bottom of the heap, the musings of a geographer. I am sure each of you has your own “rock star of the web”, so please share your favorite sites with us in the comments below.

Science not longer needs to wait for publication to be shared between peers and with the general public. The web offers us a new space to communicate, not only on that small part of our work that led to positive results, but also our negative results, frustrations and failures, which can at times be as informative and useful to the scientific community than our successes. So, wherever you stand, tell us about your ideas, and tell us about the challenges you have encountered, where you failed and where you succeeded. Because, this is what ecology is all about. Sharing knowledge across borders and cultures to understand the planet we live on and together take better care of it.

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.

Looking back on a busy field season

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

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

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

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

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

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

A calf breaching out of the water on a late afternoon. No wonder humpback whales are favored by whale-watching companies, they can be very active at the surface!

These two adult whales were part of a very active competitive group of eight individuals and displayed a peculiar behavior that included gently rolling and rubbing themselves against each other.

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

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

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

Literature cited:

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

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.

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