GEMM Lab – Page 5 – Geospatial Ecology of Marine Megafauna Laboratory

The pathway to advancing knowledge of rorqual whale distribution off Oregon

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

In September 2020, I was hired as a postdoc in the GEMM Lab and was tasked to conduct the analyses necessary for the OPAL project. This research project has the ambitious, yet essential, goal to fill a knowledge gap hindering whale conservation efforts locally: where and when do whales occur off the Oregon coast? Understanding and predicting whale distribution based on changing environmental conditions is a key strategy to assess and reduce spatial conflicts with human activities, specifically the risk of entanglement in fixed fishing gear.

Starting a new project is always a little daunting. Learning about a new region and new species, in an alien research and conservation context, is a challenge. As I have specialized in data science over the last couple of years, I have been confronted many times with the prospect of working with massive datasets collected by others, from which I was asked to tease apart the biases and the ecological patterns. In fact, I have come to love that part of my job: diving down the data rabbit hole and making my way through it by collaborating with others. Craig Hayslip, faculty research assistant in MMI, was the observer who conducted the majority of the 102 helicopter surveys that were used for this study. During the analysis stage, his help was crucial to understand the data that had been collected and get a better grasp of the field work biases that I would later have to account for in my models. Similarly, it took hours of zoom discussions with Dawn Barlow, the GEMM lab’s latest Dr, to be able to clean and process the 75 days of survey effort conducted at sea, aboard the R/V Shimada and Oceanus.

Once the data is “clean”, then comes the time for modeling. Running hundreds of models, with different statistical approaches, different environmental predictors, different parameters etc. etc. That is when you realize what a blessing it is to work with a supervisor like Leigh Torres, head of the GEMM Lab. As an early career researcher, I really appreciate working with people who help me take a step back and see the bigger picture within which the whole data wrangling work is included. It is so important to have someone help you stay focused on your goals and the ecological questions you are trying to answer, as these may easily get pushed back to the background during the data analysis process.

And here we are today, with the first scientific publication from the OPAL project published, a little more than three years after Leigh and Craig started collecting data onboard the United States Coast Guard helicopters off the coast of Oregon in February 2019. Entitled “Seasonal, annual, and decadal distribution of three rorqual whale species relative to dynamic ocean conditions off Oregon, USA”, our study published in Frontiers in Marine Science presents modern and fine-scale predictions of rorqual whale distribution off Oregon, as well as a description of their phenology and a comparison to whale numbers observed across three decades in the region (Figure 1). This research focuses on three rorqual species sharing some ecological and biological traits, as well as similar conservation status: humpback whales (Megaptera novaeangliae), blue whales (Balaenoptera musculus musculus), and fin whales (Balaenoptera physallus); all of which migrate and feed over the US West coast (see a previous blog to learn more about these species here).

*Figure 1: Graphical abstract of our latest paper published in Frontiers in Marine Science*.

We demonstrate (1) an increase in rorqual numbers over the last three decades in Oregon waters, (2) differences in timing of migration and habitat preferences between humpback, blue, and fin whales, and (3) predictable relationships of rorqual whale distribution based on dynamic ocean conditions indicative of upwellings and frontal zones. Indeed, these ocean conditions are likely to provide suitable biological conditions triggering increased prey abundance. Three seasonal models covering the months of December-March (winter model), April-July (spring) and August-November (summer-fall) were generated to predict rorqual whale densities over the Oregon continental shelf (in waters up to 1,500 m deep). As a result, maps of whale densities can be produced on a weekly basis at a resolution of 5 km, which is a scale that will facilitate targeted management of human activities in Oregon. In addition, species-specific models were also produced over the period of high occurrence in the region; that is humpback and blue whales between April and November, and fin whales between August and March.

As we outline in our concluding remarks, this work is not to be considered an end-point, but rather a stepping stone to improve ecological knowledge and produce operational outputs that can be used effectively by managers and stakeholders to prevent spatial conflict between whales and human activities. As of today, the models of fin and blue whale densities are limited by the small number of observations of these two species over the Oregon continental shelf. Yet, we hope that continued data collection via fruitful research partnerships will allow us to improve the robustness of these species-specific predictions in the future. On the other hand, the rorqual models are considered sufficiently robust to continue into the next phase of the OPAL project that aims to assess overlap between whale distribution and Dungeness crab fishing gear to estimate entanglement risk.

The curse (or perhaps the beauty?) of species distribution modeling is that it never ends. There are always new data to be added, new statistical approaches to be tested, and new predictions to be made. The OPAL models are no exception to this rule. They are meant to be improved in future years, thanks to continued helicopter and ship-based survey efforts, and to the addition of new environmental variables meant to better predict whale habitat selection. For instance, Rachel Kaplan’s PhD research specifically aims at understanding the distribution of whales in relation to krill. Her results will feed into the more general efforts to model and predict whale distribution to inform management in Oregon.

This first publication therefore paves the way for more exciting and impactful research!

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Reference

Derville, S., Barlow, D. R., Hayslip, C. E., and Torres, L. G. (2022). Seasonal, Annual, and Decadal Distribution of Three Rorqual Whale Species Relative to Dynamic Ocean Conditions Off Oregon, USA. Front. Mar. Sci. 9, 1–19. doi:10.3389/fmars.2022.868566.

Acknowledgments

We gratefully acknowledge the immense contribution of the United State Coast Guard sectors North Bend and Columbia River who facilitated and piloted our helicopter surveys. We would like to also thank NOAA Northwest Fisheries Science Center for the ship time aboard the R/V Bell M. Shimada. We thank the R/V Bell M. Shimada (chief scientists J. Fisher and S. Zeman) and R/V Oceanus crews, as well as the marine mammal observers F. Sullivan, C. Bird and R. Kaplan. We give special recognition and thanks to the late Alexa Kownacki who contributed so much in the field and to our lives. We also thank T. Buell and K. Corbett (ODFW) for their partnership over the OPAL project. We thank G. Green and J. Brueggeman (Minerals Management Service), J. Adams (US Geological Survey), J. Jahncke (Point blue Conservation), S. Benson (NOAA-South West Fisheries Science Center), and L. Ballance (Oregon State University) for sharing validation data. We thank J. Calambokidis (Cascadia Research Collective) for sharing validation data and for logistical support of the project. We thank A. Virgili for sharing advice and custom codes to produce detection functions.

New publication by GEMM Lab reveals sub-population health differences in gray whales

Dr. KC Bierlich, Postdoctoral Scholar, OSU Department of Fisheries, Wildlife, & Conservation Sciences, Geospatial Ecology of Marine Megafauna (GEMM) Lab

In a previous blog, I discussed the importance of incorporating measurement uncertainty in drone-based photogrammetry, as drones with different sensors, focal length lenses, and altimeters will have varying levels of measurement accuracy. In my last blog, I discussed how to incorporate photogrammetric uncertainty when combining multiple measurements to estimate body condition of baleen whales. In this blog, I will highlight our recent publication in Frontiers in Marine Science (https://doi.org/10.3389/fmars.2022.867258) led by GEMM Lab’s Dr. Leigh Torres, Clara Bird, and myself that used these methods in a collaborative study using imagery from four different drones to compare gray whale body condition on their breeding and feeding grounds (Torres et al., 2022).

Most Eastern North Pacific (ENP) gray whales migrate to their summer foraging grounds in Alaska and the Arctic, where they target benthic amphipods as prey. A subgroup of gray whales (~230 individuals) called the Pacific Coast Feeding Group (PCFG), instead truncates their migration and forages along the coastal habitats between Northern California and British Columbia, Canada (Fig. 1). Evidence from a recent study lead by GEMM Lab’s Lisa Hildebrand (see this blog) found that the caloric content of prey in the PCFG range is of equal or higher value than the main amphipod prey in the Arctic/sub-Arctic regions (Hildebrand et al., 2021). This implies that greater prey density and/or lower energetic costs of foraging in the Arctic/sub-Arctic may explain the greater number of whales foraging in that region compared to the PCFG range. Both groups of gray whales spend the winter months on their breeding and calving grounds in Baja California, Mexico.

Figure 1. The GEMM Lab field team following a Pacific Coast Feeding Group (PCFG) gray whale swimming in a kelp bed along the Oregon Coast during the summer foraging season.

In January 2019 an Unusual Mortality Event (UME) was declared for gray whales due to the elevated numbers of stranded gray whales between Mexico and the Arctic regions of Alaska. Most of the stranded whales were emaciated, indicating that reduced nutrition and starvation may have been the causal factor of death. It is estimated that the population dropped from ~27,000 individuals in 2016 to ~21,000 in 2020 (Stewart & Weller, 2021).

During this UME period, between 2017-2019, the GEMM Lab was using drones to monitor the body condition of PCFG gray whales on their Oregon coastal feeding grounds (Fig. 1), while Christiansen and colleagues (2020) was using drones to monitor gray whales on their breeding grounds in San Ignacio Lagoon (SIL) in Baja California, Mexico. We teamed up with Christiansen and colleagues to compare the body condition of gray whales in these two different areas leading up to the UME. Comparing the body condition between these two populations could help inform which population was most effected by the UME.

The combined datasets consisted of four different drones used, thus different levels of photogrammetric uncertainty to consider. The GEMM Lab collected data using a DJI Phantom 3 Pro, DJI Phantom 4, and DJI Phantom 4 Pro, while Christiansen et al., (2020) used a DJI Inspire 1 Pro. By using the methodological approach described in my previous blog (here, also see Bierlich et al., 2021a for more details), we quantified photogrammetric uncertainty specific to each drone, allowing cross-comparison between these datasets. We also used Body Area Index (BAI), which is a standardized relative measure of body condition developed by the GEMM Lab (Burnett et al., 2018) that has low uncertainty with high precision, making it easier to detect smaller changes between individuals (see blog here, Bierlich et al., 2021b).

While both PCFG and ENP gray whales visit San Ignacio Lagoon in the winter, we assume that the photogrammetry data collected in the lagoon is mostly of ENP whales based on their considerably higher population abundance. We also assume that gray whales incur low energetic cost during migration, as gray whale oxygen consumption rates and derived metabolic rates are much lower during migration than on foraging grounds (Sumich, 1983).

Interestingly, we found that gray whale body condition on their wintering grounds in San Ignacio Lagoon deteriorated across the study years leading up to the UME (2017-2019), while the body condition of PCFG whales on their foraging grounds in Oregon concurrently increased. These contrasting trajectories in body condition between ENP and PCFG whales implies that dynamic oceanographic processes may be contributing to temporal variability of prey available in the Arctic/sub-Arctic and PCFG range. In other words, environmental conditions that control prey availability for gray whales are different in the two areas. For the ENP population, this declining nutritive gain may be associated with environmental changes in the Arctic/sub-Arctic region that impacted the predictability and availability of prey. For the PCFG population, the increase in body condition across years may reflect recovery of the NE Pacific Ocean from the marine heatwave event in 2014-2016 (referred to as “The Blob”) that resulted with a period of low prey availability. These findings also indicate that the ENP population was primarily impacted in the die-off from the UME.

Surprisingly, the body condition of PCFG gray whales in Oregon was regularly and significantly lower than whales in San Ignacio Lagoon (Fig. 2). To further investigate this potential intrinsic difference in body condition between PCFG and ENP whales, we compared opportunistic photographs of gray whales feeding in the Northeastern Chukchi Sea (NCS) in the Arctic collected from airplane surveys. We found that the body condition of PCFG gray whales was significantly lower than whales in the NCS, further supporting our finding that PCFG whales overall have lower body condition than ENP whales that feed in the Arctic (Fig. 3).

Figure 2. Boxplots showing the distribution of Body Area Index (BAI) values for gray whales imaged by drones in San Ignacio Lagoon (SIL), Mexico and Oregon, USA. The data is grouped by phenology group: End of summer feeding season (departure Oregon vs. arrival SIL) and End of wintering season (arrival Oregon vs. departure SIL). The group median (horizontal line), interquartile range (IQR, box), maximum and minimum 1.5*IQR (vertical lines), and outliers (dots) are depicted in the boxplots. The overlaid points represent the mean of the posterior predictive distribution for BAI of an individual and the bars represents the uncertainty (upper and lower bounds of the 95% HPD interval). Note how PCFG whales at then end of the feeding season (dark green) typically have lower body condition (as BAI) compared to ENP whales at the end of the feeding season when they arrive to SIL after migration (light brown).

Figure 3. Boxplots showing the distribution of Body Area Index (BAI) values of gray whales from opportunistic images collected from a plane in Northeaster Chukchi Sea (NCS) and from drones collected by the GEMM Lab in Oregon. The boxplots display the group median (horizontal line), interquartile range (IQR box), maximum and minimum 1.5*IQR (vertical lines), and outlies (dots). The overlaid points are the BAI values from each image. **Note the significantly lower BAI of PCFG whales on Oregon feeding grounds compared to whales feeding in the Arctic region of the NCS.**

This difference in body condition between PCFG and ENP gray whales raises some really interesting and prudent questions. Does the lower body condition of PCFG whales make them less resilient to changes in prey availability compared to ENP whales, and thus more vulnerable to climate change? If so, could this influence the reproductive capacity of PCFG whales? Or, are whales that recruit into the PCFG adapted to a smaller morphology, perhaps due to their specialized foraging tactics, which may be genetically inherited and enables them to survive with reduced energy stores?

These questions are on our minds here at the GEMM Lab as we prepare for our seventh consecutive field season using drones to collect data on PCFG gray whale body condition. As discussed in a previous blog by Dr. Alejandro Fernandez Ajo, we are combining our sightings history of individual whales, fecal hormone analyses, and photogrammetry-based body condition to better understand gray whales’ reproductive biology and help determine what the consequences are for these PCFG whales with lower body condition.

References

Bierlich, K. C., Hewitt, J., Bird, C. N., Schick, R. S., Friedlaender, A., Torres, L. G., … & Johnston, D. W. (2021). Comparing Uncertainty Associated With 1-, 2-, and 3D Aerial Photogrammetry-Based Body Condition Measurements of Baleen Whales. Frontiers in Marine Science, 1729.

Bierlich, K. C., Schick, R. S., Hewitt, J., Dale, J., Goldbogen, J. A., Friedlaender, A.S., et al. (2021b). Bayesian Approach for Predicting Photogrammetric Uncertainty in Morphometric Measurements Derived From Drones. Mar. Ecol. Prog. Ser. 673, 193–210. doi: 10.3354/meps13814

Burnett, J. D., Lemos, L., Barlow, D., Wing, M. G., Chandler, T., & Torres, L. G. (2018). Estimating morphometric attributes of baleen whales with photogrammetry from small UASs: A case study with blue and gray whales. Marine Mammal Science, 35(1), 108–139.

Christiansen, F., Rodrı́guez-González, F., Martı́nez-Aguilar, S., Urbán, J., Swartz, S., Warick, H., et al. (2021). Poor Body Condition Associated With an Unusual Mortality Event in Gray Whales. Mar. Ecol. Prog. Ser. 658, 237–252. doi:10.3354/meps13585

Hildebrand, L., Bernard, K. S., and Torres, L. G. (2021). Do Gray Whales Count Calories? Comparing Energetic Values of Gray Whale Prey Across Two Different Feeding Grounds in the Eastern North Pacific. Front. Mar. Sci. 8. doi: 10.3389/fmars.2021.683634

Stewart, J. D., and Weller, D. (2021). Abundance of Eastern North Pacific Gray Whales 2019/2020 (San Diego, CA: NOAA/NMFS)

Sumich, J. L. (1983). Swimming Velocities, Breathing Patterns, and Estimated Costs of Locomotion in Migrating Gray Whales, Eschrichtius Robustus. Can. J. Zoology. 61, 647–652. doi: 10.1139/z83-086

Torres, L.G., Bird, C., Rodrigues-Gonzáles, F., Christiansen F., Bejder, L., Lemos, L., Urbán Ramírez, J., Swartz, S., Willoughby, A., Hewitt., J., Bierlich, K.C. (2022). Range-wide comparison of gray whale body condition reveals contrasting sub-population health characteristics and vulnerability to environmental change. Frontiers in Marine Science. 9:867258. https://doi.org/10.3389/fmars.2022.867258

Dive into Oregon’s underwater forests

By Lisa Hildebrand, PhD student, OSU Department of Fisheries, Wildlife, & Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

When I was younger, I aspired to be a marine mammal biologist. I thought it was purely about knowing as much about marine mammal species as possible. However, over time and with experience in this field, I have realized that in order to understand a species, you need to have a holistic understanding of its prey, habitat, and environment. When I first applied to be advised by Leigh in the GEMM Lab, I had no idea how much of my time I would spend looking at tiny zooplankton under a microscope, thinking about the different benefits of different habitat types, or reading about oceanographic processes. But these things have been incredibly vital to my research to date and as a result, I now refer to myself as a marine ecologist. This holistic understanding that I am gaining will only grow throughout my PhD as I am broadly looking at the habitat use, site fidelity, and population dynamics of the Pacific Coast Feeding Group (PCFG) of gray whales for my thesis research.

The PCFG display many foraging tactics and occupy several habitat types along the Oregon coast while they spend their summer feeding seasons here (Torres et al. 2018). Here, I will focus on one of these habitats: kelp. When you hear the word kelp, you probably conjure an image of long, thick stalks that reach from the ocean floor to the surface, with billowing fronds waving around (Figure 1a). However, this type is only one of three basic morphologies (Filbee-Dexter & Scheibling 2014) and it is called canopy kelp, which often forms extensive forests. The other two morphologies are stipitate and prostrate kelps. The former forms midwater stands (Figure 1b) while the latter forms low-lying kelp beds (Figure 1c). All three of these morphologies exist on the Oregon coast and create a mosaic of understory and canopy kelp patches that dot our coastline.

Figure 1. Examples of the three different kelp morphologies. a: bull kelp (*Nereocystis luetkeana*) is a type of canopy kelp and the dominant kelp on the Oregon coast (Source: Oregon Coast Aquarium); b: sea palm (*Postelsia palmaeformis*) is a type of stipitate kelp that forms mid-water stands (Source: Oregon Conservation Strategy); c: sea cabbage (*Saccharina sessilis*) is a type of prostrate kelp that is stipeless and forms low-lying kelp beds (Source: Central Coast Biodiversity).

One of the most magnificent things about kelp is that it is not just a species itself, but it provides critical habitat, refuge, and food resources to a myriad of other species due to its high rates of primary production (Dayton 1985). Kelp is often referred to as a foundation species due to all of these critical services it provides. In Oregon, many species of rockfish, which are important commercial and recreational fisheries, use kelp as habitat throughout their life cycle, including as nursery grounds. Lingcod, another widely fished species, forages amongst kelp. A large number of macroinvertebrates can be found in Oregon kelp forests, including anemones, limpets, snails, sea urchins, sea stars, and abalone, to name a fraction of them.

Kelps grow best in cold, nutrient-rich waters (Tegner et al. 1996) and their growth and distribution patterns are highly naturally variable on both temporal and spatial scales (Krumhansl et al. 2016). However, warm water, low nutrient or light conditions, intensive grazing by herbivores, and severe storm activity can lead to the erosion and defoliation of kelp beds (Krumhansl et al. 2016). While these events can occur naturally in cyclical patterns, the frequency of several of these events has increased in recent years, as a result of climate change and anthropogenic impacts. For example, Dawn’s blog discussed increasing marine heatwaves that represent an influx of warm water for a prolonged period of time. In fact, kelps can be useful sentinels of change as they tend to be highly responsive to changes in environmental conditions (e.g., Rogers-Bennet & Catton 2019) and their nearshore, coastal location directly exposes them to human activities, such as pollution, harvesting, and fishing (Bennett et al. 2016).

Due to its foundational role, changes or impacts to kelp can reverberate throughout the ecosystem and negatively affect many other species. As mentioned previously, kelp is naturally highly variable, and like many other ecological processes, undergoes boom and bust cycles. For over four decades, dense, productive kelp forests have been shown to transition to sea urchin barrens, and back again, in natural cycles (Sala et al. 1998; Pinnegar et al. 2000; Steneck et al. 2002; Figure 2). These transitions are called phase shifts. In a healthy, balanced kelp forest, sea urchins typically passively feed on detrital plant matter, such as broken off pieces of kelp fronds that fall to the seafloor. A phase shift occurs when the grazing intensity of sea urchins increases, resulting in them actively feeding on kelp stalks and fronds to a point where the kelp in an area can become greatly reduced, creating an urchin barren. Sea urchin grazing intensity can change for a number of reasons, including reduction in sea urchin predators (e.g., sea otters, sunflower sea stars) or poor kelp recruitment events (e.g., due to warm water temperature). Regardless of the reason, the phases tend to transition back and forth over time. However, there is concern that sea urchin barrens may become an alternative stable state of the subtidal ecosystem from which kelp in an area cannot recover (Filbee-Dexter & Scheibling 2014).

Figure 2. Screenshots from GoPro videos from 2016 (left) and 2018 (right) at the same kayak sampling station in Port Orford showing the difference between a dense kelp forest and what appears to be an urchin barren. (Source: GEMM Lab).

For example, in 2014, bull kelp canopy cover in northern California was reduced by >90% and has not shown signs of recovery since (Rogers-Bennet & Catton 2019; Figure 3). This massive decline was attributed to two major events: 1) the onset of sea star wasting disease (SSWD) in 2013 and 2) the “warm blob” of 2014-2016. SSWD affected over 20 sea star species along the coast from Mexico to Alaska, with the predatory sunflower sea star, which consumes purple sea urchins, most affected, including population declines of 80-100% along the coast (Harvell et al. 2019). Following this SSWD outbreak, the “warm blob”, which was an extreme marine heatwave in the Pacific Ocean, caused ocean temperatures to spike. These two events allowed purple sea urchin populations to grow unchecked by their predators, and created nutrient-poor and warm water conditions, which limited kelp growth and productivity. Intense grazing on bull kelp by growing urchin populations resulted in the >90% reduction in bull kelp canopy cover and has left behind widespread urchin barrens instead (Rogers-Bennet & Catton 2019). Consequently, there have been ecological and economic impacts on the ecosystem and communities in northern California. Without bull kelp, red abalone and red sea urchin populations starved, leading to a subsequent loss of the recreational red abalone (estimated value of $44 million/year) and commercial red urchin fisheries in northern California (Rogers-Bennet & Catton 2019).

Figure 3. Surface kelp canopy area pre- and post-impact from sites in Sonoma and Mendocino counties, northern California from aerial surveys (2008, 2014-2016). Figure and figure caption taken from Rogers-Bennett & Catton (2019).

As I mentioned earlier, while phase shifts between kelp forests and urchin barrens are common cycles, the intensity of the events described above in northern California are an example of sea urchin barrens potentially becoming a stable state of the subtidal ecosystem (Filbee-Dexter & Scheibling 2014). Given that marine heatwaves are only expected to increase in intensity and frequency in the future (Frölicher et al. 2018), the events documented in northern California may not be an isolated incidence.

Considering that parts of the Oregon coast, particularly the southern portion, are very similar to northern California biogeographically, and that it was not exempt from the “warm blob”, similar changes in kelp forests may be occurring along our coast. There are many individuals and groups that are actively working on this issue to examine potential impacts to kelp and the species that depend on the services it provides. For more information, check out the Oregon Kelp Alliance.

Figure 4. A gray whale surfaces in a large kelp bed during a foraging bout along the Oregon coast. (Source: GEMM Lab).

So, what does all of this information have to do with gray whales? Given their affinity for kelp habitats (Figure 4) and their zooplankton prey that aggregates there, changes to kelp ecosystems may affect gray whale health and ecology. This aspect of the complex kelp trophic web has not been examined to date; thus one of my PhD chapters focuses on the response of gray whales to changing kelp ecosystems along the southern Oregon coast. To do this, I am examining 6 years of data collected during the TOPAZ/JASPER project in Port Orford, to look at the relationships between kelp health, sea urchin density, zooplankton abundance, and gray whale foraging effort over space and time. Documenting impacts of changing kelp forests on gray whales is important to assist management efforts as healthy and abundant kelp seems critical in providing ample food opportunities for these iconic Pacific Northwest marine predators.

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References

Bennett S, et al. The ‘Great Southern Reef’: Social, ecological and economic value of Australia’s neglected kelp forests. Marine and Freshwater Research 67:47-56.

Dayton PK (1985) Ecology of kelp communities. Annual Review of Ecology and Systematics 16:215-245.

Filbee-Dexter K, Scheibling RE (2014) Sea uechin barrens as alternative stable states of collapsed kelp ecosystems. Marine Ecology Progress Series 495:1-25.

Frölicher TL, Fischer EM, Gruber N (2018) Marine heatwaves under global warming. Nature 560:360-364.

Harvell CD, et al. (2019) Disease epidemic and a marine heat wave are associated with the continental-scale collapse of a pivotal predator (Pycnopodia helianthoides). Science Advances 5(1) doi:10.1126/sciadv.aau7042.

Krumhansl KA, et al. (2016) Global patterns of kelp forest change over the past half-century. Proceedings of the National Academy of Sciences of the United States of America 113(48):13785-13790.

Pinnegar JK, et al. (2000) Trophic cascades in benthic marine ecosystems: lessons for fisheries and protected-area management. Environmental Conservation 27:179-200.

Rogers-Bennett L, Catton CA (2019) Marine heat wave and multiple stressors tip bull kelp forest to sea urchin barrens. Scientific Reports 9:15050.

Sala E, Boudouresque CF, Harmelin-Vivien M (1998) Fishing, trophic cascades and the structure of algal assemblages; evaluation of an old but untested paradigm. Oikos 82:425-439.

Steneck RS, et al. (2002) Kelp forest ecosystems: biodiversity, stability, resilience and future. Environmental Conservation 29:436-459.

Tegner MJ, Dayton PK, Edwards PB, Riser KL (1996) Is there evidence for the long-term climatic change in southern California kelp forests? California Cooperative Oceanic Fisheries Investigations Report 37:111-126.

Torres LG, Nieukirk SL, Lemos L, Chandler TE (2018) Drone up! Quantifying whale behavior from a new perspective improves observational capacity. Frontiers in Marine Science doi:10.3389/fmars.2019.00319.

A pregnancy test for whales?! Why and how?

Dr. Alejandro A. Fernández Ajó, Postdoctoral Scholar, Marine Mammal Institute – OSU Department of Fisheries, Wildlife, & Conservation Sciences, Geospatial Ecology of Marine Megafauna (GEMM) Lab.

I often receive two reactions when asked what I am currently working on; one is “Wow! That is a very cool job, it must be amazing to work with such incredible animals!”, the other is “How do you do that and why is that important?”. So, today I decided to blog about some of the reasons why it is important to develop a pregnancy test for gray whales and how we are doing this.

In a previous blogpost, I described the many ways in which whales play critical roles in sustaining marine ecosystem. Briefly, whales can enhance marine productivity by vertically and horizontally mixing of ocean waters, promoting primary production, and mitigating climate change by sequestering carbon with their large biomass and long life-span (1-3). Even after they die, their carcasses can contribute to biodiversity creating new habitat on the seafloor (4). But, over several decades, the whaling industry drastically removed whales around the globe, with some species and populations depleted to near extinction (5). Consequently, these depleted whale populations now play a diminished role in ocean ecosystem processes and their recovery is currently challenged by an increasing number of modern anthropogenic impacts. Hence, working towards whale conservation is essential for keeping a healthy marine ecosystem.

Working and designing effective strategies for conservation biology often involves gaining knowledge regarding the reproductive parameters of individual animals in wild populations. This information is critical for understanding population trends and the underlaying mechanisms that affect animal welfare and their potential for recovery. However, getting such information from free-living whales can be challenging (see Hunt et al. 2013). While we know that whales typically have long life-spans, lengthy generation times, extended parental care, and high survival rates, detailed knowledge on the life history and general reproductive biology of free-ranging whales is limited for the majority of the whale populations. In fact, much of what we do know about whale reproduction is derived from whaling records. Only recently, conservation physiology approaches (see our previous post here) have contributed alternative and non-invasive methods for monitoring key physiological processes that can help monitor a whale’s reproductive biology and determine reproductive parameters such as sexual maturity and pregnancy (6-9).

In this clip you can see an example of a fecal sample collection from a gray whale off the Oregon coast. We can look at hormones in the fecal samples which are useful indicators for endocrine assessments of free-swimming whales. Fecal sample and footage filmed under NOAA/NMFS permit #16111.

Gray whales (Eschrichtius robustus) in the Eastern North Pacific (ENP) typically undertake annual migrations between their lower latitude breeding grounds in the coastal waters of the Baja California Peninsula, Mexico, and the foraging grounds located on the Bering and Chukchi Seas (10). However, among the ENP whales a distinct subgroup of about 230 whales shorten their migration to feed in the coastal waters of Northern California, Oregon, and southeastern Alaska (11). This group of whales is known as the gray whale Pacific Coast Feeding Group (PCFG).

Since 2016, the GEMM Lab has monitored individual gray whales within the PCFG off the Oregon coast (check the GRANITE project). Gray whales have a distinct mottled skin; and each individual whale presents a unique pigmentation pattern that allows for the individual identification of whales. We can identify who is who among the whales who visit the Oregon coast. In this way, we can keep a detailed record of re-sightings of known individuals (visit our new web site to know more about the lives of individual whales that visit the Oregon coast). We have high individual re-sighting rates, so this unique opportunity helps us keep a long-term data series for individual whales to monitor their health, body condition, and reproductive status over time, and thus further develop and advance our non-invasive study methods.

We are combining behavioral and feeding ecology with drone photogrammetry and endocrinology of the same individual whales to help us understand the relationships between natural and anthropogenic drivers with biological parameters. In this way, following individual whales, we are developing sensitive biomarkers to monitor and infer about the population health, population trends, and identify stressors that impact their recovery and welfare. In particular, we are now working to develop a noninvasive approach to detect pregnancy in gray whales based on fecal hormone analyses.

In this picture you can see “Rose”, a gray whale calf, on top of her mother “Scarlett”. Scarlett is one of the most recognizable whales from the PCFG, due to a large scar on the right side of her back (not visible in this picture). She has been observed along the Pacific NW coast since 1996, so she is at least 26 years old today. We know 3 of her calves. Following individual whales like Scarlett is helping us to better understand the gray whale reproductive biology. Photo by Alejandro Fernandez Ajo taken under NOAA/NMFS permit #21678.

In marine mammals, the progesterone hormone is secreted in the ovaries during the estrous cycle and gestation, and is the predominant hormone responsible for sustaining pregnancy (12). As the hormones are cleared from the blood into the gut, they are metabolized and eventually excreted in feces; fecal samples represent a cumulative and integrated concentration of hormone metabolites (13-14), which are useful indicators for endocrine assessments of free-swimming whales. Several studies show that changes in hormone concentration correlate in meaningful ways with exposure to stressors (15-16) and changes in reproductive status (17-19). We are using our long data series of fecal hormones and individual life histories to advance our understanding on the gray whales’ reproductive biology. We are close to developing a technique that will allow us to detect pregnancy in whales based in fecal hormones analyses and photogrammetry. Stay tuned for results from this pregnancy test!

References:

1- Pershing AJ, Christensen LB, Record NR, Sherwood GD, Stetson PB (2010) The impact of whaling on the ocean carbon cycle: Why bigger was better. PLoS ONE 5(8): e12444.

2- Roman J and McCarthy JJ. 2010. The whale pump: marine mammals enhance primary productivity in a coastal basin. PLoS ONE. 5(10): e13255.

3- Morissette L, Kaschner K, and Gerber LR. 2010. “Whales eat fish”? Demystifying the myth in the Caribbean marine ecosystem. Fish Fish 11: 388–404.

4- Smith CR, Roman J, Nation JB. A metapopulation model for whale-fall specialists: The largest whales are essential to prevent species extinctions. J. Mar. Res. 77, 283–302 (2019).

5- Branch TA, Williams TM. Legacy of industrial whaling. Whales. Whal. Ocean Ecosyst. 2006, 262–278 (2006).

6- Kellar NM, Keliher J, Trego ML, Catelani KN, Hanns C, George JC, et al. Variation of bowhead whale progesterone concentrations across demographic groups and sample matrices. Endanger Species Res 2013; 22:61–72. https://doi.org/10.3354/esr00537.

7- Pallin L, Robbins J, Kellar N, Berube M, Friedlaender A. Validation of a blubber-based endocrine pregnancy test for humpback whales. Conserv Physiol 2018;6:1 11. https://doi.org/10.1093/conphys/coy031PMID:29942518.

8-Hunt KE, Robbins J, Buck CL, Bérubé M, Rolland RM (2019) Evaluation of fecal hormones for noninvasive research on reproduction and stress in humpback whales (Megaptera novaeangliae). Gen Comp Endocrinol 280: 24–34.

9-Melica, V., Atkinson, S., Calambokidis, J., Lang, A., Scordino, J., & Mueter, F. (2021). Application of endocrine biomarkers to update information on reproductive physiology in gray whale (Eschrichtius robustus). Plos one, 16(8), e0255368.

10-Swartz SL. Gray Whale. In: Wursig B, Thewissen JGM, Kovacs KM, editors. Encyclopedia of Marine Mammals (Third Edition). Elsevier;2018,p. 422–8.https://doi.org/10.1016/B978-0-12-804327-1.00140–0.

11-Calambokidis J, Darling JD, Deecke V, Gearin P, Gosho M, Megill W, et al. Abundance, range and movements of a feeding aggregation of gray whales (Eschrichtius robustus) from California to south-eastern Alaska in 1998. J Cetacean Res Manag 2002;4:267–76.

12- Bronson, F. H. (1989). Mammalian reproductive biology. University of Chicago Press.

13-Wasser SK, Hunt KE, Brown JL, Cooper K, Crockett CM, Bechert U, Millspaugh JJ, Larson S, Monfort SL (2000) A generalized fecal glucocorticoid assay for use in a diverse array of nondomestic mammalian and avian species. Gen Comp Endocrinol120:260–275.

14- Hunt, K.E., Rolland, R.M., Kraus, S.D., Wasser, S.K., 2006. Analysis of fecal glucocorticoids in the North Atlantic right whale (Eubalaena glacialis). Gen. Comp. Endocrinol. 148, 260–272. https://doi.org/10.1016/j.ygcen.2006.03.01215.

15- Lemos, L.S., Olsen, A., Smith, A., Burnett, J.D., Chandler, T.E., Larson, S., Hunt, K.E., Torres, L.G., 2021. Stressed and slim or relaxed and chubby? A simultaneous assessment of gray whale body condition and hormone variability. Mar. Mammal Sci. 1–11. https://doi.org/10.1111/mms.12877

16- Rolland, R., McLellan, W., Moore, M., Harms, C., Burgess, E., Hunt, K., 2017. Fecal glucocorticoids and anthropogenic injury and mortality in North Atlantic right whales Eubalaena glacialis. Endanger. Species Res. 34, 417–429. https://doi.org/10.3354/esr00866.

17-Rolland, R.M., Hunt, K.E., Kraus, S.D., Wasser, S.K., 2005. Assessing reproductive status of right whales (Eubalaena glacialis) using fecal hormone metabolites. Gen. Comp. Endocrinol. 142, 308–317. https://doi.org/10.1016/j.ygcen.2005.02.002

18- Valenzuela Molina M, Atkinson S, Mashburn K, Gendron D, Brownell RL. Fecal steroid hormones reveal reproductive state in female blue whales sampled in the Gulf of California, Mexico. Gen Comp Endocrinol 2018;261:127–35.https://doi.org/10.1016/j.ygcen.2018.02.015 PMID:29476760.

19- Hunt, K. E., Robbins, J., Buck, C. L., Bérubé, M., & Rolland, R. M. (2019). Evaluation of fecal hormones for noninvasive research on reproduction and stress in humpback whales (Megaptera novaeangliae). General and Comparative Endocrinology, 280, 24-34.

What drives individual specialization?

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

When I wrote my first blog on individual specialization well over a year ago, I just skimmed the surface of the literature on this topic and only started to recognize the importance of studying individual specialization. The question, “is there individual specialization in the PCFG of gray whales?” is the focus of my first thesis chapter and the results will affect all my subsequent work. Therefore, the literature and concepts of individual specialization are a focus of my literature review and studies.

In my previous blog I focused on common characteristics of individuals that are similarly specialized as an underlying driver of individual specialization. While these characteristics (often attributable to age, sex, or physical traits) are important to consider, I’ve learned that the list of drivers of individual specialization is long and that many variables are dynamic. Of all the drivers I’ve learned about, competition is among the most common.

Competition is a major driver of individual specialization, and a common driver of competition is resource availability. When resource availability decreases, whether caused by increasing population density or changing environmental conditions, competition for that resource increases. As competition increases, individuals have a choice. They can choose to engage in competition, either by racing, fighting, or sharing [1], which can be costly, or they can diffuse the competition by focusing on a different resource. This second approach would be considered niche partitioning in the prey dimension. Niche partitioning is a way for individuals to share ecological space by using different resources. Essentially, individuals can share habitat without having to engage in direct competition by pursuing different prey types [2].

This switch to different prey types can change the degree of individual specialization present in the population (Figure 1). But the direction of the change is not constant. If all individuals were pursuing the same prey type under low competition conditions but then switched to different alternate prey types under high competition, then individual specialization would increase (Figure 1a). This direction has been observed across a range of species including sharks [3], otters [4]–[7], dolphins [8], [9], stickleback fish [10], [11], largemouth bass [12], banded mongoose [13], fur seals [14], and baleen whales [15].

However, if individuals were pursuing different prey types under low competition conditions (maybe because of underlying differences such as age or sex) but then switched to the same alternate prey types under high competition, diet overlap would increase, and individual specialization would decrease (Figure 1b). Furthermore, an individual might not switch to an entirely new prey type but instead add prey items to its diet [16]. This diet expansion under competition would also decrease individual specialization. Fewer studies have reported this direction but it’s been found in the common bumblebee [17] and in several neotropical vertebrate species [18], [19].

**Figure `1.** Figure 3 from Araújo et al. 2011 [20]. Illustration of how ecological mechanisms may affect the degree of individual specialization. Arrows linking resources to individual consumers indicate resource consumption (relative thickness indicates proportional contribution).
Horizontal arrows indicate the sign (positive or negative) of the effect on the degree of individual specialization. (a) Consumers share the same preferred resource (dark gray tangle) but have different alternative resources (white and light gray triangles). As the preferred resource becomes scarce, consumers switch to different alternatives, increasing the degree of individual specialization. (b) Alternatively, consumers have distinct preferred resources, so that as resources become scarce, individuals converge to the alternative resource (dark gray triangle), reducing diet variation.

Interestingly, its hypothesized that individual specialization driven by competition is one of the factors that facilitates the formation and existence of stable groups [21]. For example, a study on resident female dolphins in Sarasota Bay, FL, USA found that females with high spatial overlap used distinct foraging specializations [8](Figure 2). This study illustrates how partitioning prey enabled spatial and social coexistence. A study on banded mongooses reached a similar conclusion [13]. They found that specialization was highest in the biggest groups (with the most competition) and not explained by sex, age, or other inherent differences. They hypothesized that specialization increasing with competition reduced conflict and allowed the groups to remain stable. This study also highlighted the role of learning to determine an individual’s specialization.

**Figure 2.** A bottlenose dolphin.
*Source: https://sarasotadolphin.org*

Learning drives the distribution of knowledge throughout a population, which can lead to either specialization or generalization. ‘One-to-one’ learning, where one individual learns from one demonstrator, tends to promote individual specialization [21]. This form of transmission drives specialization because the individuals who learn the specialization tend to then carry on using, and eventually teaching, that specialization [6]. A common example of ‘one-to-one’ learning is vertical transmission from parent to offspring. It has been shown to transmit specializations in dolphins [22] and otters [6]. ‘One-to-one’ learning can occur outside of parent-offspring pairs; non-parent-offspring ‘one-to-one’ learning has been shown to drive specialization in banded mongooses [13](Figure 3).

However, other forms of social learning can promote more generalized foraging strategies. ‘Many-to-one’ or ‘one-to-many’ learning can reduce the presence of specialization in species [13], [21] as can the presence of conformity in a group [23], [24].

**Figure 3.** A group of banded mongooses.
Source: http://socialisresearch.org/about-the-banded-mongoose-project/

The multiple drivers of specialization and their dynamic quality means that it is important to contextualize specialization. For example, a study on four species of neotropical frogs found varying degrees of specialization across multiple populations of each species [18]. The degree of specialization was dependent on a variety of drivers including predation and both intra- and inter-specific competition. Notably, the direction of the relationship between degree of specialization and each driver was species specific. This study highlights that one species may not always be more specialized than another, but that a populations’ specialization is context dependent.

Therefore, it is important to not only be aware of the degree of specialization present in a population, but to also understand its dynamics and drivers. These relationships can then be used to understand how, and why, a population may react to competition from other species, predators, and changes in resource availability [20]. A population’s specialization can also affect the specialization of other populations and community dynamics [25], therefore, it’s important to consider and study individual specialization on both the population and community level. I am excited to start using our incredible six-year dataset to start investigating these questions for PCFG gray whales, so stay tuned for results!

References

[1] M. Taborsky, M. A. Cant, and J. Komdeur, The Evolution of Social Behaviour. Cambridge: Cambridge University Press, 2021. doi: 10.1017/9780511894794.

[2] E. R. Pianka, “Niche Overlap and Diffuse Competition,” vol. 71, no. 5, pp. 2141–2145, 1974.

[3] P. Matich et al., “Ecological niche partitioning within a large predator guild in a nutrient-limited estuary,” Limnol. Oceanogr., vol. 62, no. 3, pp. 934–953, 2017, doi: https://doi.org/10.1002/lno.10477.

[4] S. D. Newsome et al., “The interaction of intraspecific competition and habitat on individual diet specialization: a near range-wide examination of sea otters,” Oecologia, vol. 178, no. 1, pp. 45–59, May 2015, doi: 10.1007/s00442-015-3223-8.

[5] M. T. Tinker, G. Bentall, and J. A. Estes, “Food limitation leads to behavioral diversification and dietary specialization in sea otters,” Proc. Natl. Acad. Sci., vol. 105, no. 2, pp. 560–565, Jan. 2008, doi: 10.1073/pnas.0709263105.

[6] M. T. Tinker, M. Mangel, and J. A. Estes, “Learning to be different: acquired skills, social learning, frequency dependence, and environmental variation can cause behaviourally mediated foraging specializations,” Evol. Ecol. Res., vol. 11, pp. 841–869, 2009.

[7] M. T. Tinker et al., “Structure and mechanism of diet specialisation: testing models of individual variation in resource use with sea otters,” Ecol. Lett., vol. 15, no. 5, pp. 475–483, 2012, doi: 10.1111/j.1461-0248.2012.01760.x.

[8] S. Rossman et al., “Foraging habits in a generalist predator: Sex and age influence habitat selection and resource use among bottlenose dolphins (Tursiops truncatus),” Mar. Mammal Sci., vol. 31, no. 1, pp. 155–168, 2015, doi: https://doi.org/10.1111/mms.12143.

[9] L. G. Torres, “A kaleidoscope of mammal , bird and fish : habitat use patterns of top predators and their prey in Florida Bay,” vol. 375, pp. 289–304, 2009, doi: 10.3354/meps07743.

[10] M. S. Araújo et al., “Network Analysis Reveals Contrasting Effects of Intraspecific Competition on Individual Vs. Population Diets,” Ecology, vol. 89, no. 7, pp. 1981–1993, 2008, doi: 10.1890/07-0630.1.

[11] R. Svanbäck and D. I. Bolnick, “Intraspecific competition drives increased resource use diversity within a natural population,” Proc. R. Soc. B Biol. Sci., vol. 274, no. 1611, pp. 839–844, Mar. 2007, doi: 10.1098/rspb.2006.0198.

[12] D. E. Schindler, J. R. Hodgson, and J. F. Kitchell, “Density-dependent changes in individual foraging specialization of largemouth bass,” Oecologia, vol. 110, no. 4, pp. 592–600, May 1997, doi: 10.1007/s004420050200.

[13] C. E. Sheppard et al., “Intragroup competition predicts individual foraging specialisation in a group-living mammal,” Ecol. Lett., vol. 21, no. 5, pp. 665–673, 2018, doi: 10.1111/ele.12933.

[14] L. Kernaléguen, J. P. Y. Arnould, C. Guinet, and Y. Cherel, “Determinants of individual foraging specialization in large marine vertebrates, the Antarctic and subantarctic fur seals,” J. Anim. Ecol., vol. 84, no. 4, pp. 1081–1091, 2015, doi: 10.1111/1365-2656.12347.

[15] E. M. Keen and K. M. Qualls, “Respiratory behaviors in sympatric rorqual whales: the influence of prey depth and implications for temporal access to prey,” J. Mammal., vol. 99, no. 1, pp. 27–40, Feb. 2018, doi: 10.1093/jmammal/gyx170.

[16] R. H. MacArthur and E. R. Pianka, “On Optimal Use of a Patchy Environment,” Am. Nat., vol. 100, no. 916, pp. 603–609, 1966, doi: 10.1086/282454.

[17] C. Fontaine, C. L. Collin, and I. Dajoz, “Generalist foraging of pollinators: diet expansion at high density,” J. Ecol., vol. 96, no. 5, pp. 1002–1010, 2008, doi: 10.1111/j.1365-2745.2008.01405.x.

[18] R. Costa-Pereira, V. H. W. Rudolf, F. L. Souza, and M. S. Araújo, “Drivers of individual niche variation in coexisting species,” J. Anim. Ecol., vol. 87, no. 5, pp. 1452–1464, 2018, doi: 10.1111/1365-2656.12879.

[19] M. M. Pires, P. R. Guimarães Jr, M. S. Araújo, A. A. Giaretta, J. C. L. Costa, and S. F. dos Reis, “The nested assembly of individual-resource networks,” J. Anim. Ecol., vol. 80, no. 4, pp. 896–903, 2011, doi: 10.1111/j.1365-2656.2011.01818.x.

[20] M. S. Araújo, D. I. Bolnick, and C. A. Layman, “The ecological causes of individual specialisation,”Ecol. Lett., vol. 14, no. 9, pp. 948–958, 2011, doi: https://doi.org/10.1111/j.1461-0248.2011.01662.x.

[21] C. E. Sheppard, R. Heaphy, M. A. Cant, and H. H. Marshall, “Individual foraging specialization in group-living species,” Anim. Behav., vol. 182, pp. 285–294, Dec. 2021, doi: 10.1016/j.anbehav.2021.10.011.

[22] S. Wild, S. J. Allen, M. Krützen, S. L. King, L. Gerber, and W. J. E. Hoppitt, “Multi-network-based diffusion analysis reveals vertical cultural transmission of sponge tool use within dolphin matrilines,” Biol. Lett., vol. 15, no. 7, p. 20190227, Jul. 2019, doi: 10.1098/rsbl.2019.0227.

[23] L. M. Aplin, D. R. Farine, J. Morand-Ferron, A. Cockburn, A. Thornton, and B. C. Sheldon, “Experimentally induced innovations lead to persistent culture via conformity in wild birds,” Nature, vol. 518, no. 7540, pp. 538–541, Feb. 2015, doi: 10.1038/nature13998.

[24] E. Van de Waal, C. Borgeaud, and A. Whiten, “Potent Social Learning and Conformity Shape a Wild Primate’s Foraging Decisions,” Science, Apr. 2013, doi: 10.1126/science.1232769.

[25] D. I. Bolnick et al., “Why intraspecific trait variation matters in community ecology,” Trends Ecol. Evol., vol. 26, no. 4, pp. 183–192, Apr. 2011, doi: 10.1016/j.tree.2011.01.009.

Back to the Future: The return of scientific conferences

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

The pandemic has taught me that certain skills – including ones I never recognized as such – can atrophy. How do I construct an outfit that involves actual pants instead of gym shorts? How do I make a lunch that is portable and can be eaten outside my home?

These are things that I’ve had to relearn over the last year, as I increasingly leave my virtual work world and move back into the physical world. Recently, the new ways in which the world is opening up again have pushed me to brush off another skill – how do I talk to other people about my work?

The pandemic has necessarily made the world a bit more insular. A year and a half into my graduate career, I’ve mostly discussed my work within the cozy cocoon of my lab groups and cohort. In particular, I’ve lived the last few months in that realm of research that is so specific and internal that almost no one else fully understands or cares about what I’m doing: I’ve spent days tangled up in oodles of models, been woken up at night by dreams about coding, and sweated over the decimal points of statistical deviance-explained values.

This period of scientific navel gazing abruptly ended this February. In the space of ten days, I presented at my first in-person conference during graduate school, gave a short talk at my first international conference, and gave my longest talk yet to a public audience. After reveling in the minutiae of research for months, it was so valuable to be forced to take a step back, think about the overarching narrative of this work, and practice telling that story to different audiences.

A February talk for the Oregon chapter of the American Cetacean Society gave me the chance to tell the story of my research to a broad audience.

Presenting this work to an in-person audience for the first time was especially rewarding. With a physical (!) poster in hand, I headed out to Newport for the annual meeting of the Oregon Chapter of The Wildlife Society. The GEMM Lab really took this conference by storm – Leigh gave a plenary talk on the meeting’s theme of “Dynamic Oceans, Shifting Landscapes”, Lisa chaired a session and gave a talk about trophic relationships between kelp and whales, and Miranda presented a poster on the new Holistic Assessment of Living marine resources off the Oregon coast (HALO) project.

This great GEMM Lab presence gave me the opportunity to reference everyone else’s work as I shared my own, and to think about the body of work we do as a group and the coherence in research themes that different projects share. I almost lost my voice by talking for the entire duration of the poster session, and was energized by the opportunity to share this work with so many interested people.

The GEMM Lab and other OSU Marine Mammal Institute members presented alongside terrestrial researchers on the theme of “Dynamic Oceans, Shifting Landscapes”.

Just a few days later, the biennial Ocean Sciences Meeting began. Dawn presented on forecasting the distribution of blue whales in New Zealand’s South Taranaki Bight region, and several members of the Krill Seeker Lab, led by my co-advisor Dr. Kim Bernard, presented their own zooplankton ecology research.

Originally scheduled for Hawaii, this meeting was instead held virtually as a safety precaution against Covid-19. Nevertheless, the diversity of talks and time spent gathering online still gave me the sense of being part of an international ocean science community. People attended from every time zone, and watching early-morning talks while wearing pajamas with Solene, Dawn, and Quin the dog is officially one of my new favorite conference experiences.

In addition to the chance to discuss science with other students and researchers, it was great to have the opportunity to step back from our normal routines a bit. The Krill Seeker Lab did the conference-organized 5K walk together (in intermittent rain, of course) and our team even came within one point of winning the trivia contest. All the while, we were hopping in and out of poster sessions and talks, realizing that virtual conferences can be just as busy as in-person ones.

Taking a 5k-long break from watching talks! From left to right: Rachel Kaplan, Kim Bernard, Giulia Wood, and Kirsten Steinke.

Over the last two years, one of the things the pandemic has made me appreciate the most is the ability to gather. Dinner with friends, holidays with family – the ability to be together is far more tentative and precious than I realized during the “before times.” Now, as we start tiptoeing back into normal life a bit more, I’m appreciating the ability to gather for science and looking forward to more conferences in the future.

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Wavelet analysis to describe biological cycles and signals of non-stationarity

By Allison Dawn, GEMM Lab Master’s student, OSU Department of Fisheries, Wildlife, and Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

During my second term of graduate school, I have been preparing to write my research proposal. The last two months have been an inspiring process of deep literature dives and brainstorming sessions with my mentors. As I discussed in my last blog, I am interested in questions related to pattern and scale (fine vs. mesoscale) in the context of the Pacific Coast Feeding Group (PCFG) of gray whales, their zooplankton prey, and local environmental variables.

My work currently involves exploring which scales of pattern are important in these trophic relationships and whether the dominant scale of a pattern changes over time or space. I have researched which analysis tools would be most appropriate to analyze ecological time series data, like the impressive long-term dataset the GEMM lab has collected in Port Orford as part of the TOPAZ project, where we have monitored the abundance of whales and zooplankton, as well as environmental variables since 2016.

A useful analytical tool that I have come across in my recent coursework and literature review is called wavelet analysis. Importantly, wavelet analysis can handle non-stationarity and edge detection in time series data. Non-stationarity is when a dataset’s mean and/or variance can change over time or space, and edge detection is the identification of the change location (in time or space). For example, it is not just the cycles or “ups and downs” of zooplankton abundance I am interested in, but when in time or where in space these cycles of “ups and downs” might change in relation to what their previous values, or distances between values, were. Simply stated, non-stationarity is when what once was normal is no longer normal. Wavelet analysis has been applied across a broad range of fields, such as environmental engineering (Salas et al. 2020), climate science (Slater et al. 2021), and bio-acoustics (Buchan et al. 2021). It can be applied to any time series dataset that might violate the traditional statistical assumption of stationarity.

In a recent review of climate science methodology, Slater et al. (2021) outlined the possible behavior of time series data. Using theoretical plots, the authors show that data can a) have the same mean and variance over time, or b) have non-stationarity that can be broken into three major groups – trend, step change, or shifts in variance. Figure 1 further demonstrates the difference between stationary vs. non-stationary data in relation to a given variable of interest over time.

Figure 1. Plots showing the possible magnitude of a given variable across a time series: a) Stationary behavior, b) Non-stationary trend, step-change, and a shift in variance. [Taken from Slater et. al (2021)].

Traditional correlation statistics assumes stationarity, but it has been shown that ecological time series are often non-stationary at certain scales (Cazelles & Hales, 2006). In fact, ecological data rarely meets the requirements of a controlled experiment that traditional statistics require. This non-stationarity of ecological data means that while widely-used methods like generalized linear models and analyses of variances (ANOVAs) can be helpful to assess correlation, they are not always sufficient on their own to describe the complex natural phenomena ecologists seek to explain. Non-stationarity occurs frequently in ecological time series, so it is appropriate to consider analysis tools that will allow us to detect edges to further investigate the cause.

Wavelet analysis can also be conducted across a time series of multiple response variables to assess if these variables share high common power (correlation). When data is combined in this way it is called a cross-wavelet analysis. An interesting paper used cross-wavelet analysis to assess the seasonal response of zooplankton life history in relation to climate warming (Winder et. al 2009). Results from their cross-wavelet analysis showed that warming temperatures over the past two decades increased the voltinism (number of broods per year) of copepods. The authors show that where once annual recruitment followed a fairly stationary pattern, climate warming has contributed to a much more stochastic pattern of zooplankton abundance. From these results, the authors contribute to the hypothesis that climate change has had a temporal impact on zooplankton population dynamics, and recruitment has increasingly drifted out of phase from the original annual cycles.

Figure 2. Cross-wavelet spectrum for immature and adult Leptodiaptomus ashlandi for 1965 through either 2000 or 2005. Plots show a) immatures and temperature, b) adults and temperature, c) immatures and phytoplankton, and d) adults and phytoplankton. Arrows indicate phase between combined time series. 0 degrees is in-phase and 180 degrees is anti-phase. Black contour lines show “cone of influence” or the 95% significance level, every value within the cone is considered significant. Left axis shows the temporal period, and the color legend shows wavelet frequency power, with low frequencies in blue and high frequencies in red. Plots show strong covariation of high common power at the 12-month period until the 1980s. This pattern is especially evident in plot c) and d). [Taken from (Winder et. al 2009)].

While wavelet and cross-wavelet analyses should not be the only tool used to explore data, due to its limitations with significance testing, it is still worth implementing to gain a better understanding of how time series variables relate to each other over multiple spatial and/or temporal scales. It is often helpful to combine multiple methods of analysis to get a larger sense of patterns in the data, especially in spatio-temporal research.

When conducting research within the context of climate change, where the concentration of CO₂ in ppm in the atmosphere is a non-stationary time series itself (Figure 3), it is important to consider how our datasets might be impacted by climate change and wavelet analysis can help identify the scales of change.

Figure 3. Plot showing the historic fluctuations of CO^2 and the recent deviation from normal levels. Source: https://globalclimate.ucr.edu/resources.html

When considering our ecological time series of data in Port Orford, we want to evaluate how changing ocean conditions may be related to data trends. For example, has the annual mean or variance of zooplankton abundance changed over time, and where has that change occurred in time or space? These changes might have occurred at different scales and might be invisible at other scales. I am eager to see if wavelet analysis can detect these sorts of changes in the abundance of zooplankton across our time series of data, particularly during the seasons of intense heat waves or upwelling.

References

Buchan, S. J., Pérez-Santos, I., Narváez, D., Castro, L., Stafford, K. M., Baumgartner, M. F., … & Neira, S. (2021). Intraseasonal variation in southeast Pacific blue whale acoustic presence, zooplankton backscatter, and oceanographic variables on a feeding ground in Northern Chilean Patagonia. Progress in Oceanography, 199, 102709.

Cazelles, B., & Hales, S. (2006). Infectious diseases, climate influences, and nonstationarity. PLoS Medicine, 3(8), e328.

Salas, J. D., Anderson, M. L., Papalexiou, S. M., & Frances, F. (2020). PMP and climate variability and change: a review. Journal of Hydrologic Engineering, 25(12), 03120002.

Slater, L. J., Anderson, B., Buechel, M., Dadson, S., Han, S., Harrigan, S., … & Wilby, R. L. (2021). Nonstationary weather and water extremes: a review of methods for their detection, attribution, and management. Hydrology and Earth System Sciences, 25(7), 3897-3935.

Winder, M., Schindler, D. E., Essington, T. E., & Litt, A. H. (2009). Disrupted seasonal clockwork in the population dynamics of a freshwater copepod by climate warming. Limnology and Oceanography, 54(6part2), 2493-2505.

Social turmoil due to the approval of an offshore oil exploration project off the coast of Argentina.

I just returned to my home country, Argentina, after over 2 years without leaving the USA due to COVID-19 travel restrictions. Being back with my family, my friends, my culture, and speaking my native language feels great and relaxing. However, I returned to a country struggling to rebound from the coronavirus pandemic. I am afraid this post pandemic scenario places Argentina in a vulnerable situation. The need for economic growth could result in decisions or policies that, in the long term, hurt the country, leaving environmental damage for potential economic growth.

Argentina holds extensive oil and gas deposits, including the world’s second largest gas formation, Vaca Muerta. Although offshore (i.e., in the ocean) oil exploration and exploitation are not yet extensively developed, the intention of offshore gas and oil drilling is on the agenda. In July 2021, a public hearing was held with the purpose to consider the environmental impact assessment for carrying out seismic exploration in the North Argentinian basin off the southern coast of the Buenos Aires province. Over 90% of the participants, including scientists, researchers, technicians from various institutions, non-governmental organizations and representatives of the fishing sector spoke against the project and highlighted the negative impacts that such activity can generate on marine life, and to other socioeconomic activities such as tourism and fishing, not only in Argentina but at the regional level.

Thousands of people marched along the beaches and the main coastal cities of Argentina to protest against the approval for a seismic explorations project in the Argentinian basin. Photo source: prensaobrera.com

Seismic prospections are usually done with the purpose for oil and gas exploitation and less frequently for research purposes. In seismic prospections, ships carry out explosions with airguns, whose sound waves reach the seabed, bounce back and are captured by receivers on the ships to map the petroleum deposits in seafloor and identify potential areas for hydrocarbon extractions. The sound emitted by the seismic airguns can reach extremely loud levels of sounds that travel for thousands of miles underwater. Such extreme high levels of sound can alter the behavior of many marine species, from the smallest planktonic species, to the largest marine mammals, masking their communication, causing physical and physiological stress, interfering with their vital functions, and reducing the local availability of prey (Di Iorio & Clark, 2010; Hildebrand, 2009; Weilgart, 2018).

Here you can listen to a short audio clip of a seismic airgun firing every ~8 seconds, a typical pattern. Close your eyes and imagine you are a whale living in this environment. Now, put the clip on loop and play it for three months straight. This would be the soundscape that whales living in a region of oil and gas exploration hear, as seismic surveys often last 1-4 months (see our previous post “Hearing is believing” for more details).

Despite the public rejection and the mounting evidence about the negative impacts and environmental risks associated with such activities, the government approved the initiation of the seismic prospection off the southern coast of Buenos Aires. In response, thousands of people marched along the beaches and the main coastal cities of Argentina to protest against the oil exploration project. The areas where the seismic surveys will be carried out overlap largely with the southern right whale’s migration routes and feeding areas during their spring and summer (Figure 1). Likewise, the area overlaps with highly productive areas in the ocean that hosts great biodiversity of species of ecological and commercial importance, including the feeding areas of seabirds, turtles and other marine mammals. Additionally, the seismic activity will endanger the health of the beaches of the coast of Buenos Aires and Uruguay where thousands of tourists spend the summer to escape from the large cities.

***Figure 1.*** The map on the left is showing (light blue squares **CAN_100**, **CAN_108**, **and CAN_114**) the areas where seismic prospections are proposes. The map on the right is showing the individual satellite track lines for eleven individual southern right whales (SRW) during the feeding season. You can observe that the proposed area for seismic explorations overlaps with critical feeding habitat for the SRW. Source: Whale Conservation Institute of Argentina (ICB).

The impacts of these activities to marine wildlife are difficult to control and monitor (Elliott et al. 2019, Gordon et al, 2003), especially for large whales that are a very challenging taxa to study (Hunt et al. 2013). We know that the ability to perceive biologically important sounds is critical to marine mammals, and acoustic disturbance through human-generated noise can interfere with their natural functions. Sounds from seismic surveys are intense and have peak frequency bands overlapping those used by baleen whales (Di Lorio & Clark, 2010); however, evidence of interference with baleen whale acoustic communication, and the effects on their health and physiology are sparse. In this context, the GEMM Lab project GRANITE (Gray Whale Response to Ambient Noise Informed by Technology and Ecology), plans to generate information to fulfill these knowledge gaps and provide tools to aid conservation and management decisions in terms of allowable noise level in whale habitats. I am hopeful such information will reach decision makers and influence their decisions, however, sometimes it is frustrating to see how evidence-based information generated with high quality standards are often ignored.

The recent approval of the seismic exploration in Argentina is an example of my frustration. There is no way that the oil industry can guarantee a low-risk of impact on biodiversity and the environment. There are too many examples of environmental catastrophes related to the oil industries at sea that speak for themselves. Moreover, the promotion of such activities goes against the compromises assumed by the country to work to mitigate the effects of Climate Change, and to achieve the reductions of the greenhouse gas emissions to comply with the Paris Agreement. Decades of research help recognized the areas that would be impacted by these seismic activities as key habitat for the life cycle of whales, penguins, seals and more. But, apparently all these scientific data are ignored at the time of weighing the tradeoffs between “economic development” and environmental impacts. As a conservation biologist, I am questioning what can be done in order to be heard and significantly influence such decisions.

References:

Di Iorio, L., & Clark, C. W. (2010). Exposure to seismic survey alters blue whale acoustic communication. Biology Letters, 6(1), 51–54. https://doi.org/10.1098/rsbl.2009.0651
Weilgart, L. (2018). The impact of ocean noise pollution on fish and invertebrates. Report for OceanCare, Switzerland.
Elliott, B. W., Read, A. J., Godley, B. J., Nelms, S. E., & Nowacek, D. P. (2019). Critical information gaps remain in understanding impacts of industrial seismic surveys on marine vertebrates. In Endangered Species Research (Vol. 39, pp. 247–254). Inter-Research. https://doi.org/10.3354/esr00968
Gordon, J., Gillespie, D., Potter, J., Frantzis, A., Simmonds, M. P., Swift, R., & Thompson, D. (2003). A review of the effects of seismic surveys on marine mammals. Marine Technology Society Journal, 37(4), 16-34.
Hunt, K. E., Moore, M. J., Rolland, R. M., Kellar, N. M., Hall, A. J., Kershaw, J., Raverty, S. A., Davis, C. E., Yeates, L. C., Fauquier, D. A., Rowles, T. K., & Kraus, S. D. (2013). Overcoming the challenges of studying conservation physiology in large whales: a review of available methods. Conservation Physiology, cot006–cot006. https://doi.org/10.1093/conphys/cot006

Drones with lasers: almost as cool as “sharks with laser beams attached to their heads”

Dr. KC Bierlich, Postdoctoral Scholar, OSU Department of Fisheries, Wildlife, & Conservation Sciences, Geospatial Ecology of Marine Megafauna (GEMM) Lab

The recent advancement in drones (or unoccupied aircraft systems, UAS) has greatly enhanced opportunities for scientists across a broad range of disciplines to collect high-resolution aerial imagery. Wildlife researchers in particular have utilized this technology to study large elusive animals, such as whales, to observe their behavior (see Clara Bird’s blog) and obtain morphological measurements via photogrammetry (see previous blog for a brief history on photogrammetry and drones). However, obtaining useful measurement data is not as easy as flying the drone and pressing record. For this blog, I will provide a brief overview on the basics of using photogrammetry to extract morphological measurements from images collected with drones, as well as the associated uncertainty from using different drone platforms.

During my PhD at Duke University, I co-developed an open-source photogrammetry software called MorphoMetriX to measure whales in images I collected using drones (Fig. 1) (Torres and Bierlich, 2020) (see this blog for some fieldwork memoirs!). The software is designed to be flexible, simple to use, and customizable without knowledge of scripting languages. Using MorphoMetriX, measurements are made in pixels and then multiplied by the ground sampling distance (GSD) to convert to standard units (e.g., meters) (Fig. 2A). GSD represents the distance on the ground each pixel represents (i.e., the linear size of the pixel) and therefore sets the scale of the image (i.e., cm per pixel). Figure 2A describes how GSD is dependent on the camera sensor, focal length lens, and altitude. Thus, drones equipped with different cameras and focal length lenses will have inherent differences in GSD as altitude increases (Fig. 2B). A larger GSD increases the length each pixel represents in a photo and results in a lower resolution image, potentially obscuring important features in the photo and introducing measurement error.

Figure 1. An example of a Pacific Coast Feeding Group gray whale measured in MorphoMetriX (Torres & Bierlich, 2020).

Figure 2: Overview of photogrammetry methods and calculating ground sampling distance (GSD). A) Photogrammetry methods for how each image is scaled to convert measurements in pixels to standard units (e.g., meters). Altitude is the distance between the camera lens and whale (usually at the surface of the water). Figure from Torres and Bierlich (2020). B) The exact (not accounting for distortion or altitude error) ground sampling distance (GSD) for two drone platforms commonly used to obtain morphological measurements of cetaceans. The difference in GSD between the P4Pro and Inspire 1 is due to the difference in sensor width and focal lengths of the cameras used. Figure from Bierlich et al. (2021).

Obtaining accurate altitude information is a key component in obtaining accurate measurements. All drones are equipped with a barometer, which measures altitude from changes in pressure. In general, barometers usually yield low accuracy in the altitude recorded, particularly for low-cost sensors commonly found on small, off-the-shelf drones (Wei et al., 2016). Dawson et al. (2017) added a laser altimeter (i.e., LightWare SF11/C, https://www.mouser.com//datasheet//2//321//28054-SF11-Laser-Altimeter-Manual-Rev8-1371857.pdf) to a drone, which yields higher accuracy in the altitude recorded. Since then, several studies have adopted use of a laser altimeter to study different species of baleen whales (i.e., Gough et al., 2019; Christiansen et al., 2018).

The first chapter of my dissertation, which was published last year in Marine Ecology Progress Series, compared the accuracy of several drones equipped with different camera sensors, focal length lenses, and a barometer vs. laser altimeter (Bierlich et al., 2021). We flew each drone over a known sized object floating at the surface and collected images at various altitudes (between 10 – 120 m). We used the known size of the floating object to determine the percent error of each measurement at each altitude. We found that 1) there is a lot of variation in measurement error across the different drones when using a barometer to measure altitude and 2) using a laser altimeter dramatically reduces measurement error for each drone (Fig. 3).

Figure 3. The % error for measurements from different drones. Black dashed line represents 0% error (true length = 1.48 m). The gray dashed lines represent under- and over-estimation of the true length by 5% (1.41 and 1.55 m, respectively).

These findings are important because if a study is analyzing measurements that are from more than one drone, the uncertainty associated with those measurements must be taken into account to know if measurements are reliable and comparable. For instance, let’s say we are comparing the body length of two different populations and found that population A is significantly longer than population B. From looking at Figure 3, that significant difference in length between population A and B could be unreliable as the difference may be due to the bias introduced by the type of drone, camera sensor, focal length lens, and whether a barometer or laser altimeter was used for recording altitude. In other words, without incorporating uncertainty associated with each measurement, how do you trust your measurement?

Hence, the National Institute of Standards and Technology (NIST) states that a measurement is complete only when accompanied by a quantitative statement of its uncertainty (Taylor & Kuyatt, 1994). In our Bierlich et al. (2021) study, we develop a Bayesian statistical model where we use the measurements of the known-sized object floating at the surface (what was used for Fig. 3) as training data to predict the lengths of unknown-sized whales. This Bayesian approach views data and the underlying parameters that generated the data (such as the mean or standard deviation) as random, and thus can be described by a statistical distribution. Using Bayes’ Theorem, a model of the observed data (called the likelihood function), is combined with prior knowledge pertaining to the underlying parameters (called the prior probability distribution) to form the posterior probability distribution, which serves as updated knowledge about the underlying parameter. For example, if someone told me they saw a 75 ft blue whale, I would not be phased. But if someone told me they saw a 150 ft blue whale, I would be skeptical – I’m using prior knowledge to determine the probability of this statement being true.

The posterior probability distribution produced by this Bayesian approach can also serve as new prior information for subsequent analyses. Following this framework, we used the known-sized objects to first estimate the posterior probability distribution for error for each drone. We then used that posterior probability distribution for error specific to each drone platform as prior information to form a posterior predictive distribution for length of unknown-sized whales. The length of an individual whale can then be described by the mean of this second posterior predictive distribution, and its uncertainty defined as the variance or an interval around the mean (Fig. 4).

Figure 4. An example of a posterior predictive distribution for total length of an individual blue whale. The black bars represent the uncertainty around the mean value (the black dot) – the longer black bars represent the 95% highest posterior density (HPD) interval, and the shorter black bars represent the 65% HPD interval.

For over half a decade, the GEMM Lab has been collecting drone images of Pacific Coast Feeding Group (PCFG) of gray whales off the coast of Oregon to measure their morphology and body condition (see GRANITE Project Blog). We have been using several different types of drones equipped with different cameras, focal length lenses, barometers, and laser altimeters. These measurements from different drones will inherently have different levels of error associated with them, so adapting these methods for incorporating uncertainty will be key to ensure our measurements are comparable and analyses are robust. To do this, we fly over a known-sized board (1 m) at the start of each flight to use as training data to generate a posterior predictive distribution for length of the an unknown-sized PCFG gray whale that we fly over (Fig. 5). Likewise, we are working closely with several other collaborators who are also using different drones. Incorporating measurement uncertainty from drones used across research labs and in different environments will help ensure robust analyses and provide great opportunity for some interesting comparisons – such as differences in gray whale body condition on their feeding grounds in Oregon vs. their breeding grounds in Baja, Mexico, and morphological comparisons with other baleen whale species, such as blue and humpback whales. We are currently wrapping up measurement from thousands of boards (Fig. 5) and whales (Fig. 1) from 2016 – 2021, so stay tuned for the results!

Figure 5. An example of a known-sized object (1 m long board) used as training data to assess measurement uncertainty.

References

Bierlich, K.C., Schick, R.S., Hewitt, J., Dale, J., Goldbogen, J.A., Friedlaender, A.S., Johnston D.J. (2021). A Bayesian approach for predicting photogrammetric uncertainty in morphometric measurements derived from UAS. Marine Ecology Progress Series. DOI: https://doi.org/10.3354/meps13814

Christiansen F, Vivier F, Charlton C, Ward R, Amerson A, Burnell S, Bejder L (2018) Maternal body size and condition determine calf growth rates in southern right whales. Mar Ecol Prog Ser 592: 267−281

Dawson SM, Bowman MH, Leunissen E, Sirguey P (2017) Inexpensive aerial photogrammetry for studies of whales and large marine animals. Front Mar Sci 4: 366

Gough, W.T., Segre, P.S., Bierlich, K.C., Cade, D.E., Potvin, J., Fish, F. E., Dale, J., di Clemente, J., Friedlaender, A.S., Johnston, D.W., Kahane-Rapport, S.R., Kennedy, J., Long, J.H., Oudejans, M., Penry, G., Savoca, M.S., Simon, M., Videsen, S.K.A., Visser, F., Wiley, D.N., Goldbogen, J.A. (2019). Scaling of swimming performance in baleen whales. Journal of Experimental Biology, 222(20).https://doi.org/10.1242/jeb.204172

Taylor, B. N., and Kuyatt, C. E. (1994). Guidelines for Evaluating and Expressing the Uncertainty of NIST Measurement Results. Washington, DC: National Institute of Standards and Technology. 1–25.

Torres, W.I., & Bierlich, K.C. (2020). MorphoMetriX: a photogrammetric measurement GUI for morphometric analysis of megafauna. Journal of Open Source Software, 5(45), 1825. https://doi.org/10.21105/joss.01825

Wei S, Dan G, Chen H (2016) Altitude data fusion utilizing differential measurement and complementary filter. IET Sci Meas Technol (Singap) 10: 874−879

The costs and benefits of automated behavior classification

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

“Why don’t you just automate it?” This is a question I am frequently asked when I tell someone about my work. My thesis involves watching many hours of drone footage of gray whales and meticulously coding behaviors, and there are plenty of days when I have asked myself that very same question. Streamlining my process is certainly appealing and given how wide-spread and effective machine learning methods have become, it is a tempting option to pursue. That said, machine learning is only appropriate for certain research questions and scales, and it’s important to consider these before investing in using a new tool.

The application of machine learning methods to behavioral ecology is called computational ethology (Anderson & Perona, 2014). To identify behaviors from videos, the model tracks individuals across video frames and identifies patterns of movement that form a behavior. This concept is similar to the way we identify a whale as traveling if it’s moving in a straight line and as foraging if it’s swimming in circles within a small area (Mayo & Marx, 1990, check out this blog to learn more). The level of behavioral detail that the model is able to track depends on the chosen method (Figure 1, Pereira et al., 2020). These methods range from tracking each animal as a simple single point (called a centroid) to tracking the animal’s body positioning in 3D (this method is called pose estimation), which range from providing less detailed to more detailed behavior definitions. For example, tracking an individual as a centroid could be used to classify traveling and foraging behaviors, while pose estimation could identify specific foraging tactics.

*Figure 1. Figure from Pereira et al. (2020) illustrating the different methods of animal behavior tracking that are possible using machine learning.*

Pose estimation involves training the machine learning algorithm to track individual anatomical features of an individual (e.g., the head, legs, and tail of a rat), meaning that it can define behaviors in great detail. A behavior state could be defined as a combination of the angle between the tail and the head, and the stride length.

For example, Mearns et al. (2020) used pose estimation to study how zebrafish larvae in a lab captured their prey. They tracked the tail movements of individual larvae when presented with prey and classified these movements into separate behaviors that allowed them to associate specific behaviors with prey capture (Figure 2). The authors found that these behaviors occurred in a specific sequence, that the behaviors kept the prey within the larvae’s line of sight, and that the sequence was triggered by visual cues. In fact, when they removed the visual cue of the prey, the larvae terminated the behavior sequence, meaning that the larvae are continually choosing to do each behavior in the sequence, rather than the sequence being one long behavior event that is triggered only by the initial visual cue. This study is a good example of the applicability of machine learning models for questions aimed at kinematics and fine-scale movements. Pose estimation has also been used to study the role of facial expression and body language in rat social communication (Ebbesen & Froemke, 2021).

Figure 2. Excerpt from figure 1 of Mearns et al. (2020) illustrating (A) the camera set up for their experiment, (B) how the model tracked the eye angles and tail of the larvae fish, (C) the kinematics extracted from the footage. In panel (C) the top plot shows how the eyes converged on the same object (the prey) during prey capture event, the middle plot shows when the tail was curved to the left or the right, and the bottom plot shows the angle of the tail tip relative to the body.

While previous machine learning methods to track animal movements required individuals to be physically marked, the current methods can perform markerless tracking (Pereira et al., 2020). This improvement has broadened the kinds of studies that are possible. For example, Bozek et al., (2021) developed a model that tracked individuals throughout an entire honeybee colony and showed that certain individual behaviors were spatially distributed within the colony (Figure 3). Machine learning enabled the researchers to track over 1000 individual bees over several months, a task that would be infeasible for someone to do by hand.

*Figure 3. Excerpt from figure 1 of Bozek et al., (2021) showing how individual bees and their trajectories were tracked.*

These studies highlight that the potential benefits of using machine learning when studying fine scale behaviors (like kinematics) or when tracking large groups of individuals. Furthermore, once it’s trained, the model can process large quantities of data in a standardized way to free up time for the scientists to focus on other tasks.

While machine learning is an exciting and enticing tool, automating behavior detection via machine learning could be its own PhD dissertation. Like most things in life, there are costs and benefits to using this technique. It is a technically difficult tool, and while applications exist to make it more accessible, knowledge of the computer science behind it is necessary to apply it effectively and correctly. Secondly, it can be tedious and time consuming to create a training dataset for the model to “learn” what each behavior looks like, as this step involves manually labeling examples for the model to use.

As I’ve mentioned in a previous blog, I came quite close to trying to study the kinematics of gray whale foraging behaviors but ultimately decided that counting fluke beats wasn’t necessary to answer my behavioral research questions. It was important to consider the scale of my questions (as described in Allison’s blog) and I think that diving into more fine-scale kinematics questions could be a fascinating follow-up to the questions I’m asking in my PhD.

For instance, it would be interesting to quantify how gray whales use their flukes for different behavior tactics. Do gray whales in better body condition beat their flukes more frequently while headstanding? Does the size of the fluke affect how efficiently they can perform certain tactics? While these analyses would help quantify the energetic costs of different behaviors in better detail, they aren’t necessary for my broad scale questions. Consequently, taking the time to develop and train a pose estimation machine learning model is not the best use of my time.

That being said, I am interested in applying machine learning methods to a specific subset of my dataset. In social behavior, it is not only useful to quantify the behaviors exhibited by each individual but also the distance between them. For example, the distance between a mom and her calf can be indicative of the calves’ dependence on its mom (Nielsen et al., 2019). However, continuously measuring the distance between two individuals throughout a video is tedious and time intensive, so training a machine learning model could be an effective use of time. I plan to work with an intern this summer to develop a machine learning model to track the distance between pairs of gray whales in our drone footage and then relate this distance data with the manually coded behaviors to examine patterns in social behavior (Figure 4). Stay tuned to learn more about our progress!

*Figure 4. A mom and calf pair surfacing together. Image collected under NOAA/NMFS permit #21678*

References

Anderson, D. J., & Perona, P. (2014). Toward a Science of Computational Ethology. Neuron, 84(1), 18–31. https://doi.org/10.1016/j.neuron.2014.09.005

Bozek, K., Hebert, L., Portugal, Y., Mikheyev, A. S., & Stephens, G. J. (2021). Markerless tracking of an entire honey bee colony. Nature Communications, 12(1), 1733. https://doi.org/10.1038/s41467-021-21769-1

Ebbesen, C. L., & Froemke, R. C. (2021). Body language signals for rodent social communication. Current Opinion in Neurobiology, 68, 91–106. https://doi.org/10.1016/j.conb.2021.01.008

Mayo, C. A., & Marx, M. K. (1990). Surface foraging behaviour of the North Atlantic right whale, Eubalaena glacialis , and associated zooplankton characteristics. Canadian Journal of Zoology, 68(10), 2214–2220. https://doi.org/10.1139/z90-308

Mearns, D. S., Donovan, J. C., Fernandes, A. M., Semmelhack, J. L., & Baier, H. (2020). Deconstructing Hunting Behavior Reveals a Tightly Coupled Stimulus-Response Loop. Current Biology, 30(1), 54-69.e9. https://doi.org/10.1016/j.cub.2019.11.022

Nielsen, M., Sprogis, K., Bejder, L., Madsen, P., & Christiansen, F. (2019). Behavioural development in southern right whale calves. Marine Ecology Progress Series, 629, 219–234. https://doi.org/10.3354/meps13125

Pereira, T. D., Shaevitz, J. W., & Murthy, M. (2020). Quantifying behavior to understand the brain. Nature Neuroscience, 23(12), 1537–1549. https://doi.org/10.1038/s41593-020-00734-z

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