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Justine Hudson’s Lab Exchange at Northern Arizona University
At the end of January, Winnipeg was under an extreme cold warning with temperatures dipping to -47°C with the wind-chill. I was ecstatic to escape the bitter cold and travel to warm, sunny, Arizona. Stepping off the plane in Phoenix was like heaven, a mere 13°C felt like beach weather. The trip from Phoenix to Flagstaff was beautiful. Seeing cacti as the sun went down over the mountains was everything that I imagined Arizona to be. By the time that I arrived in Flagstaff, it was dark and a little chilly. When I woke up the next morning, I got dressed, packed my bags for the day, and headed off to Northern Arizona University. You can imagine my surprise when I opened the door to see a fresh blanket of snow!
Between February 3rd and the 17th, I participated in a laboratory exchange at Northern Arizona University under the supervision of Dr. Loren Buck and Dr. Kathleen Hunt. The main objectives of the laboratory exchange were to 1) receive training in hormone analyses, 2) measure corticosterone from baleen plates collected from 9 bowhead whales, 3) network and collaborate with researchers from Northern Arizona University, and 4) publish peer-reviewed journal articles focused on the physiology of bowhead whales.
Baleen is a filter-feeding apparatus that is present in all mysticete whale species and grows continuously over the course of an individual’s lifetime. Hormones and stable isotopes are incorporated in to baleen as it grows, allowing researchers to examine foraging and endocrine patterns over the length of a plate, which in bowhead whales may represent 10-20 years. The goal of this project, led by Dr. Kathleen Hunt and Dr. Cory Matthews, was to assess reproduction of bowhead whales by measuring corticosterone profiles along baleen plates, in combination with previously analyzed testosterone and stable isotope profiles.
On my first day, Kathleen introduced me to everyone working in the lab and then we got started on setting up our schedule for the week. During the first week, Kathleen showed me how to properly run an enzyme immunoassay and together, we processed over 1000 samples. I also had the opportunity to present my research to Loren’s lab, which was then followed by dinner at a local restaurant. Kathleen and I finished a busy week in the lab with a lovely drive to the Grand Canyon, which was definitely a highlight of the trip!
During my second week, Kathleen showed me how to process our newly assayed data. I ran preliminary analyses, started compiling data, and packed up samples to ship back to Winnipeg so that I could assay them all again for triiodothyronine (T3), which is a metabolic hormone. We finished another busy week with a lab trip to Sedona, followed by a lovely dinner!
When applying for the RCN laboratory exchange, I hoped to receive training from experts in the field, but the experience was much more than that. Not only did I receive training, but I also met and networked with graduate students from all over the world and learned how using a physiological approach can help us answer a range of questions. Through this experience, we also formed strong multi-institutional, multinational networks between researchers from the University of Manitoba, Fisheries and Oceans Canada, and Northern Arizona University. Since returning home, our network has submitted abstracts to two international conferences and will soon be working on a peer-reviewed journal article.
I would like to thank Dr. Loren Buck for hosting me in his lab, Dr. Kathleen Hunt for the training and mentorship, Dr. Cory Matthews for facilitating this exchange, and to all lab members that took the time to talk to me about their work. I would also like to thank the RCN g2p2pop committee for this amazing opportunity. It was such a great experience and I encourage anyone interested to apply!
Past Blog Posts
Renee Jordan’s Lab Exchange at University of Oregon Accordion Closed
I am privileged to have had the opportunity to participate in an exchange with Dr. John Postlethwait’s lab! My time spent learning new techniques, attending talks, and fighting with pipettes opened my eyes to a whole new world (Disney pun intended).
Who? Me! Renee Jordan, PhD Student at Northern Arizona University
What? RCN g2p2pop laboratory exchange
When? December 2nd– 15th, 2018
Where? University of Oregon, Institute for Neuroscience
WHY! (1) Run RNA-seq library preps on Alaska blackfish gonad and liver samples, (2) train in bioinformatics associated with gene expression datasets, (3) advance my skill set in genetic laboratory techniques
My PhD focuses on understanding the contribution of environmental contaminants to health disparities on St. Lawrence Island, Alaska. St. Lawrence Island is located just 80km from Russia, which made it a strategic location for two military defense sites during the Cold War. Despite remediation and clean-up efforts, the formerly used defense site on the Northeast Cape of the island remains a point source for polychlorinated biphenyl (PCB) pollution and may pose a mounting health risk to local wildlife and Siberian Yupik residents living on the island. My research aims to evaluate the effects of current PCB exposure on cancer related gene expression, developmental pathologies, and genomic divergence in the ninespine stickleback (Pungitius pungitius) and Alaska blackfish (Dallia pectoralis). We hypothesize that PCB contamination from the formerly used defense site is significantly downregulating genes important in DNA repair and tumor suppression compared to fish from reference sites. The goals of this lab visit were to receive training on RNAseq techniques and to process blackfish samples for my project.
Lab highlight: Getting dsDNA quantification reads after four days of RNA extractions, mRNA purification, and library prep
Eugene highlight:Hiking up Spencer’s Butte (Fig. 1, 5)
The first thing I noticed upon touching down in the Eugene, Oregon airport was the moisture. Arizona is a bit lacking in that department, and landing amid a dense fog was SO refreshing. Eugene is an interesting place to explore, with quaint coffee shops, bookstores, art museums, and hat stores. On the weekend, I took an incredible hike up Spencer’s Butte (Fig. 1, 5) south of town. The pictures don’t do it justice!
My training commenced in full force on Monday morning (after frantically trying to find the lab in the labyrinth that is Huestis Hall). Dr. Tom Titus (pictured above) and I planned out 28 blackfish samples for RNA-seq analysis and began RNA extractions. During my first week, Tom trained me in Ribopure RNA extractions, Qubit assays (RNA broad range, RNA, and dsDNA high sensitivity), Dynabeads mRNA purification, and NEXTflex Rapid Directional qRNA-seq library preparation. By Friday, we had seven beautiful RNA-seq libraries ready to go for qPCR and sequencing.
Unfortunately, Murphy’s law had other plans for the next set of samples. On Tuesday, the Qubit quantification of our RNA-seq library preps revealed that we had no dsDNA… Aka, all the samples failed. Tom and I spent the rest of the week troubleshooting and running new samples through the process (which, thankfully, are working). Despite the disappointing turn of events, it was really interesting to work through possibilities with Tom and watch how he troubleshot the issue.
During my stay, I also had the chance to meet and learn from other lab members on a variety of topics, including restriction site associated DNA sequencing, caudal fin morphology and phylogeny, and bioinformatics. I am grateful to Dr. Angel Amores, Dr. Thomas Desvignes, Jason Sydes, and Pete Batzel for dedicating hours of their time to my training.
My goals in applying for the RCN exchange were to receive training on RNAseq techniques and to process samples for my doctoral studies. I can easily say that these goals were met and surpassed. The connections, skills, troubleshooting techniques, and experiences both in and out of the lab have enriched my understanding of molecular genetics and fostered new contacts for future work. I am very grateful to Dr. John Postlethwait for hosting me in his laboratory. Collaboration between our labs will continue to benefit my PhD work and professional network. Tom and I plan to continue our work on the blackfish samples over the next year.
I owe a huge thanks to Tom for his training and allowing me to prod his vast knowledge throughout my visit. I would also like to thank Thomas for his inclusiveness, Dr. Frank von Hippel for encouraging my application, and the RCN g2p2pop for making this trip possible!!!
And yes, plaid is a required color (:
Nicholas Per Huffeldt’s lab exchange at Nagoya University in Nagoya, Japan Accordion Closed
To approach ecological questions regarding persistence of species, understanding constraints imposed by the current physiology of a species is an important piece to the evolutionary puzzle, and, being an ecologist by training, my molecular skills to investigate physiological mechanisms were limited. It was under this premise that I applied for support from the g2p2pop RCN to support a Laboratory Exchange in Prof. Takashi Yoshimura’s lab in the Institute for Transformative Biomolecules at Nagoya University, Japan. My objective for the laboratory exchange was to learn innovative molecular techniques, obtain proof-of-concept data, and strengthen international collaboration among my PI, Prof. Yoshimura, and myself.
Traveling from Aarhus University in Denmark was easier than expected; I flew to Helsinki, where I met up with Prof. Barbara Helm- my supervising PI for the project. From Helsinki, it was a simple flight to Nagoya, Japan. Prof. Yoshimura picked us up from the airport, and because we arrived on a Friday, we had the weekend to overcome our jetlag. But on Monday, the work began in earnest.
During our stay, I went through the steps to learn how to quantify RNA expression from neurological tissues, along with Prof. Helm. Each day was a new task, we started with tissue dissection and then cut very thin slices of tissue for histological staining. The subsequent violet color of the nuclei made navigating the tissue easier for the next step of obtaining miniscule and precise subsamples using laser micro-dissection. Thereafter, we extracted RNA and quantified the amount of RNA using qPCR. During this process, we had guidance from two of Prof. Yoshimura’s students Okimura and Toyama. They had tremendous amounts of patience and were knowledgeable of the methods. Prof. Yoshimura has three labs and is the head of his department, but this did not stop him from making our stay productive and interesting. He was able to come help when he could.
Prof. Helm left after the first week, and I continued to hone my skills the second week. I also had the privilege to visit one of Prof. Yoshimura’s other labs at the National Institute for Basic Biology in Okazaki where he studies seasonal phenomena using medaka fish.
On the plane back to Europe, I reflected on my experience. For this ecologist, the trip was a success. I was able to learn new molecular techniques that I will use in a future project and to further my career. The trip helped build an international network of scientists that are bridging physiology and ecology, and the RCN was instrumental in making all of this happen. I owe the RCN a huge thank you for their support in this learning experience, Prof. Helm for encouraging me, and Prof. Yoshimura for his generous hospitality.
Jordyn Upton’s lab exchange at Brookfield Conservation Park in South Australia Accordion Closed
The southern hairy-nosed wombat is a keystone species, South Australia’s faunal emblem, and was listed as Near-Threatened in 2016 (IUCN Red List). Because of this new listing, Dr. Faith Walker, my Primary Investigator (PI) at Northern Arizona University (NAU), renewed her interest in the burrowing marsupial. In 2017, she and a field team headed to Brookfield Conservation Park (BCP) to collect hair samples, the first of many projects she would start that year with wombats. The hair samples were being collected to take a genetic census of the population, which was last done in the early 2000s during Dr. Walkers Ph.D. work. The census will look at how population has declined, if any wombats are still present from the original study, and if space use has changed after 17 years. This project was how I got my start at NAUs Bat Ecology and Genetics Lab, and my introduction to wombats.
As I continue my work on the genetic census, we are also starting another project in our lab: looking at diet, gut microbiome, and pathogens of the southern hairy-nosed wombat. We also wanted to sample kangaroo feces, as the western grey kangaroo (Macropus fuliginosus) is highly abundant and may be impeding wombat population recovery. Wombats are very active in the spring, and Dr. Gaughwin was making plans to take a team into the field to collect these samples for Dr. Walker. As a college student, a trip to Australia was out of my budget, so I began looking for funding to join Dr. Gaughwin’s lab, and found the G2P2Pop RCN lab exchange program.
From September 14th to September 24th I participated in a Laboratory exchange at Brookfield Conservation Park in South Australia. I was hosted by PI Dr. Matthew Gaughwin, and worked with Drs. David Taggert and Bertram Ostendorf, as well as Colin Sobek from NAU. Wombats are more active in spring, making it on opportune time to go into the field and opportunistically collect samples. Having only worked in a laboratory, I was excited to tackle the challenge of field work and an entire new way to conduct research.
During my lab exchange, I was actively involved in the field work activities. Wombats are nocturnal, so each morning we woke up with the sun to begin sampling. We drove to wombat warrens in the 1km2 study site, and sampled fresh feces from around the burrow entrances. We sampled throughout the study site, using GPS to make sure we created a fair representation of the population.
As we drove around, we would also see kangaroos running from the truck. We would wait for the kangaroos to settle down. After a few minutes we would trek out to their resting place to search for fresh feces. When it got hot in the afternoons, we would take a break, going back to camp. Every day the kangaroos would disappear around 11 a.m. and we would not see another one until the sun began setting. While on the hunt for more kangaroo feces in the late afternoon, we would also stop by wombat warrens, as they would come outside to bask in the sun before the cold night came. This was probably my favorite part of the trip, observing the wombats in their natural habitat while they are unaware of us watching. I accidentally stumbled within 20 feet of one, which was awesome because they usually were scared off when anyone on the team got within 50 feet.
We finished sampling all of our feces within the week. It was great to accomplish our goals, especially since the first few days we were very worried about not getting enough kangaroo feces since we were struggling to find fresh samples. With our extra tubes, we collected vegetation from around wombat warrens. The samples of the plants will have their DNA extracted, and we will create a genetic “barcode”, where other scientists can compare their DNA and see if they have the same plant. This will be helpful since there is a lack of information available on Australian flora in most United States databases.
While I was there, a lot of work occurred, but I did get the opportunity to explore Adelaide. The first day we landed, I went to Cleland Wildlife Park, which I recommend to anyone wanting to get a taste of Australian Wildlife. You can pet koalas during certain times of the day, and buy bags of food to hand feed kangaroos and wallaby’s.
Having never seen any marsupials in zoos before, this was a very unique and exciting opportunity for me. I also had the opportunity to meet a wallaby joey named Mikey. His mother was a victim of a hit and run, and he was being cared for by Jo, a woman working at a nonprofit. I was given the honor of bottle feeding him during his afternoon snack.
Camping in the outback was also one of the coolest experiences I have had to date. There were tropical birds flying everywhere, my favorite being the Galah. When walking through the park, I could see Emus running in the distance, and hear magpies and other birds calling to each other. I quickly got over my arachnophobia there, as there were plenty of wolf spiders, huntsman, and orb weavers. I actually came to appreciate the huntsman living on my tent, as he kept down the number of flies and mosquitoes around.
I would recommend applying for a lab exchange to anyone. The contacts and the experience I gained working in the field I made will benefit me for years to come. I would like to thank Dr. Matthew Gaughwin for being an amazing host, as well as Brookfield Conservation Park for allowing us to go into the field and sample this year. I would also like to thank my PI, Dr. Faith Walker, for encouraging me to apply for this lab exchange and the G2P2POP RCN for sponsoring this laboratory exchange.
At the American Physiological Society’s Comparative Physiology: Complexity and Integration Meeting, g2p2pop steering committee members Drs. Allyson Hindle and Loren Buck, along with member Dr. Gisele Oda, will present “Connecting Genomes to Phenomes to Populations” on Friday, October 26, 2018.
“Navigating Climate Change,” videos from our first workshop! Accordion Closed
Navigating Climate Change Featured Speaker: Dr. Tom Whitham Accordion Closed
The first g2p2pop workshop, Navigating Climate Change, will be held in Flagstaff, Arizona from September 19-21, 2018. On day 1, four speakers will be featured. Dr. Scott Goetz, Dr. Andrew Richardson, Dr. Tom Whitham, and Dr. Stephen Jackson.
Dr. Tom Whitham is a Regents’ Professor of Biological Sciences at Northern Arizona University and serves as Co-Executive Director of the Merriam-Powell Center for Environmental Research.
Part of Dr. Whitham’s research focuses on how underlying genetics shapes and impacts the local ecosystem. In a recent study published in Proceedings of the Royal Society B, Dr. Whitham and colleagues investigated how genetic variation in a foundational tree and its herbivore aphid interact. They found that the two genotypes interacted to impact arthropod community structure, but this interaction was dependent on the abundance of aphids.
In another study, Dr. Whitham and colleagues investigated how foundational tree genotype impacts the mutualistic fungal species in drought conditions. They found that specific tree and fungal genotypes were able to tolerate drought conditions better than others and that these associations held over multiple tree generations. These results suggest that there is a genetic basis to these traits.
Additionally, Dr. Whitham creates ecological niche models to better predict species distributions. In a recent study published in Global Change Biology, Whitham and colleagues incorporated genetic data to these models, which improved the accuracy of the existing models by about 12-fold. The model also showed that existing populations that are adapted to specific niches are likely to diverge further in niche as the climate changes.
Dr. Whitham’s research suggests additional ways in which we can examine community dynamics and how these communities may be differentially impacted by climate change.
Navigating Climate Change Featured Speaker: Dr. Andrew Richardson Accordion Closed
The first g2p2pop workshop, Navigating Climate Change, will be held in Flagstaff, Arizona from September 19-21, 2018. On day 1, three speakers will be featured. Dr. Scott Goetz, Dr. Andrew Richardson, Dr. Tom Whitham, and Dr. Stephen Jackson.
Dr. Andrew Richardson is a professor at Northern Arizona University in the School of Informatics, Computing, and Cyber Systems and in the Center for Ecosystem Science and Society. He is the Principle Investigator of PhenoCam Network, a system of high-resolution cameras that are used to track how phenology is changing across North America. Together with David Hollinger, he runs the AmeriFlux tower in the Bartlett Experimental Forest, which measures carbon dioxide, water, temperature, and energy.
Dr. Richardson use many different methods to better understand how climate change is impacting phenology. Recently, he and a colleague used photographs from aerial drones taken of forest canopies over different seasons. They were looking at how specific color changes in the canopy might correlate with events in the leaf life cycle to better analyze phenology data. In the study published in Sensors, they found that both green and red colors correlate to leaf aging in autumn, and the redness can track the progression of leaf fall that begins with peak redness.
In addition to this data, Dr. Richardson uses data from PhenoCam to model how phenology may shift in the changing climate. His study published in Global Change Biology shows how leaf-out dates in deciduous forests in the Northern Hemisphere may shifting by up to 11 days.
Dr. Richardson also measures the temperature of forest canopies using the Ameriflux towers equipped with thermal cameras reading at hourly intervals, as published in Agricultural and Forest Meteorology. As air temperature can be quite different from canopy temperature, Richardson and colleagues hoped to see how these dynamics differ between species and over different timescales.
Overall, this line of research has important implications for ecosystem dynamics, and we look forward to speaking with Dr. Richardson!
Aubrecht, D. M., Helliker, B. R., Goulden, M. L., Roberts, D. A., Still, C. J., & Richardson, A. D. (2016). Continuous, long-term, high-frequency thermal imaging of vegetation: Uncertainties and recommended best practices. Agricultural and forest Meteorology, 228, 315-326.
Chen, M., Melaas, E. K., Gray, J. M., Friedl, M. A., & Richardson, A. D. (2016). A new seasonal‐deciduous spring phenology submodel in the Community Land Model 4.5: impacts on carbon and water cycling under future climate scenarios. Global change biology, 22(11), 3675-3688.
Navigating Climate Change Featured Speaker: Dr. Stephen Jackson Accordion Closed
The first g2p2pop workshop, Navigating Climate Change, will be held in Flagstaff, Arizona from September 19-21, 2018. On day 1, three speakers will be featured. Dr. Scott Goetz, Dr. Andrew Richardson, Dr. Tom Whitham, and Dr. Stephen Jackson.
Dr. Stephen Jackson is the Director of the Department of the Interior Southwest Climate Adaptation Science Center and an Adjunct Professor of Geosciences and Natural Resources and Environment at the University of Arizona. He is also a Professor Emeritus of Botany at the University of Wyoming.
Dr. Jackson uses paleo-archives, such as sediment cores and tree-rings, to understand how ecosystems have responded to environmental perturbations. Recently, he and colleagues investigated vegetation dynamics in the Ozark highlands in Missouri since the last glacial maximum, about 21,000 years BP. Using sediment cores sampled for pollen, charcoal, and plant microfossils, they quantified the dominating species, rate of vegetation change, and potential reasons for turnover.
Recently, he and colleagues put forward a manuscript to Trends in Ecology and Evolution that communicated the need to account for novel species assemblages. They argued that going forward, studies should focus on the interaction of species that are invading new areas with those that have stayed in their historical range. As the climate continues to change, it is becoming increasingly important to understand these interactions as they may impact management efforts.
Dr. Jackson has put forward many perspectives papers that argue for the inclusion of paleo-ecological data into current studies and models. We look forward to hearing his perspective on how that data can be used to model genomes to phenomes to populations!
Jones, R. A., Williams, J. W., & Jackson, S. T. (2017). Vegetation history since the last glacial maximum in the Ozark highlands (USA): A new record from Cupola Pond, Missouri. Quaternary Science Reviews, 170, 174-187.
Alejandro Fernandez Ajó’s Lab Exchange at Oregon State University Accordion Closed
From July 26 to August I participated in a Laboratory exchange at the Geospatial Ecology of Marine Megafauna Laboratory (GEMM Lab) at Oregon State University at the Hatfield Marine Science Center (HMSC), Newport-OR. I was hosted by principal investigator (PI) Dr. Leigh Torres with the two main objectives of 1) collaborating and learning non-invasive fieldwork techniques for studying free-range whales and 2) interacting with, exchanging ideas, and networking with the GEMM Lab members. PhD candidate Leila Lemos lead the research specifically titled, “Evaluation of gray whale hormone and body condition variation, with response to variable ambient ocean noise conditions,” a project which aims to evaluate the hormonal variability and health of the gray whales that forage along the Oregon coast.
Marine mammals live and have evolved in an acoustic world where the production and reception of sounds plays a fundamental role for survival. Sound intervenes in the biology of cetaceans in numerous ways, from mediating the attraction and selection of mates to the search for prey and the perception of their environment. The human use of the oceans, whether for navigation, military activities, exploration for gas or petroleum resources, and tourist or recreational navigation increases the amount of sounds in the sea. Usually these sounds of anthropic origin do not represent signals for marine fauna and are considered as “noise” that can affect marine animals in different ways. Despite its importance, there is limited knowledge about the physiological stress response to human noise for cetaceans and marine mammals in general. Research into stress physiology of mysticete whales has been hampered by difficulty in obtaining physiological samples from individuals; however, new methods are available for measuring hormone levels in whales and have the potential to improve our understanding of whale physiological condition to target important conservation questions, such as the ones Leila Lemos´ project is undertaking.
Field season for this project expands between May and October each year, and the gray whales, Eschrichtius robustus, subject of this study are part of the Pacific Coast Feeding Group (PCFG) that forage in the coastal habitat off of Oregon, where they are exposed to variable ambient ocean noise conditions (e.g., storms, vessel traffic, and more recently seismic surveys). The objectives of the study are to (1) measure and characterize the coastal soundscape of Oregon, (2) determine the physiological baseline and describe the variation in reproductive and stress hormones in gray whale fecal samples, (3) evaluate the trends in gray whale body condition by demographic unit and temporal period, (4) assess the annual variation in prey availability and quality for gray whales, and (5) link these previously described data sets and results to evaluate the relationships between ambient ocean noise levels and gray whale health. The study uses a combination of methods to link whale stress with varying ambient sound level conditions. Using hydrophones to monitor coastal ambient ocean noise, fecal sample collection and analysis for stress hormones levels in gray whale’s assessment, the use of video recordings through UAS (“drone”) flights to document whale behavior and body condition, and deployment of GoPro cameras along with zooplankton sample collections to describe prey availability for whales.
During my exchange I was actively involved on the fieldwork activities which consisted of small boat-based surveys for gray whale photo-identification, photogrammetry data collection, as well as the collection of fecal and zooplankton samples. Each day we were scheduled to departure from the boat ramp at the HMSC and survey the area around Newport. During the days I have participated in the fieldwork, we surveyed the area between Otter Rock, North of Newport, and Seal Rock, South of Newport, approaching every gray whale we encountered. However, fieldwork at sea is highly dependent on weather conditions, such as fog, wind, swell, presence of whales and many other factors that can hinder the possibilities of conducting fieldwork at sea. During the time I spent with the GEMM Lab, we were very lucky with the weather where wind conditions were optimal, and whales were around most of the days. The only limiting factor was the visibility, a dense fog was present nearly every morning, but occasionally lifted after mid-day.
Once at sea and as we crossed the harbor jetty all eyes were overboard to spot a whale blow. Someone would shout, “there it blows!”- giving directions to the pilot on where to go. We imagined the boat as a clock, with the bow being the 12, the stern being 6, and so on. For example, a whale could be seen at “1 o’clock” 50 meters away, meaning about 30° to the starboard and 50 meters away. That method was particularly useful when flying the drone as the drone pilot would be looking at the control screen not able to see overboard. As the boat carefully approached the whale, the researcher would assess the whale’s behavior and would decide if they could continue to approach the whale or not. If the whale was feeding or staying stationary, the researchers would decide to stay nearby and collect the data. However, if the whale was traveling or swimming away from the boat they would leave the individual and start searching for the next one.
Once in the vicinity of the whales, tasks would be assigned to each member on board such as taking notes, photographing the whales for photo-identification, operating the drone, setting the calibration board (a board of a known length which allowed us to calculate the exact size of each pixel at various UAS altitudes and accurately measure whale lengths) and, of course piloting the boat.
Whenever one of the researchers would scream “poop!” the boat pilot would hurriedly try to approach the location where the whale defecated at which point one crew member would use a net to collect as much fecal matter as possible. If the drone was flying, the pilot would keep following the whale with the aid of another crew member which would always be taking pictures of the whale. The frame number of the pictures would be written on the notes, synchronized with the time in the iPad frame that is linked to the drone, to match the ID of the whale with the sample collected. That was probably the most stressful moment aboard, where there were only a few seconds before the poop scattered and sank deep into the ocean. Collecting the precious samples was integral to our mission. In addition to the perilousness of collecting the fecal samples, it was also critical to accurately match the identity of the whale with the fecal sample and the drone images to complete the picture.
The gray whales looked prehistoric, especially when they would arch their back to submerge beneath the sea surface where if you were lucky, you could see a series of knuckles on their backs that resembled ancient dinosaur crests. As they dived, the ideal moment for photographing their flukes arose. Everyone was prepared to take the pictures that would help identify the individual whale, and oftentimes this was also the moment when the whales would defecate. These pictures would allow us to match the samples with the whale ID. However, unlike humpback whales where the photo ID is based mainly on the unique shapes and color patterns on the underside of their flukes, gray whales were complex in that the researchers needed more aids for individual identification. For every sighting we would try to take pictures from left and right, at the first knuckle, and the fluke whenever possible. With all this information, the scientists could identify the individual whales. But for the GEMM research team I worked with, it was apparent that they know most of the individual whales very well. They could remember who was who and what that particular whale was doing days before or even in the previous seasons. They nicknamed most of them and for many of the whales they even knew their gender and whether they came with a calf in the previous years. It was fascinating!
I myself had the opportunity to re-sight one particular whale. On my first day on the boat we spotted a whale who had a very distinctive heart shaped grey spot on the underside of her/his fluke and the very last day at sea we found that one again! It is hard to explain how amazing is to get the feeling of knowing an individual, wild and magnificent animal like these whales and I can only imagine the joy Leila, Leigh, Todd, and Sharon experience when they re-sight a whale from one season to the next after their long migrations! I nicknamed that whale, just for myself, as Pluto, because of the resemblance of the mark with the large heart-shaped nitrogen glacier revealed in 2015 on Pluto by the New Horizons spacecraft.
The days when we could not go out onto the sea, we were on “standby” for weather conditions to improve and get ready to launch the boat. Those were the times when I could interact with the rest of the GEMM Lab members. Dawn Barlow is a PhD student who studies the ecology of blue whales in New Zealand; Dominique Kone is a masters student working on a project that looks at the potential to reintroduce sea otters to the Oregon coast by identifying suitable habitat and investigating their potential ecological impacts. Leila Lemos is a PhD candidate leading the gray whale project. Prof. Sharon Nieukirk, an acoustics researcher, is helping to characterize the acoustic soundscape off the Oregon Coast. Unfortunately, I was unable to meet with the last member of the GEMM Lab, Alexa Kownacki, PhD student, as she was studying the common bottlenose dolphin’s population health off in California and is conducting fieldwork in San Diego, but we are all connected via email and are exchanging ideas on methods for studying hormones on free-living whale and dolphins.
Friday, August 3rd, I presented my research plan to the GEMM lab, preliminary results and future goals, which led to a very interesting interaction with the lab members, where we exchanged ideas for plans in the future and ways to better understand the data I was generating. Additionally, we discussed the ongoing projects of the GEMM lab and again exchanged ideas. Building these new connections will greatly improve my opportunities to develop as a marine mammals’ scientist by broadening my views, learning about other projects and approaches to solve marine mammal ecology questions, as well as applying science to conservation of marine mammals and their habitats.
Furthermore, while I was at the HMSC, a humpback whale, Megaptera novaeangliae, was reported to be entangled in fishing gear off Winchester bay (76 miles South off of Newport). A rescue team from Cascadia Research, a non-profit Washington State corporation responded to the event and we were summoned to collaborate with the search of the entangled whale. Dr. Leigh Torres, Todd Chandler, and I met the group of Cascadia Research Collective (CRC) led by John Calambokidis. In total we were three boats at sea scouting the area and searching for this whale with gear. While looking for the whale we approached over 80 Humpbacks, and collected pictures for photo-identification that will contribute to the humpback whale photo-ID catalog in the North Pacific Ocean. However, despite over 8 hours at sea searching for the whale with gear, we were unable to find it and had to head back to shore with the gas tank almost empty but hearts full of wonderful memories and images of the whales, seabirds, and blue sharks that were swimming near the boat. The next day, we headed back to Newport to continue with the gray whale field work, but the Cascadia team continued the search in the following days. Hopefully, they will find and release the whale from the fishing gear.
I would highly recommend this type of laboratory exchange for building connections and networking with researchers in interdisciplinary fields of study who can synergistically collaborate in building new and novel science to solve both ecology and conservation questions. I would like to thank Dr. Leigh Torres, Leila Lemos and the GEMM Lab members for hosting me at the HMSC in Newport as well as Dr. C Loren Buck and Dr. Kathleen Hunt for encouraging me to participate in this exchange and the G2P2POP RCN for sponsoring this laboratory exchange.
Navigating Climate Change Featured Speaker: Dr. Scott Goetz Accordion Closed
The first g2p2pop workshop, Navigating Climate Change, will be held in Flagstaff, Arizona from September 19-21, 2018. On day 1, three speakers will be featured. Dr. Scott Goetz, Dr. Andrew Richardson, Dr. Stephen Jackson, and Dr. Tom Whitham.
Dr. Scott Goetz is a Professor at Northern Arizona University in the School of Informatics, Computing, and Cyber Systems. He serves as the Deputy principal investigator of NASA’s Global Ecosystem Dynamics Investigation (GEDI), a high-resolution laser precisely measuring topography and forest features, including canopy height. He is also the Science Lead of NASA’s Arctic Boreal Vulnerability Experiment (ABoVE), a long-term study of how climate change is impacting these ecosystems. Previously, he was the Deputy Director of Woods Hole Research Center.
Dr. Goetz makes use of many tools to predict how vegetation will change over time, particularly in the face of climate change. A recent publication in Environmental Research Letters describes how he and colleagues made use of Landsat satellite imagery to map plant and shrub aboveground biomass in the Arctic tundra. They found areas where summer temperatures were higher also had higher above-ground biomass overall and were more likely to be dominated by shrubs, which indicates that additional warming may exacerbate this trend.
These trends have an impact on how wildlife use and interact with the environment. For example, Zhou et al. found that moose and snowshoe hares have been expanding their ranges to include areas that are increasing in shrub density, as it is preferred foraging area and may provide shelter from predators. These maps may be of utmost importance to model how wildlife will use these areas and shift their ranges as increased warming, and subsequent changes in plant biomass, occur.
During his time at Woods Hole Research Center, Dr. Goetz and colleagues studied how corridors between protected areas in the Amazon differ in above-ground biomass. They found that these corridors are contain about 15% of the total above-ground carbon in the region and can sometimes surpass the amount of carbon found in the protected regions which they connect. Additionally, they play an important role in the passage of flora and fauna between these protected areas, as well as supporting many species themselves. These results suggest that management efforts can benefit by targeting corridors high in above-ground biomass for preservation, both for carbon sequestration and biota.
Dr. Goetz’s research represents an important link between ecosystem dynamics and climate change, with important implications how organisms will respond. We look forward to hearing from him!
Berner, L. T., Jantz, P., Tape, K. D., & Goetz, S. J. (2018). Tundra plant above-ground biomass and shrub dominance mapped across the North Slope of Alaska. Environmental Research Letters, 13(3), 035002.
Zhou, J., Prugh, L., D. Tape, K., Kofinas, G., & Kielland, K. (2017). The role of vegetation structure in controlling distributions of vertebrate herbivores in Arctic Alaska. Arctic, Antarctic, and Alpine Research, 49(2), 291-304.
The RCN’s First Meeting Accordion Closed
G2p2pop had its first organizational meeting March 8 and 9th at the University of Nevada, Las Vegas. Present we had: Loren Buck (NAU), Nika Galic (Syngenta Crop Protection), Allyson Hindle (Harvard), Frank van Breukelen (UNLV), Haley Hanson (USF), Jenifer Utz (UNLV), John Delong (UNL), Elinor Karlsson (Broad Institute), Jared Wilson (UNLV), and Sarah York (UNLV). Unfortunately, Michael Romero (Tufts) couldn’t make it due to inclement weather!
Together, our research interests ranged from animal physiology to ecological modeling to pedagogy. We assembled to begin discussions on the trajectory of the RCN, how we intend to measure success of our meetings, and to plan our first official workshop scheduled for Fall 2018. We identified the need to recruit additional modelers, specifically non-linear modelers and those working on the molecular level.
We decided on the theme and set the location for the workshops.
At these workshops, we hope to have approximately 5 plenary talks on day one that encompass the theme, followed by breakout sessions for the remainder of the time to maximize interaction between participants.
We also determined the steering committee: Loren Buck (NAU), Nika Galic (Syngenta Crop Protection), Allyson Hindle (Harvard), Frank van Breukelen (UNLV), Jenifer Utz (UNLV), John Delong (UNL), Elinor Karlsson (Broad Institute), Lynn “Marty” Martin (USF), Haley Hanson (USF), Michael Romero (Tufts), and Kenia Bicego (UNESP, Jaboticabal).
We were able to spend a little time outside of the meetings, as well… Frank van Breukelen gave us a tour of his lab, including a visit to his tenrecs!
Thank you to the meeting organizers! Looking forward to more g2p2pop meetings.
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
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