Fall 2019 Happenings

Fall 2019 Happenings

The Fall 2019 semester is in full swing here at URI and the Humphries Lab is busy squeezing in all our favorite wholesome New England Fall activities between manuscripts, scuba dives, data analysis and class schedules. Read on for an update of what everyone is up to.

First and foremost, the Humphries Lab graduated our very first PhD this summer!! Evans has set the bar high with the hardworking, calm, cool, and kind manner in which he worked through his dissertation these past years. We are so excited for his accomplishment and his next adventure as a faculty member at the University of Cape Coast, and although it is bittersweet we’re so happy to have him back with his family in Ghana. Glad you could school us in bowling one more time before departing, Evans!


In late September, the lab wrapped up annual fish habitat monitoring in partnership with some friends from the RI Department of Environmental Management. As per usual, the water was chilly, the visibility was poor, the morale was high and we still managed to have fun.

Our group has published a number of papers since our last blog update, covering research topics from snapper & grouper life histories, fishing gear selectivity, periodically harvested fishing closures, and social vulnerability in oyster fisheries. See all of the publications from the lab group on our website’s publication page.

Austin, Kelvin, Paul and Lauren spent part of the summer focused on creating engaging lesson plans covering fisheries management topics and have submitted lesson plan materials on seafood traceability and ecolabeling to SESYNC and CourseSource.

Paul, Kelvin, and Lauren on a fresh air break from work with their SESYNC group in Annapolis, MD.

Paul, Kelvin, and Lauren on a fresh air break from work with their SESYNC group in Annapolis, MD.

Lots of us are still currently in writing mode. Celeste is putting the finishing touches on her MS thesis on a dynamic energy budget model for local kelp production. Elaine is applying for research fellowships and putting together a proposal on patterns and drivers of cryptic diversity on hyperdiverse coral reefs.

On the data analysis side of things, Annie is working on balancing a model of the Narragansett Bay social-ecological system and prepping to attend the Ecopath 35 conference in Florida later this semester. Elle recently traveled to Belgium to participate in this year’s Open Sea Lab Hackathon where her team won 3rd place for their app that uses Copernicus data to teach kids how personal choices affect polar conditions!  

Elle and her Hackathon team #ByteBear placed 3rd overall among more than a dozen teams in this year’s Hackathon data science competition run by Open Sea Lab.

Elle and her Hackathon team #ByteBear placed 3rd overall among more than a dozen teams in this year’s Hackathon data science competition run by Open Sea Lab.

Kelvin has had his hands full working through the fish landings data in the large coral reef fisheries monitoring database resulting from our work in Lombok, Wakatobi, and Raja Ampat, Indonesia. Paul has been working from this database as well with two new undergraduate researchers in the lab, Ned and Cullen, to analyze fish length trends across different fishing gear types and management strategies. 

Our newest MS student Nicky returned from a successful first field season on the island of Bontosua, Indonesia to a full class schedule. While in the field with Austin, Nicky was piloting and training field assistants in collecting data for her work studying fisheries value-chains on Bontosua.

Austin has submitted his tenure dossier (WOO!) and will be back on the Kenyan coast this November, checking in with collaborators and going over some preliminary research results on local fisheries potential for supplying dietary micronutrients to local communities.

This is just a flavor of what we’re up to this academic semester! Follow the lab on Twitter at our handle @URI_fisheries to get regular updates, and Happy Fall 2019!

Lab dinner at Lauren’s house with puppy Suki in late Summer 2019

Lab dinner at Lauren’s house with puppy Suki in late Summer 2019

2019 Misool Field Excursion

2019 Misool Field Excursion

Last month a team of URI researchers composed of members of the Humphries and Lane Labs joined collaborators in Indonesia for a data collection trip to Misool Conservation and Marine Reserve in Raja Ampat, Indonesia. Raja Ampat’s coral reefs support the world’s greatest biodiversity, making it an important site for understanding Indonesia’s coral reef ecosystems.

Professors Austin Humphries and Chris Lane, and PhD students Elaine Shen and Erin Borbee joined Dr. Hawis Maduppa and undergraduate and graduate students of Bogor Agricultural University (IPB) and University of Papua (UNIPA). They were stationed on a liveaboard research vessel to collect coral reef biodiversity and fisheries data from more than 40 sites in Misool. Read on to learn more about the specific roles and activities of each of our URI researchers.

Austin was leading the trip along with Bogor Agricultural University’s Dr. Hawis Madduppa and URI Professor Chris Lane. Austin’s role was to make sure they selected appropriate sites that were intended to represent the broader Misool coral reef environment, from reefs that had abundant coral and fish that see little to no fishing pressure, to reefs more impacted by fishing and/or other factors that reduce species abundance. The overarching goal of this trip was to sample this area that represents a more "pristine" coral reef ecosystem in Indonesia, or area that has a lighter human fingerprint, to give the group a baseline of biodiversity and fisheries. This baseline is important in assessing the efficacy of management and for goal-setting when creating new policies. The team was taking underwater visual censuses as well as collecting gut contents of grouper for DNA analysis and water samples for environmental DNA. By pairing new technology and methods with traditional census techniques, they are able to study the entire foodweb and not just what we can see when underwater. Ultimately, the group is interested in how management might be able to increase fisheries production to support food security in Indonesia, while also considering the impacts on biodiversity.

Elaine was a part of the grouper gut content team, where she helped dissect and isolate over 80 grouper stomachs and intestine contents for metagenetic analysis. These groupers were collected from local fishermen who used handlines each morning to capture the fish. She also took fin clip samples of other fish species to begin building a custom genetic database for Indonesian fish. After doing lab work with Erin, Elaine visited Sekotong, Lombok, to learn about coral reef fisheries with students from the University of Mattaram (Awan, Iza, Rahmat). At landing sites and the local market, she was able to collect more unique fin clip samples, totaling her count to ~60 different coral reef fish species.

Chris and Erin were a part of the eDNA team, where they dove to collect water samples at sites varying in levels of fisheries management (open access and gear-restricted). Once collected, Chris and Erin would filter the water samples on the boat using a fancy peristaltic pump. Erin stayed with Elaine after fieldwork to process all of the genetic samples (eDNA, gut content, fin clip) at the Biodiversity and Biosystematics Lab at Bogor Agricultural University (IPB) and they mentored students through DNA extraction and PCR. Erin even celebrated her birthday in the lab!

Overall, the trip was an exhausting but highly rewarding data collection effort. Now it’s time to hit the lab and crunch the numbers so we can show you all what we learned. Stay tuned!

PS. Huge thank you to Chris Lane, Erin Borbee, Iqbal Sani, and Budi Pradbowo for photo credits!

Graduate and undergraduate researchers (left to right) Erin, Elaine, Dije, Iqbal, Ubun, and Abby teamed up for fieldwork in Misool.

Graduate and undergraduate researchers (left to right) Erin, Elaine, Dije, Iqbal, Ubun, and Abby teamed up for fieldwork in Misool.

Spring 2019 Happenings

Spring 2019 Happenings

The Humphries Lab is rolling right through these strange New England winter weather patterns and into the Spring 2019 semester! As per usual, this semester will see our group increase in size, travel across borders in the name of sustainable fisheries, and expand our minds, teaching skills, proposals, and scientific pubs! All the activity is seriously invigorating, and this upcoming semester should be a time of lots of hard work paying off for all of us. Read on for specific updates on each lab member!

Austin kicked off the new semester abroad on the Kenyan coast, getting the new USAID project named #SecureFish up and running. The project will identify conditions under which local fisheries could improve provisions of vital nutritional resources to pregnant women and young children in local communities while also sustaining marine ecosystem functioning. Austin spent 3 weeks in Kenya meeting with collaborators and local community members to establish protocols for data collection. Austin will be busy this semester teaching an Ecosystem-Based Fisheries Management course, mentoring students, and overseeing so many other research projects that really he needs his own separate blog post to cover it all.

Annie, our newest Humphries Lab member, is quickly getting oriented to her graduate program and diving into a packed class schedule that covers ecosystem-based fisheries management, big data analysis, marine protected area (MPA) management, and of course graduate seminars! She’ll be spending the semester getting going on her work with the RI C-AIM group modeling the Narragansett Bay social-ecological system.

Celeste has been hard at work contributing to the maintenance of a horde of kelp babies in their aquaculture nursery and helping to oversee their deployment at sea to grow and provide data for her kelp growth model. Celeste is working with her collaborators to parameterize the kelp model and will be teaching an undergraduate recitation course on introductory ecology.

Elaine has been working on the construction of a data analysis work-flow protocol for environmental DNA (eDNA) sampling in Indonesia and helping to lead programming as a part of the student-led CELS department Professional Learning Community (PLC), including a panel she recently co-moderated on social responsibility and equity in STEM. This semester she will be working on developing her proposal and teaching an undergraduate herpetology course.

Elle is back stateside after many months in Bali working through data and writing her first manuscript. She presented her research at the 5th International Marine Conservation Congress meeting in Malaysia and participated in the Youth Summit during the 2018 Our Ocean Conference in Bali. This semester Elle will be preparing for comprehensive exams and teaching and grading for multiple undergraduate courses.

Evans has his eyes set on a Summer 2019 graduation. He has his work cut out for him finishing up data analysis, polishing off his dissertation chapters, and preparing to defend his dissertation on sustainable management of the Ghanaian sardinella fishery. Meanwhile, Evans has also discovered the secret to reversing hair loss. No joke. But we do ask that you hold all requests for information on this front until after his successful PhD defense.

Kelvin has already been busy expanding his professional toolkit by participating in various workshops early this semester, including the 2019 SABER West conference on STEM education research and a National Institute for Mathematical and Biological Synthesis (NIMBioS) workshop on network modeling. Kelvin will continue this semester lending his expertise to various projects in the lab, such as the RI EPSCoR C-AIM effort to build an end-to-end model of the Narragansett Bay ecosystem and working with socioecological fisheries data from Wakatobi, Indonesia, to understand management tradeoffs.

Kelvin reunites with a research mentor and former graduate school classmate from University of Hawaii for dinner after the SABER West conference.

Kelvin reunites with a research mentor and former graduate school classmate from University of Hawaii for dinner after the SABER West conference.

Lauren will be spending the upcoming semester overseeing the usual wide range of research activities, from data visualizations to travel coordination to drafting manuscripts. A couple of the major projects that will be occupying Lauren’s attention in the coming months include finalizing a data matrix of Narragansett Bay fish diets for input into the ecosystem model being developed by the RI C-AIM modeling group, and handling data coming in from the USAID #SecureFish project examining marine resources in Kenya as a solution to local nutrition insecurity.

Melati will be busy this semester working to finish analyzing fish landings data and market networks from our Wakatobi, Indonesia, field site. Melati expects to graduate in May.

Melati and research collaborator Professor Wa Iba of Universitas Halu Oleo celebrate one year of successful data collection with a fish fry.

Melati and research collaborator Professor Wa Iba of Universitas Halu Oleo celebrate one year of successful data collection with a fish fry.

Paul conquered his comprehensive exams and is now enjoying working as a teaching assistant for both marine ecology and intro to biology undergraduate courses. Paul is also wrapping up his SESYNC graduate pursuit research on the impacts of hurricanes on coastal socio-ecological systems. His major goal this semester is to complete the first chapter of his dissertation and get his manuscript on periodically harvested fisheries closures published.

As always, stay tuned for highlights before classes wrap up and we break for the summer field season! Wait, it’s summer time already?!

Fall 2018 Semester Highlights

Fall 2018 Semester Highlights

The Fall 2018 academic semester is in full swing and so are we! We are a big group here at the Humphries Lab and we’ve got big to-do lists to match. Whether it’s immersing in the first required courses of a graduate degree, teaching, or studying for and annihilating comprehensive exams, we’re meeting the new challenges with that ‘back-to-school’ enthusiasm that this time of year always brings. Here’s a glimpse of what everyone is up to:

Austin (PI) has his hands full mentoring students, and teaching 2 sections of URI’s ‘Food from the Sea’ course while helping to launch the AquaFish Innovation Lab, a giant new USAID funded research partnership that will look into opportunities to use seafood to improve food security. Austin is serving as the East Africa Director on the project and will work closely with Washington University in St. Louis, Pwani University and Egerton University to lead research efforts in Kenya. This is just a flavor of the many, many on-going projects Austin is working on.

Kelvin (post-doc) has been working and succeeding on learning Ecopath modeling to assist in his work building a socio-ecological model of Narragansett Bay for the NSF EPSCoR Rhode Island Consortium for Coastal Ecology Assessment, Innovation and Modeling (C-AIM) effort. Kelvin and Austin attended an intensive 5-day Ecopath workshop at the Center for Marine Sciences at Universidade do Algarve in Faro, Portugal in early November.

Diana (postdoc) is being kept nice and busy teaching URI’s Fisheries Science (AFS 415) course. Class topics cover the foundations of aquatic species as resources, including fisheries ecology, management, and farming.

Lauren (research associate) started the Fall 2018 semester fresh back from a trip to Bali where the Humphries Lab was able to secure additional funding to continue monitoring the impact of a new coral reef restoration method on local small-scale fisheries activity. Lauren will also help Kelvin to develop curriculum for a week-long teaching module on seafood traceability in Austin’s ‘Food from the Sea’ course this Fall.

Research Associate Lauren Josephs with URI collaborators Amelia Moore and PhD student Jess Vandenberg pose for a group photo at the end of the Mars, Inc. coral reef restoration workshop in Bali.

Research Associate Lauren Josephs with URI collaborators Amelia Moore and PhD student Jess Vandenberg pose for a group photo at the end of the Mars, Inc. coral reef restoration workshop in Bali.

Evans (PhD student) is back from 8 months in Ghana, where he spent time finishing up his data collections on the Sardinella fishery in his home country. Evans is now prolifically producing figures, tables, and models of his data (learning a lot of “for” loops in R), writing up his first manuscript, and aims to graduate in 2019.

Paul (PhD student) has finished up his fieldwork in Indonesia during which he has logged an impressive 100+ dives over just a few years. Paul recently got his dissertation proposal approved and is now deep in the dark pit that is studying for comprehensive exams. We all miss him and eagerly await his return to the land of the non(read:less)-stressed.

Elle (PhD student) is working from Bali, Indonesia, this semester where she is writing her dissertation proposal and contributing to on-going fieldwork with The Nature Conservancy. Elle is also putting together a manuscript on updating the life-history parameters for the top-50 species in the demersal snapper-grouper fishery in Indonesia, and received a fellowship to take part in the Youth Leadership Summit at the Our Ocean 2018 conference in Bali.

Celeste (MS student) was able to travel to Moncton, Canada, with Austin to meet Dr. Romain Lavaud to check on his sea lettuce growth model and gain insight for her own kelp dynamic energy budget model for her Master’s thesis research on integrated kelp aquaculture. Celeste is helping to keep a blog on the larger NOAA-funded project that you can see here. She is also writing up her proposal, finishing up required courses, and learning to code in Python - she has already conquered Matlab and R.

Melati (MS student) is wrapping up data collection for her Master’s research. She spent the summer in Indonesia with collaborators completing the data collection process for her investigation of the market-chain from the coral reef Indonesian fishery in Wakatobi. Melati also oversees data collection on fish landings in Indonesia, and is being kept busy by her teaching assistantship on URI’s main campus.

Elaine (PhD student) Elaine (PhD student) is diving into her own required classes while also teaching three recitation sections for Intro Ecology. She was sponsored by the graduate school to attend the #InclusiveSciComm Workshop hosted by the Metcalf Institute here at URI and is busy thinking about research and outreach ideas that integrate what she learned.

Elaine having no problem whatsoever holding the attention of her students as she taught one of her Intro Ecology recitation classes on Halloween.

Elaine having no problem whatsoever holding the attention of her students as she taught one of her Intro Ecology recitation classes on Halloween.

Last but not least, the whole crew is looking forward to welcoming new MS student Annie Innes-Gold to the lab to study social-ecological modeling of the Narragansett Bay system this upcoming Spring 2019 semester!

Stay tuned for another productive year of building solutions to complex trans and interdisciplinary coastal problems from this excited and exciting group of individuals!

Drone shot of the lab group during the inaugural Humphries Lab retreat in Martha’s Vineyard, MA.

Drone shot of the lab group during the inaugural Humphries Lab retreat in Martha’s Vineyard, MA.

Summer 2018 Update

Summer 2018 Update

Happy field season everyone! Just a quick update on what this marvelously giant group of researchers will be getting up to this summer.

Some of us will be mostly sticking around Rhode Island:  

Austin will be around helping students get organized and set for their field work trips, as well as getting some writing done and manuscripts submitted. He’ll be working on a hydroacoustic project with menhaden in Narragansett Bay collaborating with RI Dept. of Environmental Management, Jeremy Collie at GSO, and welcoming the talented Corinne Truesdale (MS student) to the lab group for the summer to work on the project.  Austin will also be spending a month doing field work in Indonesia and setting up more teams to collect fisheries data on small islands.

Lauren will be helping to manage student travel and tie up loose ends within the bounty of research projects the lab is orchestrating this field season. Lauren will also be traveling to Bali towards the end of the summer to meet will collaborators to discuss progress on our big coral reef ecosystem restoration project with Mars Symbioscience and Hasanuddin University in Indonesia.

Celeste will be working in Point Judith Pond and Narragansett Bay monitoring oyster growth and working on dynamic energy budget (DEB) models for kelp and oysters. Celeste and Austin will also be traveling to Canada to meet with an awesome DEB modeler.

Katie will be spending the first part of the summer in full-on defense prep mode. She’ll spend the rest of the warm months volunteering on a number of shark-related projects with NOAA Fisheries, working on a shark diving boat, and setting out on the job hunt.

Diky will be defying logic by celebrating the month of Ramadan, prepping to pass in and defend his Master’s thesis, and probably still fueling the rest of the lab with amazing home-cooked Indonesian food all at the same time.

Catie Alves is joining the Humphries Lab family this summer as a visiting PhD student from the University of North Carolina at Chapel Hill, studying with Dr. John Bruno. She’ll be around campus writing up her first dissertation chapter for publication, which documents 20 years of coral reef community changes along the Belize Barrier Reef. She’ll also be preparing for comprehensive exams with mountains of reading.

(So far) Kelvin will be working on two projects, splitting his efforts between Narragansett Bay and Indonesia. For Narragansett Bay, he’ll be leading a review paper on the rich history of models that have been used to study the physical, biological, and/or socioeconomic ecosystem components of the bay. And for Indonesia, he’ll be focusing on the small-scale fisheries Lombok, analyzing their catch data to look for patterns that could be informative for ecosystem-based fisheries management. Last but not least, Kelvin will be cutting his teeth (read: his canines) as a brand-new dog-daddy with his recently adopted cairn terrier named Kelly!

Diana continues to plug away at a review paper on what we know globally about coral reef fish genetic diversity. This requires lots of database and code wrangling behind the computer screen.

Melati will be in Wakatobi, Indonesia for her second field season. She will be gathering data for a value chain analysis of fish species sold locally within the archipelago and regionally in SE Sulawesi and larger Asia, mapping local and regional market networks for fish caught within the national park boundaries.

Paul’s field season is already off and running as he meets with his SESYNC graduate pursuit team in Annapolis to work on their research project studying hurricane impacts on social-ecological systems. In addition, Paul will be traveling to Wakatobi and Lombok in Indonesia to collect data for his dissertation. Between traveling and field work he’ll will be working on his dissertation proposal.

Elle will be traveling to the 5th International Marine Conservation Congress in Kuching in Malaysia to give a talk on her work characterizing the deep-slope demersal fishery in Indonesia. Then it’s a quick stop in Jakarta to see family and back to Bali to her office with her collaborators at The Nature Conservancy to resume field work and data collection for the next chapter of her dissertation.

This summer, Evans will be in Ghana to complete his field work, and clean up his data to get ready to launch into analysis mode. He’ll also be taking advantage of time at home to review relevant literature that is not readily available on the internet but found in Ghanaian libraries in hard copies, and of course to spend precious time with his family.

We’ll check back in again soon with lots of pictures of this (fish) frenzied summer. For now, there’s kelp to measure, perspectives to document, and parameters to define.

Shown here: Austin understandably startled by the success of his recruiting skills. Drawing by Elle Wibisono.

Shown here: Austin understandably startled by the success of his recruiting skills. Drawing by Elle Wibisono.