In identifying the oyster, the students did all the research from start to finish: DNA extraction, amplified a gene that’s typically used for DNA barcoding, did the analysis, and then wrote a report on what they found.
A previously undocumented oyster species has been recognized for the first time in Hawai‘i by a team of undergraduates, graduate students, and faculty at the University of Hawai‘i at Hilo in a collaborative project with community partners.
The work was done as part of a Course-based Undergraduate Research Experience, commonly called a CURE project, by a genetics class with lab work (BIOL 376L) taught by Jolene Sutton, assistant professor of biology at UH Hilo. CURE projects are large-scale, where an entire class works together to tackle a single research question.
“We brought the oysters into the class and the students did everything from start to finish,” says Sutton, an evolutionary geneticist specializing in conservation biology. “They did the DNA extraction, amplified a gene that’s typically used for DNA barcoding, did the analysis, and then wrote a report on what they found.”
Oyster species are difficult to identify based on morphology alone, but their identities can be resolved by applying genetic and genomic technologies. Until now, four extant species of true oyster have been documented in Hawai‘i. The genetic study by the UH Hilo students expands the known range of the western Pacific Ostrea equestris, a species previously documented in China, Japan, and New Zealand, by providing the first verification of its occurrence in Hawai‘i.
Sutton’s coauthors on the paper include the nine students in the genetics class: Keinan Agonias, Nicole Antonio, Brandi Bautista, Riley Cabarloc, Maata Fakasieiki, Noreen Aura Mae Gonong, Torey Ramangmou, Lavin Uehara, and Jade Wong.
The project arose serendipitously when Haws approached Sutton with samples of oysters she had collected but could not identify. Sutton, who was already having her CURE students do DNA barcoding in the genetics lab class using pre-specified training samples, had been looking for a project that had more relevance to the community. “I wanted my students to do a project with a purpose.”
The previously undocumented oyster identified by the class as part of a large species complex known as Ostrea stentina/aupouria/equestris. “It’s a group of oysters that are closely related and very difficult to distinguish from one another,” says Sutton. “We took the analyses a little bit further and it turns out that the samples that we have in Hawai‘i are most closely related to the western Pacific branch of Ostrea equestris, which are associated with China, Japan, and New Zealand.”
The students’ findings may prove useful for the state’s aquaculture industry.
“Here in Hawai‘i we have a resurgence of aquaculture and traditional fishponds and using locally available species for aquaculture purposes, both for food and, in the case of oysters, for environmental remediation,” explains Sutton. “This task of identifying the different oysters in Hawai‘i offers some potential to diversify the markets. This could be something is marketable for food, since people do eat the Ostrea species. If this is a species that grows really well and is already here, maybe this a good option for aquaculture purposes.”
The value of a CURE classroom
Sutton says the CURE classroom format is extremely valuable for student learning and engagement.
“There are data showing that CUREs increase retention and student success,” she explains. “But we need more support for CUREs as they are a lot more effort and time given that it is real research. They require much more planning and flexibility than my other courses. The role of graduate student teaching assistants was critical to accomplishing this project the way we did and in the timeframe that we did it.”
The CURE format also made it possible for every undergraduate enrolled in the class to be published as a coauthor of a scientific paper. “It was really exciting for the students when we told them that we have this result that we think is worth publishing and we want you to be coauthors,” says Sutton.
Based on the results from spring 2019, Sutton secured additional seed funding to continue similar research for the spring 2020 semester. “We have a cohort of twelve students plus an undergraduate teaching assistant. They have been working on more oysters from more locations in Hawai‘i.”
Even with the COVID-19 interruption and the challenges associated with online lab classes, Sutton says she is prepared to teach the students remotely how to analyze the collected data using a combination of different free programs used in genetic analysis.
The work of the two graduate students was partially supported by the National Science Foundation. On the Pacific Aquaculture and Coastal Resources Center side, the work was partially supported by the Center for Tropical and Subtropical Aquaculture and the UH Sea Grant Program.
Story by Leah Sherwood, a graduate student in the tropical conservation biology and environmental science program at UH Hilo. She received her bachelor of science in biology and bachelor of arts in English from Boise State University.
Researchers at the University of Hawai‘i at Hilo waited 25 years for field results from a study investigating whether or not Hawai‘i Island’s higher-elevation tropical forests could rejuvenate after destructive cattle and pigs were fenced out. The recent discovery of new and thriving growth of keiki ʻōhiʻa and koa in the studied area is good news about the forests’ native trees and the threatened bird species for whom the trees provide habitat.
Hawai‘i Island’s tropical forests evolved without large herbivores and were ill-prepared to withstand their arrival in the 18th century. Cattle were introduced to the island in 1793, and their numbers increased rapidly, with feral cattle roaming the island freely. By 1960, 65 percent of the island was grazing land, most of which was formerly forest, and the cattle also were allowed to graze the remaining forested areas. Following the introduction of cattle, feral pigs were introduced and also caused extensive damage to forests through their rooting behavior and eating of seedlings and saplings.
In 1985, Hakalau Forest National Wildlife Refuge was established to preserve approximately 13,000 hectares of higher-elevation wet forest that had been impacted by cattle and pigs. The conservationists fenced off large tracts of the preserve and by 1992 had removed all remaining cattle, most of which had become feral. Subsequently, thousands of feral pigs were removed, mainly through hunting.
In the mid-1990s, after the cattle were removed, Hart, who was then a doctoral student studying the refuge as a bird habitat, measured and tagged 7,000 trees in some of the fenced-off areas. For the 2020 paper, Hart and his colleagues returned to the same areas he had studied 25 years earlier.
The goal of the Hakalau Forest National Wildlife Refuge project was to allow the forest to passively regenerate, mainly to improve habitat for a number of threatened and endangered native Hawaiian forest bird species, but also to increase native plant diversity and native Hawaiian forest cover.
The new paper by Hart and his colleagues demonstrates that the refuge has been largely successful. “We were able to demonstrate that passive restoration can work in these upper elevation areas,” says Hart. “It’s a positive story because the bird habitat is regenerating.”
“When we returned to those areas that I had studied 25 years ago, we found 4,000 new recruits [young trees] five cm in diameter in those same plots,” says Hart. “Going up there 25 years ago you would see mostly medium to large trees with very little understory, but now you see lots of keiki.”
Hart was particularly pleased by the fast recovery of the native koa trees (Acacia koa). “The fencing allowed this new cohort of koa trees to come up just in time,” he says. “The koa trees get big, they grow fast, and can live for 200 years, so they’re very important for the bird species up there.”
Hart says one lesson from the team’s research is that in certain cases, passive conservation management can be effective. “Often in Hawai‘i when the non-native plants come in and outcompete the native species, it requires active management and active weeding,” says Hart. “In this case, the refuge is basically doing passive management, although some maintenance of the fencing is required.”
Hart notes that the reason the restoration was successful without active management may be because the forest had not yet been completely converted into grassland, and there was still relatively intact forest left nearby, which helped the native trees to come back on their own. “Once the natives make a canopy they can shade out the invasives,” he notes.
Story by Leah Sherwood, a graduate student in the tropical conservation biology and environmental science program at UH Hilo. She received her bachelor of science in biology and bachelor of arts in English from Boise State University.
Last year team CGRG (Conservation Genomics Research Group) genetically modified Hawai‘i sourced Culex quinquefasciatus (southern house mosquito) to test stable incorporation of components of our reversible gene drive system (note two genes were inserted, not the full drive system). This work was Jared Nishimoto’s TCBES M.Sc. thesis, which he defended in July 2019, and was also developed it into an undergraduate teaching lab module.
Photos taken by Jared Nishimoto
Team CGRG is currently completing construction of the full gene drive system, and plan to use CRISPR to insert it alongside an eye-color phenotype marker. They began using CRISPR in the lab a few weeks ago, and here are some early results: white-eyed Culex pupae. One photo is a wildtype shown for comparison – it has black eyespots. These photos are from G0s (injected eggs) so the next step is to rear them to see if they have a stable germline modification (the previous modification was germline stable).
Once CGRG has a high quality reference genome data (sequencing is underway), they will be able to complete the gene drive construct and start working to incorporate it into the lab colony.
All of this work is being done strictly in laboratory colonies.
University of Hawaiʻi at Hilo’s Matthew Knope featured in Science for marine animal biodiversity research
A team of researchers led by the Biology Department at the University of Hawaiʻi at Hilo has its new study on animal biodiversity patterns on the planet featured in the February 28, 2020 issue of the journal Science.
Dr. Matthew Knope, assistant professor of biology, is lead author of “Ecologically diverse clades dominate the oceans via extinction resistance,” which demonstrates that animal biodiversity in the modern oceans is best explained by lower extinction rates in animal groups that are ecologically diverse, rather than by higher origination rates, as previously predicted. Co-authors include Andrew M. Bush, University of Connecticut, Luke O. Frishkoff, University of Texas at Arlington, Noel A. Heim, Tufts University, and Jonathan L. Payne, Stanford University.
“Animals in the oceans today are more diverse than they have ever been in the history of life on Earth and scientists have long worked to describe how they have come to be that way,” Knope said. The study examined approximately 20,000 genera of fossil marine animals across the past 500 million years, and approximately 30,000 genera of living marine animals.
“Our findings clearly show that the most ecologically diverse animal groups are also the most dominate animals in terms of numbers of genera in the modern oceans,” Knope noted. “Being a member of an ecologically flexible group makes you resistant to extinction, particular during mass extinctions, that primarily impacted ecologically homogenous groups. The oceans we see today are filled with a dizzying array of species in groups like fishes, arthropods, and mollusks, not because they had higher origination rates than groups that are less common, but because they had lower extinction rates over very long intervals of time.”
Rosemary Gillespie, professor of evolutionary biology at the University of California, Berkeley, who was not involved in the study, explained, “Understanding how biodiversity is structured, both in space and time, has always been a major focus in biology. A significant difficulty in doing so is that current patterns of biodiversity are dictated both by origination and extinction, and while we can infer origination rates through examination of extant biodiversity, elucidating the role of extinction is notoriously difficult. This study represents some of the most detailed and careful analyses of the fossil record to date, showing very clearly the importance of the ‘slow and steady’ development of lineages through time has been a key factor in dictating which lineages have achieved the highest diversity.”
Further, Michal Kowalewski, professor of invertebrate paleontology at the University of Florida, who was also not involved with the study, said, “In a clever analysis of massive data derived from the fossil record, Knope and colleagues directly address one of the critical questions of biology, as to why do certain types of animals occupy exceptionally broad spectra of ecological niches. As importantly, the study highlights the truly unique value of paleontological data for assessing core questions of biology and exploring historical roots of the modern biosphere.”
Knope further explained, “Perhaps the fable of the tortoise and the hare is apt in explaining marine animal diversification: some groups jumped out to an early diversity lead only to be surpassed by other groups that were more ecologically diverse and less evolutionarily volatile, with steady diversification rates and strong resistance to mass extinctions.”
A study led by biologists at the University of Hawai‘i at Hilo documents the loss of bird song complexity and the convergence of the songs of three species of Hawaiian honeycreepers on the island of Kaua‘i.
The three species of Hawaiian honeycreepers, ‘akeke‘e (Loxops cauruleirostris), ‘anianiau (Magumma parvus), and Kaua‘i ‘amakihi (Chlorodrepanis stejnegeri), have seen rapid declines in their population numbers in the wild due most likely to avian malaria and habitat loss. The honeycreepers forage on insects and help to pollinate plants and disperse seeds in the forests of Kaua‘i, their natural habitat.
“We did this study specifically in Kaua‘i because it is in a real crisis mode,” says Kristina Paxton, an ecologist and post-doctoral researcher at UH Hilo, who was the lead author of the study. “Their populations are crashing and malaria is probably the largest driving factor of the declines. But we are not only losing the individuals, we are losing their songs. When you go into the forest in Kaua‘i it is now quieter, and that’s losing a part of what makes the Hawaiian forest what it is. The quietness of the forest is a sign that the forest is facing challenges.”
Paxton is affiliated with the LOHE lab, a bioacoustics laboratory at UH Hilo led by Patrick Hart, professor of biology, and Adam Pack, professor of psychology. The lab goes by the Hawaiian name LOHE, which means “to perceive with the ear” and is an acronym for Listening Observatory for Hawaiian Ecosystems.
In January 2019, Dr. Cam Muir, along with 20 students and faculty members from the University of Mississippi, conducted research on the fungal recruitment by tea plants and soil ecosystems. Fungi are well known to play key roles in plant growth and can benefit plants by acting as a both mutualists and decomposers. The diversity of fungi and the impact of their species diversity on soil ecosystems is still poorly understood.
This collaboration between UH Hilo and Ole Miss has led to the recent submission of a $3.5 M grant proposal: Establishing Foundations for Ecosystem Steering. The proposal team is composed of faculty from University of Surrey (UK), Waseda University (Japan), Georgia Institute of Technology (USA), Earth-Life Science (Japan), University of Mississippi, and University f Hawai`I at Hilo (USA).
Students and faculty in lab conducting research on tissue sampling
Dr. Cam Muir teaching in "living lab"
Students from University of Mississippi at "living lab"
Faculty from "Ole Miss" conducting research on tea plants
Researchers at the University of Hawai‘i at Hilo were recently awarded a Bradshaw Medal for their provocative paper questioning a fundamental assumption of the field of restoration ecology, which is the science of restoring natural habitats that have been subject to anthropogenic disturbances.
The Bradshaw Medal, named after British ecologist and restoration pioneer Tony Bradshaw, is given by the Society for Ecological Restoration, in recognition of a scientific paper published in the Society’s major journal, Restoration Ecology, which advances the field of restoration ecology.
Cordell is also an affiliate faculty member at UH Hilo who serves in an advisory role for the tropical conservation biology and environmental sciences graduate program. Coauthors Ostertag, an ecologist, and Michaud, a hydrologist, are both professors and researchers at UH Hilo. Warman is a plant ecologist with the USDA forestry institute who also teaches at UH Hilo.
A provocative approach to native forest restoration
The provocative aspect of the paper is in its relatively accepting attitude towards nonnative, noninvasive plant species, often the traditional nemesis of ecologists. The authors argue that in some cases it is better to “give up” on the traditional goal of restoring disturbed ecosystems to their pristine native state, and instead pursue a “hybrid” approach that incorporates both native plant species and nonnative (but noninvasive) plants.
“Our perspective is that in many cases we cannot keep these areas all native,” says Ostertag. “It is just not feasible or pragmatic.”
The focus of the paper is a multiyear, multistudy restoration project called Liko Nā Pilina, which in Hawaiian means roughly “growing or budding novel relationships.” The project is an ongoing effort to restore an area of Hawaiian lowland wet forest, an ecosystem found on the northeastern sides of the Hawaiian islands and that is particularly susceptible to loss of native plant species biodiversity and domination of invasive plant species. Hawaii’s native lowland wet forests were first altered by the arrival of the Polynesians and later exploited by Western colonists for agricultural and housing purposes. The result was an altered ecosystem and loss of biodiversity. Today, remnants of the forests remain on Hawai‘i Island in patchy forest reserves in Puna and East Hawai‘i, but they remain threatened by development.
In practice, ecologists want to restore ecosystems back to their original state because the native species evolved over time to fill certain niches or functions in the overall system. This was the original goal of the research team in the Liko Nā Pilina project.
“We had originally done an experiment where we removed all the invasives from our ten-by-ten meter plots,” explains Ostertag. “We thought by removing the highly invasive species we would able to improve the germination of the native species and get them to regenerate. However, that is not really what we got. And the amount of weeding we had to do to keep out the invasives was really really intense. We estimated about 40 person hours per meter squared to do all the weeding to keep it native.”
“Weeding will kill you!” agrees Michaud, the hydrologist whose primary role was studying water flow in the study area. She and Ostertag, along with rest of the team, started to realize that the ecosystem would never return to an-all native state, and even if this were possible, the cost would be too high and payoff too low.
“We realized we needed a different strategy,” Ostertag says. “Just removing the invasives, just doing a passive restoration, was not going to work, the effort was too great. We decided that we needed to do a more active restoration that involved planting the specific species we wanted. This led us to this idea of planting a hybrid forest, making hybrid ecosystems of the native and nonnative species grow together, using nonnative species that were not invasive but that could fill important functional roles. This hypothesis led us to collecting really important data that showed that one problem is that the native community is missing certain functional roles. Therefore, by including nonnative, noninvasive species that can fill these functional roles that are currently missing, we might have more success.”
An example of a functional role that can be filled by a nonnative species is providing shade.
“We found that we were missing fast-growing species with large leaves that create a lot of shade,” explains Ostertag. “We need the shade in the environment because that’s what keeps out the highly invasive seedlings. We need to manipulate the light environment to the goldilocks level where it is just right. We needed species that closed the canopy faster and helped produce shade to keep out the undesirable invasive species but that still allowed native species’ seedlings to regenerate.”
Ostertag adds that they plan to continue to manage the forest indefinitely to support the growth of native species and prohibit the spread of invasives under their new strategy of mixing native and nonnative species to fill functional roles.
“If you are in it for the long game you can start to see real changes,” she says. “After five years, we are starting to see the canopy getting darker and starting to close, and we are really reducing our weeding effort.”
Fine tuning the approach
Ostertag emphasizes that the researchers’ hybrid restoration strategy is not appropriate in every case.
“Our strategy for mixing native and nonnative is less palatable at higher elevations, which are more native-dominated,” she says. “And if there is already high native cover in an area you may not need this method. However, at the lower elevations, which are completely dominated by these highly invasive species, we think this is a realistic approach.”
Ostertag says that winning the Bradshaw Medal was a surprise considering that the team had originally written a completely different type of data-rich paper focusing on weeding and invasive species reoccurrence. The original idea was not reviewing well and instead a new paper emerged.
“We decided we would morph our study into a story format and a lessons learned paper,” says Ostertag. “It took on more of a narrative structure. I think people like the paper because we explain our experience over a decade of work, and the trials and tribulations of this lowland wet forest restoration project.”
Their mixing of native and nonnative species may raise the eyebrows of some conservation ecologists, but Ostertag says her colleagues in Hawai‘i have been very receptive to the hybrid approach.
“Ecologists who work in Hawai‘i were enthusiastic and encouraging because they understand the huge problem that we have with invasive species here,” says Ostertag. “Hawai‘i is like an endpoint on the conservation continuum. Half of our flora is nonnative, we have these highly disturbed systems in the low elevations, and if you go to most places you don’t see native species. They are completely altered, modified systems. Once people realize this, they understand that this is a potentially viable strategy that deserves to be tested.”
About the author of this story: Leah Sherwood is a graduate student in the tropical conservation biology and environmental science program at UH Hilo. She received her bachelor of science in biology and bachelor of arts in English from Boise State University.
The Society for Ecological Restoration recently presented the Bradshaw Medal to two outstanding papers published in its peer-reviewed journal, Restoration Ecology. Named for famed British ecologist and restoration pioneer Tony Bradshaw, the award honors scientific papers that advance the field of restoration ecology in a significant way. Susan Cordell, Rebecca Ostertag, Jené Michaud, and Laura Warman published “Quandaries of a decade‐long restoration experiment trying to reduce invasive species: beat them, join them, give up, or start over?” Their study investigated the most effective way to reforest native species in Hawai’i to recover biodiversity. Ostertag is a member of the Biology department and Michaud is a member of the Geology department at UH Hilo, while Cordell and Warman are affiliated with the USDA Forest Service Institute of Pacific Islands Forestry. Full article: https://www.ser.org/news/434318/
Read the article and watch the video to learn more about how UH Hilo graduate student, Jared Nishimoto, and undergraduates under the supervision of Dr. Jolene Sutton are developing genetic technologies that will help control invasive mosquitoes in Hawaiʻi.