Biology Department News

UH Hilo students identify previously undocumented oyster species in Hawai‘i

Thursday, April 2, 2020, 1:57am by

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.

By Leah Sherwood.

At top is photo of class of students, at bottom is two images of oyster.
At top, the students in a UH Hilo genetics class who did the lab work used to identify a previously undocumented oyster species in Hawai‘i. The genetic study expands the known range of the western Pacific Ostrea equestris (bottom photos), a species previously documented in China, Japan, and New Zealand, by providing the first verification of its occurrence in Hawai‘i. Courtesy photos.

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.”

The project

Jolene Sutton
Jolene Sutton

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.

The discovery has been submitted to a journal for peer review and is currently available as a paper on the pre-print server biorxiv.org.

Sutton’s coauthors on the paper include the nine students in the genetics class: Keinan AgoniasNicole AntonioBrandi BautistaRiley CabarlocMaata FakasieikiNoreen Aura Mae GonongTorey RamangmouLavin Uehara, and Jade Wong.

Maria Haws
Maria Haws

Other coauthors are the course’s two teaching assistants, Jared Nishimoto and Jeremy Schrader, both graduate students from the tropical conservation biology and environmental science programMaria Haws, professor of aquaculture and director of the UH Hilo Pacific Aquaculture and Coastal Resources Center, along with colleagues Marni Rem-McGeachyHope HelgDaniel Wilkie, and David Littrell; and Rhiannon Chandler, executive director of Waterkeepers Hawaiian Islands.

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.

Long-term study by UH Hilo scientists shows Hawai‘i Island forests can regenerate once cattle and pigs are fenced out

Tuesday, March 31, 2020, 8:55pm by

Twenty-five years ago, a UH Hilo biologist tagged 7,000 trees in a declining Hawai‘i Island rainforest. A recent survey of the site reveals conservationists’ efforts are paying off.

By Leah Sherwood.

Patrick Hart
Patrick Hart

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.

UH Hilo scientists Patrick J. HartThomas IbanezShea Uehana, and Joshua Pang-Ching‘s paper, “Forest regeneration following ungulate removal in a montane Hawaiian wet forest,” was published January in the journal Restoration Ecology. Hart is a professor and Ibanez a post-doctoral fellow, both from UH Hilo’s biology department. Uehana and Pang-Ching are recent alumni of UH Hilo’s graduate program in tropical conservation biology and environmental science.

Three researchers (two men, one woman) each with backpack, stand in open field, forest in background.
UH Hilo research team members conducting forest surveys at Hakalau, Hawai‘i Island. From left, Shea Uehana (UH Hilo alumni, tropical conservation biology and environmental sciences graduate program), Ann Tanimoto-Johnson (graduate student), and Andrew Yoshimoto (UH Hilo biology undergraduate). Courtesy photo.

 The study

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.

Team CGRG genetically modifies Hawai‘i sourced Culex quinquefasciatus (southern house mosquito)

Monday, March 9, 2020, 10:22pm by

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.

white-eyed Culex mosquito pupae compared to black-eyed Culex mosquitor larvae

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.

 

NexTech STEM Exploration: Hawaii’s Forest Birds

Monday, March 9, 2020, 9:25pm by

Photograph of a cohort of students posing in front of banyan tree
Saturday, March 7th was a “beautiful day in the neighborhood”, with Lisa Mason filling minds and creating smiles.
A parent wrote, “Yesterday’s Bird Day was fabulous. My daughter really enjoyed it and got to learn some great things about Hawaii’s birds.”  Expert help included: Ann Tanimoto, Timon, Carmelita Villalobos, and Kristina Paxton from the UHH graduate program of Tropical Conservation Biology and Environmental Science.

Thank you Lisa Mason for designing and creating such an active learning environment. Thank you Tennville and Shannon for your logistical support. Moms and Dads, Melissa, Brian and Jolene Sutton who jumped in to help. Mahalo!

WHAT’s NEXT?

 If you are interested in Aeronautical Science at UHH on Saturday, March 21, contact Gail at 430-5898 for more information.

University of Hawaiʻi at Hilo’s Matthew Knope featured in Science for marine animal biodiversity research

Tuesday, March 3, 2020, 2:46am by

Photograph of Matt Knope

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.”

Humpback whale jumping out of oceanRosemary 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.”

The entire study is available at: https://science.sciencemag.org/cgi/doi/10.1126/science.aax6398.

More information:

https://www.scientificamerican.com/article/ability-to-take-on-diverse-roles-may-be-key-to-which-animals-survive-mass-extinction/

Biologist Narrissa Spies, UH Hilo alumna, inspires artwork for national STEM conference

Tuesday, October 8, 2019, 10:58pm by

The piece, by Laurie Sumiye, depicts Haumea, Hawaiian Earth Mother and Creation Goddess (ancestor to all indigenous Hawaiians) and is modeled after Native Hawaiian scientist and UH Hilo alumna Narrissa Spies.

By Susan Enright

Narrissa Spies, an alumna from the University of Hawai‘i at Hilo, is the inspiration behind artwork created by Laurie Sumiya for the upcoming 2019 SACNAS National Diversity in STEM Conference. The conference is a three-day event to be held Oct. 31 through Nov. 2, 2019, in Honolulu.

SACNAS stands for the Society for Advancement of Chicanos/Hispanics and Native Americans in Science, an organization that supports and promotes Chicanos/Hispanics and Native Americans in attaining advanced degrees, careers, and positions of leadership in science, technology, engineering and math fields.

SACNAS

@sacnas

Meet the muse for the artwork: SACNISTA Narrissa Spies!✨Aside from seeing her depicted in this year’s art, Narrissa is also a graduate student in @UHNews.

🔗 Learn more about Narrissa and her research on coral reefs >> https://www.hawaii.edu/news/2018/01/23/a-role-model-who-revels-in-research/ 

Images of Narrissa smiling in the lab, looking in microscope. Background image of 2019 SACNAS artwork featuring Narrissa holding a tree.
See SACNAS’s other Tweets

Spies grew up in Hilo and Kawaihae, where her childhood aspiration was to become a medical researcher. She began her studies at Hawai‘i Community College, then graduated from UH Hilo with bachelor of arts degrees in molecular biology and anthropology and a master degree in tropical conservation biology and environmental science. She received her doctor of philosophy in zoology from UH Mānoa. She is now a fish and wildlife biologist with the U.S. Fish and Wildlife Service.

About the Artwork
“‘Ano Lani; ‘Ano-Honua” by Laurie Sumiye.

Artwork of Narrissa with volcano in background, she has her hands in the ocean cradling fish, and has a tree image on her front.The piece, titled after a traditional Hawaiian proverb meaning “A heavenly nature; an earthly nature” depicts Haumea, Hawaiian Earth Mother and Creation Goddess (ancestor to all indigenous Hawaiians) and modeled after Native Hawaiian scientist and SACNAS member Narrissa Spies. In her hands, she carries the Makalai tree, a tree of life. Behind Haumea is an active volcano (representing creation), verdant green mountains, and the Scorpio and Pleiades constellations (representing the ancestors). Below her, swims a red fish (representing nourishment), an iwa bird (representing travel and clear direction), and colorful hibiscus flowers (representing the diversity and beauty of Hawaiian people and native flora). As a whole, the artwork depicts the creation story — a tale of who we are and how we got here.

The upcoming conference is the largest multidisciplinary and multicultural STEM diversity event in the country. The three-day event focuses on empowering participants for their academic and professional STEM paths. Participants are inspired by scientific research and professional development sessions, motivational keynote speakers, an expo hall, and multicultural celebrations. “At 2019 SACNAS, you can shape your own STEM story inspired by your ancestors, mentors, and peers—nourished by diversity and fueled by passion for discovery,” notes the website about the event.

To learn more about Spies and her research while at UH, see UH Hilo alumna Narrissa Spies: A role model who revels in research (UH Hilo Stories, Jan. 24, 2018).

 

Story by Susan Enright, a public information specialist for the Office of the Chancellor and editor of UH Hilo Stories. She received her bachelor of arts in English and certificate in women’s studies from UH Hilo.

A quieter forest: UH Hilo biologists document loss of bird song in Hawaiian honeycreepers on Kaua‘i

Tuesday, September 17, 2019, 7:14pm by

The researchers did the study on Kaua‘i because it is in crisis mode: bird populations are crashing due to disease and habitat loss, and with that, the species are losing their songs. 

By Leah Sherwood.

Small green bird on lehua tree.
‘Amakihi (Chlorodrepanis stejnegeri). Photo by Robby Kohley.

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.”

Kristina Paxton stands in front of a bookcase of biology books and two framed picture of birds.
Kristina Paxton. Photo by Raiatea Arcuri.

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.

Click to read full article.

Establishing Foundations for Ecosystem Steering

Thursday, September 5, 2019, 10:07pm by

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).

Dr. Matt Knope awarded the Francis Davis Award for Excellence in Undergraduate Teaching!

Wednesday, June 5, 2019, 10:03pm by

Matthew Knope, assistant professor of biology, received the Frances Davis award for Excellence in Teaching. Assistant Prof. Knope joined UH Hilo in fall 2017 and quickly became known for putting teaching and his students as his highest priorities. Colleagues praise him for demonstrating his commitment and strong ability to integrate research and teaching and to directly involve students in his research. He is considered a natural and effective teacher and a rising star in the field of ecology and evolution.

Local tour company donates $25K to UH Hilo biology program to research mosquito-borne avian disease

Monday, April 8, 2019, 7:42pm by

The gift from Hawaii Forest & Trail will support research and technologies to reduce mosquito populations that spread avian disease in Hawai‘i.

Red ‘i‘iwi drinking nectar from flower.
The ‘i‘iwi is a scarlet honeycreeper native to Hawai‘i and decreasing in numbers. Photo by Ludovic Hirlimann/Wikimedia.

A local tour company with a strong conservation mission has donated $25,000 to the biology department at the University of Hawai‘i at Hilo. The gift from Hawaii Forest & Trail will support research and technologies to reduce mosquito populations that spread avian disease in Hawai‘i.

“It’s our hope that through this donation, important research work will continue to make strides in protecting Hawaiian forest birds, including our much-loved ‘i‘iwi,” says Rob Pacheco, founder and president of the tour company.

Mosquito control

The primary reason for the continued decline of native honeycreepers is mosquito-transmitted diseases such as avian malaria and avian pox. Climate change is exacerbating the problem, and mosquitoes are beginning to move up in elevation to the last disease-free habitats on all Hawai‘i islands.

Research shows mosquito suppression can be achieved by introducing different strains of Wolbachia bacteria into mosquitoes, which drops reproduction rates. Wolbachia male-based insect control programs have been highly successful for reducing local mosquito populations around the world.

“The ultimate goal is to be able to release male mosquitoes with a different Wolbachia strain into the wild to mate with wild females, to suppress mosquito populations,” says Jolene Sutton, assistant professor of biology and top researcher into native avian disease via mosquitoes. None of the mosquitoes here are native to Hawai‘i. If we can reduce or even eliminate mosquito populations in Hawai‘i, we have a good change of saving many iconic bird species. Our research focuses on evaluating and developing novel strategies for mosquito control, including Wolbachia-based strategies and genetic ones. We want to ensure that new technologies are safe and effective.”

She adds, “This donation will go a long way to help further this work. We are very grateful to have this kind of local interest and support.”