Biology Department News

Biology Scientists awarded NSF Grant for Rapid ‘Ōhiʻa Death Research

Tuesday, August 14, 2018, 10:51pm by

ʻApapane on an ‘Ōhiʻa branch
An ‘Apapane on an ‘Ōhiʻa branch

Drs. Kristina Paxton and Patrick Hart were awarded a grant from the National Science Foundation (NSF) Grants for Rapid Response Research (RAPID) to assess the impact of Rapid ‘Ōhiʻa Death on Hawaiian forest birds. The project is entitled: “RAPID: Cascading effects of rapid and widespread mortality of a foundation tree species on animal communities in Hawaiʻi”
Rapid ‘Ōhiʻa Death or ROD, is a fungal pathogen causing rapid and widespread mortality of ‘Ōhiʻa (Metrosideros polymorpha), a foundation tree species in Hawaiian forests. ROD poses a serious threat to Hawaiʻi’s remaining native forests and the plants and animals that depend on ‘Ōhiʻa. Research focused on ROD to-date has been concentrated on understanding the pathology of the disease, how ROD is spread, and the impacts of ROD on ‘Ōhiʻa trees. However, there has not been an examination of how ROD is affecting animal communities reliant on ‘Ōhiʻa forests. ‘Ōhiʻa is an important nesting substrate and food resource for both insectivorous and nectarivorous Hawaiian forest birds, 57% of which are threatened or endangered, and there is no substitute for the volume, geographic spread, and year-round source of nectar provided by ‘Ōhiʻa. Given the foundational role of ‘Ōhiʻa in Hawaiian forest communities as the dominant tree in the canopy, the widespread or total loss of ‘Ōhiʻa would likely be catastrophic for endemic Hawaiian forest birds.

This project will use advances in recording technology to continuously record, over an extended period of time, the entire sound-producing animal community (i.e., biophony of a soundscape) within ‘Ōhiʻa forests across Hawaiʻi Island. By using soundscape analysis tools developed within the growing field of soundscape ecology the researchers will be able to rapidly assess changes in the biodiversity of audible birds, insects, and amphibian species associated with mortality of ʻŌhiʻa across the landscape. The research will also evaluate whether the diversity and composition of understory plant species moderates how reliant animal communities respond to the loss of a dominant forest tree species. The use of soundscape indices to model biodiversity following the loss of a foundation species represents a novel and relatively rapid method for assessing ecological change and would be applicable in a range of ecosystems outside Hawaiʻi.

UH Hilo genetics research team releases unprecedented genome assembly for endangered Hawaiian crow

Tuesday, August 14, 2018, 10:30pm by

The extraordinary findings of a genetic research team at the University of Hawai‘i at Hilo studying the ‘alalā (Hawaiian crow), one of the world’s most endangered bird species, are published in the current issue of the journal Genes. Biologist Jolene Sutton, an assistant professor at the University of Hawai‘i at Hilo who specializes in evolutionary genetics, led the team of UH Hilo colleagues Martin Helmkampf, a research scientist with the tropical conservation biology and environmental science program, and Renee Bellinger of the Conservation Genomics Research Group, along with collaborators from the Hawai‘i Endangered Bird Conservation Program, San Diego Zoo Global, and Pacific Biosciences, a Silicon Valley company that provides sophisticated genomic analysis systems.

The article, “A high-quality, long-read de novogenome assembly to aid conservation of Hawaii’s last remaining crow species,” describes the high-quality reference genome that was generated to assist recovery efforts for the ‘alalā.

“The quality of this assembly places it among the very best avian genomes assembled to date, comparable to intensively studied model systems,” according to a post on the UH Hilo Biology Department News website.

Researchers and conservationists are currently using this resource to better understand genetic diversity in the ‘alalā, and to develop tools that will help inform strategic pairings as part of the conservation-breeding program. This genome assembly is now publicly available.

The paper is the cover story of the August 2018 issue of Genes, a special issue on conservation genetics and genomics.

PacBio reports:

Led by Jolene Sutton, assistant professor at the University of Hawaii, Hilo, the team created an assembly which has provided critical insights into inbreeding and disease susceptibility. They found that the ‘alalā genome is substantially more homozygous compared with more outbred species, and created annotations for a subset of immunity genes that are likely to be important for conservation applications.

As reported in the latest issue of Genes — and featured on its cover — the quality of the assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems.

“Such genome-level data offer unprecedented precision to examine the causes and genetic consequences of population declines, and to apply these results to conservation management,” the authors state. “Although pair selection and managed breeding using the pedigree has kept the inbreeding level of the ‘alalā population at a relatively low level over the past 20 years, the intensive and ongoing conservation management of the species requires a more detailed approach.”

UH Hilo conservation biologists use high-tech acoustics to study Rapid ʻŌhiʻa Death impact on forest animals

Wednesday, August 8, 2018, 12:13am by

A fungal disease is ravaging native forests on Hawai‘i Island, killing huge swaths of ʻōhiʻa (Metrosideros polymorpha), the most abundant native tree in the state of Hawaiʻi. On Hawaiʻi Island, hundreds of thousands of ʻōhiʻa have already died from the fungus, Ceratocystis. Healthy trees die within a few days to a few weeks, hence the name Rapid ʻŌhiʻa Death or ROD. The disease has killed trees in all districts of Hawaiʻi Island and has the potential to kill ʻōhiʻa trees statewide.

So far, ROD research has concentrated on understanding the pathology of the disease, how it is spread, and the impacts of it on ‘ōhi‘a trees. But the decimation of the trees is destroying native forests as a whole, and in turn, posing a serious threat to the plants and animals that depend on healthy ecosystems created by ‘ōhi‘a trees.

This summer, UH Hilo biologists started a one-year study on the effects of ROD on animal communities in Hawaiʻi. The research is funded by a $197,000 grant from the National Science Foundation’s Grants for Rapid Response Research or RAPID program. The project is entitled “RAPID: Cascading effects of rapid and widespread mortality of a foundation tree species on animal communities in Hawai‘i.”

“[T]here has not been an examination of how ROD is affecting animal communities reliant on ‘ōhi‘a forests, which is an important nesting substrate and food resource for both insectivorous and nectarivorous Hawaiian forest birds, 57 percent of which are threatened or endangered,” explains lead scientist on the study Kristina Paxton, an adjunct assistant professor in the UH Hilo tropical conservation biology and environmental science program. “Given the foundational role of ‘ōhi‘a in Hawaiian forests as the dominant tree in the canopy, widespread or total loss of ‘ōhi‘a would likely be catastrophic for endemic Hawaiian forest birds.”

Acoustics: Recording the animal sounds of the forest as an indicator of biodiversity

Paxton is working on the study with colleague Patrick Hart, a UH Hilo professor of biology and a specialist in conservation of Hawaiian forests and forest birds. The team will be basing the research on high-tech recorded acoustics—bird song and other animal sounds of the forest—using technology out of the UH Hilo bioacoustics lab called the Listening Observatory for Hawaiian Ecosystems or LOHE, which was founded by Hart.

Paxton says the project will use advances in recording technology to continuously record over an extended period of time the entire sound-producing animal community within ‘ōhi‘a forests across Hawaiʻi Island.

Lab logo with bird and whale and the words: Listening Observatory for Hawaiian Ecosystems, LOHE Bioacoustics Lab, University of Hawaii at Hilo.“By using soundscape analysis tools developed within the growing field of soundscape ecology, we will be able to rapidly assess changes in the biodiversity of audible birds, insects, and amphibian species associated with the mortality of ōhi‘a across the landscape,” she says.

The research also will evaluate whether the diversity and composition of understory plant species moderates how reliant animal communities respond to the loss of a dominant forest tree species.

Paxton says the use of soundscape to assess ecological change could serve as a model in studying a range of ecosystems outside Hawaiʻi.

LOHO logo, with bird flying above, whale below - a waveform between them
LOHE Bioacoustics Laboratory at UH Hilo

Drs. Jolene Sutton, Martin Helmkampf, and Renee Bellinger publish paper on the Hawaiian crow genome on the cover of Genes

Wednesday, August 1, 2018, 8:35pm by

Drs. Jolene Sutton, Martin Helmkampf, and Renee Bellinger of the Conservation Genomics Research Group, along with collaborators from the Hawaii Endangered Bird Conservation ProgramSan Diego Zoo Global, and PacBio publish in Genes. The article, “A high-quality, long-read de novogenome assembly to aid conservation of Hawaii’s last remaining crow species” describes the high-quality reference genome that was generated to assist recovery efforts for the ‘Alalā, one of the world’s most endangered bird species. The quality of this assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems. 

Researchers and conservationists are currently using this resource to better understand genetic diversity in the ‘Alalā, and to develop tools that will help inform strategic pairings as part of the conservation-breeding program. This genome assembly is now publicly available. This paper is the “Feature Article” of the August 2018 issue of Genes, and belongs to the special issue, “Conservation Genetics and Genomics” and is also published in PACBIO, titled “Dying Breeds: How Scientists Can Save Species Through Genetics“.

Cover of Genes with ʻAlalā bird, Volume 9, Issue 8, August 2018. Impact Factor 30.191. Title is "A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawai'i's Last Remaining Crow Species".

Drs. Jolene Sutton, Martin Helmkampf, and Renee Bellinger publish paper on the Hawaiian crow genome on the cover of Genes

Wednesday, August 1, 2018, 12:15am by

Drs. Jolene Sutton, Martin Helmkampf, and Renee Bellinger of the Conservation Genomics Research Group, along with collaborators from the Hawaii Endangered Bird Conservation ProgramSan Diego Zoo Global, and PacBio publish in Genes. The article, “A high-quality, long-read de novogenome assembly to aid conservation of Hawaii’s last remaining crow species” describes the high-quality reference genome that was generated to assist recovery efforts for the ‘Alalā, one of the world’s most endangered bird species. The quality of this assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems. 

Hawaiian Crow closeup

Researchers and conservationists are currently using this resource to better understand genetic diversity in the ‘Alalā, and to develop tools that will help inform strategic pairings as part of the conservation-breeding program. This genome assembly is now publicly available. This paper is the “Feature Article” of the August 2018 issue of Genes, and belongs to the special issue, “Conservation Genetics and Genomics.

Dr. Jonathan B. Koch publishes papers the journals Ecology and Evolution and in Molecular Ecology

Tuesday, July 17, 2018, 11:27pm by

Recent Smith Conservation Fellowship awardee and member of the Conservation Genomics Research Group at UH Hilo, Dr. Jonathan Koch, was lead author on an article published in the July 2018 edition of the journal, Ecology and Evolution. The article, “Quaternary climate instability is correlated with patterns of population genetic variability in Bombus huntii” examines how 22,000 years of historic climate variability has influenced patterns of population genetic diversity in an agriculturally important bumble bee species in North America. The article is open access, and can be read in full by clicking on the link below. Dr. Koch was also a co-author on an article published in a June 2018 edition of the journal, Molecular Ecology. The article, “Distance, elevation, and environment as drivers of diversity and divergence in bumble bees across latitude and altitude” examines fine-scale patterns of genomic diversity in a widely-distributed bumble bee species in western North America using reduced-representation genome sequencing and bioinformatics. A link to the abstract of this article is below. Feel free to contact Dr. Koch if you would like access to his personal copies. Dr. Koch, the Principal Investigator of the nalo meli ‘āpa‘akuma project, explores useful ways to use genomic data to guide the management and conservation of endemic Hawaiian bees.

 

Koch et al. 2018 | https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.4294

Jackson et al. 2018 | https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.14735

Undergraduate student, Leah Martin, published in Advances in Cytology & Pathology

Friday, June 22, 2018, 1:22am by

Leah Martin
Leah Martin was a student at the Biology department. During her senior year, Leah conducted research in Li Tao’s laboratory studying the regulation of mitotic motors. Unregulated cell proliferation is the primary feature of cancer and research has focused on disrupting and halting the cell division in the cancer cells.
In her publication, ““Braking bad”: halting mitotic motors in cancer cells” (http://medcraveonline.com/ACP/ACP-03-00051.pdf), Leah reviewed the latest findings on the inhibition of cancer cells through protein modifications. Combined with her research results in the Tao lab, Leah provided her insights on the regulation of kinesin motors for the development of new anti-cancer therapies. Leah graduated in May, 2018. She is now applying for medical schools.

Dr. Li Tao publication is selected as “A Highlights from MBoC Selection”

Tuesday, March 6, 2018, 1:49am by

Dr. Li Tao’s paper was formally published on Molecular Biology of the Cell, and it was selected as “A Highlights from MBoC Selection“.

Polo kinase mediates the phosphorylation and cellular localization of Nuf/FIP3, a Rab11 effector. Mol. Biol. Cell 2017 28:11 1435-1443;

Animal cytokinesis involves both actin-myosin–based contraction and vesicle-mediated membrane addition. In many cell types, Nuf/FIP3, a Rab11 effector, mediates recycling endosome (RE)–based vesicle delivery to the cytokinesis furrow. Nuf exhibits a cell cycle–regulated concentration at the centrosome that is accompanied by dramatic changes in its phosphorylation state. However, the underlying mechanism involved in these changes is poorly understood and rarely reported. Here we use genetic, biochemical, and cell biological techniques to demonstrate that Polo kinase directly mediates Nuf cell cycle–dependent localization.

Dr. Adam Pack publishes paper in the journal Animal Behaviour

Tuesday, November 7, 2017, 12:20am by

In November, 2017, Adam Pack was the lead author on the paper “Habitat preferences by individual humpback whale mothers in the Hawaiian breeding grounds vary with the age and size of their calves”, published in the journal Animal Behaviour.”  Read the abstract.

Dr. Adam Pack stands in the Edith Kanakaole stadium, adorned with lei
Dr. Adam Pack after receiving his 2017 Excellence in Teaching Medal, awarded by the UH Board of Regents

Adam Pack introduces the “Louis M. Herman Student Research Scholarship Award”

Sunday, October 1, 2017, 2:16am by

In October, 2017, Adam Pack introduced the “Louis M. Herman Student Research Scholarship Award” at the 22nd Biennial Conference on the Biology of Marine Mammals in Halifax, Nova Scotia.  Dr. Pack also co-authored 2 talks and 2 poster presentations at the conference including “An unexpected journey: Diurnal movement into deeper waters by humpback whale (Megaptera novaeangliae) mother-calf pairs observed off Northwest Maui, Hawaii,”  “Humpback whale song as a display of male fitness: Evidence from measurements of variability in song units in conjunction with singer body size,” “Vocalizations and behavior of humpback whale (Megaptera novaeangliae) mother-calf groups in the Hawaiian wintering grounds,” and “Endocrine markers for understanding stress response and reproduction in male humpback whales (Megaptera novaeangliae) in Hawaiian and Alaskan waters”

Dr. Adam Pack stands next to his poster on Humpback Whale movement

An unexpected journey: Diurnal movement into deeper waters by humpback whale (Megaptera novaeangliae) mother-calf pairs observed off Northwest Maui, Hawaii,

Dr. Adam Pack stands with a conference attendee at his poster session