[Nagano University Press Release] New Statistical Method Shows That Extinction Risk Can Be Estimated Reliably Even with Limited Data - Published in Methods in Ecology and Evolution and Applied to Japanese Eel
IFB
On April 17, 2026, a research paper from the Institute of Freshwater Biology, Nagano University, was published in the international journal Methods in Ecology and Evolution, published by the British Ecological Society. The study develops a new statistical framework for estimating extinction risk with accurate confidence intervals, even when only limited time-series data are available.
The study further proposes an observation-error-and-autocovariance-robust (OEAR) extension based on long-run variance estimation for cases with additive observation error and short-run dependence, and applies the framework to two national harvest-index series of Japanese eel (Anguilla japonica) covering 1957 to 2020.
The core w-z method developed in the study is implemented in the R package extr, available on CRAN.
Figure. A simplified conceptual workflow of the method developed in this study, from observed time-series data to extinction-risk estimation with accurate confidence intervals, including the robust extension based on long-run variance.
Highlights of the Study
Developed a new analytical method for constructing confidence intervals for extinction probability under the drift-Wiener process, a standard model in population viability analysis (PVA).
Showed that meaningful extinction-risk estimates can still be obtained from limited data, especially when the true extinction risk is clearly low or clearly high.
Proposed a more robust OEAR estimator, based on long-run variance estimation, for data with additive observation error and short-run dependence.
Applied the method to Japanese eel and found that extinction probabilities under IUCN Criterion E remain far below the threatened-category thresholds even when confidence intervals are taken into account. Japanese eel is nevertheless currently listed as Endangered under Criterion A. The study also shows theoretically that, under the drift-Wiener model, the decline subcriteria of Criterion A systematically overestimate the extinction risk quantified by Criterion E for sufficiently large populations.
Background
The quantitative assessment of extinction risk is central to modern conservation practice, including evaluations by the IUCN Red List and CITES. However, for many years researchers have debated how reliably extinction probabilities can be estimated from short or noisy ecological time series. A widely cited concern is that, when data are limited, confidence intervals may span almost the entire 0-1 range, making the estimate practically uninformative.
At the same time, conservation practice still requires quantitative evidence. Population viability analysis (PVA) remains one of the most transparent ways to assess future extinction risk, but its usefulness depends on whether uncertainty can be evaluated in a statistically reliable way.
Purpose of the Study
This study aimed to clarify under what conditions extinction-risk estimation remains informative even under realistic data limitations, and to derive confidence intervals with accurate statistical coverage. A second goal was to extend the method to settings in which observation error and short-run temporal dependence are present.
Methods
The study focused on the drift-Wiener process, a canonical stochastic model of extinction dynamics. Instead of estimating extinction risk directly in the original model parameters, the paper introduces two transformed parameters, w and z, and carries out inference in this transformed space. Their maximum-likelihood estimators follow noncentral t distributions, making it possible to construct accurate confidence intervals for extinction probability.
The properties of the method were studied analytically and evaluated by Monte Carlo simulation. The study also introduced an OEAR extension based on HAC long-run variance estimation with AR(1) pre-whitening and a Bartlett kernel, improving robustness to additive observation error and short-run dependence while ensuring that the variance estimate remains nonnegative in finite samples.
The framework was then applied to two national Japanese eel harvest series from 1957 to 2020: a common glass-eel seed index (coastal plus inland) and an inland yellow-and-silver-eel harvest index.
Main Findings
The study shows that the width of the confidence interval for extinction probability depends not only on the amount of data, but also on effect size: how far the true extinction probability lies from the point of maximum uncertainty. This means that extinction risk can, in some cases, be estimated much more precisely than previously assumed, even from limited monitoring data.
The new confidence-interval method achieved accurate nominal coverage in simulation experiments, whereas several commonly used alternatives showed larger deviations from the nominal level. In settings with additive observation error and short-run dependence, the OEAR extension also showed stable performance and, at least within the range examined in this study, did not alter the practical threshold-based interpretation.
Japanese eel is currently listed as Endangered under IUCN Criterion A, which is based on population decline. By contrast, the extinction probabilities estimated here under IUCN Criterion E were far below the threatened-category thresholds at the relevant evaluation horizons, and the upper bounds of the confidence intervals also remained below those thresholds. This conclusion did not change across the two adopted national time series, under either the naive or OEAR approach, or under sensitivity analyses for effort-trend correction and abundance-scale calibration.
The study also shows that, under the drift-Wiener model, for sufficiently large populations, the decline subcriteria of Criterion A systematically overestimate the finite-horizon extinction risk quantified by Criterion E. This theoretical result explains the discrepancy seen above between Criterion A and Criterion E in the Japanese eel case.
Because IUCN listing can be triggered when any one of several criteria is met, such systematic overestimation creates a risk of false-positive threat classification: species that are not in fact threatened may nevertheless be ranked as threatened. As a result, conservation effort may not be directed sufficiently toward taxa facing higher extinction risk. This issue is not limited to Japanese eel, but applies broadly to marine organisms with large population sizes.
Significance and Future Outlook
The study provides an exact confidence-interval theory under the drift-Wiener process while, through the OEAR extension, offering a general framework that treats a wide class of stochastic processes with observation error and short-run dependence through an effective-diffusion approximation. A major contribution of the study is that it integrates mathematical population-dynamics models with the statistical theory of confidence intervals to provide an extinction-risk framework that can be used directly in conservation assessment.
The framework developed here should be useful for future applications of IUCN Criterion E, for methodological work on uncertainty in conservation decision-making, and for reassessing the relationships among different Red List criteria. Future work may extend the approach to broader classes of stochastic population models and to additional species of conservation concern.
Acknowledgments
This research was funded by a grant from the Japan Fisheries Agency.
Article Information
Title: Confidence Intervals for Extinction Risk: Validating Population Viability Analysis with Limited Data
The First Future Vision Council Meeting of the Institute of Freshwater Biology Was Held
IFB
On February 19, 2026, the first Future Vision Council meeting of the Institute of Freshwater Biology was held.
At the meeting, participants shared the history and current status of the Institute of Freshwater Biology and exchanged views on its role as a center for research and education, its relationship with local communities and society, and directions for its sustainable future operation.
The Institute will continue discussions with relevant stakeholders as it considers its sustainable operation and future development.
The FY2025 Year-end Report Meeting of the Chikuma River and Shinano River Research Group Was Held!
IFB
On February 12, 2026, the FY2025 year-end report meeting of the Chikuma River and Shinano River Research Group was held in person at the Chikuma River Office. At this meeting, the Institute of Freshwater Biology, Nagano University, the Nagano Prefectural Fisheries Experimental Station, and Shinshu University reported their research results related to the Ministry of Land, Infrastructure, Transport and Tourism river ecology general research group and river erosion control technology research and development program to the Chikuma River Office.
The Chikuma River and Shinano River Research Group is conducting research under the theme, “The Importance of Habitat Continuity in Rivers - Impact Assessment and Conservation Measures for River Ecosystems.” The group is examining the relationship between river ecosystems and river management from multiple perspectives, including fish biodiversity, environmental DNA, channel change, biological communities, fish passage, and migration monitoring. During the meeting, each presentation was followed by active discussion on how the research outcomes can contribute to river management and ecological conservation in the Chikuma and Shinano River systems.
FY2025 Promotion and Research Progress Meeting for the International Fisheries Resource Survey and Evaluation Project (Eel Unit) Held at the Fisheries Agency!
IFB
On January 30, 2026, the FY2025 promotion and research progress meeting for the International Fisheries Resource Survey and Evaluation Project (Eel Unit) was held in a hybrid format at the 2nd Conference Room of the Fisheries Policy Department, Fisheries Agency, Kasumigaseki, Tokyo, and online. This project on Japanese eel resource management is a commissioned and subsidized research project of the Fisheries Agency led by Professor Hiroshi Hakoyama, with participation from universities, research institutes, prefectural agencies, and private-sector partner organizations. A total of 67 participants from the Fisheries Agency, universities, prefectures, and other research and partner institutions attended the meeting, where FY2025 research outcomes were presented and future directions were discussed. Covering stock trend and sex-ratio analyses, population genetic analysis, glass eel recruitment surveys, satellite-tag studies, and extinction risk assessment, the outcomes of this project are expected to contribute to resource management by national and prefectural authorities as well as by countries and regions along the East Asian coast.
Meeting Agenda
Opening Remarks (Chief of the International Resources Section) 13:15-13:20 (5 min)
Introduction of Participants (Attendance List) 13:20-13:25 (5 min)
Review of Project Progress and Research Outcomes
1. Overall Project Summary, Hakoyama 13:25-13:35 (10 min)
2. Trend and Sex-ratio Analysis of Eel Resources, Hakoyama / Faulks / T. Kodama 13:35-14:00 (25 min)
3. Population Genetic Analysis of Eel, Sekino 14:00-14:20 (20 min)
4. Summary of Glass Eel Recruitment Surveys, Mochioka / Hakoyama 14:20-14:40 (20 min)
5. Break 14:40-14:50 (10 min)
6. Reducing Drag of Satellite Tags for Eels, Iio / Huynh 14:50-15:10 (20 min)
7. Argos Satellite Tag Survey, Hakoyama / Huynh 15:10-15:30 (20 min)
8. General Discussion 15:30-15:55 (25 min)
Closing Remarks (Chief of the International Resources Section) 15:55-16:00 (5 min)
Participated in Sediment Removal Work in the Rokkason Weir Tunnel
IFB
In January 2026, as part of routine maintenance of the Institute’s water intake system from the Chikuma River, IFB staff participated in sediment removal work in the tunnel at Rokkason Weir.
Director Hiroshi Hakoyama and technical staff member Masayuki Itoh joined the on-site work and cooperated with local stakeholders to remove accumulated sediment from the tunnel.
On 16 January 2026, the Institute of Freshwater Biology, Nagano University, hosted a discussion meeting with SEAFDEC (Southeast Asian Fisheries Development Center).
The meeting was held as part of collaborative activities under the Memorandum of Understanding (MOU) between Nagano University and SEAFDEC, which supports cooperation in research and education on inland fisheries resources and freshwater ecosystems (signed on 29 July 2019; updated on 18 July 2024).
Thank you for your continued interest in the activities of the Institute of Freshwater Biology (IFB) throughout 2025.
Information from IFB is consolidated on ifb-research.jp, and we will continue to keep it updated.
This year, we also worked on improving website performance and basic quality.
In a recent check of the top page (https://ifb-research.jp/), Google PageSpeed Insights reported 100% performance for both mobile and desktop.
In addition, the HTML validation (W3C Markup Validation Service) detected no errors or warnings.
We also confirmed a score of 100 points with Another HTML-lint (HTML5).
We will continue to maintain a website that is easy to access across a wide range of devices, including smartphones, so that essential information can be delivered reliably.
In 2026, we will keep recording our activities and sharing updates. Thank you again, and best wishes for the New Year.
The Journal of Ethology has released a new video introducing Editor Choice papers.
The video was produced and edited by Associate Professor Sakie Kodama of the Institute for Freshwater Biology.
This video provides an accessible overview of the featured research and is part of a series that highlights recent contributions in the field of ethology.
It serves as a valuable resource for students, educators, and researchers who wish to understand key findings through a clear visual format.
Abstract:
Dr. David O. Alila (University of Dar es Salaam – Tanzania) will present a seminar titled “The Evolutionary Ecology of African Annual Killifish of the Genus Nothobranchius” The talk will examine how ecological and evolutionary forces shape the extraordinary life histories, adaptations, and diversification of Nothobranchius killifish, a group of short-lived species inhabiting ephemeral wetlands across sub-Saharan Africa. Drawing on extensive fieldwork and experimental studies in Tanzania, the global hotspot of Nothobranchius diversity, Dr. Alila will highlight how ecological pressures drive rapid evolution, niche partitioning and sympatric coexistence. Importantly, he will demonstrate how these evolutionary traits underpin the species’ exceptional potential as native biological control agents against malaria mosquitoes, linking fundamental evolutionary ecology to practical, sustainable applications for biodiversity conservation and public health.
The Chikuma–Shinano River Research Group presented at the 27th River Ecology Research Meeting
IFB
On November 13, 2025, at the Tokyo Stock Exchange Conference Center in Chuo-ku, Tokyo, the “27th River Ecology Research Meeting” (organized by the River Ecology Research Association and co-organized by the Japan Society on Ecological Engineering) was held. At this meeting, the “Chikuma–Shinano River Research Group,” led by Professor Hiroshi Hakoyama of the Institute of Freshwater Biology, Nagano University, gave a research presentation.
The Chikuma–Shinano River Research Group focuses on the importance of habitat connectivity in rivers and advances research on relationships between river ecosystems and river management using diverse approaches, including fish diversity, aquatic communities, channel morphology, and environmental DNA.
Oral presentation
“The importance of habitat connectivity in rivers — impact assessment and conservation measures for river ecosystems”
Presenter: Hiroshi Hakoyama (Representative, Chikuma–Shinano River Research Group)
Selected poster presentations
“The importance of habitat connectivity in rivers — impact assessment and conservation measures for river ecosystems”
Hiroshi Hakoyama
“Relationships between fish diversity and environmental variables in the Shinano River: towards understanding habitat connectivity”
Sakie Kodama, Takeru Kodama, Leanne Faulks, Alessandra Cera, Hiroshi Hakoyama
“River fragmentation at the local scale: effects on biodiversity”
Leanne Faulks, Alessandra Cera, Sakie Kodama, Hiroshi Hakoyama
“Spatial and temporal variations of community-level profile of epilithic biofilm for assessing disturbances”
Alessandra Cera
“Relationships among dams, water quality, microbial communities, and fish assemblages in the middle reaches of the Chikuma River”
Takeru Kodama, Mitsuki Ohara, Yoshinobu Hanaoka, Koki Hada, Sakie Kodama, Leanne Faulks, Hiroshi Hakoyama
“Estimating Fish Density from Downstream eDNA Reads in an Experimental Waterway”
Mitsuki Ohara, Takeru Kodama, Hiroshi Hakoyama
“Channel changes in the middle reaches of the Chikuma–Shinano River based on cross-section survey data and aerial photographs”
Fuka Iwai, Takato Izuchi, Masafumi Toyoda
“Analysis of fish–environment relationships using integrated river data from the Ministry of Land, Infrastructure, Transport and Tourism with dam location information”
Takeru Kodama, Sakie Kodama, Leanne Faulks, Masafumi Toyoda, Hiroshi Hakoyama
“Effects of ayu on river ecosystems”
Shun Kato, Leanne Faulks, Yuji Onishi, Shinji Takahashi, Hiromi Uno
For the detailed program and further information, please refer to the website of the River Ecology Research Association.
The Encyclopedia of Theoretical Biology (Asakura Publishing) has been published.
IFB
Professor Hiroshi Hakoyama of the Institute of Freshwater Biology has contributed the following three entries to The Encyclopedia of Theoretical Biology (in Japanese) published by Asakura Publishing:
“Demographic and environmental stochasticity” pp. 50–51
“Optimal foraging” pp. 122–123
“Risk-sensitive foraging” pp. 124–125
Title: The Encyclopedia of Theoretical Biology
Publisher: Asakura Publishing Co., Ltd. (Tokyo)
Publication date: 13 November 2025
ISBN: 9784254172034
Publisher website: https://www.asakura.co.jp/detail.php?book_code=17203
Covering the whole field of biology, this encyclopedia provides an overview of theoretical ideas and mathematical methods that are useful for understanding the basic logic of biology, explained in a way that is accessible even to readers outside the field. It is organized into eight sections: Ecology & Environment, Evolution, Behavior & Society, Neuroscience, Development & Morphogenesis, Medicine, Systems Biology, and Biological Information. In addition, two chapters are devoted to common methodologies: mathematical modeling and data analysis.
The 2025 Glass Eel and Yellow Eel Research Meeting Was Held
IFB
On October 31, 2025, the 2025 Glass Eel and Yellow Eel Research Meeting was held at the meeting room of the Institute for Freshwater Biology, Nagano University (Komaki 1088, Ueda City).
Participants reported on local glass eel surveys conducted across Japan and discussed future directions for data analysis and collaborative research.
Date: October 31, 2025 (Friday), 13:30–16:00
Venue: Meeting Room, Institute for Freshwater Biology, Nagano University (Komaki 1088, Ueda City)
Agenda:
0. Opening
1. Glass eel survey in Miyazaki – Tetsuya Matsunaga / Hidekazu Hayashida (13:30–13:50)
2. Glass eel survey in Wakayama – Yoshitsugu Kaji / Toshimitsu Tanaka (13:50–14:10)
3. Glass eel survey in Kagoshima – Hiroki Nakashima (14:10–14:30)
Break (10 min, 14:30–14:40)
4. Glass eel survey in Fukuoka – Noritaka Mochioka (14:40–15:00)
5. Glass eel survey in Chiba – Junichi Hirata (15:00–15:20)
6. Glass eel survey in Shizuoka – Takahiro Yamamoto (15:20–15:40)
7. General discussion (15:40–16:00)
8. Closing
Break (10 min, 16:00–16:10)
Data Analysis Discussion (16:10–18:00, with short breaks)
9. Time-series data analysis – Hiroshi Hakoyama (16:10–16:30)
10. Discussion on analysis of survey data from each JV (16:10–18:00)
Participants shared survey results from various regions and engaged in active discussions to strengthen collaboration for future eel resource management.
Professor Hakoyama Presented at the SEAFDEC/JAIF Project End Meeting on Tropical Anguillid Eel Management in Southeast Asia
IFB
On October 31, 2025, Professor Hiroshi Hakoyama attended the Project End Meeting on “Development of Stock Assessment Methods and Strengthening of Resources Management Measures for Tropical Anguillid Eel in Southeast Asia,” organized by Southeast Asian Fisheries Development Center (SEAFDEC) and supported by the Japan‑ASEAN Integration Fund (JAIF), held in Bangkok, Thailand. For details see https://www.seafdec.org/project-end-meeting-jaif-eel-2025/.
Professor Hakoyama delivered a presentation titled “Experience from Japan in Managing the Japanese Eel (Anguilla japonica): Implications for Tropical Anguillid Eels in ASEAN (Rev. 2),” under Agenda 7-2.
In his talk, he introduced Japan’s experience and lessons learned in the sustainable management of Anguilla japonica and discussed how these insights could be applied to improve regional management frameworks for tropical anguillid eels across ASEAN Member States.
The meeting brought together representatives from ASEAN Member States, SEAFDEC departments, and partner organizations to present project outcomes, share country experiences, and discuss future directions for regional cooperation in eel resource management.
Professor Hakoyama Participated in the 2025 Nagara River Field Study Tour Organized by the River Ecology Research Association!
IFB
On October 16–17, 2025, the Nagara River Field Study Tour, organized by the River Ecology Research Association, was held, and Professor Hakoyama participated as a member of the parent committee.
During the event, participants visited the study sites of the Nagara River Research Group, and on the second day, oral presentations of research results were given.
The 2025 General Meeting of the "Association for Restoring the Blessings of the Chikuma River" Was Held!
IFB
On October 7, 2025, the 2025 General Meeting of the “Association for Restoring the Blessings of the Chikuma River” was held in the training hall on the second floor of the Kamiko Fisheries Cooperative Hall.
Under the leadership of Chairman Yoichi Tsuchiya, the Association aims to “revive the Chikuma River as a mecca for ayu fishing.” Through efforts to create a river environment that is friendly to native fish species such as ayu and ugui, and beloved by local residents, the Association seeks to contribute to the promotion of fisheries and tourism industries, as well as to regional revitalization. The Institute for Freshwater Biology (IFB) cooperates as a member organization of this Association.
At the meeting, reports on this year’s activities were presented, along with research presentations. From IFB, Professor Hiroshi Hakoyama and Researcher Takeru Kodama gave presentations on IFB’s initiatives and topics related to the water quality of the Chikuma River.
Researchers from Indonesia’s BRIN Visit the Institute of Freshwater Biology
IFB
From September 29 to October 3, 2025, Dr. Arif Wibowo, Director of the Center for Aquatic Conservation Research, and Dr. Dwi Atminarso from Indonesia’s National Research and Innovation Agency (BRIN) visited the Institute of Freshwater Biology (IFB) at Nagano University.
During their stay, the two researchers held in-depth discussions with Professor Hiroshi Hakoyama and other IFB staff members on the future directions of collaborative research on eel resource management, river ecosystem conservation, and environmental DNA (eDNA) analysis in Southeast Asia.
They also toured IFB’s research facilities and exchanged ideas on data sharing and the establishment of a long-term research collaboration framework.
This visit was conducted as part of the activities of the Eel Task Team,
aimed at strengthening international collaboration toward the sustainable use and ecological conservation of tropical and temperate eel species.
Associate Professor Sakie Kodama Appointed as Advisor to the Newly Established "Insect Ecology Research Club" in 2025!
IFB
The Insect Ecology Research Club, a new student circle at Nagano University, was founded by students who bonded during the Laboratory Course in Freshwater Biology.
The club’s activities include raising insects (such as beetles, silkworms, and bell crickets), outdoor observation and identification, and ecological research.
Abstract:
The Japanese eel was classified as Endangered IB by the Ministry of the Environment in 2013. In response, the Fisheries Agency implemented the Eel Habitat Improvement Support Project from 2016 to 2023, installing stone basket reefs (Ishikura-kago) at 86 sites across 40 rivers and 2 lakes in 19 prefectures, ranging from Iwate to Kagoshima. The project was carried out based on the precautionary principle, with effect verification mainly conducted by Kyushu University. Using eight experimental ponds at the Kagoshima Prefectural Fisheries Technology Development Center, it was demonstrated that stone baskets help reduce damage from birds.
Furthermore, six stone baskets of varying stone sizes (long diameter 10, 20, 30 cm) were installed in the brackish zone of the Saigo River in Fukutsu City, Fukuoka Prefecture. It was revealed that yellow eels prefer stones of 10 cm in diameter, while silver eels prefer 20 cm, and that individuals with high-frequency use of stone baskets had better nutritional conditions compared to those with low-frequency use. Currently, stone baskets have been installed at four sites from the freshwater zone to the estuary of the Saigo River and the Arase River in Kagoshima Prefecture, in an effort to identify effective locations for protecting individuals undergoing silvering metamorphosis.
Workshop on Biodiversity Conducted at Ueda Nishi High School UNMP (9th)
IFB
On September 23, 2025, Associate Professor Sakie Kodama and Professor Hiroshi Hakoyama from the Institute for Freshwater Biology, Nagano University, conducted a workshop titled “Thinking About Biodiversity – A Workshop with the Institute for Freshwater Biology, Nagano University” as part of the 9th Ueda Nishi Mind Project (UNMP) held at Ueda Nishi High School.
The workshop aimed to help students deepen their understanding of biodiversity conservation and invasive species control while developing scientific inquiry skills through hands-on learning.
Participants conducted fieldwork in the Chikuma River, collecting and observing planarians (Dugesia japonica)—a freshwater species known as an indicator of clean water.
Following an ecological introduction by Associate Professor Kodama, students collected planarians in the river and then observed them under microscopes at the IFB.
They also performed flow cytometry to examine ploidy variation, discovering multiple individuals with different ploidy levels within the same population—a fascinating finding for the students.
Through this experience, they learned the importance of biodiversity conservation and gained a deeper appreciation of scientific observation and analysis.
R package “extr: Extinction Risk Estimation” Released on CRAN
IFB
On September 21, 2025, Professor Hiroshi Hakoyama of the Institute for Freshwater Biology, Nagano University, released his R package “extr: Extinction Risk Estimation” on the Comprehensive R Archive Network (CRAN).
This package implements a method for estimating extinction probabilities from population time-series data under the Wiener process with drift, and includes the newly proposed approach for constructing confidence intervals for extinction risk using the w–z method (Hakoyama, 2025, arXiv preprint).
The method enables accurate extinction-risk estimation even with limited data, providing a statistically rigorous framework for validating Population Viability Analysis (PVA) and supporting IUCN Red List assessments.
