iTHEMS Biology Seminar

Towards rock-solid evolutionary genomics

May 28 (Thu) 13:00 - 14:00, 2026

Leo Speidel (RIKEN ECL Research Unit Leader, Mathematical Genomics RIKEN ECL Research Unit, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

I will present an overview of ongoing and future projects in our lab. We aim to understand how human genomes retain information about our evolutionary past; a central goal is to reconstruct a high-resolution history of humans, pushing the limits of what we can learn about our origins, past migrations, and adaptation to changing environments and survival pressures. Our genomes reveal events that would otherwise be lost to history, revealing how evolutionary forces have shaped genetic variation and influence our health today. How can we confidently infer events that occurred tens of thousands of years ago? I will discuss how converging and independent lines of genomic evidence can provide “rock-solid” support for major evolutionary events, including archaic admixture, large-scale migrations across continents, and population bottlenecks, and how we aim to extend these approaches to study the evolutionary history and origins of humans and other species.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Stochastic Thermodynamics: noise and energetics of nanoscale systems

May 21 (Thu) 13:00 - 14:00, 2026

Jean-Charles Delvenne (Professor, Applied Mathematics, Université Catholique de Louvain, Belgium)

Stochastic thermodynamics, initiated three decades ago, aims at quantifying the fluctuations of physical observables in relation with thermodynamic quantities (such as heat or entropy production). A typical result is the Thermodynamic Uncertainty Relation, which states that a high entropy production is required to obtain a favorable noise-to-signal ratio for some observables (such as displacement of a molecular motor) in stationary out-of-equilibrium systems. It is especially relevant for nanoscale systems, where the fluctuations cannot be neglected. This includes biological systems (e.g. biological motors such as kinesin along a microtubule), electronic systems (transistor-based memories), chemical reactions, etc. The talk will be both a tutorial on some basic results or applications, and a presentation of some recent results and perspectives.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Sexual conflict over floral receptivity? — theory-guided experiments of evolutionary ecology

May 14 (Thu) 16:00 - 17:00, 2026

Daisuke Kyogoku (Associate Professor, Faculty, Division of Natural Sciences, Nara Women's University)

The theory of evolutionary biology predicts that the interests (in terms of adaptation) of different individuals can conflict with one another. Specifically, mating partners can have different optima in traits such as mating rates, number of mates, number of offspring, and resource allocation to the offspring. Botanists have long recognized that pollination induces floral closure or wilting, which is typically seen as the adaptation of the pollen recipients (i.e., getting rid of costly flowers after achieving their function). However, it is also possible that floral closure or wilting is, at least in part, the outcome of the manipulation by selfish pollen. For example, pollen may secure their paternity by preventing additional pollination. Fewer seed production by the recipients can result in so much allocation of maternal resources to each fertilized egg cell that is maternally maladaptive (but paternally adaptive). Being guided by these theoretical predictions, I have been testing the hypothesis using both Taraxacum dandelions and Arabidopsis. In this talk, I will show our recent (mostly unpublished) results. Although the projects are halfway, results so far generally support the hypothesis. The ideas of related future projects and the philosophy behind the projects may also be discussed.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Cautionary tales in data analysis from gravitational-wave astronomy

April 23 (Thu) 13:00 - 14:00, 2026

Kipp Cannon (Professor, Research Center for the Early Universe (RESCEU), The University of Tokyo)

We'll look at signal detection in noisy data, and at Bayesian inference in astrophysical inverse problems. We'll look at the form these problems take in the context of gravitational-wave astronomy, but we'll focus on where attempts at solutions have gone wrong. The mistakes we make transcend disciplines, and hopefully by shining light on them others can be helped to avoid making them as well.

Venue: Hybrid Format (3F #359 and Zoom), Main Research Building

Event Official Language: English

Understanding Biological Clocks Using Methods from Applied Mathematics and Theoretical Physics

April 16 (Thu) 12:30 - 13:30, 2026

Gen Kurosawa (Senior Research Scientist, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

Imagine that you are in a room with no information about time. The room is located in a cave, where temperature and light intensity remain constant. In such an environment, would you be able to wake up tomorrow or the day after? In fact, most humans can wake up at roughly similar times on successive days. This is because we possess internal daily rhythms, known as circadian rhythms. Biological experiments have shown that such rhythms are not unique to humans, but are shared by many species on Earth. In this talk, I will introduce some open problems related to these daily rhythms, and discuss approaches based on dynamical systems theory and the renormalization group method, from the perspectives of applied mathematics and theoretical physics.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Biology Starter Meeting & Welcome 4 New Members!

April 9 (Thu) 13:00 - 15:00, 2026

Alba Nieto Heredia (Postdoctoral Researcher, Mathematical Genomics RIKEN ECL Research Unit, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))
Takehiro Tottori (Special Postdoctoral Researcher, RIKEN Center for Brain Science (CBS))
Mariia Ivonina (Postdoctoral Researcher, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))
Satsuki Hirasawa (Ph.D. Student, Graduate School of Information Science and Technology, Hokkaido University)

This is a special 2 h event of our newly renewed Biology Study Group! This year, 4 new members are joining iTHEMS Biology. They will each give us a 15 min introduction to their research. All participants will also take 2-3 min to introduce themselves and their research topic to the new members. If time permits, we'll hold a brief organizational meeting to review the running of the biology seminars in the new fiscal year. We strongly encourage all iTHEMS members, not just biology-interested ones, to join our session at least in the 1st hour, to meet the new members and learn about their research.

Venue: Hybrid Format (3F #359 and Zoom), Main Research Building

Event Official Language: English

A mathematical promenade in microscopic locomotion

April 2 (Thu) 13:00 - 14:00, 2026

Clément Moreau (CNRS Researcher, CNRS, France)

The microscopic world offers a fascinating diversity of locomotion strategies, relying primarily on the use of flagella and cilia. These slender structures, capable of complex periodic deformations, serve as a major source of inspiration for medical microrobotics. At this scale, fluid dynamics is governed by the predominance of viscosity over inertia. This low-Reynolds number regime imposes strict physical constraints, summarized by the famous « scallop theorem »: a reciprocal deformation cannot produce any net displacement. Mathematically, this is framed by the Stokes connection, which links changes in body shape to net movement in space. This presentation proposes a journey through the modeling principles of microscopic swimmers. We will see how to derive analytical solutions to the locomotion problem by simplifying degrees of freedom or by assuming small deformation amplitudes. I will then present the perspective of control theory to address the « controllability » property, i.e. the ability of a locomotor to reach any target position and shape. Finally, I will question a classic hypothesis in the field: the inextensibility of flagella. Although the literature often assumes these structures are rigid in the longitudinal direction, certain micro-organisms and artificial robots exhibit significant compression variations. I will present recent results, based on classical modeling tools, exploring the influence of compression-curvature coupling on locomotion efficiency at low Reynolds numbers.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Ecological decline and biocultural loss in Cycas revoluta landscapes of the Amami Islands

March 31 (Tue) 13:00 - 14:00, 2026

Joshua Englehardt (Professor, Center of Archeologist Studies, El Colegio de Michoacán, Mexico)

Cycads (Cycadales) are one of the world’s most ancient plant lineages, and Cycas revoluta Thunb. (‘sotetsu,’ in Japanese) has long occupied a central place in the cultural ecologies of the Ryukyu archipelago, particularly in the Amami Islands of southern Japan. Although never domesticated, C. revoluta has held enduring alimentary, ethnoecological, and symbolic saliency within local agroecological systems, ritual landscapes, and island identities for centuries. Building on recent interdisciplinary scholarship on Japanese and Ryukyuan cycad cultures, this presentation synthesizes ethnobotanical, historical, ecological, and genetic research to detail the accelerating collapse of Amami cycad biocultural heritage. The core of this talk focuses on results from ongoing fieldwork documenting the rapid spread of cycad aulacaspis scale (Aulacaspis yasumatsui Takagi), an invasive insect that now poses an existential threat to both biological C. revoluta populations and sotetsu culture across the Amami archipelago. Drawing on systematic botanical surveys, geospatial mapping, genetic sampling, and ethnographic interviews, the presentation details how ecological decline and cultural erosion are unfolding in tandem. Population-level mortality, reproductive failure, and genetic loss are paralleled by the disappearance of knowledge, practices, and senses of place historically anchored in the islands’ cycad landscapes. By situating these findings within broader discussions of cycad use in Japan and worldwide, as well as comparative biocultural heritage studies, the presentation highlights how invasive species can rapidly destabilize long-standing human-plant relationships. The Amami case underscores the urgency of integrating biological conservation with cultural documentation at moments of irreversible ecological change, offering broader insights into island resilience, heritage loss, and the fragility of biocultural systems under accelerating environmental pressures.

Venue: Seminar Room #359 (Main Venue) / via Zoom

Event Official Language: English

Toward a Mathematical Prehistory of Homo sapiens: Data Integration and Statistical Representation in PaleoAsiaDB

March 26 (Thu) 13:00 - 14:00, 2026

Kenji Okubo (Special Postdoctoral Researcher, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

This talk introduces PaleoAsiaDB, a curated database of lithic assemblages from Paleolithic Asia, and aims to initiate a discussion on its potential uses and methodological challenges. The database integrates information on tool typology, technological attributes, stratigraphy, and chronological ranges across multiple sites and periods. Archaeological assemblage data are inherently heterogeneous, combining categorical variables with hierarchical structure and, in some cases, continuous measurements. In addition, temporal information is often represented as ranges rather than precise dates, and sampling intensity varies substantially across sites. These features make it non-trivial to define consistent procedures for comparison, aggregation, and quantitative analysis. The goal of this session is to gather feedback on data representation and analysis strategies, and to clarify what types of quantitative approaches are most suitable for extracting robust patterns from archaeological assemblage data.

Venue: Seminar Room #359 (Main Venue) / via Zoom

Event Official Language: English

Mouse Limb Bud Skeletal Patterning Description and Modelling

March 19 (Thu) 13:00 - 14:00, 2026

Laura Aviñó Esteban (Ph.D. Candidate, European Molecular Biology Laboratory, Barcelona, Spain)

Understanding how complex organs reliably form during development remains a key question in biology. In this talk, I discuss how gene regulatory networks may generate skeletal patterns in the vertebrate limb, using Sox9 expression as a proxy, as it marks the earliest stages of cartilage formation. To address this, I developed new computational tools for reconstructing spatiotemporal gene expression and built models ranging from machine learning approaches to mechanistic frameworks. These analyses reveal that limb patterning cannot be explained by a single universal mechanism. Instead, different regions of the limb appear to use distinct regulatory strategies, uncovering an unexpected qualitative modularity in skeletal development. Together, these findings lead to a new hypothesis in which other systems, such as the vasculature may actively shape skeletal spacing in specific limb regions.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Chronotaxicity and Dynamic Stability: From Theory to Quantitative Measures

March 12 (Thu) 13:00 - 14:00, 2026

Aneta Stefanovska (Professor, Lancaster University, UK)

Living systems operate far from equilibrium under continuous time-varying forcing across multiple temporal and spatial scales. From neural and cardiovascular rhythms to microcirculatory dynamics and circadian cycles, physiological processes are inherently nonautonomous. Classical stability concepts based on autonomous attractors and stationary limit cycles are therefore insufficient to explain how such systems remain robust yet adaptable. In this talk, I will introduce chronotaxicity as a framework for nonautonomous oscillatory systems possessing time-dependent point attractors and contraction regions. Chronotaxic systems maintain stability under continuous forcing, providing a rigorous theoretical description of dynamic robustness. To illustrate the generality of this concept, I will show how chronotaxicity can be observed in a controlled physical experiment. I will then present a new order parameter based on angular velocity for quantifying phase dynamics in numerical simulations of coupled nonautonomous oscillators, along with the methods collected in the Multiscale Oscillatory Dynamics Analysis (MODA) toolbox for analysing time-dependent oscillatory behaviour. This approach provides a unified perspective on dynamic stability in complex systems, highlighting how living systems remain robust yet adaptable and suggesting quantitative signatures of dysfunction in health and disease. While the focus is on physiological and numerical models, it is broadly applicable to complex nonautonomous systems, underscoring its generality as a dynamical principle.

Venue: via Zoom / Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

How does the brain compute the value of odors and trigger adaptive behavior?

March 5 (Thu) 13:00 - 14:00, 2026

Hokto Kazama (Team Director, Laboratory for Circuit Mechanisms of Sensory Perception, RIKEN Center for Brain Science (CBS))

The world is filled with numerous odors that are impossible to experience all in our lifetime. Perhaps to cope with this situation, the brain is equipped with an ability to recognize whether an odor is attractive or aversive even from the first encounter and guide adaptive behavior. However, how information about the innate value of odors (attractiveness/aversiveness) is computed and transformed into appropriate behavioral outputs in the brain remains poorly understood. We are addressing this question in the olfactory circuit of fruit flies by combining behavioral analysis in virtual reality, comprehensive neuronal activity imaging, neuronal connectivity analysis, and computational modeling. In this talk, I will present our latest efforts to decipher how odor value is computed and how this information is transformed into motor-related signals in a tiny brain.

Venue: Seminar Room #359 (Main Venue) / via Zoom

Event Official Language: English

Sex ratio theory for facultative parthenogens: from fortuitously optimal stick insects to the origin of haplodiploidy in Hymenoptera

February 26 (Thu) 13:00 - 14:00, 2026

Kora Klein (Visiting Researcher, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

First, I will present one of my PhD papers which focuses on sex ratios when females can reproduce both sexually and asexually. This paper features two models: an optimality model and an evolutionary invasion analysis. More generally, it shows my style of approaching evolutionary theory. After this, I will briefly discuss the work I plan to do in the next 6 months during my JSPS fellowship where I will focus on the evolution of more conventional X-chromosomes. Short Bio: I studied biology at the Free University in Berlin. My biology studies were mostly empirical but I attended several Bachelor courses for mathematicians (calculus and stochastics) and did my Master thesis in Zurich with Hanna Kokko, a theoretical evolutionary ecologist who studies a broad range of topics. In 2020, I then continued working in Hanna Kokko’s group for my PhD and moved with her from Zurich to Mainz in 2023. During my time with Hanna Kokko, worked on various topics centered around intraspecific diversity, including projects on sexual dimorphism, sex ratio theory, intralocus sexual conflict, and a female-limited color polymorphism in a butterfly. Since then, I started my first PostDoc in 2024 with Laura Ross in Edinburgh (UK) where I modelled how the unusual genetic systems of Scarid flies could have evolved, and have now started a 6 month JSPS fellowship with Ryosuke Iritani.

Venue: #435-437, Main Research Building

Event Official Language: English

Quantitative phylogenomics

February 24 (Tue) 13:00 - 14:00, 2026

Hector Banõs (Assistant Professor, Department of Mathematics, California State University, USA)
Benjamin Teo (Postdoc, Mathematical Analysis of Cellular Systems, University of Melbourne, Australia)

This session features two speakers: Hector Banos, Assistant Professor of Mathematics at California State University, whose research focuses on phylogenetic inference and network models, and Benjamin Teo, a Postdoctoral Researcher at the University of Melbourne, working on probabilistic and computational methods for continuous trait evolution on phylogenetic networks. See below for details. 【Talk 1】 Speaker: Hector Banos Title: Bringing a Knife to a Gunfight: Pitfalls of Phylogenetic Inference under Model Misspecification Abstract: Phylogenetic networks provide a flexible framework for representing evolutionary histories that include hybridization, introgression, and other reticulate processes. However, inferring such networks remains computationally and statistically difficult. Many current methods often scale only to restricted classes of networks. Consequently, researchers frequently analyze their data using simpler models (most commonly phylogenetic trees) even when there is strong evidence that the underlying evolutionary history is more complex. In this talk, we examine the impact of model misspecification on phylogenetic inference, focusing on situations in which data are generated by a complex network but are analyzed using simpler tree or network models. I then show how this mismatch can influence the topology of inferred trees, as well as the structure of inferred networks. These results highlight the limitations and the practical consequences of using simplified models for phylogenetic inference. 【Talk2】 Speaker: Benjamin Teo Title: Adapting cluster graphs for inference of continuous trait evolution on phylogenetic networks Abstract: I consider a new approach ("loopy belief propagation") for fitting Gaussian models on a phylogenetic network to explain the data observed across present-day species for a continuous univariate or multivariate trait. We previously showed [1] that a trait evolution model coupled to a network can be readily cast as a probabilistic graphical model, so that the likelihood can be efficiently computed using a dynamic programming framework ("belief propagation") defined on an auxiliary graph ("cluster graph") that is tree-structured. Even so, maximum likelihood estimation can grow computationally prohibitive for large complex networks. Belief propagation can be applied more generally to non-tree ("loopy") cluster graphs to compute a factored energy approximation to the log-likelihood. "Loopy" belief propagation may provide a more practical trade-off between estimation accuracy and runtime. However, the influence of cluster graph structure on this trade-off is not precisely understood. We conduct a simulation study using our Julia package PhyloGaussianBeliefProp [2] to investigate how varying the maximum cluster size of a cluster graph affects this trade-off. We discuss recommended choices for maximum cluster size, and prove the equivalence of likelihood-based and factored-energy based estimates for the homogeneous Brownian motion trait model. The talk is based on our preprint [3]. I will introduce the key concepts from the ground up.

Venue: Seminar Room #359 (Main Venue) / via Zoom

Event Official Language: English

The sample complexity of species tree estimation: How many genes does it take to infer a species tree?

February 19 (Thu) 13:00 - 14:00, 2026

Max Hill (Assistant Professor, University of Hawaiʻi, USA)

In this talk, I will discuss the problem of inferring an evolutionary tree from DNA sequence data. The main focus will be on the sample complexity of this problem---i.e., the question of how much data is required to achieve high probability of correct inference. After introducing a standard stochastic model of gene and DNA evolution, I will highlight some surprising features of DNA sequence data that complicate inference. Finally, I will present an impossibility result which takes the form of an information-theoretic lower bound on the minimum amount of data needed for accurate inference when genes exhibit variation in mutation rates. No prior knowledge of phylogenetics or information theory is assumed. Based on joint work with Sebastien Roch.

Venue: Seminar Room #359 (Main Venue) / via Zoom

Event Official Language: English

Monitoring the complexity and dynamics of mitochondrial translation

February 12 (Thu) 16:00 - 17:00, 2026

Taisei Wakigawa (Research Associate, RNA Systems Biochemistry Laboratory, RIKEN Pioneering Research Institute (PRI))

Since mitochondrial translation leads to the synthesis of the essential oxidative phosphorylation (OXPHOS) subunits, exhaustive and quantitative delineation of mitoribosome traversal is needed. Here, we developed a variety of high-resolution mitochondrial ribosome profiling derivatives and revealed the intricate regulation of mammalian mitochondrial translation. Harnessing a translation inhibitor, retapamulin, our approach assessed the stoichiometry and kinetics of mitochondrial translation flux, such as the number of mitoribosomes on a transcript, the elongation rate, and the initiation rate. We also surveyed the impacts of modifications at the anticodon stem loop in mitochondrial tRNAs (mt-tRNAs), including all possible modifications at the 34th position, in cells deleting the corresponding enzymes and derived from patients, as well as in mouse tissues. Moreover, a retapamulin-assisted derivative and mito-disome profiling revealed mitochondrial translation initiation factor (mtIF) 3-mediated translation initiation from internal open reading frames (ORFs) and programmed mitoribosome collision sites across the mitochondrial transcriptome. Our work provides a useful platform for investigating protein synthesis within the energy powerhouse of the cell.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Quantitative characterization of microbial diversity and environmental adaptation

February 5 (Thu) 13:00 - 14:30, 2026

Mio Matsumoto (Junior Research Associate, Geobiology and Astrobiology Laboratory, RIKEN Pioneering Research Institute (PRI))
Shino Suzuki (Chief Scientist, Geobiology and Astrobiology Laboratory, RIKEN Pioneering Research Institute (PRI))

Event Official Language: English

Development of a real-time object tracking and response system

January 29 (Thu) 13:00 - 14:00, 2026

Isaac Planas Sitja (Postdoctoral Researcher, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

I will introduce the real-time tracking software and automatic response system that we are developing: TracktorLive. We created a modular system to overcome several issues in close-loop experiments, with the aim to automatise mechanical stimulus delivery or time-consuming actions, and provide tools for VR experiments in animals. This tracker, coded as a Python package, separates the processes into server and client functions to run several processes in parallel, which minimises the frame processing time, and allows running on low-end computers. We hope to implement LLM or AI functions as server processes in the future.

Venue: Seminar Room #359

Event Official Language: English