iTHEMS Biology Seminar

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

Evolution of sterile soldier castes in aphids

January 21 (Wed) 13:00 - 14:00, 2026

Keigo Uematsu (Assistant Professor, Keio University)

This seminar is jointly organized with the RIKEN Center for Sustainable Resource Science (CSRS). Social evolution in aphids is tightly linked to the formation of galls on their host plants. Galls provide efficient colony defense and nutritionally rich feeding sites such that colony members need not forage outside, leading to high intra-group relatedness. Typically, social aphids form a gall on their primary host plant, after which winged morphs disperse to secondary host plants and establish a free-living, open colony. Remarkably, sterile soldier castes have independently evolved twice in these open colonies, where individuals live on plant surfaces without modifying their structure. These aphids raise intriguing questions about the prerequisites for eusocial evolution and the mechanisms by which two distinct social systems are maintained within a single genome. In this talk, I will first provide an overview of the life cycle and the diversity of altruistic behaviors in gall-forming aphids, and then present our studies of the evolution of a sterile soldier caste in aphids inhabiting open colonies. From a developmental perspective, we tested the hypothesis that the sterile soldiers evolved through the co-option of pre-existing soldier phenotypes in a gall, based on similarity in morphology, transcriptome and behavior. From an ecological perspective, we investigated the kin structure and altruistic behavior of young nymphs in the open colonies of pre-eusocial species, and demonstrate that young aphids exhibit altruism by yielding feeding sites to older kin. Together, we propose that the open colonies of social aphids provide an ideal model system for studying the evolution of altruism.

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

Event Official Language: English

Enhancing the methodological framework for inferring selection with ancient DNA: theoretical insights, improvements and comparison

January 15 (Thu) 13:00 - 14:00, 2026

Lucas Sort (Postdoctoral Researcher, Mathematical Genomics RIKEN ECL Research Unit, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

Over the past decade, the emergence of ancient DNA has opened new opportunities for studying evolutionary processes. However, inferring signals of selection from such data remains a methodological challenge since controlling for population stratification, admixture, and dynamically changing demographic histories, among other confounding evolutionary processes, is difficult. In this context, ancient DNA time series data, which have proliferated, have led to the development of methods based on two main frameworks: Hidden Markov Models and Generalized Linear Mixed Models. In this work, we aim to clarify how these frameworks relate to the classical Wright–Fisher model, enabling targeted modeling improvements and producing more relevant comparisons across methods.

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

Event Official Language: English

Origin and evolutionary history of an urban underground mosquito

December 18 (Thu) 13:00 - 14:00, 2025

Yuki Haba (Postdoc, Zuckerman Institute, Columbia University, USA)

Urbanization is rapidly reshaping landscapes around the world, which poses questions about whether and how quickly animals and plants can adapt. Culex pipiens form molestus, more commonly known as the "London Underground mosquito," has been held up as a benchmark for the potential speed and complexity of urban adaptation. This intraspecific lineage within Cx. pipiens, a major West Nile virus vector, is purported to have evolved human biting and a suite of other human-adaptive behaviors in the subways and cellars of northern Europe within the past 200 years. Form molestus features prominently in textbooks as well as scholarly reviews of urban adaptation. Yet, the hypothesis of in situ urban evolution has never been rigorously tested. I will talk our recent efforts to understand the contentious origin and evolutionary history of the urban, human-biting mosquito. Our synthesis and meta-analysis of rich yet confusing literature show that its London Underground origin is unlikely (Haba and McBride 2022 Current Biology). Whole genome resequencing and population genomics of 800+ mosquitoes across ~50 countries again debunk the in situ evolution hypothesis and instead support that molestus first adapted to human environments >1000 years ago in the Mediterranean or Middle East, most likely in ancient Egypt or another early agricultural society (Haba et al. 2025 Science). I will outline implications of our results in urban evolutionary biology as well as in public health. Speaker Bio Yuki Haba, Ph.D., is an evolutionary biologist passionate about understanding how and why diverse behaviors evolve in nature. He is currently a Leon Levy Scholar in Neuroscience at Columbia University's Zuckerman Mind Brain Behavior Institute. He aims to take multi-desciplinary approaches, combining genomics, neuroscience, and field-based behavioral ecology to comprehensively understand the evolution of behavior. Yuki completed his PhD at Princeton, MA at Columbia, and undergraduate degree at the University of Tokyo. Personal webpage: https://yukihaba.github.io/

Venue: Seminar Room #359

Event Official Language: English

Widespread conservation of genetic effect sizes between human groups across traits

December 12 (Fri) 13:30 - 15:00, 2025

Simon Robert Myers (Professor, University of Oxford, UK)

Understanding genetic differences between populations is essential for avoiding confounding in genome-wide association studies and improving polygenic score (PGS) portability. We developed a statistical pipeline to infer fine-scale Ancestry Components and applied it to UK Biobank data. Ancestry Components identify population structure not captured by widely used principal components, improving stratification correction for geographically correlated traits. To estimate the similarity of genetic effect sizes between groups, we developed ANCHOR, which estimates changes in the predictive power of an existing PGS in distinct local ancestry segments. ANCHOR infers highly similar (estimated correlation 0.98 ± 0.07) effect sizes between UK Biobank participants of African and European ancestry for 47 of 53 quantitative phenotypes, suggesting that gene–environment and gene–gene interactions do not play major roles in poor cross-ancestry PGS transferability for these traits in the United Kingdom, and providing optimism that shared causal mutations operate similarly in different populations.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Self-organized mechano-chemical instabilities drive the emergence of tissue morphogenesis in digit organoids

December 11 (Thu) 13:00 - 14:00, 2025

Antoine Diez (Research Scientist, Mathematical Application Research Team, Division of Applied Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

Tissue morphogenesis is an emergent phenomenon: macroscopic structures cannot be predicted from a mere list of genes and cells. We examine here how digits arise from a spherical limb bud and present a framework linking microscopic cellular behavior to morphogenesis. To extract digit morphogenesis in vitro, we created a limb-mesenchyme organoid that breaks symmetry and forms digit-like cartilage. Analyzing cell behavior, iterating between experimental evidence and cellular-based models, shows that microscopic mechanisms like differential adhesion between distal and proximal autopod cells, chemotaxis toward Fgf8b, and biased traction can drive tissue-wide deformations by convergent extension that eventually lead to the formation of digit structures. Taking the continuum limit of these microscopic rules yields a modified Cahn–Hilliard equation, that is well known to describe fluid interfaces and so-called fingering instabilities, but that is shown here to recapitulate well organoid morphogenesis. Taken together, this work suggests that the emergence of “fingers” can be explained in a theoretical framework as a type of fingering instability.

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

Event Official Language: English

Biological Background of Duplicated Sequence Evolution: A Focus on Gene Conversion

December 4 (Thu) 13:00 - 14:00, 2025

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

Duplicated sequences—such as gene families, tandem arrays, and segmental duplications—are common in many genomes. Their evolution is shaped by several biological processes, including mutation, recombination, duplication, deletion, and gene conversion. Among these, gene conversion is especially important because it can make nearby copies more similar, while leaving distant copies free to diverge. In this seminar, I will give a broad and accessible overview of the biological background related to duplicated sequences, with a particular focus on what is known about gene conversion. I will summarize well-established patterns such as its dependence on genomic distance, sequence similarity, and recombination context. These biological features are often studied separately, so organizing them in one place can help provide a clearer foundation. The goal of the talk is to outline the biological principles that motivate thinking about duplicated sequences in a more formal or quantitative way in the future. I will not discuss specific model details. Instead, this presentation will serve as background preparation for later theoretical work.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

From phase reduction to hypergraphs: the higher-order dynamics of coupled phase oscillators

November 27 (Thu) 13:00 - 14:00, 2025

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

Networks are powerful tools in the modeling of complex systems, but they do not always capture the right interactions when multiple units are involved simultaneously. Such many-body interactions are encoded by higher-order structures which can be thought as extensions of networks. Over the last years, higher-order networks have been the focus of great excitement, since this novel framework has enormous potential for applications. In this talk, I will give an overview of higher-order interactions and their effects on nonlinear dynamics. I will introduce the basics of dynamics on networks and its extension to the case of higher-order interactions. As examples of the effects on nonlinear dynamics, I will discuss the case of phase reduction for systems with higher-order interactions and show the effects on synchronization dynamics.

Venue: Seminar Room #359 / via Zoom

Event Official Language: English