iTHEMS生物学セミナー

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

2026年2月26日(木) 13:00 - 14:00

コーラ・クライン (理化学研究所 数理創造研究センター (iTHEMS) 数理基礎部門 訪問研究員)

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.

会場: 研究本館 435-437号室

イベント公式言語: 英語

Quantitative phylogenomics

2026年2月24日(火) 13:00 - 14:00

ヘクター・バニョス (Assistant Professor, Department of Mathematics, California State University, USA)
ベンジャミン・テオ (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.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

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

2026年2月19日(木) 13:00 - 14:00

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.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

Monitoring the complexity and dynamics of mitochondrial translation

2026年2月12日(木) 16:00 - 17:00

脇川 大誠 (理化学研究所 開拓研究所 (PRI) 岩崎RNAシステム生化学研究室 リサーチアソシエイト)

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.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

Quantitative characterization of microbial diversity and environmental adaptation

2026年2月5日(木) 13:00 - 14:30

松本 美緒 (理化学研究所 開拓研究所 (PRI) 鈴木地球・惑星生命科学研究室 大学院生リサーチ・アソシエイト)
鈴木 志野 (理化学研究所 開拓研究所 (PRI) 鈴木地球・惑星生命科学研究室 主任研究員)

イベント公式言語: 英語

Development of a real-time object tracking and response system

2026年1月29日(木) 13:00 - 14:00

イザク・プラナス シッジャ (理化学研究所 数理創造研究センター (iTHEMS) 数理基礎部門 特別研究員)

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.

会場: セミナー室 (359号室)

イベント公式言語: 英語

Evolution of sterile soldier castes in aphids

2026年1月21日(水) 13:00 - 14:00

植松 圭吾 (慶応義塾大学)

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.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催 (メイン会場) / via Zoom

イベント公式言語: 英語

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

2026年1月15日(木) 13:00 - 14:00

リュカ・ソール (理化学研究所 数理創造研究センター (iTHEMS) 数理基礎部門 数理遺伝学理研ECL研究ユニット 特別研究員)

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.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

Origin and evolutionary history of an urban underground mosquito

2025年12月18日(木) 13:00 - 14:00

羽場 優紀 (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/

会場: セミナー室 (359号室)

イベント公式言語: 英語

Widespread conservation of genetic effect sizes between human groups across traits

2025年12月12日(金) 13:30 - 15:00

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.

会場: via Zoom / セミナー室 (359号室)

イベント公式言語: 英語

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

2025年12月11日(木) 13:00 - 14:00

アントワーヌ・ディエズ (理化学研究所 数理創造研究センター (iTHEMS) 数理展開部門 数学応用研究チーム 研究員)

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.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

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

2025年12月4日(木) 13:00 - 14:00

大窪 健児 (理化学研究所 数理創造研究センター (iTHEMS) 数理基礎部門 基礎科学特別研究員)

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.

会場: via Zoom / セミナー室 (359号室)

イベント公式言語: 英語

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

2025年11月27日(木) 13:00 - 14:00

リッカルド・ムオロ (理化学研究所 数理創造研究センター (iTHEMS) 数理基礎部門 基礎科学特別研究員)

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.

会場: セミナー室 (359号室) / via Zoom

イベント公式言語: 英語

Adaptive navigation strategies in adversarial predator-prey contexts

2025年11月20日(木) 13:00 - 14:00

西海 望 (新潟大学 教育研究院 自然科学系 特任准教授)

Animal navigation has long been a central topic in behavioral biology. In predator-prey systems, both predators and prey must navigate strategically - predators to capture prey and prey to reach safety - each evolving to outsmart the other through coevolution. To uncover the essence of these navigation strategies, I have investigated behavioral mechanisms across taxa. In bats, my collaborators and I found that they integrate multiple sensory and flight tactics to keep erratically flying moths within detection range. In pigeons, we discovered that individuals anticipating drone attacks adjust their positions toward the rear within the flock. I will also introduce an experimental framework that enables controlled interactions between real animals and virtual agents driven by reactive motion control, allowing quantitative tests of navigation efficiency. Through this seminar, I aim to highlight how studies of predator-prey navigation can bridge biology and engineering, providing insights into adaptive decision-making in dynamic environments.

会場: セミナー室 (359号室) / via Zoom

イベント公式言語: 英語

A genealogy-based framework to infer the demographic history, genetic structure, and phenotype association

2025年11月11日(火) 14:00 - 15:00

Charleston Chiang (Associate Professor, University of Southern California, USA)

We propose a conceptual analogy in population genetics to the central dogma of molecular biology. While the central dogma describes the flow of information from DNA to RNA to protein, we posit that under neutrality, a population's demography shapes its underlying genealogy, which in turn determines patterns of genetic variation that give rise to phenotypic variation. At the center of this analogous dogma is the genetic genealogies. Recent advances in inferring the Ancestral Recombination Graph (ARG), a complete record of a population's genealogies, have enabled us to develop a suite of methods that interrogates each stage these fundamental and connected components:

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

Semiotic Rupture and the Emergence of Writing: Toward a Multimodal Model of Representational Innovation

2025年11月6日(木) 13:00 - 14:00

Joshua Englehardt (Professor, Center of Archeologist Studies, El Colegio de Michoacán, Mexico)
Michael D. Carrasco (Associate Dean for Research / Associate Professor, College of Fine Arts, Florida State University, USA)

Writing is a unique—and distinctively human—creation, one which arose independently in only six locations worldwide. From these primary sites of innovation, this relatively recent technology spread across the world. Its development is routinely lauded as one of humanity’s most important inventions, among its “greatest intellectual and cultural achievements,” and a key to human evolution. The scholar Florian Coulmas labels it “the single most important sign system ever invented on our planet. This presentation presents a theoretical framework for modeling the emergence, development, and structure of writing and other visual representational systems through a formal, processual lens. Building on Noam Chomsky’s distinction between internal language (I-language) and its externalization as E-language, we model writing as the mediated product of E-language and propose a set of visual analogues: I-image and E-image, understood as structurally similar generative systems. We offer a formal, cross- and multimodal model of writing and its development that treats it not as a codified extension of speech, but as a recursive reorganization of visual and linguistic generative systems. Rather than asking what writing is, we ask how it and other semiotic systems emerge. What tensions, pressures, and interactions catalyze their formation, transformation, and typological diversity? We contend that the semiotic dynamics that give rise to writing are not isolated or unique events, but are grounded in deeper processes, such as those underlying the emergence of image-making, that are already established in the cognitive evolution of Homo sapiens and plausibly present in ancestral hominins. That is, we see writing not as a spontaneous invention but as an emergent semiotic modality grounded in cognitive evolution and cultural externalization.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

Inferring Phylogenetic Networks in the Genomic Era

2025年10月30日(木) 13:00 - 14:00

孔 星植 (理化学研究所 数理創造研究センター (iTHEMS) 数理基礎部門 研究員)

While phylogenetic trees (i.e., branching diagrams that depict the evolutionary history of different organisms) have been essential for understanding species evolution, they do not fully capture certain evolutionary processes, such as hybridization. In these cases, a phylogenetic network, which extends a phylogenetic tree by allowing two branches to merge into one and create reticulations, is needed. However, existing methods for estimating networks from genomic data become computationally prohibitive as dataset size and topological complexity increase. In this talk, I present the performance of popular computational methods that detect hybridization from genomic data as an alternative to the network inference, discussing their significance and limitations. I then explain how phylogenetic networks generalize trees to represent complex evolutionary histories and explore the biological interpretations that can be drawn from various branching patterns. Finally, I introduce PhyNEST (Phylogenetic Network Estimation using SiTe patterns), a novel method that efficiently and accurately infers phylogenetic networks directly from sequence data using composite likelihood. PhyNEST is implemented as an open-source Julia package and is available at https://github.com/sungsik-kong/PhyNEST.jl.

会場: 研究本館 3階 359号室 (メイン会場) / via Zoom

イベント公式言語: 英語