iTHEMS Biology Seminar

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

Adaptive navigation strategies in adversarial predator-prey contexts

November 20 (Thu) 13:00 - 14:00, 2025

Nozomi Nishiumi (Specially Appointed Associate Professor, Academic Assembly Institute of Science and Technology, Niigata University)

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.

Venue: Seminar Room #359, Seminar Room #359 / via Zoom

Event Official Language: English

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

November 11 (Tue) 14:00 - 15:00, 2025

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:

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

Event Official Language: English

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

November 6 (Thu) 13:00 - 14:00, 2025

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.

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

Event Official Language: English

Inferring Phylogenetic Networks in the Genomic Era

October 30 (Thu) 13:00 - 14:00, 2025

Sungsik Kong (Research Scientist, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

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.

Venue: #359, 3F, Main Research Building (Main Venue) / via Zoom

Event Official Language: English

Sequence-encoded protein condensation: a statistical physics perspective

October 23 (Thu) 13:00 - 14:00, 2025

Kyosuke Adachi (Research Scientist, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

Event Official Language: English

Why complexity persists: Evolutionary dynamics of the amylase locus in primates

October 16 (Thu) 12:30 - 13:45, 2025

Charikleia Karageorgiou (Postdoctoral Fellow, University at Buffalo, USA)

The amylase locus is among the most structurally variable regions of the human genome, frequently linked to starch digestion, metabolic traits, and dietary adaptation. Yet the causes of its recurrent duplication and exceptional variability remain unresolved. Why is this locus particularly prone to structural change? To address these questions, we analyzed 98 modern human genomes using long-read sequencing and optical mapping, alongside 53 high-quality primate assemblies. We identified 30 distinct amylase haplotypes in humans and documented more than 15 lineage-specific expansions and contractions across primates. Structural complexity appears to have been initiated by lineage-specific LTR insertions and subsequently shaped by non-allelic homologous recombination, with occasional contributions from microhomology-mediated break-induced replication. Independent duplications and salivary expression gains evolved repeatedly across primate lineages, but extensive within-species structural polymorphism is largely unique to humans. We further detected signatures of positive selection among primate paralogs, and dietary correlations with copy number suggest recurrent adaptive roles for amylase variation. The persistence of structural variation in this locus points to a unique combination of elevated mutational input, relaxed constraint, and ongoing selection, highlighting broader principles in the evolution of structurally unstable loci.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Homo lupo lupus est: Man is a wolf to wolves.

October 9 (Thu) 14:00 - 15:00, 2025

Carlos Sarabia (Postdoctoral Researcher, Evolutionary Population Genetics Lab, Institute of Evolutionary Biology (IBE-CSIC), Spain)

The gray wolf (Canis lupus) is one of the most emblematic wild species in human history: revered as a symbol of strength and wildness, although unforgivably persecuted as a competitor and pest. Across Europe and much of Eurasia, wolves would still dominate as apex predators... were it not for millennia of human pressure. Today, their evolutionary trajectory is shaped not only by climate fluctuations and habitat loss, but also by a uniquely flexible species boundary. Due to their unique karyotype, canids can admix freely with other related species, a capacity that both threatens the genetic integrity of wild canids like wolves and enriches our understanding of hybridization as a driver of adaptation. In this talk, we will explore recent studies on wolf demography under human pressure and climatic change, with particular attention to admixture with domestic dogs and the consequences for their survival in increasingly anthropized environments. Finally, we will observe how the wolf's distinctive genomic architecture makes it a powerful model for testing population genetics theoretical frameworks and for applying state-of-the-art computational tools, offering new insights into the understanding of evolution as a force for change.

Venue: via Zoom

Event Official Language: English

From Data to Discovery: Chronobiology in Translation

October 1 (Wed) 13:00 - 14:00, 2025

Bharath Ananthasubramaniam (Professor, Institute for Theoretical Biology, Humboldt University of Berlin, Germany)

Disruption of circadian rhythms is increasingly linked to a range of pathologies. To harness circadian biology for disease prevention and treatment, we must first establish causal relationships between rhythm disruption and the underlying clock mechanisms. This requires both the ability to quantify the “clock state” and to define what constitutes “disruption.” While significant progress has been made in model organisms, translating these insights to humans presents distinct challenges for quantitative chronobiology. In this talk, I will highlight how we have leveraged novel computational methods and high-throughput molecular datasets to begin addressing these obstacles.

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

Event Official Language: English

The evolution of conditional dispersal promotes cooperation

September 25 (Thu) 13:00 - 14:00, 2025

Iris Prigent (Ph.D. Student, Department of Ecology and Evolution, University of Lausanne, Switzerland)

Kin selection is an important mechanism for the evolution of cooperative behaviours across multiple taxa. While limited dispersal can foster kin selection by generating a genetic correlation between cooperating individuals, it also increases competition among relatives, constraining the evolution of cooperation. Prior theory has explored the co-evolution of dispersal and cooperation but typically assumes dispersal is independent of social cues. Here, we use mathematical modelling to examine whether socially-mediated dispersal, whereby individuals adjust their dispersal based on social context, can mitigate kin competition and thus enhance cooperation. We model the joint evolution of: (i) the probability of cooperating within social groups; and (ii) the probability of dispersing conditional on the number of individuals that have cooperated within the group, leading to a reaction norm for dispersal. We show that when the probability of dispersal increases with the number of cooperators, cooperation is favoured because it increases the fitness of relatives. The joint evolution of the two traits can lead to the differentiation of two types of individuals, one that always cooperates and another that never does. Although both types evolve dispersal norms such that they disperse more often when there are more cooperators in the group, cooperators evolve a steeper norm, reflecting greater sensitivity to their social environment. Our study shows that dispersal responses to the environment can vary between individuals based on their own social tendency, which can help explain why dispersal proclivities may differ between genotypes and between environments within a single population.

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

Event Official Language: English

Cross-species transcriptome analysis using Gromov-Wasserstein optimal transport

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

Yuya Tokuta (Program-Specific Researcher, Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University Institute for Advanced Study (KUIAS))

Sequence homology underpins cross-species analysis but cannot identify evolutionarily distinct genes that play analogous regulatory roles. Furthermore, ethical restrictions on human experiments necessitate analytical frameworks that translate insights from other animals to humans. To address these challenges, we developed Species-OT, a cross-species transcriptome analysis framework based on Gromov-Wasserstein optimal transport, which quantitatively compares the geometry of transcriptome distributions. Given a pair of bulk or single-cell RNA-sequencing datasets, Species-OT returns a gene-to-gene correspondence capturing probabilistic alignments of regulatory roles, and a transcriptomic distance quantifying overall divergence. Applied pairwise, Species-OT yields a transcriptomic discrepancy array and a hierarchical clustering tree analogous to a phylogenetic tree. We validated Species-OT using bulk RNA-seq data from human, mouse, and macaque germ cell specification as well as scRNA-seq data from pluripotent stem cells of six mammalian species. Species-OT identified evolutionarily related and distinct gene correspondences including biologically unexplored candidates, while transcriptomic discrepancies recapitulated expected species relationships. This is joint work with T. Nakamura, K. Fujiwara, M. Imamura, M. Nagano, M. Saitou, Y. Imoto, and Y. Hiraoka.

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

Event Official Language: English

Identifying signatures of natural selection through the genome using mixed models

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

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

Identifying signatures of selection has traditionally relied on detecting traces in modern day genomes. In particular, the length of linkage disequilibrium (LD) blocks in modern day genomes has often been used as an indicator of selection. However, in recent years, the emergence of ancient DNA has enabled new approaches to infer selection that directly use genetic data from the past and reconstruct the evolutionary history of genomes. In this presentation, I will introduce a methodological framework that was recently proposed to identify variants under selection across the genome: mixed models. Mixed models have long been applied in the Genome-Wide Association Study (GWAS) literature, as they effectively account for population structure and easily integrate confounders. In this context, I will present the framework and outline our plans to further improve current approaches.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Synthesizing the evolutionary invasion analysis for high-dimensional population dynamics

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

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

I will present a linear-algebraic (spectral) method for analyzing nonnegative matrices to study the dynamics of natural selection. This is a joint project with Troy Day (Queen's University, Canada). Within adaptive dynamics theory, evolutionary invasion analysis provides a powerful framework for studying adaptive evolution. It allows us to evaluate (i) whether a new type of individuals (mutants) can successfully invade and replace the resident type, and (ii) whether recurrent substitutions converge to an equilibrium that resists further invasion (an evolutionary Nash equilibrium). A central task is to quantify the reproductive success of mutants, which corresponds to computing the spectral radius (largest eigenvalue) of a nonnegative matrix. However, the high dimensionality of population dynamics often makes the analytical treatment of eigenvalues intractable. To address this problem, we have developed a methodology that applies to any high-dimensional adaptive dynamics system. I will first introduce the principles of adaptive dynamics and the associated eigenvalue problem. I will then present our new method, which translates the high-dimensional eigenvalue problem into another, lower-dimensional eigenvalue problem of arbitrary size, using (i) Perron–Frobenius theory and (ii) graph-theoretic arguments.

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

Event Official Language: English