iTHEMS Biology Seminar

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

The link between ecology and evolution in the speciation process

August 28 (Thu) 13:00 - 14:00, 2025

José Said Gutiérrez-Ortega (Research Scientist, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

Both ecological and evolutionary processes shape biodiversity, but these are usually studied separately. Ecologists focus on current dynamics, while evolutionary biologists examine long-term changes. The intersection between the two perspectives lies in understanding speciation: the process of how new species arise. Understanding speciation can clarify how ecological processes build up into the global patterns we see in evolution, and in turn, how evolutionary trends promote ecological processes. Using observational data compiled from macroecological and phylogenetic methods on multiple plant and animal groups, I suggest that the ecological patterns left by the factors promoting speciation in a community correspond to the speciation/extinction dynamics within that community. This ecological-phylogenetic correspondence represents a connection between the ongoing and the long-term dynamics, an idea that may unify the disciplines of ecology and evolution. I expect this talk can promote discussion on the topics of eco-evolutionary dynamics, so that I can get some feedback from you, and that we can create chances for collaboration.

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

Event Official Language: English

Detecting ghost ancestors in the human lineage

August 21 (Thu) 13:00 - 14:00, 2025

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))

Event Official Language: English

Dynamic Scaling Analysis for Enzymatic Degradation and Network Growth of DNA Liquid Droplets

August 14 (Thu) 13:00 - 14:00, 2025

Michio Tateno (JSPS Overseas Research Fellow, Material Research Laboratory, University of California Santa Barbara, USA)

In this talk, I will introduce two novel pattern formation dynamics exhibited by phase-separated liquid droplets composed of DNA nanoparticles: 1) By enzymatically inactivating the phase-separation ability of the nanoparticles, we observed the process by which droplets gradually disappeared. Notably, the droplet-size distribution density remained unchanged, while only the total number of droplets decreased over time. 2) We also observed the formation of a novel two-dimensional wire-like network pattern, in which two types of droplets are arranged in a one-dimensional, alternating manner. We confirmed that the characteristic size of the network follows power-law growth over nearly two decades, with a universal growth exponent that is independent of droplet viscosity and inter-droplet wetting affinity. We analyze these results within the framework of the dynamic scaling hypothesis and discuss the physical mechanisms underlying these behaviors.

Event Official Language: English

iTHEMS Biology welcomes another new member!

August 7 (Thu) 13:00 - 14:15, 2025

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

This meeting will be used to welcome another new members to the iTHEMS Biology Study Group: Dr. Sungsik Kong, who is joining iTHEMS Fundamental Division as a Research Scientist. He will give us a 15-20 min talk to introduce his research. If time permits, let's also use this time to catch up on each other's current research. I hope that many people will join us to welcome this new member and come meet him and hear about his research.

Venue: Changed to Zoom only

Event Official Language: English

Targeting SARS-CoV-2 RNA: Insights for RNA-Directed Drug Discovery

July 31 (Thu) 13:00 - 14:30, 2025

Mariia Ivonina (Postdoctoral Fellow, Platform for Inter/Transdisciplinary Energy Research (Q-PIT), Kyushu University)

Traditional pharmacology fights virus infections by targeting proteins including enzymes, receptors, and structural proteins to break up the viral machinery. Nucleic acid-targeting therapies, on the other hand, can act directly on the genetic code of viruses, blocking their replication or translation in host cells. Coronaviruses and HIV are examples of RNA viruses that use a process called -1 programmed ribosomal frameshifting (-1 PRF) to produce their viral proteins. In this process, the translating ribosome is forced to shift into the alternative reading frame, replicating mRNA in the wrong order. Using small-molecule compounds to block this mechanism could be a promising way to neutralize such viruses. It is difficult to experimentally study the interactions between RNA and a drug candidate to understand where the drug binds and how it changes the shape of the viral RNA. I will discuss how Molecular Dynamics simulations are used to explore the conformational dynamics of mRNA structural elements and to investigate what happens when an antiviral agent binds to it. Additionally, I will show how the quantum-chemical orbital interaction analysis we developed, called Through-Space/Through-Bond Energy Decomposition Analysis (TS/TB-EDA), reveals which RNA nucleotides, at the atomic level, are critical for binding. This molecular modelling approach reveals strategies for targeting structured RNA elements — a crucial step toward expanding the arsenal of RNA-targeting therapeutics for future pandemics.

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

Event Official Language: English

Self-organization mechanism of adaptive colony size sensing in ants

July 17 (Thu) 13:00 - 14:00, 2025

Kazuki Tsuji (Professor, Department of Environmental Sciences and Technology, University of the Ryukyus)

Social insects such as ants and termites are superorganisms, and traits of a colony change in a manner similar to the growth of an individual. The most common pattern is that reproductive castes are produced only when the colony size exceeds a certain threshold, which is well known to be adaptive. This means that social insects can “sense” their own colony size. However, how they achieve this even without visual information in a dark environment was yet largely unknown. We empirically tested the self-organization hypothesis on the proximate mechanism using ant colonies. In Diacamma colonies the monogynous queen is known to increase the effort devoted to queen pheromone–transmission behaviour (patrolling) as the colony grows, as if she perceives colony size. The negative feedback hypothesis assumes that through repeated physical contacts with workers the queen monitors the physiological state (fertility) of workers and increases her patrolling effort when she encounters more fertile workers. Supporting this hypothesis, we found that queens increased patrol effort in response to a higher ratio of fertile workers under the experimental condition of constant colony size. Furthermore, supplementary experiments suggested that cuticular hydrocarbons can mediate the observed queen–worker communication of fertility state. However, when the colony size exceeds a certain value, information transmission fails, resulting in the production of the next generation of reproductive caste. Such a self-organising mechanism of sensing colony size may also operate in other social insects living in small colonies.

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

Event Official Language: English

iTHEMS Biology welcomes a new member!

July 3 (Thu) 16:00 - 17:00, 2025

Aina Colomer i Vilaplana (Postdoctoral Researcher, Mathematical Genomics RIKEN ECL Research Unit, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

This meeting will be used to welcome a new members to the iTHEMS Biology Study Group: Postdoc Aina Colomer, who is joining Unit Leader Leo Speidel's Mathematical Genomics RIKEN ECL Research Unit. She will give us a 15-20 min talk to introduce her research. If time permits, let's also use this time to catch up on each other's current research. I hope that many people will join us to welcome this new member and come meet her and hear about her research.

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

Event Official Language: English

Simulating the spread of infection in networks with quantum computers

June 26 (Thu) 13:00 - 14:00, 2025

Xiaoyang Wang (Postdoctoral Researcher, Quantum Mathematical Science Team, Division of Applied Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

Many classical stochastic processes can be modeled as Markovian processes, including the spreading of infection in networks. Simulating the Markovian processes using classical computers is generally unscalable for large networks. In this seminar, I will introduce the Hamiltonian evolution on quantum computers and how the Markovian spreading of infection can be efficiently simulated using the Hamiltonian evolution. In particular, we analytically and numerically analyze the evolution of a specifically designed Hamiltonian, and prove that the evolution simulates a classical Markovian process, which describes the well-known epidemiological stochastic susceptible and infectious (SI) model. As an example, we simulate the infection spreading process of the SARS-CoV-2 variant Omicron in a small-world network. The simulation results are qualitative consistent with the infection spreading in the west coast of USA.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Programmed chromosome eliminations in flies

June 19 (Thu) 13:00 - 14:00, 2025

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

Species that break the traditional rules of genetics and inheritance offer perhaps some of the best opportunities to study fundamental biological questions. Sciarids (fungus gnats) are a species-rich family of flies with highly unorthodox chromosome inheritance. Asymmetric male meiotic divisions result in elimination of the paternal genome every generation, and maternally-controlled eliminations of chromosomes in the developing embryo determine offspring sex. I use a combination of genomics, population genetics, and cytogenetics to understand both the mechanisms and the evolution of this system. I will discuss how these approaches have allowed us to uncover some fascinating biology as well as tackle broader biological questions.

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

Event Official Language: English

Inferring Castration Status and Age-at-Death from Sheepskin Parchments

June 12 (Thu) 13:00 - 14:00, 2025

Ciarán O'Connor (Ph.D. Student, Department of Genetics, Trinity College Dublin, Ireland)

Secondary products such as traction from cattle, wool from sheep, and mobility from horses are invaluable outputs from rearing livestock. The innovative herd management practice of castration enables non-breeding males to be managed safely beyond typical ages of slaughter, greatly improving the productivity of livestock herds. Although osteological methods can identify some morphological differences between castrated and intact males, it is difficult to make clear distinctions between them. However, methylation values are affected by the considerable hormonal changes that occur as a result of castration. For example, castrated male sheep have shown lower biological ages compared to age-matched intact rams (Sugrue et al., 2021). Furthermore, age-at-death has been predicted from reconstructed methylation values in ancient horses, informing on culling practices (Liu et al., 2023). Using an aDNA-specific bisulfite sequencing approach, we have reconstructed CpG methylation values from sheepskin parchments. We have developed machine learning models trained on modern sheep in order to infer traits of interest such as castration and age-at-death. The informative CpG sites have been incorporated into a target capture set to enable cost-effective sequencing of additional samples. This will enable the characterisation of these traits in ancient sheep across time periods, geographical locations, and archaeological contexts.

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

Event Official Language: English

Ecology and Evolution of Mammal-Microbe Interactions

May 29 (Thu) 16:00 - 17:00, 2025

Taichi A Suzuki (Assistant Professor, Biodesign Center for Health Through Microbiomes, Arizona State University, USA)

A critical open question in microbiome research is identifying key host-microbial interactions that influence host fitness. While the disruption of coevolved host-microbial interactions is known to affect host fitness in simpler systems (e.g., insects and their symbionts), understanding the extent and consequences of host-microbial coevolution in more complex systems (e.g., mammals and their gut microbiota) remains a major challenge. My research has identified multiple species of gut microbes in adults and children that share a parallel evolutionary history with humans by analyzing paired human genotypes and bacterial strain genotypes. In another line of work, I applied a selection experiment demonstrating that selection and transmission of the microbiome and its metabolites can alter mouse locomotion behavior within four rounds of microbiome transfer, without any changes to the mouse genome. Finally, I will briefly outline my future plans to study the effects of disrupting evolutionary stable host-microbial associations on the phenotypes of deer mice (Peromyscus spp.) in the Madrean Sky Islands and genetically diverse human populations in Arizona. Biosketch: Assistant Professor at Arizona State University since 2023. MS at University of Arizona, PhD at University of California Berkeley, and Postdoc at Max Planck Institute for Biology. My group integrates evolutionary genomics, microbial ecology, and biomedical research to study host-microbial interactions using wild rodents and humans.

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

Event Official Language: English

Moss sporophytes and their consumers: an overlooked interaction

May 22 (Thu) 13:00 - 14:00, 2025

Yume Imada (Assistant Professor, Division of Biological Sciences, Graduate School of Science, Kyoto University)

The evolution of plant-feeding in animals is deeply intertwined with the unintentional transport of diaspores. Zoochory (the dispersal of plant diaspores by animals) has been extensively studied in flowering plants, particularly with regard to seeds and fruits. Bryophytes, in contrast, have poorly been investigated, despite possessing traits favorable for animal-mediated dispersal: they are small, easily transported, and exhibit high totipotent capacity. It has long been believed that bryophytes are rarely consumed by animals. However, our field survey into sporophyte-feeding across diverse forest-dwelling mosses (the largest clade of bryophytes) revealed the ubiquity of spore consumption. This finding prompts a re-evaluation of the ecological function of the sporophyte in the alternation of generations in mosses. Moreover, our data suggest that this interaction may be framed within the mutualism–antagonism continuum. Finally, I aim to clarify key questions surrounding the reproduction and dispersal of spore-producing plants, particularly bryophytes.

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

Event Official Language: English