iTHEMS生物学セミナー

Plasticity in the endogenous rhythms and the adaptation to the tidal environment in a freshwater snail

2023年12月14日(木) 16:00 - 17:00

​横溝 匠 (千葉大学 理学研究院 特別研究員 PD)

Organisms have diverse biological clocks synchronized with environmental cycles　depending on their habitats. The change in endogenous rhythms could contribute to range expansion in a novel rhythmic environment. For example, the Anticipation of tidal changes has driven the evolution of circatidal rhythms in some marine species. I am interested in the genetic and non-genetic changes in the biological rhythms and adaptation to tidal environments in the freshwater snail, Semisulcospira reiniana. Chronobiological analyses of behavior and gene expression revealed that snails had habitat-specific endogenous rhythms: individuals in a nontidal population showed the circadian rhythm while those in a tidal population showed the circadian and circatidal rhythms. The entrainment to the simulated tidal cycles increased the strength of circatidal activity only in snails in a tidal population. Although the circatidal rhythms in the transcriptome were clearer in individuals entrained to tidal cycles, the number of circatidal rhythmic transcripts was greater in a tidal population than in a nontidal population. These results suggest biological rhythms in the snails plastically change at the molecular level, but the strength of circatidal rhythm is different between populations. Finally, transcriptome-wide population genetic analysis revealed that these two populations can be clearly distinguished genetically, though the genetic distance was very small. Thus, genetic differentiation in biological rhythms could result from the evolution of a small number of genes. These findings suggest that adaptive plasticity and genetic changes in the biological rhythms play an important role in coping with tidal environments.

会場: via Zoom

イベント公式言語: 英語

Translating between evolutionary game theory and theoretical ecology

2023年12月5日(火) 16:30 - 17:30

Arne Traulsen (Director, Department for Theoretical Biology, Max Planck Institute for Evolutionary Biology, Germany)

Both theoretical ecology and evolutionary game theory describe the dynamics of interacting populations. More than 40 years ago, Hofbauer and Sigmund established a mathematical equivalence between the Lotka-Volterra equations and the replicator dynamics from evolutionary game theory. However, this equivalence has not been exploited by empiricists so far. One of the issues is dimensionality: An ecological interaction of two species corresponds to an evolutionary game between three types. Only when we focus on a special case with identical growth rates, it is possible to translate without this trick, leading to a more direct equivalence between the frameworks. Consequently, one has to be particularly careful how to classify interactions and how to assess dynamical outcomes. For example, a ‘Prisoner's Dilemma’ interaction where the `cooperators' have a higher intrinsic growth rate than `defectors' can result in stable coexistence of the two types and may ultimately not represent a social dilemma at all.

会場: via Zoom

イベント公式言語: 英語

Evolution by gene and genome duplications

2023年11月28日(火) 16:00 - 17:00

ジェフリ・フォーセット (理化学研究所 数理創造プログラム (iTHEMS) 上級研究員)

Each organism typically has (tens of) thousands of genes in its genome that perform various molecular and cellular functions, but how did these genes originate? The answer for most genes is by the duplication of another gene. In fact, all the genes (the entire genome) can get duplicated simultaneously on some instances. Thus, gene and genome duplications are considered key driving forces of evolution and are one of the most important topics in molecular evolutionary biology. In this talk, I will introduce the background and basic concepts related to gene and genome duplications. The talk will be aimed at non-experts so non-biologists are also welcome to attend.

会場: via Zoom

イベント公式言語: 英語

X's Fast and Slow

2023年11月21日(火) 16:00 - 17:00

トーマス・ヒッチコック (理化学研究所 数理創造プログラム (iTHEMS) 基礎科学特別研究員)

Sex chromosomes have long been suggested to undergo distinct evolutionary dynamics to the rest of the genome. Their distinct ploidy and transmission genetics may result in differing strengths of selection, magnitude of drift, and mutation rates to the autosomes, particularly if there are sex differences. Consequently, a body of theory and empirical work has developed investigating such differences, and how they might manifest in the rates of change between populations, and the diversity observed within populations. I will briefly review the theoretical basis of these comparisons, how we can infer rates of evolutionary change from genetic data, and what we can learn from non-model systems, particularly focusing on fungus gnats and pea aphids.

会場: via Zoom

イベント公式言語: 英語

Patterns of fern community assembly throughout the American continent: Do the mechanisms of species diversification also vary with latitude?

2023年11月7日(火) 16:00 - 17:00

ホセ サイード・グティエレス オルテガ (理化学研究所 数理創造プログラム (iTHEMS) 基礎科学特別研究員)

The global latitudinal gradient of biodiversity, a pattern suggesting that the low-latitude (tropical) areas have more species than the high-latitude (temperate) areas, represents the most conspicuous pattern of correlation between the environmental/geographic variation and biodiversity distribution. Yet, the relative roles of all ecological, geographic, and historical variables that can explain the gradient are unclear. Specifically, it is because we do not have a clear link between latitude and the underlying mechanisms that originate and extinct species throughout the gradient. In other words, we lack a connection between the “macroevolutionary patterns" and “microevolutionary processes”. I am researching the community assembly of ferns from the American continent, as it seems to be a group that can give some answers to what causes the latitudinal gradient of biodiversity and how the gradient is related to the processes of speciation and extinction. Regarding the community assembly, as expected, I found that the fern community clearly follows the latitudinal gradient: the number of species and localities colonized by ferns decrease with latitude. Also, this pattern is associated to a strong phylogenetic structure: the community at each latitudinal area is dependent of the previously colonizing genera (in other words, genera tend to diversify within specific latitudinal spans; most of them are restricted to the tropics). These results suggest that the fern community from the American continent follows the latitudinal gradient, and that it is a good representer of this pattern. Then, using linear regressions, I tested some classical hypotheses that have been proposed to explain the latitudinal gradient (e.g., that tropical environments, being more thermodynamically active, promote higher speciation rates). However, my results so far, suggest that none of the previously proposed hypotheses give a satisfactory explanation: there is no a single factor that can link the gradient with the processes of speciation or extinction. Rather, my data suggest that to promote speciation, the relative roles of environmental differentiation, geographic isolation, niche divergence, and time since divergence between sister species pairs vary with latitude. For example, to become new species, species near the equator did not need much geographic isolation or niche divergence from their sister counterparts (i.e., near the equator, species pairs tend to be more sympatric and present higher niche overlap). I hope my talk can stimulate some discussion about how to approach and treat the data that I have compiled, and that we can create opportunities for further collaboration.

会場: via Zoom

イベント公式言語: 英語

Mathematical modelling of the host response to inhalational anthrax across different scales

2023年10月31日(火) 16:00 - 17:00

ビバリン・ウイリアムス (Postdoctoral Fellow, School of Mathematics, University of Leeds, UK)

Inhalational anthrax, caused by the bacterium Bacillus anthracis, is a disease with very high fatality rates. Due to the significant risk posed if the bacterium was to be intentionally used as a bioweapon, it is important to be able to defend against such an attack and to make optimal decisions about treatment strategies. Mechanistic mathematical models can help to quantify and improve understanding of the underlying mechanisms of the infection. In this talk, I will present a multi-scale mathematical model for the infection dynamics of inhalational anthrax. This approach involves constructing individual models for the intracellular, within-host, and population-level infection dynamics, to define key quantities characterising infection at each level, which can be used to link dynamics across scales. I will begin by introducing a model for the intracellular infection dynamics of B. anthracis, which describes the interaction between B. anthracis spores and host cells. The model can be used to predict the distribution of outcomes from this host-pathogen interaction. For example, it can be used to estimate the number of bacteria released upon rupture of an infected phagocyte, as well as the timing of phagocyte rupture and bacterial release. Next, I will show how these key outputs can be used to connect the intracellular model to a model of the infection at the within-host scale. The within-host model aims to provide an overall understanding of the early progression of the infection, and is parametrised with infection data from studies of rabbits and guinea pigs. Furthermore, this model allows the probability of infection and the time to infection to be calculated. Building a model that offers a realistic mechanistic description of these different animal responses to the inhalation of B. anthracis spores is an important step towards eventually extrapolating the model to describe the dynamics of human infection. This would enable predictions of how many individuals would become infected in different exposure scenarios and also on what timescale this would occur.

会場: via Zoom / 研究本館 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

Population genetics in microchannels

2023年10月17日(火) 16:00 - 17:00

Anzhelika Koldaeva (沖縄科学技術大学院大学 (OIST) 生物複雑性ユニット 研究員)

Spatial constraints, such as rigid barriers, affect the dynamics of cell populations, potentially altering the course of natural evolution. In this paper, we investigate the population genetics of Escherichia coli proliferating in microchannels with open ends. Our analysis is based on a population model, in which reproducing cells shift entire lanes of cells toward the open ends of the channel. The model predicts that diversity is lost very rapidly within lanes but at a much slower pace among lanes. As a consequence, two mixed, neutral E. coli strains competing in a microchannel must organize into an ordered regular stripe pattern in the course of a few generations. These predictions are in quantitative agreement with our experiments. We also demonstrate that random mutations appearing in the middle of the channel are much more likely to reach fixation than those occurring elsewhere. Our results illustrate fundamental mechanisms of microbial evolution in spatially confined space.

会場: via Zoom

イベント公式言語: 英語

Do higher-order interactions promote coexistence in diverse ecological communities?

2023年10月10日(火) 10:00 - 11:00

Theo Gibbs (Ph.D. Student, Lewis-Sigler Institute for Integrative Genomics, Princeton University, USA)

A central assumption in most ecological models is that the interactions in a community operate only between pairs of species. However, two species may interactively affect the growth of a focal species. Although interactions among three or more species, called higher-order interactions, have the potential to modify our theoretical understanding of coexistence, ecologists lack clear expectations for how these interactions shape community structure. In this talk, I will analyze two different sets of assumptions for how higher-order interactions impact the dynamics of competing species and show that they lead to differing outcomes. When higher-order interactions are sampled from unconstrained probability distributions, they are unlikely to generate widespread coexistence. In fact, using an analytical technique from statistical physics, I will show many — though not all — of the qualitative rules derived for pairwise interactions still apply to the higher-order case. Higher-order interactions that have specific relationships with the underlying pairwise interactions, however, can stabilize coexistence in diverse communities. I will conclude by briefly discussing ongoing experimental work that seeks to determine whether or not the dynamics of annual plant communities are structured by higher-order interactions.

会場: via Zoom

イベント公式言語: 英語

How is host-symbiont specificity determined? ---Host’s partner-choice mechanisms and symbiont’s motility

2023年10月3日(火) 16:00 - 17:00

菊池 義智 (国立研究開発法人産業技術総合研究所 (AIST) 生物プロセス研究部門北海道センター 研究グループ長)

Microbial symbiosis is omnipresent in animals and plants, playing a crucial role in the evolution of these organisms. While some organisms have developed mechanisms for vertical symbiont transmission, in most cases, these microbial partners are acquired from the surrounding environment, where the enormously diverse microorganisms inhabit. How, then, do these hosts ensure specificity with their symbiotic partners among such diverse environmental microorganisms? And how has this host-symbiont specificity evolved? We are addressing these questions using the bean bug Riptortus pedestris as our model. The insect acquires Caballeronia insecticola from the soil and symbioses with it in the gut crypts. Recently, we revealed that the entrance to the gut symbiotic organ is a narrow tube, just a few micrometers in diameter, filled with a mucus-like matrix. This constricted region helps the host insect select the symbiotic bacterium from the many other soil microbes. Notably, to pass through the constricted region, Caballeronia shows a unique motility called “drill motility”, where the bacterium wraps its flagella around its body. In this presentation, I will introduce the evolutionary process of both host insects and symbiotic bacteria and will discuss the pivotal role played by bacterial motility in the context of host-symbiont specificity.

会場: via Zoom

イベント公式言語: 英語

Response to sounds in the cochlea of the inner ear

2023年9月26日(火) 16:00 - 17:00

太田 岳 (大阪大学 大学院医学系研究科薬理学講座統合薬理学 助教)

We hear sounds. The acoustic wave passes through the ear canal and oscillates the ear drum. The middle ear bones conduct the mechanical input into the cochlea, the primary sensory organ of hearing. A sensory epithelium, a sheet-like tissue inside the snail-like structure, decomposes the sound frequencies into each component along the coil. The sound stimulation evokes nanometer-scale motions in the epithelium which contains hair cells. The cells expose their hair bundles to endolymph, the extracellular solution characterized by high [K+]. The epithelium vibration changes the open probability of mechanosensitive channels on the bundles and modulates the ion entering from the fluid. Inner hair cells release neurotransmitters to the auditory nerves and outer hair cells shrink and elongate their soma depending on the receptor potentials. The electromotive response amplifies the vibration of the sensory epithelium and contributes to the faint sound sensitivity and sharp frequency selectivity. With developed technique, we observed the sound-evoked vibrations in the sensory epithelium. In this seminar, I will introduce the physiological background of the cochlear physics and the recent results.

会場: via Zoom

イベント公式言語: 英語

Predicting future biodiversity with species distribution models: current applications, persistent issues, and where to go from here

2023年9月19日(火) 16:00 - 17:00

ジェイミイ・キャス (東北大学 大学院理学研究科 准教授)

There is much current interest in macroecology to make predictions of future biodiversity patterns in order to inform both regional and global priorities for conservation and sustainability of ecosystem functions and services. Species distribution models use data on species' occurrence records, environmental predictor variables, and sometimes other data sources to estimate niche relationships and distribution extents—these models can also be combined to make biodiversity estimates. As the field of species distribution modeling has grown considerably over the past two decades, many approaches now exist to build models, evaluate their performance, and use them to make predictions for unsampled areas and times. I will provide an overview of current techniques to predict future distributions of species and biodiversity, detail some issues with these techniques concerning uncertainty and realism of predictions, and contribute my humble thoughts on where the field should go from here.

会場: via Zoom

イベント公式言語: 英語

Parameter Fitting for Glucose Homeostasis - Searching for Methods to Predict and Diagnose

2023年9月12日(火) 16:00 - 17:00

ガブリエル・グレス (東北大学 材料科学高等研究所 (AIMR) 数学連携グループ 特任研究員)

The human body regulates glucose through a complex web of biological interactions, for which state-of-the-art models require dozens of variables and parameters to even emulate. But while we've had devices to measure glucose levels as far back as the 1980's, nearly all of the remaining variables and parameters cannot be measured directly to this day. While continuous glucose monitors have greatly improved the health of diabetic patients, there are still many barriers in the diagnosis of at-risk patients as well as accurately dispersing insulin to counteract future trends in glucose levels. While glucose readings are only a small window into one of many factors of how the human body maintains glucose homeostasis, we search for ways to leverage the high-frequency and high-volume data to improve the state of diagnosis and prediction in diabetic patients.

会場: 研究本館 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

Landscape structure drives eco-evolution in host parasite systems

2023年8月24日(木) 16:00 - 17:00

Jhelam Deshpande (Ph.D. Student, Biodiversity: dynamics, interactions and conservation team, Institute of Evolutionary Science of Montpellier, France)

As all biological and many artificial systems, hosts and their parasites are most often spatially structured. Besides this highly relevant spatial context, parasites may change through time due to to evolutionary processes, including mutation and selection. These facts imply that we must study host-parasite systems taking into account space and evolution. Past work has mainly focused on simple spatial structures, but how parasites evolve in realistically complex landscapes remains unclear, hampering the translation of theoretical predictions to real ecological systems.Therefore, we here develop an eco-evolutionary metapopulation model of host-parasite interactions in which hosts and parasites disperse through realistically complex spatial graphs. Parasite virulence, a parasite life-history trait of central importance that here impacts host reproduction, is able to evolve. Our model therefore captures the eco-evolutionary feedback loop between host demography and parasite evolution in space. In order to gain a general understanding of parasite eco-evolution in space, we analyse our model for spatial networks that represent terrestrial (represented by random-geometric graphs; RGG) and riverine aquatic (represented by optimal channel networks; OCN) landscapes. We find that evolved virulence is generally a function of host dispersal, with a unimodal relationship in aquatic and a saturating relationship in terrestrial landscape, and this is driven by higher order network properies. Consistent with previous work, we show that our results are driven by kin selection, because dispersal and landscape structure impact both patterns of relatedness and availability of susceptible hosts. Our model yields readily testable predictions, including that terrestrial parasites should be more virulent than aquatic parasites are low dispersal rates and vice versa as dispersal increases. These differences in evolved virulence directly lead to differences in system stability, with more virulent parasites more often leading to host extinction. Thus, in this study we highlight the role of landscape structure in driving eco-evolutionary dynamics of parasites.

会場: via Zoom

イベント公式言語: 英語

Mating system of buckwheat

2023年8月17日(木) 16:00 - 17:00

ジェフリ・フォーセット (理化学研究所 数理創造プログラム (iTHEMS) 上級研究員)

Buckwheat (soba in Japanese) has a slightly unusual mating system called heterostylous self-incompatibility where two types of individuals coexist, one that produces flowers with a long style (female part of the flower) and short stamen (male part of the flower), and the other that produces flowers with a short style and long stamen. Mating is only successful when it occurs between the different types of individuals. It is a bit similar to sexual dimorphism where males and females coexists but in this case all individuals have both male and female organs. In this talk, I will introduce the basics of this mating system in buckwheat and some work we have been doing. In particular, I will talk about its genetic architecture and some parallels observed with other plants in which a similar mating system evolved independently. The talk will be aimed at non-experts so non-biologists are also welcome to attend.

会場: via Zoom

イベント公式言語: 英語

Evolution of dormant egg production and their hatching rate in Aedes albopictus

2023年7月13日(木) 16:00 - 17:00

桑野 友輔 (総合研究大学院大学 博士課程)

Mosquitoes are important insect vectors of infectious diseases in humans, and knowledge of their population dynamics is pivotal in disease control. Some mosquito species have dormancy in their life history to survive harsh environments. However, the population dynamics of mosquitoes have not yet been well understood due to the lack of field and experimental data on dormancy. For that reason, I modeled the population dynamics of mosquitoes that face environmental fluctuations and examine the evolution of egg dormancy strategy to survive harsh periods. I found that the ESS dormancy fraction monotonically increases with the period of environmental fluctuation. Next, I analyzed evolutionary traits of the dependence of the dormancy rate and the hatching rate from dormant egg on soil moisture content and conducted evolutionary simulations using actual weather measurement in Tokyo. The results of the hatching rate from dormant egg showed that two mosquito phenotypes having distinctly different responses to soil moisture were selected.

会場: via Zoom

イベント公式言語: 英語

Journal Club: Inference of hydrodynamic equations for active matter

2023年6月29日(木) 16:00 - 17:00

足立 景亮 (理化学研究所 生命機能科学研究センター (BDR) 生体非平衡物理学理研白眉研究チーム 基礎科学特別研究員)

イベント公式言語: 英語

The role of fluid dynamics in microbial ecology

2023年6月22日(木) 14:00 - 15:00

Douglas R. Brumley (Senior Lecturer, Applied Mathematics, University of Melbourne, Australia)

Bacterial motility, symbioses, and marine nutrient cycling unfold at the scale of individual microbes, and are inherently dynamic. In this talk, I will discuss the role that fluid flows play in shaping the ecology of microbes, both in the open ocean as well as around coral surfaces. In each case, I will demonstrate how iteratively combining video-microscopy, image processing and mathematical modelling can resolve features of microbial lifestyles that are difficult or impossible to see otherwise, and show how single-cell measurements can be connected to bulk processes at the population-level.

会場: 研究本館 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

Phase reduction beyond the Kuramoto model

2023年6月15日(木) 14:00 - 15:00

Iván León (東京工業大学 工学院 システム制御系 研究員)

Many biological, engineering and natural systems can be modeled as populations of coupled oscillators where each oscillator behaves periodically. When these units are coupled to each other, emergent phenomena, as synchronization, appears. However, dealing with those systems is usually difficult due to the large number of degrees of freedom. Conditionality reduction techniques to obtain simple tractable models are usually considered. The most common method is "phase reduction" that allows to capture the dynamics of each oscillator with just one variable, the phase. The succeed of the method was clear when the Kuramoto model, derived through phase reduction, gave a simple explanation to collective synchronization. Despite this success, phase reduction is often limited to the Kuramoto model because of the challenge to obtain analytical expressions. The porpoise of this talk is to make clear that phase reduction beyond Kuramoto model is possible. On the first part of the talk we introduce phase reduction and its limitations. Then we show how it is possible to obtain analytical phase reduced model for weakly nonlinear oscillators. Finally, we talk about second order phase reduction where higher order corrections are included to capture the qualitative dynamics and improve accuracy.

会場: 研究本館 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