Biology subjects

Tachiki, Y.

Publications and source records attributed to Tachiki, Y..

5 recordsLinked to original sources

bioRxiv2026

Genomic basis of rapid urban evolution revealed by the subgenome-resolved genome of octoploid Oxalis corniculata

Urbanization is a major driver of contemporary evolution, yet the genomic basis of urban adaptation remains poorly understood, particularly in non-model plants with complex polyploid genomes. Here, we investigate the genetic mechanisms underlying leaf color variation in the octoploid Oxalis corniculata, a phenotype associated with heat tolerance in urban environments. By integrating high-fidelity long-read sequencing and chromosome conformation capture, we generated the subgenome-resolved, chromosome-scale genome assemblies for both red- and green-leaved lines, resolving four distinct subgenomes. LTR insertion timing revealed a two-step hybridization history that established this octoploid genome within the last 1 million years. Leveraging a nationwide citizen science initiative, we collected and analyzed over 1,700 samples across a broad geographic range. We identified a major locus on one subgenome underlying this variation and implicate a coding-sequence repeat-length polymorphism in a MYB transcription factor as the candidate causal variant. This simple sequence repeat likely acts as a molecular "tuning knob" for rapid adaptation to urban heat islands. This study provides a new baseline for evolutionary ecological genomics in plants and highlights the power of integrating advanced genomics with public participation to forecast evolutionary responses in an increasingly urbanized world.

genomics↗

bioRxiv2026

Evolutionary branching of male emergence timing: Trade-offs and variance asymmetry as drivers of dimorphism.

Classical models of protandry predict unimodal male emergence timing, yet empirical observations in butterflies and bees reveal dimorphism: early-emerging small males coexist with late-emerging large males. The evolutionary mechanisms underlying such discrete alternative reproductive strategies in emergence timing remain poorly understood. In this study, we developed a mathematical model using an adaptive dynamics framework to investigate the conditions under which dimorphic male emergence timing evolves. We explored two potential mechanisms: (1) a trade-off between emergence timing and male competitiveness, and (2) differences in the variance of emergence timing between the sexes. Our analysis demonstrates that both mechanisms produce evolutionary branching, and that extreme variance asymmetry between sexes can generate multiple branching events, yielding three or more distinct male clusters. These findings provide a theoretical foundation for understanding the evolution of alternative reproductive strategies in emergence timing, with implications for other systems where reproductive success depends on temporal overlap between the sexes. We provide testable predictions that a positive correlation between emergence timing and male body size or competitiveness should be observed under the trade-off mechanism, and that the variance in emergence timing within each male morph should be smaller than that of females under the variance asymmetry mechanism.

evolutionary biology↗

bioRxiv2022

Scale space calibrates present and subsequent spatial learning in Barnes maze in mice

Animals including humans are capable of representing different scale spaces from smaller to larger ones. However, most laboratory animals live their life in a narrow range of scale spaces like home-cages and experimental setups, making it hard to extrapolate the spatial representation and learning process in large scale spaces from those in conventional scale spaces. Here, we developed a 3-meter diameter Barnes maze (BM3), then explored whether spatial learning in Barnes maze (BM) is calibrated by scale spaces. In the BM3, mice exhibited lower learning rate compared to a conventional 1-meter diameter Barnes maze (BM1), suggesting that the BM3 requires more trial-and-error and larger computational resources to solve the task than the BM1. Analyzing network structures of moving trajectories, betweenness centrality would contrast spatial learning in a larger scale space with that in a smaller one, as it diverges between the BM1 and the BM3 along with the learning progression. We then explored whether prior learning in either BM scale calibrates subsequent spatial learning in the other BM scale, and found asymmetric facilitation such that the prior learning in the BM3 facilitated the subsequent learning in the BM1, but not vice versa. Network structures of trajectories in the subsequent BM scale were changed by both prior and subsequent BM scale. These results suggest that scale space calibrates both the present and subsequent BM learning. This is the first study to explore and demonstrate scale-dependent spatial learning in Barnes maze in mice. Significance StatementAnimals are capable of representing different scale spaces. However, whether scale space calibrates goal-directed spatial learning remains unclear. The Barnes maze is a well-established experimental paradigm to evaluate spatial learning in rodents. Here, we developed a larger scale 3-meter diameter Barnes maze (BM3) then compared various navigation features in mice between the BM3 and a conventional 1-meter diameter Barnes maze (BM1). We demonstrated that learning on the BM3 required more computational resources than in the BM1, prompting mice to exploit unique navigation patterns. Such learning experiences in the BM3 facilitated subsequent spatial learning in the BM1, but not vice versa. These results suggest that scale space calibrates immediate and subsequent spatial learning.

animal behavior and cognition↗

bioRxiv2021

Cell cycle difference creates cortical tension difference that separates germ layer fates.

The segregation of germ layer fates is a fundamental step for embryogenesis, but the underlying molecular mechanism is unclear. In ascidians, mRNA localization coupled to nuclear migration and subsequent asymmetrical partitioning of the mRNA separates mesodermal and endodermal fates. The lack of quantitative characterization of nuclear and mRNA localization has hindered our understanding of the molecular basis of fate separation. Here, we quantitatively examined the movement of the nucleus and changes in cell shape and found that the nucleus moves to the mesodermal cell side across the region of the future cleavage furrow. However, this migration was not decisive for the asymmetric distribution of Not mRNA. Asymmetry of surface tension, caused by cell cycle difference between animal and vegetal hemisphere cells, deformed the mesendoderm cell and determined the position of the cleavage furrow, thereby ensuring the asymmetric partitioning of Not mRNA and segregation of fates. This study demonstrates how cell cycle control and the physical force relationships between cells are involved in the segregation of developmental fates.

developmental biology↗

bioRxiv2020

Eco-evolutionary dynamics of prior selfing rate promotes the coexistence without niche partitioning under reproductive interference

O_LIWhen the two or more plants species share the same pollinators, pollinator-mediated reproductive interference make coexistence difficult. Recent studies suggested prior autonomous selfing mitigate reproductive interference, could enabling coexistence without pollination niche partitioning (pre-emptive selfing hypothesis). However, there are no studies to test whether evolution of prior selfing promote the coexistence, considering eco-evolutionary dynamics of population size, selfing rate and inbreeding depression. C_LIO_LITo examine conditions that the evolution of prior selfing promote coexistence under mutual reproductive interference especially in the point of view for pollinator availability and dynamics of inbreeding depression, we constructed individual-based model in which two plant species compete against each other in the form of mutual reproductive interference and can evolve prior autonomous selfing rate. We expected that purging of deleterious mutations could cause evolutionary rescue because inferior species could rescue population density through the evolution of prior selfing if the strength of inbreeding depression decreases with an increase of populations selfing rate. C_LIO_LIOur simulation demonstrated that the evolution of prior selfing could promote the coexistence while reproductive interference caused competitive exclusion without evolution. We found that lower pollinator availability tended to prefer rapid evolutionary shift to higher prior selfing rate, it neutralizes the negative effect of reproductive interference, and population dynamics exhibit neutral random walk in both species. When the strength of inbreeding depression decreased with an increase in populations selfing rate, moderate pollinator availability resulted in long-term coexistence in which relative-abundance-dependent selection on the prior selfing rate rescue population density of inferior species intermittently. C_LIO_LISynthesis. We showed that the evolution of prior selfing could increase population growth rate of inferior species and consequently enable the long-term coexistence with evolutionary rescue. This is the new mechanisms explaining co-evolutionary coexistence of closely related plant species without niche partitioning and consistent with recent studies reported that closely related mixed-mating species are sympatrically growing even under the mutual reproductive interference. C_LI

ecology↗