Biology subjects

Katsuhara, K. R.

Publications and source records attributed to Katsuhara, K. R..

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↗

bioRxiv2024

Allopolyploidy enhances survival advantages for urban environments in the native plant genus Commelina

Background and AimsUrbanization-induced environmental changes have profound effects on the geographical distribution limits in natural plant species. Polyploidization, an influential dynamic genome change, may determine survival potentials of plant species in urban environments. This study focused on the native plants, Commelina communis L. (Cc) and closely related subspecies, C. communis f. ciliata (Masam.) Murata (Ccfc) which have different chromosome numbers (e.g. Cc: 2n = 88, Ccfc: 2n = 46). The aim is to investigate polyploidization effects on natural plant distribution in urban environments. MethodsThe geographical distribution across urban-rural gradients was investigated at a total of 218 sites in Japan. Stomata size and density were measured and compared between Cc and Ccfc. Flow cytometry was used to determine genome size and polyploidy. Chromosome karyotyping was performed by using the GISH method. Key resultsUrban areas were exclusively dominated by Cc, while Cc and Ccfc coexisted in rural areas. Cc had larger and fewer stomata and more than twice genome size than Ccfc. GISH results indicated that Cc possesses Ccfc and another unknown genome, suggesting allopolyploidy. ConclusionsThese results show that the ploidy difference affects the geographical distribution, the stomata traits, and genome size between Cc and Ccfc. In addition, GISH results indicate that Cc has Ccfc and another unknown genome, suggesting Cc is an allopolyploid and these two species of the genus Commelina are distinct. Therefore, not only polyploid but also allopolyploid contributes to Cc to enhance survival potentials in urban environments compared to Ccfc. This is the first investigation to clarify the distribution difference related to urban environments, the difference in stomata traits and genome size, and to conduct chromosome composition in Commelina species.

ecology↗

bioRxiv2022

Negative legacy effects of past forest use on plant diversity in semi-natural grasslands on ski slopes

Over the past century, grassland and forest ecosystems globally have been heavily influenced by land use changes driven by diverse socioeconomic activities. Ski resorts are a modern land-use type associated with biodiversity loss in mountain ecosystems worldwide. Below the treeline, by contrast, some ski slopes have been shown to provide suboptimal semi-natural habitats for native grassland plants and animals, depending on specific construction and management practices. We compared environmental factors and grassland vegetation between two types of ski slopes in central Japan with different land-use histories: slopes constructed on old pastures (pasture slopes) and slopes constructed by clearing secondary forests or Larix kaempferi plantations established on abandoned pastures during the 1940s-1990s (forest slopes). We examined the effects of land use history and machine grading as well as other environmental factors on ski slope vegetation, including total species richness and the richness of native, endangered, and exotic plants, using a total of 108 plots of 2 m x 10 m. Compared to pasture slopes, forest slopes exhibited significantly lower richness of total plants and native grassland species, including endangered species. Forest slopes were more graded than pasture slopes, resulting in lower native and higher exotic grassland species richness. A significantly lower duration of direct sunlight on forest slopes than on pasture slopes possibly decreased endangered species diversity. The lower species richness on forest slopes may be partly caused by seed dispersal limitations. Our findings demonstrate that ski slopes have good potential to support numerous native grassland plant species, including endangered species, but this potential is significantly and negatively affected by forest use history and concomitant environmental changes. The conservation of semi-natural conditions on pasture slopes as habitats for native grassland species can be promoted through the maintenance of annual mowing practices, avoidance of machine grading, and wider ski courses. NomenclatureYonekura & Kajita (2003) BG Plants: index of Japanese names and scientific names (YList; http://ylist.info/index.html)

plant biology↗

bioRxiv2020

The effects of temporal continuities of grasslands on the diversity and species composition of plants

Semi-natural grasslands are ecosystems rich in biodiversity. However, their decline has been reported worldwide, and identification of grasslands with high conservation priority is urgently required. Recently, an increasing number of studies have reported that past vegetation history affects current biological communities. To evaluate whether the temporal continuity of grasslands promotes biodiversity, and thus can be an indicator of conservation priority, we studied vascular plant communities in old (160- 1000s years) and new (52-70 years after deforestation) grasslands, as well as in forests, of Sugadaira Highland in central Japan. The number of plant species was highest in old grasslands, followed by new grasslands and forests. This pattern was much clearer in the number of grassland-dependent native and grassland-dependent endangered species, indicating the role of old grasslands as refugia for those species. The species composition differed between old and new grasslands. New grasslands had species compositions in between those of old grasslands and forests, suggesting that the plant community in new grasslands retains the influence of past forestation for more than 52 years after deforestation. Eleven indicator species were detected in old grasslands, but none in new grasslands, suggesting the uniqueness of the plant community in old grasslands. We conclude that the temporal continuity of grasslands increases plant diversity and can be an indicator of grasslands with high conservation priority.

ecology↗

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↗