Biology subjects

Isagi, Y.

Publications and source records attributed to Isagi, Y..

5 recordsLinked to original sources

bioRxiv2026

Molecular evolutionary evidence for coexistence within oak hybrid zones.

Resource allocation trade-offs in seedlings have been widely proposed to facilitate the coexistence of tree species; however, whether selection can maintain the underlying genetic variation under gene flow remains insufficiently investigated. Using a natural hybrid zone between two East Asian oaks, we evaluated whether loci associated with allocation trade-offs showed signatures of selection despite hybridisation. Acorns collected across the zone were cultivated in a common garden, where we quantified 25 seedling growth and functional traits, and analysed whole-genome variation. We identified trade-offs between leaf function and plant architecture. Trait-associated genomic regions demonstrated strong inter-chromosomal linkage disequilibrium in the hybrids, consistent with genetic coupling, and exhibited elevated interspecific differentiation and more pronounced genetic clines. These results indicate that multilocus selection counteracts gene flow through the development of genetic coupling, thereby maintaining resource allocation trade-offs that may contribute to tree coexistence.

evolutionary biology↗

bioRxiv2026

LeafContourEFD: a reproducible workflow for elliptic Fourier analysis with orientation normalization and lateral asymmetry

PremiseElliptic Fourier analysis is widely used to quantify leaf shape variation, but inconsistent normalization and orientation alignment can introduce biologically irrelevant variation. In addition, a reproducible workflow from raw images to normalized elliptic Fourier descriptors (EFDs) is still lacking. Methods and ResultsWe developed LeafContourEFD, a GUI application for reproducible leaf morphometrics. It integrates image segmentation, contour extraction, EFD calculation, and an extended normalization framework, termed oriented true EFD normalization, based on a user-defined biological reference axis. Analyses of Quercus serrata, Q. crispula, and Triadica sebifera showed that existing normalization methods can introduce orientation-related variance when the first-harmonic major axis does not match the leaf base-to-tip axis. In contrast, oriented true normalization removed these artifacts, yielding clearer shape transitions along principal components allowing shape variation among leaves to be captured while preserving biologically meaningful lateral asymmetry. ConclusionsLeafContourEFD improves interpretability and reproducibility in outline-based morphometrics and provides transparent outputs and metadata for data sharing and cross-study comparisons.

plant biology↗

bioRxiv2025

Hybridization during the adaptive radiation of Oxera (Lamiaceae) in New Caledonia: Is flower shape shift driven by introgression?

Recent genomic studies have suggested that hybridization may play a significant role in adaptive radiation, rapid speciation, and convergent evolution. The genus Oxera, a plant taxon thought to have diversified at its beginning through adaptive radiation in New Caledonia, provided an opportunity to investigate these processes. Within the robusta subclade of Oxera, characterized by bird-pollinated yellow-orange flowers, convergent evolution of flower shape is likely to have occurred. We aimed to elucidate the hybridization history of the robusta subclade by whole genome sequencing and MIG-seq data. Our analyses revealed an ancestral introgression from O. coriacea to O. sympatrica, whose flowers are remarkably similar to each other. Among the introgressed genomic regions, we identified several genes potentially involved in flower shape development. O. sympatrica and its sympatric sister species exhibit distinct flower shapes, and pollinator-mediated reproductive isolation presumed to be a major barrier between them. The ancestral introgression uncovered in this study may have driven the convergent evolution of flower shape in the robusta subclade and played a crucial role in the speciation process of O. sympatrica. These finding contribute to our understanding of the interplay between hybridization, adaptive radiation, and speciation process.

evolutionary biology↗

bioRxiv2023

Phylogeographical evidence for historical long-distance dispersal in the flightless stick insect Ramulus mikado

Exploring how organisms overcome geographical barriers to dispersal is a fundamental question in biology. Passive long-distance dispersal events, although infrequent and unpredictable, have a considerable impact on species range expansions. Despite limited active dispersal capabilities, many stick insect species have vast geographical ranges, indicating that passive long-distance dispersal is vital for their distribution. A potential mode of passive dispersal in stick insects is via the egg stage within avian digestive tracts, as suggested by experimental evidence. However, detecting such events under natural conditions is challenging due to their rarity. To indirectly assess the importance of historical avian-mediated dispersal, we examined the population genetic structure of the flightless stick insect Ramulus mikado based on a multifaceted molecular approach (COI haplotypes, nuclear SSR markers, and genome-wide SNPs). Subsequently, we identified unique phylogeographic patterns, including the discovery of identical COI genotypes spanning considerable distances, which substantiates the notion of passive long-distance genotypic dispersal. Overall, all the molecular data revealed low and mostly non-significant genetic differentiation among populations, with identical or very similar genotypes across distant populations. We propose that long-distance dispersal facilitated by birds is the most plausible explanation for the unique phylogeographic pattern observed in this flightless stick insect.

evolutionary biology↗

bioRxiv2020

Geographic and subsequent biotic isolations led to a diversity anomaly of Heterotropa (Aristolochiaceae) in insular versus continental regions of the Sino-Japanese Floristic Region

The Sino-Japanese Floristic Region is highly diverse with respect to temperate plants. However, the reasons for this diversity are poorly understood because most studies have only considered geographic isolation caused by climatic oscillations. Heterotropa (genus Asarum; Aristolochiaceae) diverges here and shows high species diversity in insular systems (63 species) compared to continental areas (25 species). Heterotropa shows low dispersal ability with small distribution ranges, implying diversification by geographic events, and high floral diversity, implying pollinator-mediated diversification. To reveal how abiotic and biotic factors have shaped the diversity anomaly of Heterotropa, we conducted phylogenetic analysis using ddRAD-seq and chloroplast genome datasets including 79 species, estimation of floral trait evolution, and comparison of isolation factors within clades based on distribution range and floral trait analysis. Phylogenetic analysis indicates that Heterotropa originated in mainland China and expanded to the Japanese Archipelago in the Miocene, and the major clades almost correspond to geographic distributions. Floral traits evolved repeatedly in the tip nodes within the clades. Although the major clades include a high proportion of species pairs showing isolation by floral traits, there are no conditional relationships between two isolation factors, indicating that most species pairs with floral trait isolation are distributed allopatrically. The repeated exposure and submergence of land-bridges caused by climatic oscillations would have led to significant population fragmentation in insular systems. Thus, the diversity anomaly of Heterotropa would have resulted from geographic and climatic events during the Miocene, while subsequent repeated floral trait evolution would have followed geographic isolation during the Pleistocene.

plant biology↗