Biology subjects

Suyama, Y.

Publications and source records attributed to Suyama, Y..

14 recordsLinked to original sources

bioRxiv2026

Genome-wide evidence for cryptic multi-generational introgression between invasive Bursaphelenchus xylophilus and native B. mucronatus

Hybridization between invasive and native species can generate novel genetic variation with ecological and evolutionary consequences, yet introgression often remains cryptic. We investigated natural hybridization between the invasive pinewood nematode Bursaphelenchus xylophilus, the causal agent of pine wilt disease, and native Bursaphelenchus mucronatus in Japan. Using multiplexed inter-simple sequence repeat genotyping by sequencing, we genotyped 342 field-collected nematodes and then conducted pedigree-calibrated analysis using HIest v2.0, based on 48 highly informative diagnostic single-nucleotide polymorphisms (SNPs), followed by ADMIXTURE, complementary NeighborNet and principal component analyses of a broader 2,756-SNP dataset. The results identified nine high-confidence hybrids (2.6%) across two consecutive years (2023-2024), including relatively balanced F1-like individuals and strongly parentally biased advanced backcross-like individuals, demonstrating recurrent, multigenerational introgression. Four hybrids (44.4%) were undetectable using a single-locus diagnostic marker, showing that advanced introgression can escape conventional surveillance. Chemotaxis assays detected no volatile-mediated pre-mating discrimination, whereas post-mating barriers were incomplete and asymmetric. Crosses with B. xylophilus as the maternal parent showed reduced hatchability, particularly with B. mucronatus mucronatus, while reciprocal crosses generally retained higher hatchability, although some showed reduced fecundity. These results provide a mechanistic basis for natural gene flow in a recent secondary contact zone. Because B. mucronatus kolymensis is widespread in Europe and produces viable hybrid offspring with B. xylophilus in both directions, pathogen establishment could create new opportunities for introgression. Our findings reveal cryptic, multigenerational introgression between an invasive forest pathogen and its native congener, highlighting the importance of genomic surveillance for forest disease management and invasion-risk assessment under climate change.

evolutionary biology↗

bioRxiv2026

Nationwide multi-omics profiling of Japanese jack mackerel reveals geographic gut microbiome structuring despite host panmixia

Host genetic markers often fail to resolve regional origins in highly connected or panmictic marine species. The Japanese jack mackerel, Trachurus japonicus, is a commercially important fishery species around Japan that shows little or no detectable population structure. Here, we used nationwide multi-omics profiling to compare host genomic variation and gut microbiome composition in wild T. japonicus collected from coastal regions across Japan. We generated MIG-seq data for 43 individuals and 16S rRNA gene profiles for 24 individuals; after quality filtering, 19 individuals remained for matched host-microbiome comparison. Genome-wide host SNP analyses showed weak or absent geographic population structure, consistent with previous evidence of panmixia in Japanese waters. In contrast, gut microbiome composition showed geographic structuring based on Bray-Curtis dissimilarity and PERMANOVA, and this pattern was not explained by proximity to river mouths or host-related variables. Locality- or individual-associated bacterial lineages contributed to the observed differences in the microbiome, while chloroplast-associated and Cyanobacteria-assigned ASVs suggested recent dietary or environmental input. These results indicate that gut microbiome can show regional biological variation not apparent from host genetic markers alone. Our study provides a proof-of-concept example of integrating host genomics and gut microbiome profiling to evaluate regional characteristics and origins in highly connected marine animals.

microbiology↗

bioRxiv2026

Recurring daytime and nighttime modes of VOC emissions in a cool-temperate oak forest

Plants emit substantial amounts of biogenic volatile organic compounds (VOCs) that link plant physiological activity to ecological interactions and atmospheric chemistry. However, the processes regulating VOC emissions within the forest air and at the interface directly above the canopy remain poorly characterized. In this study, we investigated forest-scale VOC dynamics in a cool-temperate deciduous forest dominated by Quercus crispula using high-time- and high-mass-resolution proton-transfer-reaction time-of-flight mass spectrometry (PTR-ToF-MS) integrated with positive matrix factorization (PMF). This non-targeted, process-oriented framework was applied to forest-interior and canopy-top atmospheres during rain-free summer days in 2024 and 2025 to extract dominant modes of VOC emissions. The PMF consistently resolved two recurring modes characterized by the daytime and nighttime enhancement patterns. The daytime mode was dominated by isoprene and its oxidation products and demonstrated strong light- and temperature-dependence, whereas the nighttime mode was enriched in mono- and sesquiterpenes. The daytime contribution exhibited a pronounced morning-afternoon asymmetry, indicating non-linear physiological and canopy-scale controls. These patterns were reproducible across the years. This study demonstrates that combining PTR-ToF-MS with PMF enables robust, top-down identification of recurring modes of forest VOC variability within and above forest canopies, linking leaf-level physiology and ecosystem-scale atmospheric exchange. HighlightForest-scale VOC emissions were resolved into recurring daytime and nighttime modes using a non-targeted PTR-ToF-MS and PMF framework.

physiology↗

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↗

bioRxiv2025

Common garden experiments suggest terpene-mediated interactions between phyllosphere microbes and Cryptomeria japonica

Plant-microbe interactions in the phyllosphere provide invaluable information on plant ecology, with implications for ecosystem functioning and plant-atmosphere feedbacks. The composition of phyllosphere microbial communities varies significantly depending on host lineages, geographic regions, and climatic conditions. However, the factors driving these variations in interactions with plants remain poorly understood. Biogenic volatile organic compounds (BVOCs) emitted by plants may be important in these interactions. Here, we quantified the composition of phyllosphere microbial communities and terpene emissions from leaves of Japanese cedar (Cryptomeria japonica) trees grown in two common gardens from cuttings collected from natural populations across Japan. Amplicon sequencing revealed that bacterial and fungal communities differed significantly between gardens and among host population origins. Analysis of BVOC profiles showed that the camphene emission rate was associated with bacterial community composition, whereas that of {beta}-farnesene was linked to fungal community composition. The relative abundances of certain putative plant pathogens and the emission rates of most monoterpenes were correlated with the climatic conditions at the origin sites of cedar trees. These findings highlight the intricate relationships between phyllosphere microbial communities and terpene emission from host trees and suggest the role of climatic factors in shaping these interactions.

plant biology↗

bioRxiv2025

Transcriptome differentiation in Cryptomeria japonica trees with different origins growing in the north and south of Japan

Cryptomeria japonica is a coniferous species widely distributed throughout Japan and therefore adapted to various environments. To seek genes involved in the local adaptation of this species, individuals with different origins growing at three common gardens located in the south, central and north of Japan were subjected to transcriptome analysis. The transcriptome assembly, guided by whole-genome sequence of C. japonica, resulted in 77,212 transcripts from 56,203 genes. Individuals were clustered into three genetic groups based on single nucleotide polymorphisms (SNPs) detected in 12,389 genes among them. Weighted gene co-expression network analysis (WGCNA) identified 25 gene modules. Comparison of representative gene expression patterns for each co-expression gene module with genetic differentiation predicted by SNPs revealed that one module exhibited a negative correlation and another a positive correlation across all three common gardens. While defense response genes were highly expressed in individuals from the Pacific Ocean side of Japan (omote-sugi), terpenoid metabolism genes were more expressed in individuals originating from the Sea of Japan side (ura-sugi). These results suggest that local adaptation associated with the alteration of gene regulation occurred in biotic stress response genes in C. japonica.

plant biology↗

bioRxiv2025

Genetic diversity and conservation insights for the baobab Adansonia suarezensis in northern Madagascar: a whole genome SNP analysis

Madagascar is home to seven unique baobab species in the genus Adansonia, all threatened by climate change, habitat destruction, and deforestation. Previous studies have highlighted the vulnerability of baobabs, particularly A. suarezensis, without delving into the specific genetic structure of its populations. In this paper we examine the genetic structure, diversity, and connectivity of seven populations of A. suarezensis, using genome-wide Single Nucleotide Polymorphism (SNP) data. The results revealed significant genetic differentiation between inland and coastal populations, with the Mahory population forming a distinct genetic cluster characterized by high heterozygosity but low polymorphism, indicative of historical bottlenecks. In contrast, northern populations showed greater admixture and gene flow but higher inbreeding coefficients in coastal regions, such as Ambilo and Cap dAmbre, suggesting localized inbreeding depression. Additionally, historical climatic shifts and potential anthropogenic dispersal are explored as contributing factors to the current genetic patterns. This study highlights the importance of understanding genetic dynamics for conservation, emphasizing habitat restoration and targeted management strategies to preserve the evolutionary potential of A. suarezensis and ensure its long-term survival.

genetics↗

bioRxiv2024

Insights from Genetic Studies: SNP Analyses Confirm White Clover Naturalization in Brazil

White clover (Trifolium repens) is a stoloniferous legume herb native to Eurasia, which had been introduced and spread globally. In Brazil, it was introduced as forage crop. While previous studies focused mainly on its agricultural benefits, much remains unclear about its territorial dynamics, introduction process and potential threats in Brazil. This study aims to estimate the genetic diversity of naturalized white clover populations in Brazil and assess the influence of cultivars into these populations diversity. Through MIG-Seq analysis, 1097 SNPs show that Brazilian populations have 94% within-population variation. Additionally, two mountainous areas clustered together, while rural and urban areas formed a second cluster. Cultivars are less diverse and have 27% of their genetic variability between them. We found that some populations admixture with cultivated varieties, while more isolated mountainous populations were singular in their genetic background. We can conclude that it is possible that parts of the populations are originally native, brought during European immigration, while others appear to have similar cultivar ancestry, indicating possible biological escapes from cultivars into naturalized populations. Considering ecological data and our genetic findings, it is confirmed that white clover is indeed naturalized in Brazil.

genetics↗

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↗

bioRxiv2023

The molecular clock in long-lived tropical trees is independent of growth rate

The rates of appearance of new mutations play a central role in evolution. However, mutational processes in natural environments and their relationship with growth rates are largely unknown, particular in tropical ecosystems with high biodiversity. Here, we examined the somatic mutation landscapes of two tropical trees, Shorea laevis (slow-growing) and S. leprosula (fast-growing), in central Borneo, Indonesia. Using newly-constructed genomes, we identified a greater number of somatic mutations in tropical trees than in temperate trees. In both species, we observed a linear increase in the number of somatic mutations with physical distance between branches. However, we found that the rate of somatic mutation accumulation per meter of growth was 3.7-fold higher in S. laevis than in S. leprosula. This difference in the somatic mutation rate was scaled with the slower growth rate of S. laevis compared to S. leprosula, resulting in a constant somatic mutation rate per year between the two species. We also found that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. These findings suggest that somatic mutations accumulate with absolute time and older trees have a greater contribution towards generating genetic variation. Significance StatementThe significance of our study lies in the discovery of an absolute time-dependent accumulation of somatic mutations in long-lived tropical trees, independent of growth rate. Through a comparative analysis of somatic mutation landscapes in slow- and fast-growing species, we observed a clock-like accumulation of somatic mutations in both species, regardless of their growth rates. Although the majority of somatic mutations were restricted to a single branch, we also identified mutations present in multiple branches, likely transmitted during growth. Our findings suggest that older trees make a greater contribution towards generating genetic variation.

evolutionary biology↗

bioRxiv2022

Extremely low level of genetic diversity in Gentiana yakushimensis, an endangered species in Yakushima Island, Japan

Rare or endangered species largely contributing to global biodiversity are essential components of ecosystems. Because genetic diversity depends not only on apparent population size but also demographic processes, the conservation priority of endangered species based on population genetics needs to be assessed by comparison with common congeners and demographic events. In this study, we performed population genetic analysis for Gentiana yakushimensis Makino, a rare and endangered plant species with an isolated distribution on Yakushima Island, Japan. We performed comparison of genetic diversity with the congener (Gentiana triflora Pall. var. japonica (Kusn.) H.Hara), demographic inference, and bottleneck test based on genome-wide single nucleotide polymorphisms. The result was that G. yakushimensis had an extremely low genetic diversity level and a high inbreeding coefficient level compared to those of the congener. The population of G. yakushimensis was estimated to experience an expansion during the Last Glacial Maximum and a recent bottleneck by the demographic inference and the bottleneck test. Therefore, the low level of genetic diversity of this species might have resulted from the impact of the recent bottleneck and the long-term maintenance of a small population size. Due to the long lifespan of the genus Gentiana, the current level of genetic diversity probably does not reflect a large part of recent demographic events, which requires long-term monitoring of changes in genetic diversity to identify the time lag between the reduction in apparent population size and genetic diversity as a future outlook.

genetics↗

bioRxiv2022

Inferring future changes in gene flow under climate change in riverscapes

Global climate change poses a significant threat to the habitat connectivity of cold-water-adapted organisms, leading to species extinctions. Because gene flow is itself a functional connectivity among wild populations, if gene flow is modeled by landscape variables, changes in population connectivity could be predicted. In this study, using a model-based riverscape genetics technique and a hydrological model to estimate water temperature, we inferred the determinants of and future changes in gene flow of the fluvial sculpin Cottus nozawae in the upstream section of the Sorachi River, Hokkaido, Japan. As a result of model selection, stream order, water temperature, slope, and distance were detected as landscape variables affecting the strength of gene flow in each stream section. In particular, the trend of greater gene flow in sections with higher stream order and lower temperature fluctuations or summer water temperatures was pronounced. The map from the model showed that gene flow is overall prevented in small tributaries in the southern area, where spring-fed environments are less prevalent. Estimating future changes in gene flow using future water temperature predictions, genetic connectivity was predicted to decrease dramatically until the end of the 21st century under IPCC representative concentration pathway scenario 8.5 (RCP8.5).

ecology↗

bioRxiv2021

A strategic sampling design revealed the local genetic structure of cold-water fluvial sculpin: a focus on groundwater-dependent water temperature heterogeneity

A key piece of information for ecosystem management is the relationship between the environment and population genetic structure. However, it is difficult to clearly quantify the effects of environmental factors on genetic differentiation because of spatial autocorrelation and analytical problems. In this study, we focused on stream ecosystems and the environmental heterogeneity caused by groundwater and constructed a sampling design in which geographic distance and environmental differences are not correlated. Using multiplexed ISSR genotyping by sequencing (MIG-seq) method, a fine-scale population genetics study was conducted in fluvial sculpin Cottus nozawae, for which summer water temperature is the determinant factor in distribution and survival. There was a clear genetic structure in the watershed. Although a significant isolation-by-distance pattern was detected in the watershed, there was no association between genetic differentiation and water temperature. Instead, asymmetric gene flow from relatively low-temperature streams to high-temperature streams was detected, indicating the importance of low-temperature streams and continuous habitats. The groundwater-focused sampling strategy yielded unexpected results and provided important insights for conservation.

ecology↗

bioRxiv2021

High-Throughput Sequencing of 5S-IGS rDNA in Fagus L. (Fagaceae) reveals complex evolutionary patterns and hybrid origin of modern species

Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind-pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high-throughput sequencing (HTS) of the 5S intergenic spacers (5S-IGS) for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata - F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4,963 unique 5S-IGS variants reflect a complex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra-genomic competition between two or more paralogous-homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years. Significance statementThe evolution of extra-tropical wind-pollinated tree genera involves dynamic speciation processes. High-throughput sequencing of the multi-copy, potentially multi-locus 5S rDNA reveals a complex history of hybrid origins, lineage sorting and mixing, and intra-genomic competition between paralogous-homeologous loci in the core group of Eurasian beech trees (genus Fagus) and their distant relative, F. japonica. The modern species are genetic mosaics and represent a striking case of at least 55 million years of ongoing reticulate evolution.

evolutionary biology↗