Biology subjects

Takenaka, M.

Publications and source records attributed to Takenaka, M..

13 recordsLinked to original sources

bioRxiv2026

Comparing the Influence of Habitat Configuration on Population Connectivity and Genetic Structure Using Congeneric Species Across Multiple Taxa

Abstract Habitat configuration influences population connectivity and, consequently, genetic structure. River networks provide heterogeneous, hierarchically arranged environments that shift drastically from upstream to downstream. We compared congeneric species across Ephemeroptera, Plecoptera, and Trichoptera, emphasizing longitudinal replacement (upstream to downstream) and the rarely studied wet rock (hygropetric) habitats. We surveyed six rivers on the Muroto Peninsula, Japan, qualitatively sampling aquatic insects at 63 sites. Cluster analysis based on the environmental data classified surveyed sites into four clusters. We analyzed a total of 10 species from four genera that exhibit longitudinal replacement patterns within genera. Genetic analyses based on the mitochondrial cytochrome c oxidase subunit I region revealed that upstream species showed higher genetic diversity than downstream species. In contrast, species adapted to hygropetric exhibited the lowest genetic differentiation among all habitat types. A novel contribution of this study is the inclusion of hygropetric species. The surprisingly low differentiation in hygropetric species suggests high connectivity, similar to lentic species. By comparing congeneric taxa across orders within environmentally similar rivers, we reduce phylogenetic and environmental confounds, strengthening inference that habitat configuration and dispersal traits jointly shape genetic structure. These findings provide a new perspective on riverine spatial ecology and underscore the importance of microhabitat-aware comparisons for evolutionary inference.

zoology↗

bioRxiv2026

Genetic structures of the Japanese stone loach Barbatula oreas (Cypriniformes: Nemacheilidae) in Sakhalin and Hokkaido: back dispersal from Hokkaido to Sakhalin

Understanding how dispersal and vicariance shape species distributions is a central goal in biogeography, yet the role of islands as sources of continental diversity remains poorly resolved. While multiple dispersal routes from the Eurasian continent to the Japanese Archipelago have been proposed, back dispersal from islands to the mainland is rarely documented, particularly in primary freshwater taxa constrained by marine barriers. Here, we investigated the population genetic structure and phylogeographic history of the Japanese stone loach Barbatula oreas, distributed in Hokkaido and Sakhalin, using mtDNA, nDNA, and genome-wide SNP data. We identified two differentiated Northern and Southern lineages within Hokkaido that diverged during the Pleistocene, indicating that geological events such as paleo-catchment reorganization, mountain uplift, and volcanic activity have shaped the present population structure. Ancestral area reconstruction based on mtDNA phylogeny identified Hokkaido as the origin of B. oreas and revealed dispersal from Hokkaido to Sakhalin, indicating back dispersal from islands toward the mainland. This pattern contrasts with the prevailing hypothesis of southward colonization from the continent via Sakhalin to Hokkaido. Additionally, low genetic differentiation between Hokkaido and Sakhalin suggested genetic exchange across the strait, consistent with paleo-catchment reconstruction indicating past catchment connectivity between the regions. These results highlight the combined roles of geological dynamics and sea-level fluctuations in shaping genetic structure, challenge the conventional continent-to-island dispersal paradigm. Moreover, our study demonstrates that island systems can act as biodiversity sources--not merely sinks--and provides a rare empirical example of back dispersal in primary freshwater species.

Molecular Biology↗

bioRxiv2026

Spatial transcriptomic analysis reveals coordinated gene expression in ovarian clear cell carcinoma and adjacent endometriosis in UK and Japanese patients

PurposeOvarian clear cell carcinoma (OCCC) is strongly associated with endometriosis and shows geographic variation in incidence. We investigated whether OCCC and adjacent endometriosis exhibit distinct transcriptional states and whether these patterns differ between United Kingdom (UK) and Japanese cohorts. Experimental DesignWe performed whole-transcriptome spatial profiling on specimens from 16 OCCC cases (8 UK, 8 Japan) in which tumor and endometriosis were both present. Gene expression was analyzed in tumor, endometriosis and stroma. ARID1A status was assessed by immunohistochemistry. ResultsMedian age was 59 years (range 26-82). 13/16 cases (81.3%) had early-stage disease. Tissue compartment rather than cohort of origin was the dominant source of variation across endometriosis and tumor regions. Endometriosis was enriched for inflammatory and immune-related pathways compared to tumor, whilst there was greater representation of chromatin and protein-DNA complex assembly pathways in tumor regions. These patterns were conserved across both cohorts and after stratification by ARID1A status. Mesenchymal-associated gene expression scores also significantly differed across stroma, endometriosis and tumor with clear compartmental separation. Cell type deconvolution analyses showed clear compositional differences between stromal and epithelial disease compartments. ConclusionsOCCC and coexisting endometriosis are transcriptionally distinct, with the dominant contrast being compartmental rather than geographic. ARID1A alone is unlikely to account for the principal spatial transcriptional states identified here. Further analyses will be required to ascertain whether these differences reflect genuine biological differences between OCCC and coexisting endometriosis or represent different stages of endometriosis-associated tumorigenesis. Translational RelevanceOvarian clear cell carcinoma often arises in association with endometriosis, yet the biological transition between these lesions remains poorly understood. Using spatial transcriptomics in matched tumor and adjacent endometriosis from Japanese and UK cohorts, we showed that endometriosis is characterized by inflammatory and antigen-presentation features, whereas tumor regions showed chromatin-organization and oncogenic transcriptional states. These patterns were largely maintained irrespective of ARID1A status and geographic background. In addition, spatial deconvolution suggested differences in local immune composition, with tumor regions showing relatively greater neutrophil- and T cell-associated signals. Together, our data suggest that OCCC and coexisting endometriosis share a spatially linked tissue context, but that tumor regions have distinct transcriptional profile and microenvironment that may be involved in the malignant transformation and inform interpretation of molecular classification in endometriosis-associated OCCC.

pathology↗

bioRxiv2026

L3R-seq: A long-read 3'RACE approach for deep quantitative analysis of RNA processing

Long-read sequencing technologies offer the potential to capture multiple RNA processing events within single molecules, but standard protocols suffer from quantification biases and sequencing errors that limit their utility for precise analysis. Here, we describe Long-read 3 RACE-seq (L3R-seq), a targeted long-read sequencing method that ligates a unique molecular identifier (UMI)-containing adapter to the 3 end of RNA molecules prior to reverse transcription and PCR amplification. By grouping cDNA reads sharing the same UMI and generating a consensus sequence for each original RNA molecule, L3R-seq corrects random sequencing errors and mitigates PCR-duplicate-driven quantification biases. The method enables simultaneous, per-molecule analysis of RNA editing, 3 end cleavage and trimming, and polyadenylation status. Along with a step-by-step protocol for library preparation and sequencing with the Oxford Nanopore Technologies (ONT) platform, we describe an accompanying bioinformatic pipeline for consensus generation and extraction of RNA features. As an example, we apply L3R-seq to the mitochondrial mRNA ccmC from Arabidopsis thaliana, a transcript subject to extensive C-to-U editing and non-canonical 3 end processing. The workflow is readily adaptable to other RNAs targets and is transferable to the Pacific Biosciences (PacBio) platform.

bioinformatics↗

bioRxiv2026

Ancient Ryukyu Jomon contributed to past and current genetic structure of Japanese populations

Characterized by the earliest use of pottery, the Jomon culture was a unique Neolithic culture that spread throughout the Japanese Archipelago. Previous archaeological evidence suggests that Jomon hunter-gatherers colonized the southernmost islands, the Ryukyu Archipelago, by approximately 7,000 years before present (YBP). However, genetic characteristics of the Ryukyu Jomon population and its contribution to the modern population have not been elucidated yet. In this study, we newly sequenced 273 modern and 25 ancient (6,700-900 YBP) whole genomes collected across the Ryukyu Archipelago. Our analysis demonstrated a genetic differentiation between the Hondo (Japanese mainland) and Ryukyu Jomon, dating back to [~]6,900 YBP. After the divergence from the Hondo Jomon, the Ryukyu Jomon experienced severe bottlenecks, with an effective population size of [~]2,000. Admixture between the Ryukyu Jomon and migrants from the historic Hondo population occurred [~]1,000 YBP, which corresponds to the widespread adoption of iron tools and agriculture in the Central Ryukyus. Different demographic histories between modern Hondo and Ryukyu populations resulted in different rates of Jomon ancestry in these populations. By providing a new perspective on the peopling of the Ryukyu Archipelago, this study significantly enhances our understanding of cultural transitions in the region.

evolutionary biology↗

bioRxiv2025

Phylo-MIP: Phylogeny-based Molecular Identification Pipeline for DNA metabarcoding, and assessment of insect communities in subalpine river ecosystems

AbstractEnvironmental DNA metabarcoding is a powerful tool for biodiversity assessment; however, species identification often relies on sequence similarity searches (BLAST), which are limited by incomplete reference databases and result in frequent misidentifications or unclassified taxa. To overcome these challenges, we designed a novel analytical pipeline, Phylo-MIP, which integrates phylogenetic analysis and species delimitation. Phylo-MIP combines sequence alignment, haplotype thinning, phylogenetic tree construction, and multiple species delimitation methods (bPTP, bPTP-ML, mPTP) to objectively identify Molecular Operational Taxonomic Units (MOTUs) without relying on reference databases. As a validation, we applied Phylo-MIP to previously published eDNA data from river in Kanagawa Prefecture, detecting approximately 28% more species than only BLAST-based methods. We also conducted a eDNA survey in the subalpine zone of Kamikochi, Nagano Prefecture, Japan, where Phylo-MIP revealed distinct community structures associated with specific aquatic environments. Phylo-MIP enables non- invasive and efficient biodiversity monitoring, even in protected areas, and offers a reproducible framework for ecological research. This approach has the potential to become a new standard method in river ecology, taxonomy, conservation biology, and ecosystem management.

molecular biology↗

bioRxiv2023

Screening for novel RyR2 inhibitors by ER Ca2+ monitoring

Type 2 ryanodine receptor (RyR2) is a Ca2+ release channel on the endoplasmic/sarcoplasmic reticulum (ER/SR) that plays a central role in the excitation-contraction coupling in the heart. Hyperactivity of RyR2 has been linked to ventricular arrhythmias in patients with catecholaminergic polymorphic ventricular tachycardia (CPVT) and heart failure, where spontaneous Ca2+ release via hyperactivated RyR2 depolarizes diastolic membrane potential to induce triggered activity. In such cases, drugs that suppress RyR2 activity are expected to prevent the arrhythmias, but there is no clinically available RyR2 inhibitors at present. In this study, we searched for RyR2 inhibitors from a well-characterized compound library using a recently developed ER Ca2+-based assay, where the inhibition of RyR2 activity was detected by the increase in ER Ca2+ signals from R-CEPIA1er, a genetically encoded ER Ca2+ indicator, in RyR2-expressing HEK293 cells. By screening 1535 compounds in the library, we identified three compounds (chloroxylenol, methyl orsellinate and riluzole) that greatly increased the ER Ca2+ signal. All of the three compounds suppressed spontaneous Ca2+ oscillations in RyR2-expressing HEK293 cells and correspondingly reduced the Ca2+-dependent [3H]ryanodine binding activity. In cardiomyocytes from RyR2-mutant mice, the three compounds effectively suppressed abnormal Ca2+ waves without substantial effects on the action-potential-induced Ca2+ transients. These results confirm that ER Ca2+-based screening is useful for identifying modulators of ER Ca2+ release channels and suggest that RyR2 inhibitors have potential to be developed as a new category of antiarrhythmic drugs. Significance statementWe successfully identified three compounds having RyR2 inhibitory action from a well-characterized compound library using an ER Ca2+-based assay, and demonstrated that these compounds suppressed arrhythmogenic Ca2+ wave generation without substantially affecting physiological action-potential induced Ca2+ transients in cardiomyocytes. This study will facilitate the development of RyR2 specific inhibitors as a potential new class of drugs for life-threatening arrhythmias induced by hyperactivation of RyR2.

pharmacology and toxicology↗

bioRxiv2023

Definitive environmental DNA research on aquatic insects: Analysis optimization using the recently developed MtInsects-16S primers set

Long-term biodiversity monitoring is necessary for the conservation and management of water resources. Notably, aquatic insects have been used as an indicator of water quality because they provide important basic information about freshwater ecosystems and water resources. Although environmental DNA (eDNA) surveys can enable easy and effective biomonitoring of aquatic insects, previous studies have not successfully detected all insect species, and there has been frequent amplification of nontarget taxa (e.g., algae and diatoms). Therefore, we developed a universal primers set, MtInsects-16S, for eDNA analyses of insects in the mtDNA 16SrRNA region. Furthermore, a well-established database of aquatic insects, especially the MtInsects-16S DNA region of Ephemeroptera, Plecoptera, and Trichoptera in Kanagawa Prefecture, which was the target area in this study, was constructed. Therefore, in this study, we conducted eDNA analyses using a universal primers set and using a well-established database. We conducted and compared capture surveys at the same sites to examine the detection capability of eDNA for Insecta. As a result, eDNA analyses using MtInsects- 16S not only detected almost all of the captured species but also detected many more species without amplifying nontarget taxa. This study demonstrated the application of eDNA analyses with unprecedented accuracy and reliability. It was also shown that community structure by eDNA reflected a relatively narrow range at the water sampling point. Although the data accumulation for constructing locally specific databases is an urgent issue, using the MtInsects-16S region is expected to be a breakthrough in the metabarcoding of insects.

zoology↗

bioRxiv2022

Phylogeography of Geothelphusa freshwater crabs: unexpected dual dispersal routes via land and sea

AimDispersal is an important factor that determines the potential for colonization to pioneer sites. Most decapods employ seaward migration for reproduction with a planktonic larval phase. However, true freshwater crabs spend their entire life cycle in freshwater. Therefore, it is expected that genetic regionality can be easily detected. In this study, we focused on the genetic structures of true freshwater crabs, Geothelphusa crabs. Herein, we reveal the evolutionary history and dispersal patterns of freshwater crustaceans, for which there is limited knowledge to date. LocationJapanese Islands TaxonGeothelphusa dehaani (Decapoda, Potamidae) MethodsWe collected and genetically analyzed 283 specimens at 138 localities from freshwater habitats across the Japanese Islands. Phylogenetic analyses were conducted on 1,796 bp of the combined dataset (mtDNA COI, 16S, and nDNA ITS1, histone H3) and 569 bp of the mtDNA COI dataset. The demographic history of G. dehaani was simulated using Approximate Bayesian Computation analysis. A salt tolerance experiment was conducted to confirm the survival rate in seawater. ResultsThe resulting of phylogenetic relationships detected 10 clades that were highly likely to be monophyletic. These 10 clades genetically exhibited an explicit pattern of geographical differentiation. Also, we confirmed the salt tolerance ability of these Japanese freshwater crabs. Main conclusionsThe highlights of this study were the discovery of several cryptic species/lineages or undescribed species, and the completely different heterogeneous dual dispersal pathways detected within a single species; i.e., both land and ocean routes. As a result of phylogenetic analysis, it was concluded that Japanese crabs are basically genetically divided by straits. However, strong evidence for dispersion via ocean currents was also detected (i.e., a "sweepstake"), and it was also determined that G. dehaani could survive in seawater. This is the first observation of such a unique mode of expansion of a species distribution area.

zoology↗

bioRxiv2021

Development of novel PCR primer sets for DNA metabarcoding of aquatic insects, and the discovery of some cryptic species

DNA barcoding is a powerful tool that provides rapid, accurate, and automatable species identification by using standardized genetic region(s). It can be a powerful tool in various fields of biology such as for revealing the existence of cryptic species and/or rare species and in environmental science such as when monitoring river biota. Biodiversity reduction in recent times has become one of the most serious environmental issues on a worldwide scale. DNA barcoding techniques require the development of sets of universal PCR primers for DNA metabarcoding. We tried to develop universal primer sets for the DNA barcoding of all insect groups. In this study, we succeeded in designing not only universal primer sets for DNA barcoding regions of almost all insects, which were designed to include a hypervariable site between highly conserved sites, but also primer sets for longer fragment sequences for registration in a database. We confirmed successful amplification for 14 orders, 43 families, and 68 species with DNA barcoding in the mtDNA 16S rRNA region, and for 13 orders, 42 families, and 66 species with DNA barcoding in the mtDNA 12S rRNA region. A key feature is that the DNA fragments of the DNA barcoding regions amplified by these primer sets are both short at about 200-bp, and longer fragment sequences will increase the level of data registration in the DNA database. Such resulting database enhancements will serve as a powerful tool for increasingly accurate assessment of biodiversity and genetic diversity.

ecology↗

bioRxiv2021

Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

Previous research indicates that the human genetic diversity found in Wallacea - islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves - has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Here, we provide new insights into this regions demographic history based on genome-wide data from 16 ancient individuals (2600-250 yrs BP) from islands of the North Moluccas, Sulawesi, and East Nusa Tenggara. While the ancestry of individuals from the northern islands fit earlier views of contact between groups related to the Austronesian expansion and the first colonization of Sahul, the ancestry of individuals from the southern islands revealed additional contributions from Mainland Southeast Asia, which seems to predate the Austronesian admixture in the region. Admixture time estimates for the oldest individuals of Wallacea are closer to archaeological estimates for the Austronesian arrival into the region than are admixture time estimates for present-day groups. The decreasing trend in admixture times exhibited by younger individuals supports a scenario of multiple or continuous admixture involving Papuan- and Asian-related groups. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.

genomics↗

bioRxiv2021

Complete loss of mitochondrial complex I genes in mistletoes (Viscaceae) and evidence of polyadenylated mitochondrial transcripts shown by whole transcriptome sequencing

The profound absence of mitochondrial complex I (NADH-ubiquinone oxidoreductase) genes from the mitogenome of Viscum spp. and the rapid rates of molecular evolution characterizing most of their remaining mitochondrial genes raise questions regarding the possible transfer of the entire nad gene set to the nucleus, as well as for the functionality of the remaining highly divergent genes. Using whole transcriptome sequencing in three species of Viscaceae: V. album, V. crassulae, and Phoradendron leucarpum we were able to confirm transcription of all previously identified genes. However, we did not detect any nad gene transcripts, thus, providing further evidence of the complete loss of complex I in Viscaceae. The results from transcriptome sequencing also revealed that levels and patterns of RNA editing were not different from those found in autotrophic plant species. Hence, RNA editing is not a means of restoring conserved domains or folding sites of the proteins coded for by the divergent mitochondrial genes. Since we were able to recover mitochondrial genes transcripts following a sequencing protocol targeted towards polyadenylated mRNA molecules, it is suggested that mitochondrial genes undergo post-transcriptional polyadenylation in Viscaceae.

evolutionary biology↗

bioRxiv2020

Development of microsatellite markers for a giant water bug, Appasus japonicus, distributed in East Asia

We developed microsatellite markers for Appasus japonicus (Hemiptera: Belostomatidae). This belostomatid bug is distributed in East Asia (Japanese Archipelago, Korean Peninsula, and Mainland China), and often listed as endangered species in the Red List or the Red Data Book at the national and local level in Japan. Here we describe twenty novel polymorphic microsatellite loci developed for A. japonicus, and marker suitability was evaluated on 56 individuals from four A. japonicus populations (Nagano, Hiroshima, and Yamaguchi prefecture, Japan, and Chungcheongnam-do, Korea). The number of alleles per locus ranged 1-12 (mean = 2.5), and average observed and expected heterozygosity, and fixation index per locus were 0.270, 0.323, and 0.153, respectively. The 20 markers described here will be useful for investigating the genetic structure of A. japonicus populations, which can contribute in population genetics studies of this species.

molecular biology↗