Biology subjects

Shigeta, S.

Publications and source records attributed to Shigeta, S..

3 recordsLinked to original sources

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↗

bioRxiv2025

Changes over a 10-year Period in the Distribution Ranges and Genetic Hybridization of Three Pelophylax Pond Frogs in Central Japan

In this study, we focused on interspecial interactions in Central Japan where three closely related pond frog species, Pelophylax nigromaculatus, Pelophylax porosus porosus and Pelophylax porosus brevipodus (two species and two subspecies) are distributed and are in contact and/or overlap. The presence or absence of hybridization between these species was evaluated by comparing the sequences of the mitochondrial DNA Cyt-b (586-bp) and the nuclear gene Tyrosinase (747-bp) regions of each specimen collected. By comparing interspecific hybridization in the same area in both 2010 (119 specimens) and 2020 (152 specimens), we clarified population distributions and corresponding genetic dynamics over a 10-year period; there was no major change in the degree of interspecific hybridization between P. nigromaculatus and P. p. brevipodus in the Ina Basin, but it was revealed that the proportion of "pure"-bred Pelophylax p. brevipodus remained low. On the other hand, in the Matsumoto Basin, interspecific hybridization between P. nigromaculatus and P. p. porosus was evaluated to have progressed slightly. The proportion of "pure"-bred Pelophylax p. porosus declined to less than half, while the proportion of hybrid individuals showed a tendency to increase. Moreover, the dispersal of P. nigromaculatus was confirmed in areas along the Sai River, where only the pure-bred P. p. porosus was previously known to inhabit. Since the three frogs targeted in this study are all "Red List" species that are endangered, continuous monitoring of population structures and genetic dynamics is required.

ecology↗

bioRxiv2020

Novel candidates of pathogenic variants of the BRCA1 and BRCA2 genes in a 3,552 Japanese whole-genome sequence dataset (3.5KJPNv2)

Identification of pathogenic germline variants yet no clinical evidence in BRCA genes has become important in patient care of hereditary breast and ovarian cancer syndrome (HBOC). Computational scoring and prospective cohort studies may help to identify such pathogenic variants. We annotated the variants in the BRCA1 and BRCA2 genes from a dataset of 3,552 whole-genome sequences obtained from members of the genome cohorts by Tohoku Medical Megabank Project (TMM) with the InterVar software. Computational impact scores (CADD_phred and Eigen_raw) and minor allele frequencies (MAF) of pathogenic (P) and likely pathogenic (LP) variants in ClinVar are used for filtration criteria. Familial predispositions in cancers among the 35,000 TMM genome cohort participants are analyzed to verify the pathogenicity. Seven potentially pathogenic variants were newly identified. Carriers of these potential pathogenic variants and definite P and LP variants among participants of the TMM prospective cohort show a statistically significant preponderance in cancer onset in sisters in the self-reported cancer history. Filtering by computational scoring and MAF is useful to identify potential pathogenic variants in BRCA genes for Japanese population. These results will be helpful to follow up the carriers of variants of uncertain significance in the HBOC genes.

genetics↗