Biology subjects

Tsuji, S.

Publications and source records attributed to Tsuji, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Feeding ecology and ecological risks of the invasive fish Coreoperca herzi revealed by gut content DNA and environmental DNA metabarcoding

Understanding the dietary patterns of introduced predators is essential for assessing their impacts on freshwater ecosystems. Here, we investigated the feeding ecology of the invasive Korean perch (Coreoperca herzi) introduced to the Oyodo River system, Japan, by integrating gut content DNA metabarcoding and environmental DNA (eDNA) metabarcoding. Fifty specimens were collected, and prey taxa were identified using metabarcoding targeting fish, aquatic insects, and crustaceans. In parallel, eDNA metabarcoding of habitat water samples was used to assess prey availability and selectivity. The results revealed that the Korean perch prey extensively on aquatic insects and fish. Aquatic insect prey were dominated by epilithic clinger taxa inhabiting stone surfaces, particularly mayflies, suggesting visual-mediated prey selection. Fish predation was frequently detected even in small individuals (<100 mm SL), in contrast to previous studies based on conventional methods, indicating that piscivory begins early and ontogenetic dietary shifts are not pronounced. Furthermore, quantitative fish eDNA analysis showed a positive relationship between eDNA concentrations of prey species and predation frequency, indicating opportunistic feeding on abundant, size-accessible prey. By applying two metabarcoding approaches, this study provides an integrated assessment of prey utilisation and environmental context, highlighting ecological risks posed by the Korean perch to freshwater communities in Japan.

ecology↗

bioRxiv2026

Predicting establishment risk of the Korean perch Coreoperca herzi in Japan using species distribution modelling: Insights for invasive fish management

Invasive freshwater fishes pose serious threats to native biodiversity and ecosystem functioning, but management resources for prevention and control are limited. The Korean perch, Coreoperca herzi, a predatory freshwater fish native to the Korean Peninsula, has recently established itself in the Oyodo and Tone River system in Japan and has begun causing serious negative impacts on the ecosystem. This study aimed to predict the spatial distribution of potential establishment risk of the Korean perch within the Japanese archipelago by using a species distribution model based on occurrence records from the native range and environmental variables. Presence records were obtained from the Global Biodiversity Information Facility and combined with hydroclimatic variables from WorldClim and HydroATLAS. A random forest algorithm modified for class-imbalanced data was employed. Model tuning and evaluation were conducted using catchment-based spatial cross-validation to enhance spatial transferability, and predictive performance was assessed using the area under the curve (AUC) and the true skill statistic (TSS). The final model achieved high predictive accuracy (AUC = 0.80; TSS = 0.56) on an independent test dataset. River discharge, river slope, and maximum summer water temperature were identified as key predictors of habitat suitability. Projection of the model onto Japanese river networks indicated that environmentally suitable habitats for Korean perch are widely distributed, particularly in mid- to upstream reaches of rivers. These results provide a spatial basis for prioritising monitoring and eradication and highlight the importance of preventive management in high-risk catchments before invasion or at early invasion stages.

ecology↗

bioRxiv2026

Lhcf9 is a novel negative regulator of non-photochemical quenching in the diatom Chaetoceros gracilis

Photosynthetic organisms in aquatic environments experience rapid fluctuations in light intensity, light quality, and carbon availability, requiring tight regulation of photosynthetic energy conversion. In marine diatoms, non-photochemical quenching (NPQ), particularly energy-dependent quenching (qE), plays a central role in dissipating excess excitation energy as heat. However, excessive NPQ can reduce photosynthetic efficiency under light-limiting or carbon-rich conditions, and how this trade-off is regulated remains poorly understood. Here, we identify CgLhcf9, a previously uncharacterized light-harvesting complex (LHC) protein, as a negative regulator of qE-type NPQ in the centric diatom Chaetoceros gracilis. Expression of CgLhcf9 is induced under low red-light and high CO2 conditions and strongly suppressed by blue light, indicating regulation by both light quality and carbon availability. Functional analyses using CgLhcf9 knockout and overexpression lines reveal that CgLhcf9 suppresses qE: NPQ induction is enhanced in the absence of CgLhcf9, whereas its accumulation downregulates NPQ without affecting other established qE effectors, including Lhcx1 or xanthophyll cycle pigments. Notably, CgLhcf9 accumulation improves cellular growth under light-limiting conditions. These results identify CgLhcf9 as a novel LHC-type regulator that fine-tunes photosynthetic energy dissipation in response to environmental signals. Our findings establish a regulatory mechanism that balances photoprotection, electron transport, and carbon fixation, advancing our understanding of how marine diatoms optimize photosynthesis under fluctuating light and CO2 conditions. Significance statementPhotosynthetic microalgae must balance light-driven electron transport with carbon fixation to maximize growth under fluctuating light and CO2 conditions. While non-photochemical quenching (NPQ) protects photosystems from excess light, excessive NPQ can limit photosynthetic efficiency when light or carbon is limiting. Here, we identify the antenna protein CgLhcf9 as a negative regulator of energy-dependent NPQ in the marine diatom Chaetoceros gracilis. CgLhcf9 integrates light-quality and CO2 signals to suppress NPQ without altering canonical quenching effectors, thereby improving growth under light-limiting conditions. This study reveals a regulatory role for a light-harvesting complex protein in tuning the balance between photoprotection and photosynthetic efficiency, providing insight into how marine diatoms coordinate electron transport and carbon fixation in dynamic environments.

plant biology↗

bioRxiv2025

High-resolution insights into the geographic differentiation and hybridisation of Odontobutis gobies through integrated eDNA and SNP analyses

Understanding fine-scale population genetic structure is essential for biodiversity conservation and evolutionary research, but conventional phylogeographic studies often face labour and financial cost constraints. This study proposes a two-step survey strategy that integrates environmental DNA (eDNA) analysis and PCR-based genome-wide SNP genotyping, aiming to evaluate its effectiveness by comprehensively characterising the population structure of widely distributed species. As a model system, we selected the odontobutid gobies, Odontobutis obscurus and O. hikimius, which occur in western Japan. Initially, water samples were collected from 335 sites across western Japan. Subsequently, tissue sampling for SNP analysis was conducted at 49 sites representing the regional groups and species. The eDNA analysis revealed two major mitochondrial clades within O. obscurus, each comprising multiple geographically distinct groups. Subsequently, tissue sampling and SNP analysis were conducted at representative sites of each regional group and species. Nuclear genomic SNP data (661 loci) corroborated the deep divergence between the two clades of O. obscurus and, unexpectedly, indicated that O. hikimius, whose range lies at their boundary, originated through hybridisation between them. Geographic patterns of the regional groups inferred from both mitochondrial and nuclear data were largely explained by historical geological events such as mountain uplift and ancient river system dynamics, and provide unprecedentedly detailed insight into the population structuring of the focal species. This study demonstrates that the integration of eDNA and SNP analyses provides a cost-effective and scalable approach for high-resolution phylogeographic surveys.

molecular biology↗

bioRxiv2025

Detection of environmental DNA of the Indo-Pacific humpback dolphins in Hong Kong waters using quantitative PCR

Environmental DNA (eDNA) analysis is a promising method to enhance the sensitivity and efficiency of biodiversity monitoring. In Hong Kong, the Indo-Pacific humpback dolphin (Sousa chinensis) is an iconic marine mammal inhabiting shallow coastal regions, playing a vital role in the local biodiversity. However, their population is declining, highlighting the need for effective monitoring methods for S. chinensis. In this study, we developed a species-specific qPCR assay for detecting S. chinensis eDNA. We designed primers and a probe targeting the Cytb region of mitochondrial DNA. Specificity tests and evaluations of the limit of detection and quantification demonstrated that the primers and probe possess sufficient specificity and sensitivity to detect S. chinensis eDNA. Our qPCR method was further validated by detecting S. chinensis eDNA in water samples collected from areas where S. chinensis individuals were sighted. Analysis of 56 coastal water samples collected over two seasons revealed that S. chinensis utilizes the western and southern Lantau regions of Hong Kong waters. With further enhancements to the eDNA-based survey method, including larger water volumes, broader spatial coverage, and targeting other cetaceans and fish, our framework will aid in the conservation of S. chinensis in Hong Kong waters.

ecology↗

bioRxiv2025

A Practical and Cost-Effective Approach to Long-Fragment eDNA Sequencing for High-Resolution Genetic Diversity Assessment

Environmental DNA (eDNA) analysis is increasingly recognised as a valuable method for assessing genetic diversity. However, its resolution and applicability are limited by the short length of sequences that can be analysed (typically < 400 bp) and high analytical costs. This study developed a practical, low-cost long-fragment eDNA analysis method using commercial full-length plasmid sequencing via a nanopore platform and evaluated its effectiveness in assessing population genetic structure. 1 L of surface water was collected from 52 sites across Hokkaido, Japan, targeting Barbatula oreas. Two mitochondrial regions (ND5 and cyt b; approximately 1,000 bp each) were species-specifically amplified, circularised, and sequenced. Library preparation took 2.5 hours, with a total cost per sample of 4,390 JPY ({approx}25.55 EUR, {approx}29.87 USD). High-quality reads were obtained from 34 samples, allowing for the reconstruction of multiple haplotypes per region through haplotype phasing. The eDNA concentration required to achieve a 50% sequencing success was within a range easily attainable for common species. Phylogenetic analysis using 62 concatenated haplotypes (1,968 bp) obtained from each sample identified two clades and multiple regional subgroups, providing higher-resolution phylogeographic information than the previous study. Furthermore, the differentiation of each clade and group was suggested to reflect geological and climatic events. These results demonstrate the feasibility and utility of long-fragment eDNA analysis for evaluating genetic diversity, and its broad application is anticipated in ecological research, conservation management, and environmental policy formulation.

molecular biology↗

bioRxiv2025

Evolutionary origin and functional mechanism of Lhcx in the diatom photoprotection

Diatoms are red-lineage algae that utilize the light-harvesting complex (LHC) subfamily Lhcx for photoprotection via non-photochemical quenching (NPQ); however, its evolutionary origin and molecular mechanism remain poorly understood. Through molecular phylogenetic analysis, we show that diatom Lhcxs and green algal Lhcsrs evolved from a common ancestor, with green plants subsequently acquiring them via horizontal gene transfer. To investigate the functional role of Lhcx1, we generated knockout mutants of Chaetoceros gracilis, a diatom with low Lhcx redundancy. The lhcx1 mutants nearly abolished NPQ, and time-resolved fluorescence measurements revealed that Lhcx1-mediated quenching occurs in energetically detached antenna complexes. Clear-native PAGE with Amphipol further indicated that CgLhcx1 interacts with the FCP L-dimer, functioning as a peripheral antenna for the C2S2M2 PSII-FCPII supercomplex. Notably, under high-light acclimation, lhcx1 mutants exhibited higher PSII effective quantum yields than wild type, attributable to reduced antenna size and enhanced carbon fixation capacity. The absence of NPQ accelerated high-light acclimation and was accompanied by increased xanthophyll accumulation, indicating that compensatory mechanisms can enhance overall photosynthetic efficiency. Together, these findings reveal the evolutionary origin of Lhcx/Lhcsr proteins and define the molecular basis of Lhcx1-mediated photoprotection in diatoms, providing fundamental insights into LHC-based photoprotection across photosynthetic lineages.

plant biology↗

bioRxiv2025

Developing terrestrial environmental DNA sampling methods for detecting arboreal invasive reptiles: a case study of the green anole in the Ogasawara Island, Japan

Early detection of invasive alien species is essential for preventing establishment and mitigating ecological impacts, particularly in island ecosystems harbouring evolutionarily isolated endemic species. Recently, despite increasing reptile introductions and their suggested widespread impacts, methods for monitoring arboreal invasive reptiles remain limited. This study addressed the need for practical detection tools by developing terrestrial environmental DNA (eDNA) sampling methods that collect DNA from leaf surfaces to detect the arboreal invasive green anole (Anolis carolinensis) in the Ogasawara Islands, Japan. Two methods, wiping leaf surfaces with gauze and rinsing with sprayed water, were tested. At an invaded site, green anoles were successfully detected in eight out of 10 samples in both methods. Although no significant difference in eDNA concentration was observed, the wiping method was selected for its greater simplicity. Subsequently, the relationship between green anole population density and eDNA concentrations detected using the wiping method was investigated, suggesting a significant positive relationship. This is the first report demonstrating that terrestrial eDNA concentrations can reflect arboreal reptile population density, suggesting potential applications in quantitative terrestrial biodiversity assessments. Furthermore, the successful detection of eDNA even in the extremely low-density habitat of the green anole demonstrates the usefulness of eDNA-based surveys for early detection of invasions. The method developed here may be broadly applicable to terrestrial biodiversity monitoring, especially in tree-dwelling taxa. Given accelerating biological invasions and biodiversity loss, this approach is expected to benefit managers, conservationists, and researchers concerned with terrestrial ecosystems.

molecular biology↗

bioRxiv2024

p16High immune cell - controlled disease tolerance as a broad defense and healthspan extending strategy

The ability of an organism to overcome infectious diseases has traditionally been linked to killing invading pathogens. Accumulating evidence, however, indicates that, apart from restricting pathogen loads, organismal survival is coupled to an additional yet poorly understood mechanism called disease tolerance. Here we report that p16High immune cells play a key role in establishing disease tolerance. We found that the FDA-approved BNT162b2 mRNA COVID-19 vaccine is a potent and rapid inducer of p16High immune subsets both in mice and humans. In turn, p16High immune cells were indispensable for counteracting different lethal conditions, including LPS-induced sepsis, acute SARS-CoV-2 infection and ionizing irradiation. Mechanistically, we propose that activation of TLR7 or a low physiological activity of STING is sufficient to induce p16High immune subset that, in turn, establishes a low adenosine environment and disease tolerance. Furthermore, containing these signals within a beneficial range by deleting MDA5 that appeared sufficient to maintain a low activity of STING, induces p16High immune cells and delays organ deterioration upon aging with improved healthspan. Our data highlight the beneficial role of p16High immune subsets in establishing a low adenosine environment and disease tolerance.

cell biology↗

bioRxiv2024

Low-invasive, wide-field, and cellular resolution two-photon imaging of neural population activity in brainstem and nucleus tractus solitarii

Brain-viscera communication plays a crucial role in regulating mental health, with the vagus nerve being a key structure mediating this interaction. Clinically, artificial vagus nerve stimulation (VNS) is used to treat various neuropsychiatric disorders, highlighting the importance of vagal afferent fibers in regulating emotion. The nucleus tractus solitarii (NTS) is a brainstem structure proposed to receive signals from vagal afferents and relay them to brain networks for emotion regulation. However, due to the anatomical complexity and difficulty in accessing the deep-brain NTS region in living animals, the mechanisms remain unclear. Here, we developed a wide-field and deep-brain two-photon imaging method using a double-prism based optical interface. This approach enables the identification of cellular-resolution neural activities in the NTS while preserving the cerebellum, which covers the NTS and is important for emotion regulation, intact. We systematically evaluated how NTS neurons respond to VNS and a gastrointestinal hormone, suggesting the usefulness of this method for investigating the role of the vagus-NTS pathway in vivo.

neuroscience↗

bioRxiv2024

A novel VCP modulator, KUS121, attenuates atherosclerosis progression by maintaining intracellular ATP and mitigating ER stress in endothelial cells

BackgroundEndoplasmic reticulum (ER) stress signaling pathways have pivotal roles in atherosclerosis progression. Recently, we have developed Kyoto University Substance (KUS) 121, which selectively inhibits ATPase activities of valosin-containing protein (VCP) and consequently saves intracellular ATP consumption and mitigates ER stress. Methods and ResultsWe assessed the efficacy of KUS121 against atherosclerosis by its daily injection into Apoe-/- mice fed with Western Diet (WD) for 8 weeks. Consequently, KUS121 treatment reduced atherosclerosis progression by approximately 40% in atherosclerotic plaques. Interestingly, we found that C/EBP homologous protein (CHOP), an established ER stress marker, was mainly expressed in plaque endothelium. Therefore, we assessed the action of KUS121 in endothelial cells using the human endothelial cell line (EA.hy926 cells). As a result, KUS121 prevented ER stress-induced apoptosis and downregulated the IRE1 (Inositol-requiring enzyme) -associated inflammatory pathways. Consistent with these in vitro findings, KUS121 treatment also significantly reduced endothelial apoptosis assessed by TUNEL staining and inflammation examined by immunostaining of Nuclear factor kappa B (NF-{kappa}B) and Intercellular adhesion molecule (ICAM) 1 at plaque endothelium. We also demonstrated that KUS121 maintained ATP levels in EA.hy926 cells and atherosclerotic plaque lesions using the single-wavelength or the FRET-based fluorescent ATP sensor. Supplementation of intracellular ATP by Methyl pyruvate (MePyr) attenuated ER stress-induced apoptotic and inflammatory pathways in endothelial cells, which could be the main mechanism how KUS121 reduces ER stress. ConclusionsKUS121 can be a new therapeutic option for atherosclerotic diseases by maintaining intracellular ATP levels and attenuating ER stress-induced apoptosis and inflammation in plaque endothelium.

pathology↗

bioRxiv2023

A novel spawning survey: identifying spawning times and locations of jack mackerel in a semi-closed bay using environmental DNA analysis

Understanding spawning ecology is important for species/population management and conservation. However, conventional surveys are often time- and labour-consuming and invasive. To address these challenges, environmental DNA (eDNA) analysis has emerged as a promising method for spawning surveys. This study investigated the spawning season and diurnal changes in eDNA concentrations targeted Japanese jack mackerel in Maizuru Bay, Japan, to assess the potential of eDNA-based spawning surveys in the marine environment. First, to estimate the spawning season, eDNA concentrations at sunset and sunrise were compared monthly for one year at three sites. As Japanese jack mackerel are nocturnal spawners, eDNA concentration will increase at night during the spawning season. A significant increase in eDNA concentration was observed between sunset and sunrise in July, suggesting that this period corresponded to the spawning season. This was confirmed by egg collection surveys using a plankton net. Second, to investigate diurnal changes in eDNA concentrations during the spawning season, time-series sampling was conducted every three hours for 24 hours in July. The results indicated that eDNA concentration showed a significant diurnal change with a peak between 9 PM and midnight, which is suggested to be their spawning time window. This study successfully estimated the spawning season of Japanese jack mackerel and demonstrated the potential of eDNA-based spawning surveys for the first time in marine environments. These surveys are expected to contribute to the advancement of this field as a new approach to overcoming traditional challenges in marine spawning surveys. HighlightsO_LIThe potential of eDNA for spawning surveys was assessed in jack mackerel. C_LIO_LIMonthly morning and evening eDNA sampling identified spawning activity in July. C_LIO_LIEgg surveys using a plankton net confirmed the spawning event. C_LIO_LITime-series sampling showed a diurnal change in eDNA concentrations in July. C_LIO_LIeDNA analysis is thus applicable for detecting spawning in marine species. C_LI

ecology↗

bioRxiv2023

Identification of fish spawning based on size-selected sampling and diurnal concentration changes of environmental DNA resulting from sperm-release

Spawning is one of the most significant aspects of fish life history, so understanding spawning is critical for the conservation and management of species. Recently, an efficient and non-invasive spawning detection method for spawning behaviour has been proposed, utilising the increased environmental DNA (eDNA) concentration and nuclear/mitochondrial eDNA ratio associated with fish spawning. However, little is known about the characteristics and dynamics of sperm-derived eDNA, which is key to detection. This study focused on changes in eDNA particle size distribution (PSD) and concentrations pre-, post-, and during spawning of Ayu, Plecoglossus altivelis. Firstly, PSD changes between pre- and post-spawning were investigated by comparing concentrations and proportions of eDNA obtained from filters with different pore sizes. Secondly, the diurnal changes in eDNA concentration were monitored at the peak of the spawning season by collecting river water every one or three hours. Results showed that eDNA related to sperm-head size increased at post-spawning, and eDNA concentrations had significant diurnal changes with a peak during the spawning time window. These findings suggest that semi-selective recovery of sperm-derived eDNA based on particle size and/or sampling during the spawning time window with increased concentrations can improve the detection sensitivity of eDNA-based spawning surveys. This study provides essential basic information for advancing eDNA-based spawning surveys and contributes to their further development.

molecular biology↗

bioRxiv2023

An engineered ACE2 decoy broadly neutralizes Omicron subvariants and shows therapeutic effect in SARS-CoV-2-infected cynomolgus macaques

The Omicron variant continuously evolves under the humoral immune pressure obtained by vaccination and SARS-CoV-2 infection and the resultant Omicron subvariants exhibit further immune evasion and antibody escape. Engineered ACE2 decoy composed of high-affinity ACE2 and IgG1 Fc domain is an alternative modality to neutralize SARS-CoV-2 and we previously reported its broad spectrum and therapeutic potential in rodent models. Here, we show that engineered ACE2 decoy retains the neutralization activity against Omicron subvariants including the currently emerging XBB and BQ.1 which completely evade antibodies in clinical use. The culture of SARS-CoV-2 under suboptimal concentration of neutralizing drugs generated SARS-CoV-2 mutants escaping wild-type ACE2 decoy and monoclonal antibodies, whereas no escape mutant emerged against engineered ACE2 decoy. As the efficient drug delivery to respiratory tract infection of SARS-CoV-2, inhalation of aerosolized decoy treated mice infected with SARS-CoV-2 at a 20-fold lower dose than the intravenous administration. Finally, engineered ACE2 decoy exhibited the therapeutic efficacy for COVID-19 in cynomolgus macaques. Collectively, these results indicate that engineered ACE2 decoy is the promising therapeutic strategy to overcome immune-evading SARS-CoV-2 variants and that liquid aerosol inhalation can be considered as a non-invasive approach to enhance efficacy in the treatment of COVID-19.

microbiology↗

bioRxiv2022

Capsid-mediated chromatin state of the AAV vector genome controls host species range

Recombinant adeno-associated viral vectors (rAAVs) are among the most commonly used vehicles for in vivo based gene therapies. However, it is hard to predict which AAV capsid will provide the most robust expression in human subjects due to the observed discordance in vector-mediated transduction between species. We used a primate specific capsid, AAV-LK03, and demonstrated that the limitation of this capsid towards transduction of mouse cells was unrelated to cell entry and nuclear transport but rather due to depleted histone H3 chemical modifications related to active transcription, namely H3K4me3 and H3K27ac, on the vector DNA itself. A single-amino acid insertion into the AAV-LK03 capsid enabled efficient transduction and the accumulation of active histone marks on the vector chromatin in mouse without compromising transduction efficiency in human cells. Our study suggests that the capsid protein itself is involved in determining the chromatin status of the vector genome, most likely during the process of uncoating. Programming viral chromatin states by capsid design may enable facile DNA transduction between vector and host species.

molecular biology↗

bioRxiv2022

Age-associated sleep-wake patterns are altered with Prdm13 signaling in the dorsomedial hypothalamus and dietary restriction in mice

Old animals display significant alterations in sleep-wake patterns such as increases in sleep fragmentation and sleep propensity. Here we demonstrated that dorsomedial hypothalamus-specific PR-domain containing protein 13-knockout (DMH-Prdm13-KO) mice recapitulated age-associated sleep alterations such as sleep fragmentation and increased sleep attempts during sleep deprivation (SD). These phenotypes were further exacerbated during aging, with increased adiposity and decreased physical activity, resulting in shortened lifespan. Dietary restriction (DR), a well-known anti-aging intervention in diverse organisms, ameliorated age-associated sleep alterations, whereas these effects of DR were abrogated in DMH-Prdm13-KO mice. Moreover, overexpression of Prdm13 in the DMH ameliorated sleep fragmentation and excessive sleepiness during SD in old mice. Therefore, maintaining Prdm13 signaling in the DMH might play an important role to control sleep-wake patterns during aging.

physiology↗

bioRxiv2022

Environmental DNA phylogeography: successful reconstruction of phylogeographic patterns of multiple fish species from a cup of water

Phylogeography is an integrative field of science linking micro- and macro-evolutionary processes, contributing to the inference of vicariance, dispersal, speciation, and other population-level processes. Phylogeographic surveys usually require considerable effort and time to obtain numerous samples from many geographical sites covering the distribution range of target species; this associated high cost limits their application. Recently, environmental DNA (eDNA) analysis has been useful not only for detecting species but also for assessing genetic diversity; hence, there has been growing interest in its application to phylogeography. As the first step of eDNA-based phylogeography, we examined (1) data screening procedures suitable for phylogeography and (2) whether the results obtained from eDNA analysis accurately reflect known phylogeographic patterns. For these purposes, we performed quantitative eDNA metabarcoding using group-specific primer sets in five freshwater fish species belonging to two taxonomic groups from a total of 94 water samples collected from western Japan. As a result, three-step data screening based on the DNA copy number of each haplotype detected successfully eliminated suspected false positive haplotypes. Furthermore, eDNA analysis could almost perfectly reconstruct the phylogenetic and phylogeographic patterns obtained for all target species with the conventional method. Despite existing limitations and future challenges, eDNA-based phylogeography can significantly reduce survey time and effort and is applicable for simultaneous analysis of multiple species in single water samples. eDNA-based phylogeography has the potential to revolutionise phylogeography.

molecular biology↗

bioRxiv2022

Quantitative environmental DNA metabarcoding reflects quantitative capture data of fish community obtained by electrical shocker

The simultaneous conservation of species richness and evenness is important to effectively reduce biodiversity loss and keep ecosystem health. Environmental DNA (eDNA) metabarcoding has been used as a powerful tool for identifying community composition, but it does not necessarily provide quantitative information due to several methodological limitations. Thus, the quantification of eDNA through metabarcoding is an important frontier of eDNA-based biomonitoring. Particularly, the qMiSeq approach has recently been developed as a quantitative metabarcoding method and has attracted much attention due to its usefulness. The aim here was to evaluate the performance of the qMiSeq approach as a quantitative monitoring tool for fish communities by comparing the quantified eDNA concentrations with the results of fish capture surveys. The eDNA water sampling and the capture surveys using the electrical shocker were conducted at a total of 21 sites in four rivers in Japan. As a result, we found significant positive relationships between eDNA concentrations of each species quantified by qMiSeq and both the abundance and biomass of each captured taxon at each site. Furthermore, for seven out of eleven taxa, a significant positive relationship was observed between quantified DNA concentrations by sample and the abundance and/or biomass. In total, our results demonstrated that eDNA metabarcoding with the qMiSeq approach is a suitable and useful tool for quantitative monitoring of fish communities. Due to the simplicity of the eDNA analysis, the eDNA metabarcoding with qMiSeq approach would promote further growth of quantitative monitoring of biodiversity. HighlightsO_LIeDNA analysis and capture surveys of fishes were conducted at a total of 21 sites. C_LIO_LIQuantitative eDNA metabarcoding (qMiSeq) successfully quantified the eDNA of fishes. C_LIO_LIFor each site, the estimated eDNA conc. reflected the abundance and biomass of fishes. C_LIO_LIFor each taxon, the estimated eDNA conc. were comparable among sites. C_LIO_LIqMiSeq is a suitable and useful tool for quantitative monitoring of fish community. C_LI

ecology↗