Biology subjects

Kondo, N. I.

Publications and source records attributed to Kondo, N. I..

3 recordsLinked to original sources

bioRxiv2025

Application of environmental DNA-based assessment for upstream-downstream comparison of river macroinvertebrates in a metal-contaminated river

Environmental DNA (eDNA) is a powerful tool for biological monitoring with the potential to overcome weaknesses of conventional macroinvertebrate surveys in running waters. However, the ability of eDNA to detect changes of macroinvertebrate communities immediately downstream of a perturbation, particularly in upstream-downstream comparisons, has not been adequately explored. To address this issue, we investigated the potential of eDNA-based assessment of a perturbation by comparing the results with macroinvertebrate surveys in a river influenced by the inflow of a metal-contaminated tributary. Both methods revealed distinctly lower richness of taxa and zero-radius operational taxonomic units (ZOTUs) at the metal-contaminated tributary site compared to other study sites. Results from collection of macroinvertebrates indicated that most richness and abundance metrics were significantly reduced at three metal-contaminated sites located 150-750 m downstream from the inflow of the tributary. In contrast, the eDNA-based assessment revealed similar ZOTU richness at a reference site and the downstream, contaminated sites. Although statistically not significant because sample sizes were small, eDNA-based non-metric multidimensional scaling revealed some separation between the reference site and two downstream sites. However, no separation was apparent between the reference site and the site immediately downstream. This result suggested that eDNA at a site 150 m downstream from the inflow was likely affected by downstream drift of eDNA from the upstream reference area. That drift complicated assessment of the community a short distance from the perturbation. The site separation detected by eDNA-based assessment was promising, but the ZOTUs that contributed to the separation were mainly from dipteran taxa rather than from metal-sensitive mayflies, which were significantly lower in abundance at the downstream, contaminated sites. Developing reliable local DNA barcoding information, particularly for these mayflies, may help overcome the limitations of making evaluations over relatively small spatial scales, such as upstream-downstream comparisons.

ecology↗

bioRxiv2022

Genetic differentiation of water penny beetles may be associated with the formation process of the ancient Lake Biwa.

BackgroundWater flow is one of several factors that determine the habitats of aquatic insects. The conversions of stagnant (lentic) and running (lotic) water are physiologically and ecologically constrained. In general, aquatic insect species only occur in one of these environments. Though Eubrianax ramicornis (Coleoptera: Psephenidae) usually resides in rivers, however, it is also known to occur near the shores of Lake Biwa in Japan. Here, we investigated the genetic differences between the two Eubrianax species of Lake Biwa and its inflowing rivers, and other regions of Japan for the first time. Lake Biwa is an ancient lake and about four million years old. Though over 60 endemic species were described from Lake Biwa, they are mostly fish and molluscs, with only two species of aquatic insects. There are few reports of endemic aquatic insects in other ancient lakes, too. Discussion of the endemism of Eubrianax and its promoting factors is expected to provide insights into the evolution of aquatic insects in ancient lakes. MethodsWe surveyed and morphologically identified psephenid larvae in Lake Biwa and its inflowing rivers during the summers of 2017 and 2018 (Hayashi, 2009: Hayashi & Sota, 2009). We conducted phylogenetic analyses of two regions of COI and estimated the ages of population divergence based on fossil records of Eubrianax beetles in Lake Biwa as well as those of previously reported populations in other regions. We also analyzed two COI regions of the E. ramicornis haplotypes in Lake Biwa. ResultsFour psephenid species were identified among the samples collected in Lake Biwa and its inflowing rivers. Of these, E. ramicornis was collected only at the Lake Biwa shore whereas its congeneric E. granicollis was collected only from the rivers inflowing the lake. The phylogenetic analyses showed that E. ramicornis of Lake Biwa were clearly differentiated from those in previously reported regions and this divergence was estimated to have occurred 1.40 MYA. At that time, there was no lake at the location of present-day Lake Biwa. It is thought that rivers and their dammed flood plains to the east, with gravel and sand supplied by the rising Suzuka Mountains further to the east. Such an environments is preferable for E. ramicornis and they were thought to have become isolated from the surrounding rivers during the formation of Lake Biwa. On the contrary, there was no genetic differentiation between the E. granicollis population at the Lake Biwa inflow rivers and those elsewhere. Hence, E. granicollis might have migrated to the Lake Biwa watershed later than E. ramicornis and maintained gene flow over a wide area. The genetic differentiation of E. ramicornis reported here for the first time suggests that a species with a wide distribution may rather be evolving endemic to Lake Biwa. Reports on the endemism of aquatic insects in ancient lakes are scarce. This study is expected to bring new perspectives to the study of insect evolution in ancient lakes.

ecology↗

bioRxiv2021

Multispecies site occupancy modeling and study design for spatially replicated environmental DNA metabarcoding

O_LIEnvironmental DNA (eDNA) metabarcoding has become widely applied to gauge biodiversity in a noninvasive and cost-efficient manner. The detection of species using eDNA metabarcoding is, however, imperfect owing to various factors that can cause false negatives in the inherent multi-stage workflow. C_LIO_LIImperfect detection in the multi-stage workflow of eDNA metabarcoding also raises an issue of study design: namely, how available resources should be allocated among the different stages to optimize survey efficiency. C_LIO_LIHere, we propose a variant of the multispecies site occupancy model for eDNA metabar-coding studies where samples are collected at multiple sites within a region of interest. This model describes the variation in sequence reads, the unique output of the high-throughput sequencers, in terms of the hierarchical workflow of eDNA metabarcoding and interspecific heterogeneity, allowing the decomposition of the sources of variation in the detectability of species throughout the different stages of the workflow. We also introduced a Bayesian decision analysis framework to identify the study design that optimizes the efficiency of species detection with a limited budget. C_LIO_LIAn application of the model to freshwater fish communities in the Lake Kasumigaura watershed, in Japan, highlighted a remarkable inhomogeneity in the detectability of species, indicating a potential risk of the biased detection of specific species. Species with lower site occupancy probabilities tended to be difficult to detect as they had lower capture probabilities and lower dominance of the sequences. The expected abundance of sequence reads was predicted to vary by up to 23.5 times between species. C_LIO_LIAn analysis of the study design suggested that ensuring multiple within-site replications of the environmental samples is preferred in order to achieve better species detection efficiency, provided that a throughput of tens of thousands of sequence reads was secured. C_LIO_LIThe proposed framework makes the application of eDNA metabarcoding more error-tolerant, allowing ecologists to monitor ecological communities more efficiently. C_LI

ecology↗