Quantitative environmental DNA metabarcoding shows high potential as a novel approach to quantitatively assess fish community

水に含まれる環境DNAから「どんな魚」が「どれだけいるか」を同時に推定 --定量的な魚類群集モニタリングを容易に実現--. 京都大学プレスリリース. 2023-01-20.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 the 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

Revising the distribution of a threatened goby, Apocryptodon punctatus (Perciformes, Oxudercidae), in Japan with the discovery of an isolated population

Five specimens of a threatened goby, Apocryptodon punctatus (21.2–40.1 mm in standard length), were collected at a mudflat site of Kushima City, Miyazaki Prefecture, Kyushu, southern Japan over two seasons, autumn (September 2015) and spring (April 2016). A review of distributional records of A. punctatus revealed that this population represents the southernmost record of the species in Japanese waters, and is isolated ca. 200 km south-southwest from the nearest point of the main range of the species along the Pacific coast of Japan. Publicising this population will help conserve it and its vulnerable habitat

Revising the distribution of a threatened goby, Apocryptodon punctatus (Perciformes, Oxudercidae), in Japan with the discovery of an isolated population

Five specimens of a threatened goby, Apocryptodon punctatus (21.2–40.1 mm in standard length), were collected at a mudflat site of Kushima City, Miyazaki Prefecture, Kyushu, southern Japan over two seasons, autumn (September 2015) and spring (April 2016). A review of distributional records of A. punctatus revealed that this population represents the southernmost record of the species in Japanese waters, and is isolated ca. 200 km south-southwest from the nearest point of the main range of the species along the Pacific coast of Japan. Publicising this population will help conserve it and its vulnerable habitat

Revising the distribution of a threatened goby, Apocryptodon punctatus (Perciformes, Oxudercidae), in Japan with the discovery of an isolated population

Five specimens of a threatened goby, Apocryptodon punctatus (21.2–40.1 mm in standard length), were collected at a mudflat site of Kushima City, Miyazaki Prefecture, Kyushu, southern Japan over two seasons, autumn (September 2015) and spring (April 2016). A review of distributional records of A. punctatus revealed that this population represents the southernmost record of the species in Japanese waters, and is isolated ca. 200 km south-southwest from the nearest point of the main range of the species along the Pacific coast of Japan. Publicising this population will help conserve it and its vulnerable habitat

Using environmental DNA analyses to assess the occurrence and abundance of the endangered amphidromous fish Plecoglossus altivelis ryukyuensis

The Ryukyu ayu Plecoglossus altivelis ryukyuensis is an endangered amphidromous fish that inhabits rivers in the Ryukyu Archipelago (Japan). Populations of the species have declined dramatically. Consequently, the Ryukyu ayu has been registered as a natural monument in Japan and monitoring surveys with direct catching are restricted legally. This restriction, unfortunately, makes monitoring of population abundances difficult and creates a barrier to both advancing understanding of the species’ status and the development of appropriate conservation plans.We developed a non-invasive monitoring methodology using eDNA analyses. We designed a specific quantitative PCR assay for the Ryukyu ayu using the mitochondrial ND4 region. Using this primer/probe set, we conducted eDNA analyses in three rivers on Amami-Ohshima Island. The DNA fragments were amplified from the eDNA extracted from natural water in each river. The numbers of DNA fragments detected were positively correlated with individual counts of fish obtained by visual snorkelling surveys. Our method does not contravene restrictions and facilitates abundance monitoring of this endangered fish species

CHARACTERISTICS OF BED-LEVEL FLUCTUATION BASED ON COLLABORATIVE MONITORING AT MANGROVE FOREST DOWN THE DAM IN OKUKUBI RIVER, OKINAWA

Influence of hydraulic conditions on the bed-level fluctuation of mangrove forest during flood was clarified at the Okukubi River in Okinawa Island, Japan. Bed-level changes were monitored every one month from June 2012 to July 2015 at 18 stations. While non-dimensional shear stress during a flood was estimated by two-dimensional bed deformation analysis. Then relationship between observed bed-level change and non-dimensional shear stress was evaluated from correlation analysis. Bed-level change negatively correlates with non-dimensional shear stress during large flood. While during small flood, bed-level change doesn't correlates with non-dimensional shear stress. These results represent that bed-level fluctuation is occurred at sites where large non-dimensional shear stress is keeping during large floods. This condition can apply to selecting priority site in order to restoration of degraded mangrove forest

Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water

環境DNA分析に基づく新しい系統地理調査 --バケツ一杯の水から魚の地域分化を解明--. 京都大学プレスリリース. 2023-03-08.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 revolutionize phylogeography