Hideyuki Doi

Summary Environmental DNA ( eDNA ) analysis for detecting the presence of aquatic and terrestrial organisms is an established method, and the eDNA concentration of a species can reflect its abundance/biomass at a site. However, attempts to estimate the abundance/biomass of aquatic species using eDNA concentrations in large stream and river ecosystems have received little attention. We determined the eDNA concentration and abundance/biomass of a stream fish, Plecoglossus altivelis , by conducting

An environmental DNA (eDNA) analysis method has been recently developed to estimate the distribution of aquatic animals by quantifying the number of target DNA copies with quantitative real-time PCR (qPCR). A new quantitative PCR technology, droplet digital PCR (ddPCR), partitions PCR reactions into thousands of droplets and detects the amplification in each droplet, thereby allowing direct quantification of target DNA. We evaluated the quantification accuracy of qPCR and ddPCR to estimate speci

Environmental DNA (eDNA) has been used to investigate species distributions in aquatic ecosystems. Most of these studies use real-time polymerase chain reaction (PCR) to detect eDNA in water; however, PCR amplification is often inhibited by the presence of organic and inorganic matter. In droplet digital PCR (ddPCR), the sample is partitioned into thousands of nanoliter droplets, and PCR inhibition may be reduced by the detection of the end-point of PCR amplification in each droplet, independent

The use of environmental DNA (eDNA) methods for community analysis has recently been developed. High-throughput parallel DNA sequencing (HTS), called eDNA metabarcoding, has been increasingly used in eDNA studies to examine multiple species. However, eDNA metabarcoding methodology requires validation based on traditional methods in all natural ecosystems before a reliable method can be established. To date, relatively few studies have performed eDNA metabarcoding of fishes in aquatic environment

ABSTRACT Aim To estimate the potential effect of global climate change on the phenological responses of plants it is necessary to estimate spatial variations at larger scales. However, previous studies have not estimated latitudinal patterns in the phenological response directly. We hypothesized that the phenological response of plants varies with latitude, and estimated the phenological response to long‐term climate change using autumn phenological events that have been delayed by recent climat

Nitrogen and carbon stable isotopic compositions (<i>δ</i>¹⁵N and <i>δ</i>¹³C) of consumers have been used for physiological and food web studies. Previous studies have shown <i>δ</i>¹⁵N and <i>δ</i>¹³C values are affected by several biological and environmental factors during starvation, but the generality of the effect of starvation on <i>δ</i>¹⁵N and <i>δ</i>¹³C values has not yet been tested. Here, we performed a meta-analysis

Abstract Although ecologists have recognized the importance of spatial structure within food webs, this aspect of ecosystems remains difficult to characterize quantitatively. Stable‐isotope techniques have recently been used to provide evidence of spatial structure within aquatic food webs. Here, I review current literature on spatial patterns of autochthonous and allochthonous resources in aquatic food webs in lakes and rivers. Across various habitats and ecosystems, the factors determining the

Environmental DNA (eDNA) metabarcoding is a recently developed method to assess biodiversity based on a high-throughput parallel DNA sequencing applied to DNA present in the ecosystem. Although eDNA metabarcoding enables a rapid assessment of biodiversity, it is prone to species detection errors that may occur at sequential steps in field sampling, laboratory experiments, and bioinformatics. In this study, we illustrate how the error rates in the eDNA metabarcoding-based species detection can be

CR Climate Research Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials CR 36:181-190 (2008) - DOI: https://doi.org/10.3354/cr00741 Heterogeneous intra-annual climatic changes drive different phenological responses at two trophic levels Hideyuki Doi1,4,*, Oscar Gordo2, Izumi Katano3 1School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, Washington 98195, USA 2Departame

The first step toward solving the problems caused by an invasive alien species is to know the distribution of the species. However, species in underwater environments are difficult to investigate. The recent development of environmental DNA (eDNA) analysis has made it possible to investigate the distribution of a target species simply by analyzing the DNA in the water. To date, few investigators have used eDNA detection of aquatic plants. We established an eDNA detection method for Egeria densa,

Abstract Climate change is inducing changes in the phenological timings of organisms. Genetic diversity could influence phenological responses to climate change, but empirical evidence is very limited. We estimated the regional variation across Japan in flowering and leaf budburst dates of plants based on a dataset of phenological timings from 1953 to 2005. The observed plants' genetic diversities varied according to human cultivation. The within‐species variations of phenological response to te

Abstract We conducted experiments to determine isotope changes in the deposit‐feeding chironomid larvae Chironomus acerbiphilus during feeding, starvation and metamorphosis. Isotope changes in chironomid larvae occurred mainly during growth and rarely afterward. This finding indicates that chironomid isotope turnover mainly occurs in conjunction with growth and suggests that chironomid larvae only break down newly assimilated food for energy during periods of no growth. Chironomid δ 13 C values