title: A novel environmental DNA approach to quantify the cryptic invasion of non-native genotypes.
abstract: The invasion of non-native species that are closely related to native species can lead to competitive elimination of the native species and/or genomic extinction through hybridization. Such invasions often become serious before they are detected, posing unprecedented threats to biodiversity. A Japanese native strain of common carp (Cyprinus carpio) has become endangered owing to the invasion of non-native strains introduced from the Eurasian continent. Here, we propose a rapid environmental DNA-based approach to quantitatively monitor the invasion of non-native genotypes. Using this system, we developed a method to quantify the relative proportion of native and non-native DNA based on a single-nucleotide polymorphism using cycling probe technology in real-time PCR. The efficiency of this method was confirmed in aquarium experiments, where the quantified proportion of native and non-native DNA in the water was well correlated to the biomass ratio of native and non-native genotypes. This method provided quantitative estimates for the proportion of native and non-native DNA in natural rivers and reservoirs, which allowed us to estimate the degree of invasion of non-native genotypes without catching and analysing individual fish. Our approach would dramatically facilitate the process of quantitatively monitoring the invasion of non-native conspecifics in aquatic ecosystems, thus revealing a promising method for risk assessment and management in biodiversity conservation.
authors: Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, 584-8540, Japan.|Institute for Sustainable Sciences and Development, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8530, Japan.
authors: Kimiko
authors: http://orcid.org/0000-0002-1375-3875
authors: K
authors: Uchii
authors: Institute for Sustainable Sciences and Development, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8530, Japan.|Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, 650-0047, Japan.
authors: Hideyuki
authors: H
authors: Doi
authors: Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe, 657-8501, Japan.
authors: Toshifumi
authors: T
authors: Minamoto
mesh_terms: D058448:Biota; D004247:DNA / Q000032:analysis* / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification; D005838:Genotype; D006801:Humans; D058865:Introduced Species; D007564:Japan; D056186:Metagenomics / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water; D004247:DNA
keywords: SNP; common carp; cryptic invasion; cycling probe technology; environmental DNA; invasive species