MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

Miya, Masaki; Sato, Yukuto; Fukunaga, Tsukasa; Sadõ, Tetsuya; Poulsen, Jan Yde; Sato, Keiichi; Minamoto, Toshifumi; Yamamoto, Satoshi; Yamanaka, Hiroki; Araki, Hideki; Kondo, Michio; Iwasaki, Wataru

doi:10.1098/rsos.150088

Cited by 905 publications

(1,156 citation statements)

References 49 publications

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“…2014; Miya et al . 2015). The ocean imposes an additional set of physical and chemical constraints affecting eDNA distribution and detection probability; currents, tides, wind and salinity all impact eDNA degradation rates and persistence in seawater (Thomsen et al .…”

Section: Introductionmentioning

confidence: 99%

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

et al. 2015

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Preserving biodiversity is a global challenge requiring data on species’ distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species’ distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource‐intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by significant unknowns surrounding error rates of detection and relevant spatial resolution of eDNA surveys. Here, we report the results of a 2.5 km eDNA transect surveying the vertebrate fauna present along a gradation of diverse marine habitats associated with a kelp forest ecosystem. Using PCR primers that target the mitochondrial 12S rRNA gene of marine fishes and mammals, we generated eDNA sequence data and compared it to simultaneous visual dive surveys. We find spatial concordance between individual species’ eDNA and visual survey trends, and that eDNA is able to distinguish vertebrate community assemblages from habitats separated by as little as ~60 m. eDNA reliably detected vertebrates with low false‐negative error rates (1/12 taxa) when compared to the surveys, and revealed cryptic species known to occupy the habitats but overlooked by visual methods. This study also presents an explicit accounting of false negatives and positives in metabarcoding data, which illustrate the influence of gene marker selection, replication, contamination, biases impacting eDNA count data and ecology of target species on eDNA detection rates in an open ecosystem.

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Section: Introductionmentioning

confidence: 99%

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

et al. 2015

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“…We designed our primers by modifying previously developed MiFish/MiMammal primers [1,9], which corresponded to regions in the mitochondrial 12S rRNA gene (insert length = ca. 171 bp), and we named our primers MiBird-U ( U indicates universal ).…”

Section: A Primer Designmentioning

confidence: 99%

“…Environmental DNA (eDNA) is genetic material that persists in an environment and is derived from organisms living there, and researchers have recently been using eDNA to detect the presence of macro-organisms, including those living in aquatic/semiaquatic ecosystems [1][2][3][4][5]. For example, several fish species inhabiting a river can be detected by amplifying and sequencing DNA fragments extracted from water samples [6] by using methodologies such as quantitative PCR and eDNA metabarcoding.…”

Section: Introductionmentioning

confidence: 99%

“…To this end, we modified a previously reported universal primer set for fish/mammals, (MiFish/MiMammal [1,9]) such that the primer set accommodated bird-specific variations, and conducted avian eDNA metabarcoding. During the primer design, we did not try to eliminate the capability of detecting mammalian species, because simultaneous detection of mammals along with birds may be advantageous, especially for ecologists who are interested in co-occurrence patterns and potential interactions among various animal species.…”

Section: Introductionmentioning

confidence: 99%

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Demonstration of the potential of environmental DNA as a tool for the detection of avian species

Ushio

Murata

Sadõ

et al. 2017

Preprint

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Birds play unique functional roles in the maintenance of ecosystems, such as pollination and seed dispersal, and thus monitoring bird communities (e.g., monitoring bird species diversity) is a first step towards avoiding undesirable consequences of anthropogenic impacts on bird communities. In the present study, we hypothesized that birds, regardless of their main habitats, must have frequent contact with water and that tissues that contain their DNA that persists in the environment (environmental DNA; eDNA) could be used to detect the presence of avian species. To this end, we applied a set of universal PCR primers (MiBird, a modified version of fish/mammal universal primers) for metabarcoding avian eDNA. We confirmed the versatility of MiBird primers by performing in silico analyses and by amplifying DNAs extracted from bird tissues. Analyses of water samples from zoo cages of birds with known species composition suggested that the use of MiBird primers combined with the Illumina MiSeq platform could successfully detect avian species from water samples. Additionally, analysis of water samples collected from a natural pond detected five avian species common to the sampling areas. The present findings suggest that avian eDNA metabarcoding would be a complementary detection/identification tool in cases where visual detection and identification of bird species is difficult.

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“…* Positions corresponding with those of AP012526 (Miya et al 2015). ** Nucleotide sites with non-synonymous substitutions.…”

Section: G a C G G G C G G G T A A T G C A G Hap02 T G A C G G A C Gmentioning

confidence: 99%

Natural habitats uncovered? – Genetic structure of known and newly found localities of the endangered bitterling Pseudorhodeus tanago (Cyprinidae)

Saitoh¹,

Suzuki²,

Ozaki³

et al. 2017

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Overuse of natural resources by humans is a major threat to biodiversity. Overuse often involves species of economic or esthetic value, and fish are a typical example for a group that is exploited both for economic reasons (for human consumption) and for esthetic reasons (e.g. by aquarists). Pseudorhodeus tanago (Tanaka, 1909) (formerly known as Tanakia tanago) is a small colorful but legally protected (fishing, keeping and transfer are banned) bitterling fish distributed around Tokyo, Japan. Whereas it is critically endangered and more and more habitat loss has occurred, at least four stocks have been newly found during the last decade. To explore whether emergence of these newly found habitats is a consequence of incomplete survey, we genotyped mitochondrial cytochrome b sequence of P. tanago from 17 localities and an illegal home aquarium. Populations known by the past extensive survey (13 localities) showed geographically structured population genetic characteristics. Population-specific haplotypes were common indicating past divergence and bottleneck events. Four (north, {center + west}, south_1, south_2) or five RESEARCH ARTICLE Launched to accelerate biodiversity conservation A peer-reviewed open-access journalKenji Saitoh et al. / Nature Conservation 17: 19-33 (2017) 20 (north, center, west, south_1, south_2) geographic groups were detectable as for these known localities. On the other hand, newly found stocks were polymorphic and showed identical haplotypes from distant known localities. If we assume historical basis of distribution and genetic characteristics of these newly found stocks, it must be a series of unlikely geological events and haplotype sorting. We discuss potential issues posed by these questionable stocks.

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MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

Cited by 905 publications

References 49 publications

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

Demonstration of the potential of environmental DNA as a tool for the detection of avian species

Natural habitats uncovered? – Genetic structure of known and newly found localities of the endangered bitterling Pseudorhodeus tanago (Cyprinidae)

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