Species traits and ecosystem characteristics affect species detection by <scp>eDNA</scp> metabarcoding in lake fish communities

Doi, Hideyuki; Matsuoka, Shiro; Matsuzaki, Shin‐ichiro S.; Nagano, Mariko; Sato, Hirotoshi; Yamanaka, Hiroki; Matsuhashi, Saeko; Yamamoto, Satoshi; Minamoto, Toshifumi; Araki, Hideki; Ikeda, Kazuko; Kato, Atsuko; Kumei, Kouichi; Maki, Nobutaka; Mitsuzuka, Takashi; Takahara, Teruhiko; Toki, Kimihito; Ueda, Natsuki; Watanabe, Takeshi; Yamazoe, Kanji; Miya, Masaki

doi:10.1111/fwb.14107

Cited by 4 publications

(3 citation statements)

References 52 publications

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“…There are a number of caveats and limitations when working with eDNA as a range of factors impact the persistence of DNA in the environment, such as species traits (i.e. body size, shape, habitat preference) as well as ecosystem size (Doi et al ., 2023). When using eDNA approaches that target an entire biological community, i.e.…”

Section: Methods For Measuring the Impact Of Disturbance On Native Fr...mentioning

confidence: 99%

An integrative approach to assess the impact of disturbance on native fish in lakes

Thomson‐Laing,

Schallenberg,

Kelly

et al. 2023

Biological Reviews

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Freshwater fish are in a perilous state with more than 30% of species considered critically endangered. Yet significant ecological and methodological complexities constrain our ability to determine how disturbances are impacting native fish communities. We review current methods used to assess the responses of fish communities, especially native fish, to disturbances, with a focus on lakes. These methods include contemporary population surveys, manipulative experimental approaches, paleolimnological approaches and Indigenous Knowledge and social histories. We identify knowledge gaps, such as a lack of baseline data for native fish, an inability to assess the impact of historical disturbances, stressor response dynamics in contemporary multi‐stressor environments, and natural disturbance regimes. Our assessment of the current methods highlights challenges to filling these knowledge gaps using the reviewed methods. We advocate strongly for the implementation of an integrative approach that combines emerging technologies (i.e. molecular‐based techniques in contemporary surveys and paleolimnology) and underutilised knowledge streams (i.e. Indigenous Knowledge and social histories) which should be used in concert with conventional methods. This integrative approach will allow researchers to determine the key drivers of decline and the degree of change, which will enable more informed and successful management actions.

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Section: Methods For Measuring the Impact Of Disturbance On Native Fr...mentioning

confidence: 99%

An integrative approach to assess the impact of disturbance on native fish in lakes

Thomson‐Laing,

Schallenberg,

Kelly

et al. 2023

Biological Reviews

View full text Add to dashboard Cite

show abstract

“…We used an eDNA dataset of sh communities from 18 lakes in Japan as previously reported (Doi et al 2023). Details of the study sites, sampling, sample treatments, and DNA sequencing have been described by Doi et al (2023). Brie y, 18 lakes across Japan were selected as study sites (Fig.…”

Section: Fish Community Datamentioning

confidence: 99%

“…Environmental data on lake morphology as used by Doi et al (2023) were used in the present study. Lake morphology data (surface area [km 2 ], maximum water depth [m], altitude [m], and perimeter [km]) and lake type (trophic status and water type [brackish or freshwater]) were obtained from Tanaka (1992).…”

Section: Environmental Datamentioning

confidence: 99%

Assessing the impact of biological invasion on fish community structures in Japanese lakes: A macroecological approach using environmental DNA metabarcoding

Oba,

Doi

2024

Preprint

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The biological invasion of aquatic ecosystems has negative effects on competition and predation. These ecological impacts on native communities may also affect two processes that are important in determining community structures, namely, the environmental and spatial processes. Here, we using lake fish community composition estimated through environmental DNA metabarcoding, we examined the effects of invasive species on the community structure determination processes in lakes. The objective was to describe the relationship between fish diversity and invasive species in lakes and to estimate the explanatory power of environmental factors with regard to variation in community composition among lakes using direct gradient analysis, i.e., distance-based redundancy analysis. Further, we employed variation partitioning to examine how the explanatory power of environmental factors and spatial structures for variation in community composition varied with the presence of invasive species. The environmental slope analysis showed that the explanatory power of environmental factors for variation in community composition among lakes was higher in communities without invasive species. A comparison of the relative importance of environmental factors and spatial structure in determining community composition between communities, excluding invasive species, and communities with invasive species showed that the relative importance of environmental factors was higher in communities without invasive species, highlighting the possibility of differences in dispersal abilities between native and invasive species.

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From DNA to diagnostics: A case study using macroinvertebrate metabarcoding to assess the effectiveness of restoration measures in a Dutch stream

van der Lee,

Polling,

van der Laan

et al. 2024

Science of The Total Environment

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Species traits and ecosystem characteristics affect species detection by eDNA metabarcoding in lake fish communities

Cited by 4 publications

References 52 publications

An integrative approach to assess the impact of disturbance on native fish in lakes

An integrative approach to assess the impact of disturbance on native fish in lakes

Assessing the impact of biological invasion on fish community structures in Japanese lakes: A macroecological approach using environmental DNA metabarcoding

From DNA to diagnostics: A case study using macroinvertebrate metabarcoding to assess the effectiveness of restoration measures in a Dutch stream

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