Environmental <scp>DNA</scp> phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water

Tsuji, Satsuki; Shibata, Naoki; Inui, Ryutei; Nakao, Ryohei; Akamatsu, Yoshihisa; Watanabe, Katsutoshi

doi:10.1111/1755-0998.13772

Cited by 9 publications

(18 citation statements)

References 107 publications

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“…Moreover, DNA retrieved from environmental or community samples could represent a better alternative than traditional sampling in the case of particularly abundant and diverse populations, for which getting a representative sample of individuals would be very time consuming and costly. It could also be particularly useful for particular fields where only presence-absence data are required such as phylogeography, as shown by Pedersen et al (2021) or Tsuji et al (2023). To date, the effect of quantification biases on population genetics metrics is a rather speculative field with little empirical testing.…”

Section: Issue # 2: Correl Ati On B E T Ween Obs Erved and True Allel...mentioning

confidence: 99%

Opportunities and inherent limits of using environmental DNA for population genetics

Couton,

Viard,

Altermatt

2023

Environmental DNA

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Molecular techniques using DNA retrieved from community or environmental samples, in particular environmental DNA (eDNA), are becoming increasingly popular for detecting individual species, assessing biodiversity, and quantifying ecological indices. More recently, eDNA has also been proposed as a template for population genetics, and several studies have already tested the feasibility of this approach, mostly looking at vertebrate species. Their results along with general opportunities offered by these types of “community‐based” samples, such as the possibility to target multiple species at the same time, have generated great enthusiasm and expectations for using eDNA in population genetics. However, not every aspect of population genetics can be addressed by eDNA‐based data and some inherent limitations may challenge its conclusions. Here, we firstly review the state of current knowledge of DNA retrieved from environmental and community samples for population genetics. Then, focusing on eDNA, we summarize the opportunities but also detail four main limitations of its use for population‐level inferences, namely, (1) the difficulty to retrieve a species‐specific dataset, (2) the potential lack of correlation between observed and true allelic frequencies, (3) the loss of individual information in multi‐locus genotyping and linkage between loci, and (4) the uncertainty about the individuals contributing to the sampled DNA pool (e.g., number, life‐stage, or sex). Some of these limitations might be overcome with the development of new technologies or models that account for the specificities of eDNA. Others, however, are inherent, and their effect on the inferences must be thoroughly evaluated. The possibility of gaining insights into genetic diversity and population structure from DNA retrieved from community and environmental samples is appealing for scientists, conservation managers, and other practitioners. Yet, to avoid false expectations and incorrect inferences, it is imperative that these limitations are known and considered alongside the opportunities and advantages.

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Section: Issue # 2: Correl Ati On B E T Ween Obs Erved and True Allel...mentioning

confidence: 99%

Opportunities and inherent limits of using environmental DNA for population genetics

Couton,

Viard,

Altermatt

2023

Environmental DNA

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“…Environmental DNA (eDNA) technique has been widely employed for species detection (Ficetola et al., 2008), the creation of species catalogs for specific sites (Klymus et al., 2017; Miya et al., 2015), and analysis of intraspecific genetic diversity (Andres et al., 2023; Sigsgaard et al., 2016; Tsuji et al., 2023). Due to its non‐invasive nature and lack of requirement for expert species identification, the eDNA technique has been gaining momentum as a standard in ecological monitoring.…”

Section: Introductionmentioning

confidence: 99%

“…

Environmental DNA (eDNA) technique has been widely employed for species detection (Ficetola et al, 2008), the creation of species catalogs for specific sites (Klymus et al, 2017;Miya et al, 2015), and analysis of intraspecific genetic diversity (Andres et al, 2023;Sigsgaard et al, 2016;Tsuji et al, 2023). Due to its non-invasive nature and lack of requirement for expert species identification, the eDNA technique has been gaining momentum as a standard in ecological monitoring.Recently, environmental RNA (eRNA) has also begun to attract attention for its potential utility as well as eDNA (Cristescu, 2019).As eRNA is less stable than eDNA (Jo et al, 2022;Kagzi et al, 2022), eRNA can reduce false positives associated with detecting dead organisms, thereby providing a real-time 'snapshot' of a living species (Giroux

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mentioning

confidence: 99%

Relative gene expression analysis of catalase in environmental RNA from Japanese medaka exposed to toxic chemicals

Hiki,

Watanabe,

Yamamoto

2024

Environmental DNA

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Environmental RNA (eRNA) has the potential as a non‐invasive tool for assessing the physiological status of macro‐organisms, yet the quantitative method for relative gene expression analysis is still underexplored. To bridge this gap, this study introduces a relative quantification method for eRNA, employing quantitative PCR (qPCR) to evaluate the expression of the antioxidant gene, catalase (cat), in the Japanese medaka Oryzias latipes exposed to two toxic chemicals for 96 h: chlorpyrifos (CPS) and carbamazepine. Our results showed that, in eRNA, genes frequently used as a reference for tissue or cells in conventional expression analysis correlated with each other. Also, one of them (elfa) exhibited less variability, showing its potential suitability as a reference gene in eRNA analyses. Additionally, cat expression levels in eRNA increased with increasing CPS concentrations, in a concentration‐response manner. These results suggest the promising potential of qPCR applications for eRNA in the monitoring of an organism's health and response to environmental changes. However, we observed disparities in gene expression levels of cat and beta‐actin (actb) between eRNA and whole fish body, indicating eRNA might have a biased origin. Further research is needed to uncover the origin of eRNA and determine the limitations and applicability domain of eRNA analysis.

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“…Thus, the intraspecific phylogeographic pattern of B. toni might provide insights into the palaeogeological and climatic events that have shaped the distribution and diversity of living organisms on the Hokkaido island. Although eDNA analyses have captured large‐scale intraspecific genetic diversity (Tsuji et al., 2023; Weitemier et al., 2021), no studies have addressed the novel histories of freshwater fishes over evolutionary timescales using eDNA till date.…”

Section: Introductionmentioning

confidence: 99%

Environmental DNA unveils deep phylogeographic structure of a freshwater fish

Yatsuyanagi,

Kanbe,

Fujii

et al. 2024

Molecular Ecology

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Phylogeography bears an important part in ecology and evolution. However, current phylogeographic studies are largely constrained by limited numbers of individual samples. Using an environmental DNA (eDNA) assay for phylogeographic analyses, this study provides detailed information regarding the history of Siberian stone loach Barbatula toni, a primary freshwater fish across the whole range of Hokkaido, Japan. Based on an eDNA metabarcoding on 293 river water samples, we detected eDNA from B. toni in 189 rivers. A total of 51 samples, representing the entire island, were then selected from the B. toni eDNA‐positive sample set for the subsequent analyses. To elucidate the phylogeographic structure of B. toni, newly developed eDNA metabarcoding primers (Barba‐cytb‐F/R) were applied to these samples, specifically targeting their haplotypic variation in cytochrome b. After a bioinformatic processing to mitigate haplotypic false positives, a total of 50 eDNA haplotypes were identified. Two regionally restricted, genetically distinct lineages of the species were revealed as a result of phylogeographic analyses on the haplotypes and tissue‐derived DNA from B. toni. According to a molecular clock analysis, they have been genetically isolated for at least 1.5 million years, suggesting their ancient origin and colonisation of Hokkaido, presumably in the glacial periods. These results demonstrate how freshwater fishes can alter their distributions over evolutionary timescales and how eDNA assay can deepen our understanding of phylogeography.

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

Abstract: Since its emergence in 1980s, the field of phylogeography has rapidly developed as an integrative field of science linking micro-and macro-evolutionary processes (

Cited by 9 publications

References 107 publications

Opportunities and inherent limits of using environmental DNA for population genetics

Opportunities and inherent limits of using environmental DNA for population genetics

Relative gene expression analysis of catalase in environmental RNA from Japanese medaka exposed to toxic chemicals

Environmental DNA unveils deep phylogeographic structure of a freshwater fish

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