Plant species identification using fecal DNAs from red-eared slider and Reeves’ pond turtle in agricultural canals for rural ecosystem conservation

Koizumi, Noriyuki; Mori, Akio; Mineta, Takuya; Sawada, Eiji; Watabe, Keiji; Takemura, Tamiko

doi:10.1007/s10333-016-0576-5

Cited by 5 publications

(3 citation statements)

References 17 publications

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“…However, these techniques have several limitations, including the loss of information due to difficulties identifying prey and plant matter present in faeces. To our knowledge, no metabarcoding study exploring the European pond turtle diet have been conducted, and metabarcoding studies of reptile diets are scarce (Brown et al., 2012; Kartzinel & Pringle, 2015; Koizumi et al., 2017).…”

Section: Methodsmentioning

confidence: 99%

“…HTS has been used to assess the diet composition of a wide taxonomic range of animals. Animals whose diets have been successfully investigated have included mammals (Buglione et al., 2018; De Barba et al., 2014; Esnaola et al., 2018; Robeson et al., 2017), birds (Crisol‐Martinìez et al., 2016; Han & Oh, 2018), reptiles (Caut et al., 2019; Kartzinel & Pringle, 2015; Koizumi et al., 2017), fish (Barbato et al., 2019; Harms‐Tuohy et al., 2016; Riccioni et al., 2018) and arthropods (Kamenova et al., 2018; Kennedy et al., 2020; Krehenwinkel et al., 2016). For most species, faecal samples, in contrast to stomach contents, can easily be obtained, with a minimal level of interaction and harm inflicted on the studied animal.…”

Section: Introductionmentioning

confidence: 99%

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A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758)

Ducotterd

Crovadore

Lefort

et al. 2020

Molecular Ecology Resources

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High‐throughput sequencing has become an accurate method for the identification of species present in soil, water, faeces, gut or stomach contents. However, information at the species level is limited due to the choice of short barcodes and based on the idea that DNA is too degraded to allow longer sequences to be amplified. We have therefore developed a long DNA metabarcoding method based on the sequencing of short reads followed by de novo assembly, which can precisely identify the taxonomic groups of organisms associated with complex diets, such as omnivorous individuals. The procedure includes 11 different primer pairs targeting the COI gene, the large subunit of the ribulose‐1,5‐bisphosphate carboxylase gene, the maturase K gene, the 28S rRNA and the trnL‐trnF chloroplastic region. We validated this approach using 32 faeces samples from an omnivorous reptile, the European pond turtle (Emys orbicularis, L. 1758). This metabarcoding approach was assessed using controlled experiments including mock communities and faecal samples from captive feeding trials. The method allowed us to accurately identify prey DNA present in the diet of the European pond turtles to the species level in most of the cases (82.4%), based on the amplicon lengths of multiple markers (168–1,379 bp, average 546 bp), and produced by de novo assembly. The proposed approach can be adapted to analyse various diets, in numerous conservation and ecological applications. It is consequently appropriate for detecting fine dietary variations among individuals, populations and species as well as for the identification of rare food items.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758)

Ducotterd

Crovadore

Lefort

et al. 2020

Molecular Ecology Resources

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“…Identification and control of introduction pathways, control and eradication of established invasive nonnative species. (Berry et al, 2020); (Koizumi et al, 2016); (Koizumi et al, 2017) Safeguard and restore freshwater connectivity System-scale infrastructure planning, dam reoperation and removal, levee repositioning, passes. Pitt et al (2021); (Ghaffari et al, 2014); (Ihlow et al, 2014); (Tucker et al, 2012); (Gaillard et al, 2015); (Ward et al, 2013)…”

Section: Prevent and Control Nonnative Species Invasions In Freshwater Habitatsmentioning

confidence: 99%

Impacts of dams on freshwater turtles: a global review to identify conservation solutions

Bárcenas-García

Michalski

Morgan

et al. 2021

Preprint

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Dams create many impacts on freshwater ecosystems and biodiversity. Freshwater turtles are at direct and indirect risk due to changes caused by damming including the loss of terrestrial and aquatic nesting and feeding habitats, changes to resource availability and reduced dispersal. We reviewed the global scientific literature that evaluated the impact of dams on freshwater turtles, and carried out additional searches of literature published in seventeen languages for studies evaluating actions to mitigate the impact of dams. The search produced 43 published articles documenting dam impacts on 29 freshwater turtle species from seven families (Chelidae, Chelydridae, Emydidae, Geoemydidae, Kinosternidae, Podocnemididae and Trionychidae) in 13 countries. More than a third of studies (41.9%, n = 18) focused on nine North American species of the Emydidae. Few studies were found from Europe and Asia and none from Africa. The number of studies, life-history stage studied and threat status differed significantly between temperate and tropical latitudes. Most studies were from temperate latitudes, where studies focused more on adults and less threatened species compared with tropical latitudes. Studies evaluated dam impacts as barriers and changes to water flow and quality, but no studies were found that assessed turtles and changes to land cover or mercury caused by dams. More than half of the studies (59%, n = 24) suggested actions to help mitigate dam impacts. Yet, only four studies on three temperate and one tropical species documented the effect of interventions (dam removal, flow management, artificial pond maintenance and community-based action). These findings demonstrate a lack of documented evidence evaluating dam impacts on freshwater turtles particularly in tropical regions. This lack of evidence reinforces the importance of strengthening and maintaining robust long-term studies of freshwater turtles needed to develop effective conservation actions for this group of vertebrates.

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The feeding behaviour of the European pond turtle (Emys orbicularis, L. 1758) is not a threat for other endangered species

Ducotterd

Crovadore

Lefort

et al. 2020

Global Ecology and Conservation

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Plant species identification using fecal DNAs from red-eared slider and Reeves’ pond turtle in agricultural canals for rural ecosystem conservation

Cited by 5 publications

References 17 publications

A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758)

A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758)

Impacts of dams on freshwater turtles: a global review to identify conservation solutions

The feeding behaviour of the European pond turtle (Emys orbicularis, L. 1758) is not a threat for other endangered species

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