Environmental DNA detection of the giant freshwater crayfish (<i>Astacopsis gouldi</i>)

Trujillo‐González, Alejandro; Hinlo, Rheyda; Godwin, Sam; Barmuta, Leon A.; Watson, Anne; Turner, Perpetua A. M.; Koch, Amy; Gleeson, Dianne

doi:10.1002/edn3.204

Cited by 3 publications

(3 citation statements)

References 36 publications

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“…This also applies to the aquarium pet trade, where poaching may threaten natural populations of crayfish (Faulkes, 2015). DNA barcoding with species‐specific COI primers has been used to detect rare crayfishes via eDNA (e.g., Cowart et al., 2018; Trujillo‐Gonzalez et al., 2021). While this is likely to continue being reliable for species detection, provided primer design was done with adequate reference sequences, we urge caution when using “universal” invertebrate COI primers such as those used in metabarcoding studies (e.g., Drake et al., 2023).…”

Section: Discussionmentioning

confidence: 99%

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DNA barcoding is currently unreliable for species identification in most crayfishes

Allison,

Pickich,

Barnett

et al. 2024

Ecology and Evolution

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DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (NH) per species, and another that focused on total number of sequences (NS; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the NH and NS datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the NH dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial‐based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species‐level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.

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Section: Discussionmentioning

confidence: 99%

“…This also applies to the aquarium pet trade, where poaching may threaten natural populations of crayfish (Faulkes, 2015). DNA barcoding with species-specific COI primers has been used to detect rare crayfishes via eDNA (e.g., Cowart et al, 2018;Trujillo-Gonzalez et al, 2021).…”

Section: Local Barcoding Gapsmentioning

confidence: 99%

DNA barcoding is currently unreliable for species identification in most crayfishes

Allison,

Pickich,

Barnett

et al. 2024

Ecology and Evolution

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“…These approaches often involve scat surveys, hair snare traps, gathering imagery from camera traps or call broadcast (Long et al., 2007; Thomas et al., 2020). Innovative technologies to monitor elusive fauna, such as eDNA sampling or drone‐assisted thermal imaging, are also important emerging methods to study elusive species (Cristescu et al., 2021; Karp, 2020; Neice & Mcrae, 2021; Trujillo‐Gonzalez et al., 2021; Witt et al., 2020). However, regardless of the methods used, if elusive species are also rare, the encounter frequency for indirect survey methods can be so low that it can be difficult to know whether failure to find traces is due to absence (i.e.…”

Section: Introductionmentioning

confidence: 99%

Detection dogs can help researchers with elusive forest owl conservation

Gill,

Cristescu,

Cisterne

et al. 2024

Austral Ecology

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Elusive fauna are often studied indirectly, via traces they leave behind, or via other non‐invasive survey methods. Critically endangered Tasmanian masked owls are both rare and elusive, which hampers conservation efforts. Spotlighting and call playback often have low success rates in accurately determining the presence/absence of Tasmanian masked owls. Using indirect survey techniques for traces such as owl pellets can be more efficient and provide a more reliable source of detailed data regarding presence/absence, diet, health, population structure and environmental contaminants. However, pellets can be difficult for researchers to find in the field. We evaluate whether detection dogs are effective in finding owl pellets in two steps: an experimental trial comparing the performance of a dog team to that of an ecologist with significant field experience with masked owls; and in a pilot field study where the dog team searched potential owl habitat in Tasmanian forests. During the experimental trials, the dog team significantly outperformed the ecologist. The dog team was more sensitive, finding 89% versus 40% of pellets present for the ecologist, and took half as long to search an equivalent‐sized search area. The combined efficiency of the dog team was 4.5 times greater than that of an ecologist working alone. During the pilot study, in searching areas of potential masked owl habitat, no pellets were found. However, when sites were visited where owls were known to have been recently sighted, the dog team were able to find large numbers of owl pellets suitable for collection and potential data extraction. Our trials suggest that dogs can find owl pellets with considerably greater sensitivity and efficiency than ecologists working alone and that they would be best used in combination with targeted surveys, especially when the detection and subsequent collection of as many pellets as possible is desirable for DNA extraction or other analysis.

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Testing multiple environmental DNA substrates for detection of the cryptic and Critically Endangered burrowing freshwater crayfish Engaewa pseudoreducta

Dawkins,

Nevill,

Chambers

et al. 2024

Environmental DNA

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Effective conservation of endangered species depends on knowledge of their distributions, but species detection can often be challenging. An example of this is provided by the Critically Endangered Margaret River burrowing crayfish (Engaewa pseudoreducta), which is highly cryptic. Due to the burrowing habit of this crayfish, detection of this species currently requires a great deal of effort, the results are often non‐conclusive, and, as it involves manual excavation of their burrows, the habitat of this and other species is destroyed in the detection process. In response to these challenges, this study developed and optimized a species‐specific probe‐based qPCR assay targeting the 16S gene region to detect the target species from environmental samples. Three test substrates—chimney pellets (soil expelled by a crayfish as it digs its burrow), burrow scrapes (soil lining the inside of a burrow), and burrow water (water that is filling the burrow space)—were tested from 11 crayfish burrows thought to have been constructed by the target species to see if eDNA could be detected. DNA from the target species was successfully amplified from both chimney pellets (6/11 samples) and burrow scrapes (3/11 samples); however, E. pseudoreducta was not detected in any water samples. As previously stated, sampling techniques to confirm the presence of this species have relied on burrow excavation (resulting in habitat destruction) and were often not definitive; therefore, replacing the traditional survey method with a noninvasive eDNA‐based technique could be of enormous benefit to the management and conservation of this (and similar) species.

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Environmental DNA detection of the giant freshwater crayfish (Astacopsis gouldi)

Abstract: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Cited by 3 publications

References 36 publications

DNA barcoding is currently unreliable for species identification in most crayfishes

DNA barcoding is currently unreliable for species identification in most crayfishes

Detection dogs can help researchers with elusive forest owl conservation

Testing multiple environmental DNA substrates for detection of the cryptic and Critically Endangered burrowing freshwater crayfish Engaewa pseudoreducta

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