Detection of an Enigmatic Plethodontid Salamander Using Environmental DNA

Pierson, Todd W.; McKee, Anna M.; Spear, Stephen F.; Maerz, John C.; Camp, Carlos D.; Glenn, Travis C.

doi:10.1643/ch-14-202

Cited by 20 publications

(19 citation statements)

References 14 publications

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“…These findings may explain why the species was not detected during the numerous amphibian surveys that have been conducted in the Hula area over the last 60 years, all of which applied the commonly used survey methods for amphibians (i.e., direct observations, sampling with hand-held nets and bioacoustic monitoring). Our study demonstrated that in contrast to traditional sampling tools, the eDNA approach is highly effective in detecting the presence of the Hula painted frog, as previous studies have indeed shown in other rare and elusive species (Goldberg et al, 2011;Jerde et al, 2011;Laramie et al, 2015;Olson et al, 2012;Pierson et al, 2016 observations of all amphibian species in spring 2016 compared to spring 2015 (unpublished data). As eDNA is expected to increase during the breeding period due to more frequent visits of adults to the water, as well as to potential male aggression and injuries and the release of gametes into the water (Spear et al, 2015), the noted reduction in eDNA-positive sites of the Hula painted frog in spring 2016 might be a result of a less suitable year for amphibian reproduction in the Hula area due to low rainfall.…”

Section: Discussionsupporting

confidence: 70%

“…These findings may explain why the species was not detected during the numerous amphibian surveys that have been conducted in the Hula area over the last 60 years, all of which applied the commonly used survey methods for amphibians (i.e., direct observations, sampling with hand‐held nets and bioacoustic monitoring). Our study demonstrated that in contrast to traditional sampling tools, the eDNA approach is highly effective in detecting the presence of the Hula painted frog, as previous studies have indeed shown in other rare and elusive species (Goldberg et al., ; Jerde et al., ; Laramie et al., ; Olson et al., ; Pierson et al., ; Pilliod et al., ; Sigsgaard et al., ; Spear et al., ; Thomsen et al., ; Wilcox et al., ). The data even suggest that for this extremely elusive species, eDNA might be the only efficient tool for a reliable detection of the species’ presence.…”

Section: Discussionsupporting

confidence: 68%

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Living quarters of a living fossil—Uncovering the current distribution pattern of the rediscovered Hula painted frog (Latonia nigriventer) using environmental DNA

et al. 2017

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One of the greatest challenges of effective conservation measures is the correct identification of sites where rare and elusive organisms reside. The recently rediscovered Hula painted frog (Latonia nigriventer) has not been seen for many decades and was therefore categorized extinct. Since its rediscovery in 2011, individuals from the critically endangered species have been found, with great effort, only in four restricted sites. We applied the environmental DNA (eDNA) approach to search for new populations of the Hula painted frog in suitable aquatic habitats. We further used the eDNA data to classify the landscape factors associated with the species distribution and to predict its suitable habitats. We sampled 52 aquatic sites in the Hula Valley during the spring of 2015 and 2016 and amplified the samples with a species-specific qPCR assay. DNA of the Hula painted frog was detected in 22 of the sites, all of which clustered within three main areas. A boosting classification model showed that soil type, vegetation cover and the current and former habitats are all key predictors of the frog's current distribution. Intriguingly, the habitat suitability models reveal a high affinity of the species to its long-lost habitat of the historical wetlands. Our findings encourage a series of informed searches for new populations of this threatened frog and provide guidance for future conservation management programmes. In the era of global conservation crisis of amphibians, developing the eDNA approach, a reliable detection method for many critically endangered and elusive amphibians, is of particular importance.

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Section: Discussionsupporting

confidence: 70%

“…These findings may explain why the species was not detected during the numerous amphibian surveys that have been conducted in the Hula area over the last 60 years, all of which applied the commonly used survey methods for amphibians (i.e., direct observations, sampling with hand‐held nets and bioacoustic monitoring). Our study demonstrated that in contrast to traditional sampling tools, the eDNA approach is highly effective in detecting the presence of the Hula painted frog, as previous studies have indeed shown in other rare and elusive species (Goldberg et al., ; Jerde et al., ; Laramie et al., ; Olson et al., ; Pierson et al., ; Pilliod et al., ; Sigsgaard et al., ; Spear et al., ; Thomsen et al., ; Wilcox et al., ). The data even suggest that for this extremely elusive species, eDNA might be the only efficient tool for a reliable detection of the species’ presence.…”

Section: Discussionsupporting

confidence: 68%

Living quarters of a living fossil—Uncovering the current distribution pattern of the rediscovered Hula painted frog (Latonia nigriventer) using environmental DNA

et al. 2017

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“…Inhibition is common in eDNA field studies and is addressed through various protocols. Employing special buffers during extraction (e.g., cetyltrimethylammonium-bromide CTAB), applying clean-up kits (e.g., Zymo One Step), using BSA in PCR reactions, and diluting template for PCR reactions are common ways of minimizing the effect of inhibitory compounds [24,[104][105][106][107]. Common environmental inhibitors include plant secondary compounds such as polysaccharides, pectin, xylan, phenols, and tannins [108,109].…”

Section: Inhibitionmentioning

confidence: 99%

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (Chrysemys picta) eDNA Under Field Conditions

et al. 2019

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Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, and present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have shown mixed results in detecting the presence of these animals under field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored non-avian reptile eDNA quantification by sampling four lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months to detect differences in eDNA using a qPCR assay amplifying the COI gene of the mtDNA genome. Only one sample of the highest-density pond amplified eDNA for a positive detection. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present the “shedding hypothesis”—the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms—as a potential challenge for eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles.

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“…CTAB), applying clean-up kits (e.g. Zymo One Step), using BSA in PCR reactions, and diluting template for PCR reactions are common ways of minimizing the effect of inhibitory compounds [51,100,109,145,146]. Common environmental inhibitors include plant secondary compounds such as polysaccharides, pectin, xylan, phenols and tannins [147,148].…”

Section: Inhibitionmentioning

confidence: 99%

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (<em>Chrysemys picta</em>) eDNA under Field Conditions

Adams¹,

Hoekstra²,

Muell³

et al. 2019

Preprint

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Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, as well as present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have been successful mostly in detecting the presence of these animals in field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored this matter by sampling lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months, attempting to detect differences in eDNA accumulation using a qPCR assay. Only one sample of the highest density pond readily amplified eDNA. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present a “shedding hypothesis”–the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms–as a potential challenge for turtle eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles.

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Detection of an Enigmatic Plethodontid Salamander Using Environmental DNA

Cited by 20 publications

References 14 publications

Living quarters of a living fossil—Uncovering the current distribution pattern of the rediscovered Hula painted frog (Latonia nigriventer) using environmental DNA

Living quarters of a living fossil—Uncovering the current distribution pattern of the rediscovered Hula painted frog (Latonia nigriventer) using environmental DNA

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (Chrysemys picta) eDNA Under Field Conditions

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (<em>Chrysemys picta</em>) eDNA under Field Conditions

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