Detecting frogs as prey in the diets of introduced mammals: a comparison between morphological and <scp>DNA</scp>‐based diet analyses

Egeter, Bastian; Bishop, Phillip J.; Robertson, Bruce C.

doi:10.1111/1755-0998.12309

Cited by 55 publications

(69 citation statements)

References 71 publications

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“…It also confirms the importance of developing a morphological identification tool based on body scales instead of bones to measure skink predation by rodents. DNA-based methods of diet analysis are increasingly popular and may significantly improve prey detection and identification in the rodent diet (Egeter et al 2015;Zarzoso-Lacoste et al 2016). But such methods require access to prey DNA, which is not possible in our context because of the rarity and patrimonial status associated with most Caledonian skink species.…”

Section: Discussionmentioning

confidence: 99%

Invasive rodents, an overlooked threat for skinks in a tropical island hotspot of biodiversity

Thibault¹,

Brescia²,

Jourdan³

et al. 2017

NZ J Ecol

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Squamata are one of the most threatened groups among island vertebrates, facing high pressure from exotic species. However, the contribution of small terrestrial reptiles in invasive rodents' diet remains poorly investigated, partly because of the lack of tools for accurately identifying chewed prey fragments in gut contents. The New Caledonia archipelago (South Pacific) hosts an exceptional terrestrial squamata fauna (105 species, 91.6% endemic) that are faced with many invasive species (rodents, feral cats, feral pigs, ants) and strong human pressures. Our study aimed to evaluate the frequency of occurrence of endemic skink remains by gut content analysis of two species of invasive rodents. Four rodent trapping sessions were implemented at two ultramafic sites and for two distinct habitats (closed canopy forest and open shrubland habitat). A total of 284 rats were trapped from two species (the ship rat Rattus rattus and the Pacific rat R. exulans) over 1200 trap nights. Combined analysis of stomach and caecum contents provided far more information than traditional stomach analysis alone. Analyses showed that 15.9% of rat samples included remains of at least 12 different skink species out of the 23 present. Six species are classified as threatened by the IUCN, the most endangered being Marmorosphax taom (CR) and Kanakysaurus viviparus (EN). This study provides new prospects for the assessment of invasive rodent impacts and new insights into the respective impacts of two sympatric invasive rodent species on native skinks.

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Section: Discussionmentioning

confidence: 99%

Invasive rodents, an overlooked threat for skinks in a tropical island hotspot of biodiversity

Thibault¹,

Brescia²,

Jourdan³

et al. 2017

NZ J Ecol

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“…After morphological analysis, samples were homogenized and DNA was extracted following Egeter, Bishop, and Robertson (), using the Qiagen DNeasy blood and tissue kit (Qiagen). All PCR plates included two positive controls (DNA from Archey's and Hochstetter's frogs) and negative controls (every eighth well).…”

Section: Methodsmentioning

confidence: 99%

“…Aerosol‐resistant pipette tips were used throughout all PCR procedures. As a qualitative assessment of the prevalence of potential false negatives (e.g., Oehm, Juen, Nagiller, Neuhauser, & Traugott, ), where adequate DNA was not extracted or PCR inhibition may have occurred, all stomach samples were subject to PCR using “universal” 12S vertebrate primers (L1091/H1478; Kocher et al, ), using PCR conditions as detailed by Egeter, Bishop et al (). This provided an estimation of the number of samples resulting in amplifiable DNA in general.…”

Section: Methodsmentioning

confidence: 99%

“…Equation 2 assumed that a sample being positive, that is, resulting in sequence(s) matching a frog species, was the result of an ingestion event occurring during the sampling period (i.e., on the night the sample was obtained). We consider that this assumption was likely to hold true due to the following rationale: Archey's frogs are active only between dusk and dawn (Cree, ), and ship rats are also primarily nocturnal (Dowding & Murphy, ; Hooker & Innes, ). Daylight hours during the study periods ranged from 12 to 15.5 hr. Detection probability of frog tissue in ship rat stomach contents using DNA‐based diet analysis under laboratory conditions was previously found to be very low c. 12 hr after ingesting frog tissue (<0.1; Egeter, Bishop et al, ). Furthermore, detection probabilities in the laboratory study were likely to be higher than under field conditions as rats in the laboratory were fed ad libitum, which is known to increase detection probabilities over time (Dodd, ). Therefore, even if a rat ingested frog tissue just before daybreak, but was not caught in a trap until the earliest possible time during the following trapping session (dusk of the same day), frog DNA would not be detected. …”

Section: Methodsmentioning

confidence: 99%

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Using molecular diet analysis to inform invasive species management: A case study of introduced rats consuming endemic New Zealand frogs

Egeter

Roe

Peixoto

et al. 2019

Ecology and Evolution

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The decline of amphibians has been of international concern for more than two decades, and the global spread of introduced fauna is a major factor in this decline. Conservation management decisions to implement control of introduced fauna are often based on diet studies. One of the most common metrics to report in diet studies is Frequency of Occurrence (FO), but this can be difficult to interpret, as it does not include a temporal perspective. Here, we examine the potential for FO data derived from molecular diet analysis to inform invasive species management, using invasive ship rats ( Rattus rattus ) and endemic frogs ( Leiopelma spp.) in New Zealand as a case study. Only two endemic frog species persist on the mainland. One of these, Leiopelma archeyi , is Critically Endangered (IUCN 2017) and ranked as the world's most evolutionarily distinct and globally endangered amphibian (EDGE, 2018). Ship rat stomach contents were collected by kill‐trapping and subjected to three methods of diet analysis (one morphological and two DNA‐based). A new primer pair was developed targeting all anuran species that exhibits good coverage, high taxonomic resolution, and reasonable specificity. Incorporating a temporal parameter allowed us to calculate the minimum number of ingestion events per rat per night, providing a more intuitive metric than the more commonly reported FO. We are not aware of other DNA‐based diet studies that have incorporated a temporal parameter into FO data. The usefulness of such a metric will depend on the study system, in particular the feeding ecology of the predator. Ship rats are consuming both species of native frogs present on mainland New Zealand, and this study provides the first detections of remains of these species in mammalian stomach contents.

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“…However, invasive mammals can have a variable diet between native and introduced ranges (Ballari & Barrios‐García ), making it difficult to predict what they will consume in their introduced range. DNA metabarcoding is a promising method: it allows the identification of multiple dietary components of hundreds of individuals and increases prey detection from 2% using morphological diagnostics to 70% using metabarcoding (Pompanon et al , Egeter et al ).…”

Section: Negative Impactsmentioning

confidence: 99%

Genetic tools in the management of invasive mammals: recent trends and future perspectives

2020

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Invasive non‐native species are now considered to be one of the greatest threats to biodiversity worldwide. Therefore, efficient and cost‐effective management of species invasions requires robust knowledge of their demography, ecology and impacts, and genetic‐based techniques are becoming more widely adopted in acquiring such knowledge. We focus on the use of genetic tools in the applied management of mammalian invasions globally, as well as on their inherent advantages and disadvantages. We cover tools that are used in: 1) detecting and monitoring mammalian invaders; 2) identifying origins and invasive pathways; 3) assessing and quantifying the negative impacts of invaders; and 4) population management and potential eradication of invasive mammals. We highlight changes in sequencing technologies, including how the use of techniques such as Sanger sequencing and microsatellite genotyping, for monitoring and tracing invasive pathways respectively, are now giving way to the use of high‐throughput sequencing methods. These include the emergence of environmental DNA (eDNA) metabarcoding for the early detection of invasive mammals, and single nucleotide polymorphisms or whole genomes to trace the sources of invasive populations. We are now moving towards trials of genome‐editing techniques and gene drives to control or eradicate invasive rodents. Genetic tools can provide vital information that may not be accessible with non‐genetic methods, for the implementation of conservation policies (e.g. early detection using systematic eDNA surveillance, the identification of novel pathogens). However, the lack of clear communication of novel genetic methods and results (including transparency and reproducibility) to relevant stakeholders can be prohibitive in translating these findings to appropriate management actions. Geneticists should engage early with stakeholders to co‐design experiments in relation to management goals for invasive mammals.

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Detecting frogs as prey in the diets of introduced mammals: a comparison between morphological and DNA‐based diet analyses

Cited by 55 publications

References 71 publications

Invasive rodents, an overlooked threat for skinks in a tropical island hotspot of biodiversity

Invasive rodents, an overlooked threat for skinks in a tropical island hotspot of biodiversity

Using molecular diet analysis to inform invasive species management: A case study of introduced rats consuming endemic New Zealand frogs

Genetic tools in the management of invasive mammals: recent trends and future perspectives

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