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

Abstract

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.

Modelling technical and biological biases in macroinvertebrate community assessment from bulk preservative using multiple metabarcoding markers

“…Databases for each marker consisted of sequences that met the following criteria: (a) they corresponded to the target amplicon region; (b) they contained the anticipated primer binding sites; and (c) they extended beyond primer binding sites. Criteria (a) and (b) were implemented to reduce bias in results, since running an in silico PCR without first confirming that all sequences correspond to the target amplicon region can produce false negatives (as noted by Egeter et al., 2019 ). The purpose of requirement (c) was to avoid having sequences that may not have had primers removed prior to being made public, which is a known issue with public barcoding sequences (Elbrecht & Leese, 2017a ).…”

“…silico PCR without first confirming that all sequences correspond to the target amplicon region can produce false negatives (as noted by Egeter et al, 2019). The purpose of requirement (c) was to avoid having sequences that may not have had primers removed prior to being made public, which is a known issue with public barcoding sequences (Elbrecht & Leese, 2017a).…”

Identification of novel bacterial biomarkers to detect bird scavenging by invasive rats

“…Molecular diet analysis of fecal material is gaining traction among molecular ecologists as a noninvasive method to study diet and trophic interactions, particularly for invasive species (Egeter et al., 2019; Zarzoso‐Lacoste et al., 2016). However, molecular techniques in diet analysis are not without issue, and some ambiguity can exist such as repeatability in food item detection (Forin‐Wiart et al., 2018) and PCR bias (Nichols et al., 2018).…”

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

“…Previous assessments of the impact of invasive rats Rattus rattus on endemic amphibians in New Zealand relied on abundance estimates of native frog species in comparison with arrival patterns of the invasive rat (Egeter et al ). Inconsistencies between observers caused doubt, but DNA metabarcoding clarified the rat's consumption of New Zealand's native frog species and its contribution to the population declines (Egeter et al ). The sensitivity achieved from next‐generation sequencing methods allows multiple prey items to be identified to the species level and generates a comprehensive account of multiple animals' resource use and overlap.…”