DNA metabarcoding reveals introduced species predominate in the diet of a threatened endemic omnivore, Telfair’s skink (Leiolopisma telfairii)

Abstract

Introduced species can exert disproportionately negative effects on island ecosystems, but their potential role as food for native consumers is poorly studied. Telfair's skinks are endemic omnivores living on Round Island, Mauritius, a globally significant site of biodiversity conservation. We aimed to determine the dietary diversity and key trophic interactions of Telfair's skinks, whether introduced species are frequently consumed, and if diet composition changes seasonally between male and female skinks. We used DNA metabarcoding of skink fecal samples to identify animals (COI) and plants (ITS2) consumed by skinks. There were 389 dietary presence counts belonging to 77 dietary taxa found across the 73 Telfair's skink fecal samples. Introduced taxa were cumulatively consumed more frequently than other categories, accounting for 49.4% of all detections, compared to cryptogenic (20.6%), native (20.6%), and endemic taxa (9.5%). The most frequently consumed introduced species was the ant, Pheidole megacephala, present in 40% of samples. Blue latan palm, Latania loddigesii, was the most frequently consumed endemic species, present in 33% of samples but was only detected in the dry season, when fruits are produced. We found a strong seasonal difference in diet composition explained by the presence of certain plant species solely or primarily in one season and a marked increase in the consumption of animal prey in the dry season. Male and female skinks consumed several taxa at different frequencies. These results present a valuable perspective on the role of introduced species in the trophic network of their invaded ecosystem. Both native and introduced species provide nutritional resources for skinks, and this may have management implications in the context of species conservation and island restoration.

Using DNA metabarcoding to explore spatial variation in diet across European Hawfinch populations

“…This study provides the first detailed insight into the diet of mainland European Hawfinch populations, and further strengthens the use of high-throughput sequencing in utilizing metabarcoding to infer omnivorous dietary information (Robeson et al 2018, da Silva et al 2020, Tercel et al 2022. This study also shows that identifying the drivers of dietary differentiation within and between populations is important in our understanding of how species adjust to fluctuating environmental conditions.…”

“…To estimate sampling completeness of Hawfinch diet, we used calculated Hill number coverage-based sampling curves of the three most commonly used species diversity measures; species richness (Hill-richness), Shannon's entropy (Hill-Shannon), and Simpson's index (Hill-Simpson) for each country (Denmark and Germany). Hill-richness is the most sensitive to rare species, while Hill-Shannon can respond to both high and very low rarity values, with Hill-Simpson most sensitive to differences in low rarity values (the relative abundance of common species; Roswell et al 2021, Tercel et al 2022. For all diversity estimates, 95% confidence intervals were plotted (Chao and Jost 2012).…”

The predator problem and PCR primers in molecular dietary analysis: Swamped or silenced; depth or breadth?

“…There are some circumstances that may modify these relationships, notably different sample types or predator physiologies (Figure 1). The predator DNA present in faecal samples, often used in dietary metabarcoding (Kaunisto, Roslin, Sääksjärvi, & Vesterinen, 2017;Pompanon et al, 2012;Rytkönen et al, 2019;Tercel et al, 2022), may be more degraded than that of gut contents of whole-body extracts, but prey DNA is also likely to be more degraded.…”

“…The choice of either attempting to silence or potentially being swamped by predator DNA is an insidious one given the financial, practical and experimental implications. The increased adoption of multiprimer (often multimarker, i.e., across multiple genes) metabarcoding (e.g., Batuecas et al, 2022; Cuff, Tercel, et al, 2022; da Silva et al, 2019, 2020; Stenhouse et al, 2021; Tercel et al, 2022) offers the option of using both approaches in synergy, but is by no means a panacea. Multimarker metabarcoding has been more generally suggested as a means of overcoming the issues associated with PCR primer bias (Browett et al, 2021; Cuff, Windsor, et al, 2022; da Silva et al, 2019).…”

“…The amplification of consumer DNA is most relevant to dietary analyses of predatory animals, and specifically in studies for which the PCR primers used amplify a sufficiently broad taxonomic range, consequently amplifying DNA of both the predator and its prey (e.g., reptiles feeding on both vertebrates and invertebrates; Tercel et al, 2022 ; bats feeding on a broad range of insects; Tournayre et al, 2020 ; spiders predating invertebrates including other spiders; Cuff, Tercel, et al, 2022 ). Other instances may be affected by this problem, such as metabarcoding‐based assessment of parasitism (Miller et al, 2021 ), filter‐feeding (Siegenthaler et al, 2018 ) or use of invertebrate‐aggregated DNA for biodiversity surveys (“iDNA”; Cutajar & Rowley, 2020 ; Drinkwater et al, 2021 ).…”