Questioning the proverb ‘more haste, less speed’: classic versus metabarcoding approaches for the diet study of a remote island endemic gecko

Abstract

Dietary studies can reveal valuable information on how species exploit their habitats and are of particular importance for insular endemics conservation as these species present higher risk of extinction. Reptiles are often neglected in island systems, principally the ones inhabiting remote areas, therefore little is known on their ecological networks. The Selvagens gecko Tarentola (boettgeri) bischoffi, endemic to the remote and integral reserve of Selvagens Archipelago, is classified as Vulnerable by the Portuguese Red Data Book. Little is known about this gecko's ecology and dietary habits, but it is assumed to be exclusively insectivorous. The diet of the continental Tarentola species was already studied using classical methods. Only two studies have used next-generation sequencing (NGS) techniques for this genus thus far, and very few NGS studies have been employed for reptiles in general. Considering the lack of information on its diet and the conservation interest of the Selvagens gecko, we used morphological and DNA metabarcoding approaches to characterize its diet. The traditional method of morphological identification of prey remains in faecal pellets collected over a longer period was compared with metabarcoding of samples collected during rapid surveys. Molecular results revealed that this species is a generalist, feeding on invertebrate, plant and vertebrate items, whereas the morphological approaches were unable to detect the latter two. These results opened up new questions on the ecological role of the Selvagens gecko that deserves to be further explored, such as the possible predation on seabirds, plant services or trophic competition with the sympatric Madeira lizard Teira dugesii. Metabarcoding identified a greater diversity of dietary items at higher taxonomic resolution, but morphological identification enabled calculation of relative abundances and biomasses of ingested arthropods, and detected a dietary shift on invertebrate preys between seasons. Results of this study highlight the global applicability of rapid metabarcoding surveys for understudied taxa on remote islands that are difficult to access. We recommend using the metabarcoding approach, even if 'speedy' sampling only is possible, but we must highlight that disregarding long-term ecological data may lead to 'hasty' conclusion.How to cite this article Gil V, Pinho CJ, Aguiar CAS, Jardim C, Rebelo R, Vasconcelos R. 2020. Questioning the proverb 'more haste, less speed': classic versus metabarcoding approaches for the diet study of a remote island endemic gecko. PeerJ 8:e8084 http://doi.org/10.7717/peerj.8084

Digging in a 120 years-old lunch: What can we learn from collection specimens of extinct species?

“…An alternative explanation for the absence of vertebrates could be due to the small sample size and technical limitations, such as the lack of power of the 12S primers to amplify the highly degraded DNA of our samples. However, these markers have been effectively used to amplify museum samples [ 98 ] and were used in a variety of dietary studies with successful results [ 68 , 99 ]. Moreover, the other markers worked very well on these samples despite being more than 100 years old and possibly poorly preserved for DNA amplification.…”

A review of applications of environmental DNA for reptile conservation and management

“…For example, the trophic niches of many lizard species have not been defined, partly due to challenges in identifying prey taxa in fecal pellets (Pereira et al, 2019 ). DNA metabarcoding of fecal samples can identify prey at a high taxonomic resolution and reveal previously unknown aspects of species diet (Gil et al, 2020 ; Jarman et al, 2013 ; Lopes et al, 2019 ). Using DNA metabarcoding, Pinho et al ( 2018 ) showed that the Endangered giant wall gecko ( Tarentola gigas ) predates one of the world's rarest bird species, the Raso lark ( Alauda razae ) in the Capo Verde Archipelago off the west coast of Africa.…”

“…Not only was predation occurring, the Raso lark was the most frequent vertebrate signature found in the gecko's feces (Lopes et al, 2019 ), creating an interesting conservation dilemma in relation to management of these two threatened species. In another study, Gil et al ( 2020 ) used DNA metabarcoding to show that a gecko previously assumed to be insectivorous, was actually a generalist. This resulted in a greater understanding of its role in the ecological network (Gil et al, 2020 ).…”

“…In another study, Gil et al ( 2020 ) used DNA metabarcoding to show that a gecko previously assumed to be insectivorous, was actually a generalist. This resulted in a greater understanding of its role in the ecological network (Gil et al, 2020 ). Hence DNA metabarcoding, especially when used for dietary analysis, shows great promise for effective identification of trophic niches and reconstruction of food webs (Ficetola et al, 2019 )—aspects of reptile ecology that are often poorly understood.…”

Evaluating the Efficiency of DNA Metabarcoding to Analyze the Diet of Hippocampus guttulatus (Teleostea: Syngnathidae)

“…A recent study based on morphological examination of stomach contents revealed the presence of only a few soft-bodied prey items, such as nematodes [20]. Indeed, traditional diet methods tend to underestimate the frequency of occurrence of prey items with totally digested body parts, such as soft-bodied arthropods [24], while these methods tend to more easily detect hard-bodied groups [25]. Although it has been shown that the prey's DNA is recoverable from seahorse feces [15], there have been no published studies demonstrating the use of highly sensitive and non-invasive molecular techniques to evaluate the entire spectrum of seahorses' dietary items despite the sensitive conservation status.…”