Amplicon metagenomics of dung beetles (Coleoptera, Scarabaeidae, Scarabaeinae) as a proxy for lemur (Primates, Lemuroidea) studies in Madagascar

Abstract

Dung beetles (Scarabaeidae, Scarabaeinae) are among the most cost-effective and informative biodiversity indicator groups, conveying rich information about the status of habitats and faunas of an area. Yet their use for monitoring the mammal species, that are the main providers of the food for the dung beetles, has only recently been recognized. In the present work, we studied the diet of four endemic Madagascan dung beetles (Helictopleurus fissicollis (Fairmaire), H. giganteus (Harold), Nanos agaboides (Boucomont), and Epilissus splendidus Fairmaire) using high-throughput sequencing and amplicon metagenomics. For all beetle species, the ⅔–¾ of reads belonged to humans, suggesting that human feces are the main source of food for the beetles in the examined areas. The second most abundant were the reads of the cattle (Bos taurus Linnaeus). We also found lower but significant number of reads of six lemur species belonging to three genera. Our sampling localities agree well with the known ranges of these lemur species. The amplicon metagenomics method proved a promising tool for the lemur inventories in Madagascar.

Diet shift in giant Madagascan dung beetle Helictopleurus giganteus (Coleoptera: Scarabaeidae: Scarabaeinae) studied by amplicon metagenomics

“…The present results are congruent with those obtained in the previous study (Frolov et al 2023). All samples in the present analysis, regardless of the collecting locality and methods, yielded similar composition of amplicon reads, with almost all reads belonging to human and cow.…”

“…These primers amplify a short (90-95 bp) yet informative region of lrRNA and were designed to be specific for mammals (Taylor 1996). They were successfully used in a few recent works (Drinkwater et al 2021;Ji et al 2022;Frolov et al 2023). NGS libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit, checked with Qubit (high-sensitive reagents) and real-time PCR for quantification, and Bioanalyzer for size distribution detection.…”

“…Short but specific DNA markers can be amplified by standard PCR protocol to limit DNA sequencing to mostly those taxa that are of interest for the researcher, for example, mammals (Kerley et al 2018;Drinkwater et al 2021). The amplicon metagenomic method was shown as a promising tool for the lemur inventories in Madagascar (Frolov et al 2023). However, the trophic associations of different dung beetle species and their food producers are still poorly known.…”

Towards holistic insect monitoring: species discovery, description, identification and traits for all insects

“…This requires that the larvae and adults are first associated via megabarcoding [62]. Even tools that were initially developed only for vertebrate detection via invertebrate derived DNA (iDNA) can now also be used for revealing species interactions between insects and vertebrates [63][64][65][66][67], and plants [68]. The study of iDNA is particularly scalable and cost-effective when applied to insect faeces or regurgitates, as neither substrate requires DNA extraction [69].…”