Establishing Silphids in the invertebrate DNA toolbox: a proof of concept

Abstract

Environmental DNA (eDNA) analyses are an increasingly popular tool for assessing biodiversity. eDNA sampling that uses invertebrates, or invertebrate DNA (iDNA), has become a more common method in mammal biodiversity studies where biodiversity is assessed via diet analysis of different coprophagous or hematophagous invertebrates. The carrion feeding family of beetles (Silphidae: Coleoptera, Latreille (1807)), have not yet been established as a viable iDNA source in primary scientific literature, yet could be useful indicators for tracking biodiversity in forested ecosystems. Silphids find carcasses of varying size for both food and reproduction, with some species having host preference for small mammals; therefore, iDNA Silphid studies could potentially target small mammal communities. To establish the first valid use of iDNA methods to detect Silphid diets, we conducted a study with the objective of testing the validity of iDNA methods applied to Silphids using both Sanger sequencing and high throughput Illumina sequencing. Beetles were collected using inexpensive pitfall traps in Alberta, Michigan in 2019 and 2022. We successfully sequenced diet DNA and environmental DNA from externally swabbed Silphid samples and diet DNA from gut dissections, confirming their potential as an iDNA tool in mammalian studies. Our results demonstrate the usefulness of Silphids for iDNA research where we detected species from the genera Anaxyrus, Blarina, Procyon, Condylura, Peromyscus, Canis, and Bos. Our results highlight the potential for Silphid iDNA to be used in future wildlife surveys.

Keywords: Biodiversity surveys; Carrion; Invertebrate-derived DNA; Pitfall trapping; Silphidae; Staphylinoidea.

Figure 1. Model for pitfall trap using a cone and platform configuration of plastic mesh to separate Silphid beetles from bait attractant.

Figure made by Katherine Higdon and Hunter Higdon.

Figure 2. Comprehensive workflow of methods to conduct the iDNA study in its entirety from the field to the lab and ending with the bioinformatic pipeline to be followed.

Conceptualization by Katherine Higdon and Melanie Ottino. All photos and drawings contained within created by Katherine Higdon.

Figure 3. Percent of target diet OTU identity per individual sample across replicates from Illumina sequencing data in 2022.

Identified to genus in all cases except for Cyprinidae and Salamandroidea which are identified to family. All figures and drawings created within by Katherine Higdon and Hunter Higdon.