Home is where the hollow is: Revealing vertebrate tree hollow user biodiversity with eDNA metabarcoding

• Published in: Environmental DNA (Hoboken, N.J.) N.J.), 2022-09, Vol.4 (5), p.1078-1091
• Main Authors: Newton, Joshua P., Bateman, Philip W., Heydenrych, Matthew J., Mousavi‐Derazmahalleh, Mahsa, Nevill, Paul
• Format: Article
• Language: English
• Subjects: Biodiversity; biomonitoring; Cameras; Cryptic species; DNA barcoding; Environmental DNA; Eucalyptus; Eucalyptus gomphocephala; Forests; metabarcoding; Monitoring methods; National parks; Nesting; Population decline; Reptiles & amphibians; Species richness; Substrates; Taxa; terrestrial; tree hollows; Trees; vertebrate; Vertebrates
• ISSN: 2637-4943; 2637-4943
• DOI: 10.1002/edn3.313

Tree hollows are essential for many vertebrate species, providing both nesting sites and shelter. Globally, old hollow‐bearing trees are in decline resulting in many dependent species being under threat. It is, therefore, imperative that vital hollow‐bearing trees are preserved, but it is logistically difficult to rapidly determine which hollows are being used and by which taxa. Here, we investigate the efficacy of eDNA metabarcoding as a survey tool for vertebrate hollow users. We compared the identity and richness of hollow‐inhabiting vertebrate taxa using eDNA metabarcoding of both sediment from the tree hollows, and material collected using roller swabs. Samples (n = 138) were collected from hollow‐bearing tuart trees (Eucalyptus gomphocephala; N = 28), within both an urban remnant and a relatively undisturbed forested area of South‐West Western Australia. We detected a wide range of vertebrate taxa, including cryptic species such as the brush‐tailed phascogale (Phascogale tapoatafa), while also providing ecologically informative data, such as hollow use by invasive Rainbow Lorikeet (Trichoglossus moluccanus) within the study areas. Our results showed variation in the species detected between methods, with the roller swab method detecting a greater number of species and a higher mean species richness per sample than hollow sediment did. The species detected from both methods did not perfectly overlap, highlighting the value of using multiple methods or substrates to detect a greater number of taxa. Our results suggest eDNA metabarcoding from tree hollow samples offers a sensitive and resource‐efficient method of monitoring vertebrate hollow users, if enough hollows are sampled. This provides not only a broad biodiversity assessment tool, but also an effective method for detecting taxa that may be elusive using other methods. Tree hollows are essential for many vertebrate species, providing both nesting sites and shelter but it is logistically difficult to rapidly determine which hollows are being used and by which taxa. Here, we present an environmental DNA (eDNA) metabarcoding method testing the use of two substrates with a single assay to determine the ability of eDNA metabarcoding to detect vertebrate hollow users within tree hollows. Our results suggest eDNA metabarcoding from tree hollow samples offers a sensitive and resource efficient method for monitoring vertebrate hollow users, proving not only a broad biodiversity assessment tool, but also a