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

Abstract

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eDNA metabarcoding of log hollow sediments and soils highlights the importance of substrate type, frequency of sampling and animal size, for vertebrate species detection

“…Tree hollows in standing or fallen trees have a role in providing shelter, foraging, thermoregulation (Gibbons, 2002), and reproduction (Flanagan-Moodie et al, 2018), for a range of taxa. Therefore, collecting eDNA samples from tree hollows is expected to be an effective way of assessing vertebrate biodiversity, particularly due to the confined space within the log and long-term use by several species (Newton et al, 2022). Furthermore, abiotic conditions found in log hollows (lower ambient temperatures, reduced light) favor eDNA persistence (Tsuji et al, 2017;Gutiérrez-Cacciabue et al, 2016).…”

Sampling environmental DNA from trees and soil to detect cryptic arboreal mammals

“…Next, our focal trees were not chosen to occur near any special attractants or areas of multi-species use, such as saltlicks or water sources, which has proven successful in other vertebrate eDNA studies 18 , 25 , 31 , 32 , 56 . It is possible that adding a broader range of soil sampling sites, including some targeted towards other guilds (e.g., burrow users 32 , 56 ), would have yielded a more complete inventory.…”

“…Visual transect surveys are another common, fieldwork-intensive survey method for canopy-dwelling mammals that, when targeting nocturnal species, must be conducted at night via spotlight 4 , 8 , 9 . In the past two decades, advances in technology and an increasingly acute need for monitoring data have spurred a flurry of research into novel methods to enhance detection of these cryptic arboreal species, including bioacoustics 12 , 13 , drone- or canopy-mounted cameras 8 , 14 , scent detection dogs 15 , and eDNA-based methods 16 – 18 . The ability to survey for arboreal mammals based on shed DNA may have distinct advantages over conventional methods that require separate surveys for diurnal and nocturnal species (e.g., visual methods), or have difficulty discriminating among groups of species (e.g., acoustic methods 19 ).…”

“…For fully terrestrial species, eDNA detection techniques represent a rapidly expanding area of research 22 – 24 . Building off of early efforts at recovering DNA from physical traces such as tracks, hair, and scat 25 , 26 , mammal researchers have recently branched out into sampling communities using eDNA that has been deposited or transported into ponds and rivers 16 , 27 – 30 or left on attractants such as natural saltlicks or hollow logs 31 , 32 , including for some cryptic arboreal species 18 . While such approaches are appealing for their ability to produce community-level inventories at large spatial scales, sampling is limited to wherever such natural features occur and is therefore inadequate for finer-scale monitoring.…”

“…Extending these terrestrial eDNA-based techniques to sample for cryptic arboreal species could involve either testing soil beneath individual trees or using surface sampling techniques to recover eDNA from bark. A newly developed tool for sampling surface eDNA using damp commercially available paint rollers performed exceptionally well for recovering arthropod DNA from tree bark 33 and reptile DNA from cover objects 24 , and for identifying the vertebrate occupants of tree holes 18 . However, it has yet to be extended to sampling the surface of tree trunks to detect arboreal mammals despite its obvious promise.…”