A central principle of threatened species management is the requirement for detailed understanding of species habitat requirements. Difficult terrain or cryptic behaviour can, however, make the study of habitat or microhabitat requirements difficult, calling for innovative data collection techniques. We used high-resolution terrestrial LiDAR imaging to develop three-dimensional models of log piles, quantifying the structural characteristics linked with occupancy of an endangered cryptic reptile, the western spiny-tailed skink (Egernia stokesii badia). Inhabited log piles were generally taller with smaller entrance hollows and a wider main log, had more high-hanging branches, fewer low-hanging branches, more mid- and understorey cover, and lower maximum canopy height. Significant characteristics linked with occupancy were longer log piles, an average of three logs, less canopy cover, and the presence of overhanging vegetation, likely relating to colony segregation, thermoregulatory requirements, and foraging opportunities. In addition to optimising translocation site selection, understanding microhabitat specificity of E. s. badia will help inform a range of management objectives, such as targeted monitoring and invasive predator control. There are also diverse opportunities for the application of this technology to a wide variety of future ecological studies and wildlife management initiatives pertaining to a range of cryptic, understudied taxa.
The microhabitat requirements of many animals are relatively subtle, and relate to small differences in localised habitat structure30,31, especially for relatively sessile species32,33 A novel option for assessment of localised habitat structure is LiDAR (light detection and ranging34), a non-destructive tool that rapidly and precisely digitises an object or site into a three-dimensional (3D) point cloud34,35. LiDAR has been applied to the broad-scale assessment of numerous fauna habitats, including forests36,37,38, tidal flats39, subtidal coastal zones40, and rivers41,42, but most of these have been at relatively large scales at square metre resolutions. At a smaller scale, terrestrial LiDAR allows for detailed scanning of microhabitat structure without obstruction from overhanging canopy or vegetation. We propose that the ultra-high-resolution (10 mm) precise characterisation of the physical environment provided by terrestrial LiDAR scanning provides a unique opportunity to gain an in-depth understanding of log pile microhabitat requirements for fauna of conservation concern.
Coarse woody debris, such as fallen log piles, are often critical habitat features for threatened fauna such as numbats (Myrmecobius fasciatus)43, chuditch (Dasyurus geoffroii)44, and the western spiny-tailed skink (Egernia stokesii badia)45. However, not all log pile sites are equally suitable for species habitation, and species-specific preferences for features such as log diameter, canopy cover and presence of adjacent trees can influence site suitability46. Here, to our knowledge, we report the first study using ultra high-resolution terrestrial LiDAR to quantify the microhabitat characteristics of fallen log piles, using this approach to estimate the suitability of log piles for an endangered cryptic reptile subspecies (western spiny-tailed skinks). We aimed to determine if the skinks exhibited a high selectivity for certain structural features of log pile habitat, such as structural complexity with multiple logs providing potential refuge options, or associated features such as degree of vegetation cover (e.g., canopy gaps for basking) through comparison of log piles known to be inhabited and uninhabited by the species. Such detailed analysis of log pile characteristics and understanding skink microhabitat specificity will provide crucial information in the design of future habitat improvement for management efforts, highlighting the applicability of the technology for the assessment of other complex microhabitat structures, potentially including the specific structures of specialised roosting habitats in some species of bats47,48 or nesting hollows or sites of endangered parrots49,50 to better understand sites for protection, translocation, or replication in restoration and other threatened species management.
Distribution records of Egernia stokesii badia (orange) according to records maintained by the Atlas of Living Australia ( , accessed 16 December2021), and the location of the study site (black), with different LiDAR scanning locations (pink).
All research and animal observational experiments were carried out and approved by the Animal Ethics Office of Curtin University (ARE2018-28) and conformed with all relevant guidelines and regulations. Scans were taken during the end of the austral winter and beginning of spring, to capture the peak abundance of annual plants. A total of 39 log piles (22 inhabited and 17 uninhabited), was scanned and three-dimensional (3D) point clouds generated for quantification of the 14 structural characteristics. The laser scanning data for this investigation were collected using a terrestrial LiDAR scanner, the Maptek I-Site 8800 (Maptek, Adelaide, Australia), which has a resolution of 10 mm46 and a range of up to 2000 m55. The LiDAR scanner was set up using a tripod on a standard tribrach mount, and a marked post was installed at each log pile site so that the scanner could be manually aligned to the top of the post using the survey alignment telescope for each scan. The scanner was placed in three to five positions around each log pile, depending on how large the log pile was, to create overlapping scans for development of a full 360-degree view of target log piles. Scan positions were targeted to ensure scanner positioning maximised capture of internal log structure within hollows. The LiDAR system position was coupled with a differential GPS system so that points were recorded with an xyz coordinate56.
Point clouds of each site were filtered to isolate each log pile system (Fig. 3C), and the physical characteristics of each log pile were measured discretely: (i) maximum canopy height, (ii) number of logs, (iii) length of log system, (iv) number of branches above and below/adjacent to the main log, (v) log structure height, (vi) diameter of widest hollow, (vii) the presence of overhanging vegetation, (viii) the position of the log pile (majority resting on ground or raised), (ix) orientation of the log pile, and (x) the diameter of the widest section of log (Table S1).
Skinks also generally occupied log piles with overhanging vegetation combined with reduced canopy cover, indicating that the presence of vegetation, particularly at mid-storey height, adjacent to and overhanging log piles is important. Microhabitat variability helps to facilitate behavioural thermoregulation of ectotherms, and vegetation cover at a site of long-term residence is likely to be particularly important in an arid environment where vegetation is highly scattered70. Microhabitats that provide complex shading have been found to increase the activity budget of other arid-dwelling lizard species during hot weather, with vegetation also acting as a temperature buffer during cooler months70. Presence of vegetation around log piles in arid habitats can also increase the abundance and richness of reptiles, probably due to a range of benefits including increased food availability, predator refuge, and options for behavioural thermoregulation71,72,73. The effects of cover on predation are mixed: some taxa are more susceptible to predation in habitats with less vegetative cover74. Similarly, many species also preferentially forage in areas of vegetation75,76,77. However, other studies show that predation can increase if cover provides perches for ambush predators78,79, likely why skinks preferred less vegetation cover at canopy height. Therefore, selection of log piles with overhanging vegetation either benefits both thermoregulatory capacity and refuge from predation by skinks or is a trade-off between the two.
Within Australia, many semi-arid and arid dwelling lizard species are uncommon, with their distribution often correlated with habitat, microhabitat, or diet specificity80. As inappropriate habitat selection is one of the major reasons that herpetofauna translocations often fail81, we predicted that microhabitat structure may limit log pile suitability for skink colonies, contributing to their limited distribution within the landscape. Our results support a degree of microhabitat selectivity by skinks, with occupation linked to log pile length, number of logs, canopy cover, and overhanging vegetation. Log pile length and composition can be easily manipulated when selecting translocation sites or introducing coarse woody debris to restoration sites. However, selection of sites with reduced canopy cover, but overhanging mid-storey, may take longer to influence through management. Biomass and vegetation complexity at the understorey and mid-storey height can be significantly reduced by introduced grazers82,83, retaining the canopy layer which they cannot reach. As skink habitat both in our study, and regionally occurs in areas with a long history of pastoralism and landscape degradation from grazing and mining operations84, restoration efforts and establishment of exclusion zones may be required to recover appropriate vegetation structure prior to any translocations into the area. In areas of mining restoration, while coarse woody debris can be introduced into the landscape, growth of surrounding vegetation cover may take time to establish85,86, lea