Analysing the effects of distance, taxon and biomass on vertebrate detections using bulk-collected carrion fly iDNA

Invertebrate-derived DNA (iDNA) metabarcoding from carrion flies is a powerful, non-invasive tool that has value for assessing vertebrate diversity. However, unknowns exist around the factors that influence vertebrate detections, such as spatial limits to iDNA signals or if detections are influenced by taxonomic class or estimated biomass of the vertebrates of interest. Using a bulk-collection method, we captured flies from within a zoo and along transects extending 4 km away from this location. From 920 flies, we detected 28 vertebrate species. Of the 28 detected species, we identified 9 species kept at the zoo, 8 mammals and 1 bird, but no reptiles. iDNA detections were highly geographically localized, and only a few zoo animals were detected outside the zoo setting. However, due to the low number of detections in our dataset, we found no influence of the taxonomic group or the estimated biomass of animals on their detectability. Our data suggest that iDNA detections from bulk-collected carrion flies, at least in urban settings in Australia, are predominantly determined by geographic proximity to the sampling location. This study presents an important step in understanding how iDNA techniques can be used in biodiversity monitoring.

Spider webs capture environmental DNA from terrestrial vertebrates

Environmental DNA holds significant promise as a non-invasive tool for tracking terrestrial biodiversity. However, in non-homogenous terrestrial environments, the continual exploration of new substrates is crucial. Here we test the hypothesis that spider webs can act as passive biofilters, capturing eDNA from vertebrates present in the local environment. Using a metabarcoding approach, we detected vertebrate eDNA from all analyzed spider webs (N = 49). Spider webs obtained from an Australian woodland locality yielded vertebrate eDNA from 32 different species, including native mammals and birds. In contrast, webs from Perth Zoo, less than 50 km away, yielded eDNA from 61 different vertebrates and produced a highly distinct species composition, largely reflecting exotic species hosted in the zoo. We show that higher animal biomass and proximity to animal enclosures increased eDNA detection probability in the zoo. Our results indicate a tremendous potential for using spider webs as a cost-effective means to monitor terrestrial vertebrates.

On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces

OBJECTIVE

Roller swabbing of surfaces is an effective way to obtain environmental DNA, but the current DNA extraction method for these samples is equipment heavy, time consuming, and increases potential contamination through multiple handling. Here, we used rollers to swab a dog kennel and compared three DNA extraction approaches (water filtration, roller trimming and direct buffer) using two different platforms (Qiacube, Kingfisher). DNA extraction methods were evaluated based on cost, effort, DNA concentration and PCR result.

RESULTS

The roller trim method emerged as the optimal method with the best PCR results, DNA concentration and cost efficiency, while the buffer-based methods were the least labour intensive but produced mediocre PCR results and DNA concentrations. Additionally, the Kingfisher magnetic bead extractions generally ranked higher in all categories over the Qiacube column-based DNA extractions. Ultimately, the ideal DNA extraction method for a particular study is influenced by logistical constraints in the field such as the size of the roller, the availability of cold storage, and time constraints on the project. Our results demonstrate the strengths and weaknesses of each approach, allowing for informed decision making by researchers.

eDNA metabarcoding of avocado flowers: 'Hass' it got potential to survey arthropods in food production systems?

In the face of global biodiversity declines, surveys of beneficial and antagonistic arthropod diversity as well as the ecological services that they provide are increasingly important in both natural and agro-ecosystems. Conventional survey methods used to monitor these communities often require extensive taxonomic expertise and are time-intensive, potentially limiting their application in industries such as agriculture, where arthropods often play a critical role in productivity (e.g. pollinators, pests and predators). Environmental DNA (eDNA) metabarcoding of a novel substrate, crop flowers, may offer an accurate and high throughput alternative to aid in the detection of these managed and unmanaged taxa. Here, we compared the arthropod communities detected with eDNA metabarcoding of flowers, from an agricultural species (Persea americana-'Hass' avocado), with two conventional survey techniques: digital video recording (DVR) devices and pan traps. In total, 80 eDNA flower samples, 96 h of DVRs and 48 pan trap samples were collected. Across the three methods, 49 arthropod families were identified, of which 12 were unique to the eDNA dataset. Environmental DNA metabarcoding from flowers revealed potential arthropod pollinators, as well as plant pests and parasites. Alpha diversity levels did not differ across the three survey methods although taxonomic composition varied significantly, with only 12% of arthropod families found to be common across all three methods. eDNA metabarcoding of flowers has the potential to revolutionize the way arthropod communities are monitored in natural and agro-ecosystems, potentially detecting the response of pollinators and pests to climate change, diseases, habitat loss and other disturbances.

Use of carrion fly iDNA metabarcoding to monitor invasive and native mammals

Severely fragmented habitats increase the risk of extirpation of native mammal populations through isolation, increased edge effects, and predation. Therefore, monitoring the movement of mammal populations through anthropogenically altered landscapes can inform conservation. We used metabarcoding of invertebrate-derived DNA (iDNA) from carrion flies (Calliphoridae and Sarcophagidae) to track mammal populations in the wheat belt of southwestern Australia, where widespread clearing for agriculture has removed most of the native perennial vegetation and replaced it with an agricultural system. We investigated whether the localization of the iDNA signal reflected the predicted distribution of 4 native species-echidna (Tachyglossus aculeatus), numbat (Myrmecobius fasciatus), woylie (Bettongia penicillata), and chuditch (Dasyurus geoffroii)-and 2 non-native, invasive mammal species-fox (Vulpes vulpes) and feral cat (Felis catus). We collected bulk iDNA samples (n = 150 samples from 3428 carrion flies) at 3 time points from 3 conservation reserves and 35 road edges between them. We detected 14 of the 40 mammal species known from the region, including our target species. Most detections of target taxa were in conservation reserves. There were a few detections from road edges. We detected foxes and feral cats throughout the study area, including all conservation reserves. There was a significant difference between the diversity (F3, 98  = 5.91, p < 0.001) and composition (F3, 43  = 1.72, p < 0.01) of taxa detections on road edges and conservation reserves. Conservation reserves hosted more native biodiversity than road edges. Our results suggest that the signals from iDNA reflect the known distribution of target mammals in this region. The development of iDNA methods shows promise for future noninvasive monitoring of mammals. With further development, iDNA metabarcoding could inform decision-making related to conservation of endangered taxa, invasive species management, and impacts of habitat fragmentation.

Ecological Considerations When Designing Mitigation Translocations: An Australian Reptile Case Study

Translocation science has made considerable progress over the last two decades; however, reptile translocations still frequently fail around the world. Major knowledge gaps surround the basic ecology of reptile species, including basic factors such as habitat preference, which have a critical influence on translocation success. The western spiny-tailed skink (Egernia stokesii badia) is used here as a case study to exemplify how empirical research can directly inform on-ground management and future translocation planning. A combination of studies, including LiDAR scanning of microhabitat structures, camera trapping, plasticine replica model experiments and unbounded point count surveys to assess predation risk, and visual and DNA analysis of dietary requirements, were all used to better understand the ecological requirements of E. s. badia. We found that the skinks have specific log pile requirements, both native and non-native predator management requirements, and a largely herbivorous, broad diet, which all influence translocation site selection and management planning. The use of E. s. badia as an Australian case study provides a clear strategic framework for the targeted research of meaningful ecological factors that influence translocation decision-making. Similar approaches applied to other reptile species are likely to fundamentally increase the capacity for effective management, and the likelihood of future successful translocations.

Detection of vertebrates from natural and artificial inland water bodies in a semi-arid habitat using eDNA from filtered, swept, and sediment samples

Biomonitoring is vital for establishing baseline data that is needed to identify and quantify ecological change and to inform management and conservation activities. However, biomonitoring and biodiversity assessment in arid environments, which are predicted to cover 56% of the Earth's land surface by 2100, can be prohibitively time consuming, expensive, and logistically challenging due to their often remote and inhospitable nature. Sampling of environmental DNA (eDNA) coupled with high-throughput sequencing is an emerging biodiversity assessment method. Here we explore the application of eDNA metabarcoding and various sampling approaches to estimate vertebrate richness and assemblage at human-constructed and natural water sources in a semi-arid region of Western Australia. Three sampling methods: sediment samples, filtering through a membrane with a pump, and membrane sweeping in the water body, were compared using two eDNA metabarcoding assays, 12S-V5 and 16smam, for 120 eDNA samples collected from four gnammas (gnamma: Australian Indigenous Noongar language term-granite rock pools) and four cattle troughs in the Great Western Woodlands, Western Australia. We detected higher vertebrate richness in samples from cattle troughs and found differences between assemblages detected in gnammas (more birds and amphibians) and cattle troughs (more mammals, including feral taxa). Total vertebrate richness was not different between swept and filtered samples, but all sampling methods yielded different assemblages. Our findings indicate that eDNA surveys in arid lands will benefit from collecting multiple samples at multiple water sources to avoid underestimating vertebrate richness. The high concentration of eDNA in small, isolated water bodies permits the use of sweep sampling that simplifies sample collection, processing, and storage, particularly when assessing vertebrate biodiversity across large spatial scales.

Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects

Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.

DNA metabarcoding identifies urban foraging patterns of oligolectic and polylectic cavity-nesting bees

Urbanisation modifies natural landscapes resulting in built-up space that is covered by buildings or hard surfaces and managed green spaces that often substitute native plant species with exotics. Some native bee species have been able to adapt to urban environments, foraging and reproducing in these highly modified areas. However, little is known on how the foraging ecology of native bees is affected by urbanised environments, and whether impacts vary among species with different degrees of specialisation for pollen collection. Here, we aim to investigate the responses of native bee foraging behaviour to urbanisation, using DNA metabarcoding to identify the resources within nesting tubes. We targeted oligolectic (specialist) and polylectic (generalist) cavity-nesting bee species in residential gardens and remnant bushland habitats. We were able to identify 40 families, 50 genera, and 23 species of plants, including exotic species, from the contents of nesting tubes. Oligolectic bee species had higher diversity of plant pollen in their nesting tubes in residential gardens compared to bushland habitats, along with significantly different forage composition between the two habitats. This result implies a greater degree of forage flexibility for oligolectic bee species than previously thought. In contrast, the diversity and composition of plant forage in polylectic bee nesting tubes did not vary between the two habitat types. Our results suggest a complex response of cavity-nesting bees to urbanisation and support the need for additional research to understand how the shifts in foraging resources impact overall bee health.

Revealing microhabitat requirements of an endangered specialist lizard with LiDAR

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.

Metal(loid) pollution, not urbanisation nor parasites predicts low body condition in a wetland bioindicator snake

Urban ecosystems and remnant habitat 'islands' therein, provide important strongholds for many wildlife species including those of conservation significance. However, the persistence of these habitats can be undermined if their structure and function are too severely disrupted. Urban wetlands, specifically, are usually degraded by a monoculture of invasive vegetation, disrupted hydrology, and chronic-contamination from a suite of anthropogenic pollutants. Top predators-as bioindicators-can be used to assess and monitor the health of these ecosystems. We measured eight health parameters (e.g., parasites, wounds and scars, tail loss and body condition) in a wetland top predator, the western tiger snake, Notechis scutatus occidentalis. For three years, snakes were sampled across four wetlands along an urban gradient. For each site, we used GIS software to measure the area of different landscapes and calculate an urbanisation-landscape score. Previously published research on snake contamination informed our calculations of a metal-pollution index for each site. We used generalised linear mixed models to assess the relationship between all health parameters and site variables. We found the metal-pollution index to have the most significant association with poor body condition. Although parasitism, tail loss and wounds differed among sites, none of these parameters influenced body condition. Additionally, the suite of health parameters suggested differing health status among sites; however, our measure of contemporary landscape urbanisation was never a significant predictor variable. Our results suggest that the health of wetland predators surrounding a rapidly growing city may be offset by higher levels of environmental pollution.

Mitigation translocation as a management tool

Mitigation translocation is a subgroup of conservation translocation, categorized by a crisis-responsive time frame and the immediate goal of relocating individuals threatened with death. However, the relative successes of conservation translocations with longer time frames and broader metapopulation- and ecosystem-level considerations have been used to justify the continued implementation of mitigation translocations without adequate post hoc monitoring to confirm their effectiveness as a conservation tool. Mitigation translocations now outnumber other conservation translocations, and understanding the effectiveness of mitigation translocations is critical given limited global conservation funding especially if the mitigation translocations undermine biodiversity conservation by failing to save individuals. We assessed the effectiveness of mitigation translocations by conducting a quantitative review of the global literature. A total of 59 mitigation translocations were reviewed for their adherence to the adaptive scientific approach expected of other conservation translocations and for the testing of management options to continue improving techniques for the future. We found that mitigation translocations have not achieved their potential as an effective applied science. Most translocations focused predominantly on population establishment- and persistence-level questions, as is often seen in translocations more broadly, and less on metapopulation and ecosystem outcomes. Questions regarding the long-term impacts to the recipient ecosystem (12% of articles) and the carrying capacity of translocation sites (24% of articles) were addressed least often, despite these factors being more likely to influence ultimate success. Less than half (47%) of studies included comparison of different management techniques to facilitate practitioners selecting the most effective management actions for the future. To align mitigation translocations with the relative success of other conservation translocations, it is critical that future mitigation translocations conform to an established experimental approach to improve their effectiveness. Effective mitigation translocations will require significantly greater investment of time, expertise, and resources in the future.

At What Cost? Trade-Offs and Influences on Energetic Investment in Tail Regeneration in Lizards Following Autotomy

Caudal autotomy, the ability to shed a portion of the tail, is a widespread defence strategy among lizards. Following caudal autotomy, and during regeneration, lizards face both short- and long-term costs associated with the physical loss of the tail and the energy required for regeneration. As such, the speed at which the individual regenerates its tail (regeneration rate) should reflect the fitness priorities of the individual. However, multiple factors influence the regeneration rate in lizards, making inter-specific comparisons difficult and hindering broader scale investigations. We review regeneration rates for lizards and tuatara from the published literature, discuss how species' fitness priorities and regeneration rates are influenced by specific, life history and environmental factors, and provide recommendations for future research. Regeneration rates varied extensively (0-4.3 mm/day) across the 56 species from 14 family groups. Species-specific factors, influencing regeneration rates, varied based on the type of fracture plane, age, sex, reproductive season, and longevity. Environmental factors including temperature, photoperiod, nutrition, and stress also affected regeneration rates, as did the method of autotomy induction, and the position of the tail also influenced regeneration rates for lizards. Additionally, regeneration could alter an individual's behaviour, growth, and reproductive output, but this varied depending on the species.

Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow

Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant 'islands'. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which 'islands' of habitat are most in need of management and protection.

Interactions between the introduced European honey bee and native bees in urban areas varies by year, habitat type and native bee guild

European honey bees have been introduced across the globe and may compete with native bees for floral resources. Compounding effects of urbanization and introduced species on native bees are, however, unclear. Here, we investigated how honey bee abundance and foraging patterns related to those of native bee abundance and diversity in residential gardens and native vegetation remnants for 2 years in urbanized areas of the Southwest Australian biodiversity hotspot and assessed how niche overlap influenced these relationships. Honey bees did not overtly suppress native bee abundance; however, complex relationships emerged when analysing these relationships according to body size, time of day and floral resource levels. Native bee richness was positively correlated with overall honeybee abundance in the first year, but negatively correlated in the second year, and varied with body size. Native bees that had higher resource overlap with honey bees were negatively associated with honey bee abundance, and resource overlap between honey bees and native bees was higher in residential gardens. Relationships with honey bees varied between native bee taxa, reflecting adaptations to different flora, plus specialization. Thus, competition with introduced bees varies by species and location, mediated by dietary breadth and overlap and by other life-history traits of individual bee species.

Snake scales record environmental metal(loid) contamination

Wetland snakes, as top predators, are becoming globally recognised as bioindicators of wetland contamination. Livers are the traditional test organ for contaminant exposure in organisms, but research is moving towards a preference for non-lethal tissue sampling. Snake scales can be used as an indicator of exposure, as many metals bind to the keratin. We used laser ablation with inductively coupled plasma-atomic emission spectroscopy and mass spectrometry (LA-ICP-MS) to quantify the concentrations of 19 metals and metalloids (collectively referred to 'metals' hereafter) in Western tiger snake (Notechis scutatus occidentalis) scales from four wetlands along an urban gradient, and compared them to concentrations measured in captive tiger snake scales. We conducted repeat measures to determine the concentration accuracy of each metal using LA-ICP-MS. Concentrations in wild Western tiger snake scales were significantly higher than in reference tiger snake scales for most metals analysed, suggesting accumulation from environmental exposure. We compared the scale concentrations to sediment concentrations of sampled wetlands, and found inter-site differences between mean concentrations of metals in scales parallel patterns recorded from sediment. Four metals (Mn, As, Se, Sb) had strong positive correlations with liver tissue contents suggesting scale concentrations can be used to infer internal concentrations. By screening for a larger suite of metals than we could using traditional digestive methods, we identified additional metals (Ti, V, Sr, Cs, Tl, Th, U) that may be accumulating to levels of concern in tiger snakes in Perth, Western Australia. This research has progressed the use of LA-ICP-MS for quantifying a suite of metals available in snake scales, and highlights the significance of using wetland snake scales as a non-lethal indicator of environmental contamination.

Toxic time bombs: Frequent detection of anticoagulant rodenticides in urban reptiles at multiple trophic levels

Anticoagulant rodenticides (ARs) are regularly used around the world to control pest mammals. Second-generation anticoagulant rodenticides (SGARs) are highly persistent in biological tissue and have a high potential for bioaccumulation and biomagnification. Consequently, exposure and poisoning of non-target organisms has been frequently documented, especially in countries with unregulated AR sales and usage. Most of this research has focussed on rodent-predators, usually raptors and predatory mammals, although exposure has also been documented in invertebrates and insectivorous fauna. Few studies have explored non-target exposure in reptiles, despite species sharing similar trophic positions and dietary preferences to other exposed fauna. We tested three abundant urban reptile species in Perth, Western Australia that differ in diet and trophic tiers for multiple AR exposure, the dugite Pseudonaja affinis (rodent-predator), the bobtail Tiliqua rugosa (omnivore) and the tiger snake Notechis scutatus occidentalis (frog-predator). We found frequent exposure in all three species (91% in dugites, 60% in bobtails and 45% in tiger snakes). Mean combined liver concentrations of ARs of exposed individuals were 0.178 mg/kg in dugites, 0.040 mg/kg in bobtails and 0.009 mg/kg in tiger snakes. High exposure frequency and liver concentration was expected for the dugite. Exposure in the other species is more surprising and implies widespread AR contamination of the food web. We discuss the likelihood of global AR exposure of urban reptiles, highlight the potential for reptiles to be important vectors of ARs in the food web and highlight implications for humans consuming wild reptiles.

When one tail isn't enough: abnormal caudal regeneration in lepidosaurs and its potential ecological impacts

Abnormal caudal regeneration, the production of additional tails through regeneration events, occurs in lepidosaurs as a result of incomplete autotomy or sufficient caudal wound. Despite being widely known to occur, documented events generally are limited to opportunistic single observations - hindering the understanding of the ecological importance of caudal regeneration. Here we compiled and reviewed a robust global database of both peer-reviewed and non-peer reviewed records of abnormal regeneration events in lepidosaurs published over the last 400 years. Using this database, we qualitatively and quantitatively assessed the occurrence and characteristics of abnormal tail regeneration among individuals, among species, and among populations. We identified 425 observations from 366 records pertaining to 175 species of lepidosaurs across 22 families from 63 different countries. At an individual level, regenerations ranged from bifurcations to hexafurcations; from normal regeneration from the original tail to multiple regenerations arising from a single point; and from growth from the distal third to the proximal third of the tail. Species showing abnormal regenerations included those with intra-vertebral, inter-vertebral or no autotomy planes, indicating that abnormal regenerations evidently occur across lepidosaurs regardless of whether the species demonstrates caudal autotomy or not. Within populations, abnormal regenerations were estimated at a mean ± SD of 2.75 ± 3.41% (range 0.1-16.7%). There is a significant lack of experimental studies to understand the potential ecological impacts of regeneration on the fitness and life history of individuals and populations. We hypothesised that abnormal regeneration may affect lepidosaurs via influencing kinematics of locomotion, restrictions in escape mechanisms, anti-predation tactics, and intra- and inter-specific signalling. Behaviourally testing these hypotheses would be an important future research direction.

The Broad-Scale Analysis of Metals, Trace Elements, Organochlorine Pesticides and Polycyclic Aromatic Hydrocarbons in Wetlands Along an Urban Gradient, and the Use of a High Trophic Snake as a Bioindicator

Wetlands and their biodiversity are constantly threatened by contaminant pollution from urbanisation. Despite evidence suggesting that snakes are good bioindicators of environmental health, the bioaccumulation of contaminants in reptiles is poorly researched in Australia. We conducted the first broad-scale analysis of 17 metals and trace elements, 21 organochlorine pesticides, and 14 polycyclic aromatic hydrocarbons in the sediments (4 samples per site, December 2018) from four wetlands along an urban gradient in Perth, Western Australia, and from the livers (5 livers per site, February-April 2019) of western tiger snakes Notechis scutatus occidentalis captured at those sites. All 17 metals and trace elements were detected in the sediments of wetlands as well as 16 in the livers of tiger snakes. Arsenic, Cu, Hg, Pb, Se, and Zn were at concentrations exceeding government trigger values in at least one sediment sample. Two organochlorine pesticides and six of seven polycyclic aromatic hydrocarbons were detected in the sediments of a single wetland, all exceeding government trigger values, but were not detected in tiger snakes. Metals and trace elements were generally in higher concentration in sediments and snake livers from more heavily urbanised wetlands. The least urbanised site had some higher concentrations of metals and trace elements, possibly due to agriculture contaminated groundwater. Concentrations of nine metals and trace elements in snake livers were statistically different between sites. Arsenic, Cd, Co, Hg, Mo, Sb, and Se near paralleled the pattern of contamination measured in the wetland sediments; this supports the use of high trophic wetland snakes, such as tiger snakes, as bioindicators of wetland contamination. Contamination sources and impacts on these wetland ecosystems and tiger snakes are discussed herein.

The evolution of autotomy in leaf-footed bugs

Sacrificing body parts is one of many behaviors that animals use to escape predation. This trait, termed autotomy, is classically associated with lizards. However, several other taxa also autotomize, and this trait has independently evolved multiple times throughout Animalia. Despite having multiple origins and being an iconic antipredatory trait, much remains unknown about the evolution of autotomy. Here, we combine morphological, behavioral, and genomic data to investigate the evolution of autotomy within leaf-footed bugs and allies (Insecta: Hemiptera: Coreidae + Alydidae). We found that the ancestor of leaf-footed bugs autotomized and did so slowly; rapid autotomy (<2 min) then arose multiple times. The ancestor likely used slow autotomy to reduce the cost of injury or to escape nonpredatory entrapment but could not use autotomy to escape predation. This result suggests that autotomy to escape predation is a co-opted benefit (i.e., exaptation), revealing one way that sacrificing a limb to escape predation may arise. In addition to identifying the origins of rapid autotomy, we also show that across species variation in the rates of autotomy can be explained by body size, distance from the equator, and enlargement of the autotomizable appendage.

Re-regeneration to reduce negative effects associated with tail loss in lizards

Many species of lizard use caudal autotomy, the ability to self-amputate a portion of their tail, regenerated over time, as an effective anti-predation mechanism. The importance of this tactic for survival depends on the degree of predation risk. There are, however, negative trade-offs to losing a tail, such as loss of further autotomy opportunities with the regenerated tail vertebrae being replaced by a continuous cartilaginous rod. The common consensus has been that once a tail has been autotomised and regenerated it can only be autotomised proximal to the last vertebral autotomy point, as the cartilage rod lacks autotomy planes. However, anecdotal evidence suggests that although the regenerated portion of the tail is unable to autotomise, it can re-regenerate following a physical shearing event. We assessed re-regeneration in three populations of the King’s skink (Egernia kingii), a large lizard endemic to south-west Western Australia and surrounding islands. We show that re-regeneration is present at an average of 17.2% across the three populations, and re-regenerated tissue can comprise up to 23.3% of an individual’s total tail length. The ability to re-regenerate may minimise the costs to an individual’s fitness associated with tail loss, efficiently restoring ecological functions of the tail.

The ecology and evolution of autotomy

Autotomy, the self-induced loss of a body part, occurs throughout Animalia. A lizard dropping its tail to escape predation is an iconic example, however, autotomy occurs in a diversity of other organisms. Octopuses can release their arms, crabs can drop their claws, and bugs can amputate their legs. The diversity of organisms that can autotomize body parts has led to a wealth of research and several taxonomically focused reviews. These reviews have played a crucial role in advancing our understanding of autotomy within their respective groups. However, because of their taxonomic focus, these reviews are constrained in their ability to enhance our understanding of autotomy. Here, we aim to synthesize research on the ecology and evolution of autotomy throughout Animalia, building a unified framework on which future studies can expand. We found that the ability to drop an appendage has evolved multiple times throughout Animalia and that once autotomy has evolved, selection appears to act on the removable appendage to increase the efficacy and/or efficiency of autotomy. This could explain why some autotomizable body parts are so elaborate (e.g. brightly coloured). We also show that there are multiple benefits, and variable costs, associated with autotomy. Given this variation, we generate an economic theory of autotomy (modified from the economic theory of escape) which makes predictions about when an individual should resort to autotomy. Finally, we show that the loss of an autotomizable appendage can have numerous consequences on population and community dynamics. By taking this broad taxonomic approach, we identified patterns of autotomy that transcend specific lineages and highlight clear directions for future research.

New light in the dark - a proposed multidisciplinary framework for studying functional ecology of groundwater fauna

Groundwaters provide the vast majority of unfrozen freshwater resources on the planet, but our knowledge of subsurface ecosystems is surprisingly limited. Stygofauna, or stygobionts -subterranean obligate aquatic animals - provide ecosystem services such as grazing biofilms and maintaining water quality, but we know little about how their ecosystems function. The cryptic nature of groundwaters, together with the high degree of local endemism and stygofaunal site-specific adaptations, represent major obstacles for the field. To overcome these challenges, and integrate biodiversity and ecosystem function, requires a holistic design drawing on classical ecology, taxonomy, molecular ecology and geochemistry. This study presents an approach based on the integration of existing concepts in groundwater ecology with three more novel scientific techniques: compound specific stable isotope analysis (CSIA) of amino acids, radiocarbon analysis (¹⁴C) and DNA analyses of environmental samples, stygofauna and gut contents. The combination of these techniques allows elucidation of aspects of ecosystem function that are often obscured in small invertebrates and cryptic systems. Carbon (δ¹³C) and nitrogen (δ¹⁵N) CSIA provides a linkage between biogeochemical patterns and ecological dynamics. It allows the identification of stygofaunal food web structures and energy flows based on the metabolic pathway of specific amino groups. Concurrently, ¹⁴C provides complementary data on the carbon recycling and incorporation within the stygobiotic trophic webs. Changes in groundwater environmental conditions (e.g. aquifer recharge), and subsequent community adaptations, can be pinpointed via the measurementof the radiocarbon fingerprint of water, sediment and specimens. DNA analyses are a rapidly expanding approach in ecology. eDNA is mainly employed as a biomonitoring tool, while metabarcoding of individuals and/or gut contents provides insight into diet regimes. In all cases, the application of the approaches in combination provides more powerful data than any one alone. By combining quantitative (CSIA and ¹⁴C) and qualitative (eDNA and DNA metabarcoding) approaches via Bayesian Mixing Models (BMM), linkages can be made between community composition, energy and nutrient sources in the system, and trophic function. This suggested multidisciplinary design will contribute to a more thorough comprehension of the biogeochemical and ecological patterns within these undervalued but essential ecosystems.

Anatomy of the cavernous muscles of the kangaroo penis highlights marsupial-placental dichotomy

The mammalian penis is a complex hydraulic organ of cavernous (spongy) tissue supported by both smooth and skeletal muscle structures. In placental mammals, the paired ‎Musculus ischiocavernosi anchor the corpora cavernosa to the pelvis (at the ischium), and the paired M. bulbospongiosi converge as they envelop the base of the corpus spongiosum. Male marsupials have a dramatically different anatomy, however, in which both sets of paired muscles remain separate, have a bulbous, globular shape and do not have any direct connection to the pelvis. Here we provide the first detailed anatomical investigation of the muscles of the penis in the western grey kangaroo (Macropus fuliginosus) incorporating dissection, histology, vascular casting and computed tomography. The M. ischiocavernosus and M. bulbospongiosus form massive, multipennate bodies of skeletal muscle surrounding the paired roots of the corpus cavernosum and corpus spongiosum, respectively. Bilateral vascular supply is via both the artery of the penis and the ventral perineal artery. Histological examination reveals cavernous tissues with substantial smooth muscle supported by fibroelastic trabeculae, surrounded by the thick collagenous tunica albuginea. The M. ischiocavernosus and M. bulbospongiosus are known to function during erection of the penis and ejaculation via muscular contraction increasing blood pressure within cavernous vascular tissues. The thick muscular anatomy of the kangaroo would be well suited to this function. The absence of any connection to the bony pelvis in marsupials suggests the possibility of different mechanisms of action of these muscles with regard to reduction of venous return, eversion from the cloaca, or movements such as penile flips, which have been described in some placental mammals. This highlights a greater diversity in form and function in the evolution of the mammalian penis than has been previously considered.

Influences of behaviour and physiology on body mass gain in the woylie (Bettongia penicillata ogilbyi) post-translocation

Context Temperament can affect an individual’s fitness and survival if it also influences behaviours associated with predator avoidance, interactions with conspecifics, refuge selection and/or foraging. Furthermore, temperament can determine an individual’s response to novel stimuli and environmental challenges, such as those experienced through translocation. Increasing our understanding of the effect of temperament on post-translocation fitness is thus necessary for improving translocation outcomes. Aims The aim was to test whether differences in an individual’s behaviour or physiology could help predict body mass changes post-translocation in the woylie (brush-tailed bettong, Bettongia penicillata ogilbyi). In the absence of predation (due to release into a predator-free exclosure), body mass was used as a proxy for an individual’s success in securing resources in the new habitat, and therefore fitness. Methods Forty woylies were translocated from two predator-free exclosures to a larger exclosure, all in Western Australia. Behavioural and physiological measures were recorded during trapping, processing, holding, and release, and again at re-capture ~100 days post-release. Key results Translocated woylies generally increased in body mass post-translocation. This suggests that, in the absence of predation, the selected candidates were able to cope with the stress of translocation and possessed the behavioural plasticity to successfully find resources and adapt to a novel environment. The strongest predictors of body mass gain were sex, heart rate lability and escape behaviour when released (a convoluted escape path). Conclusions There was no significant difference in body mass between males and females pre-translocation but females showed greater mass gain post-translocation than did males, which could reflect greater investment in reproduction (all females had pouch young). Heart rate lability and escape behaviour are likely to reflect reactivity or fearfulness, a significant temperament trait in the context of translocation success. Implications Behavioural measures that can be easily incorporated into the translocation process – without increasing stress or affecting welfare of individuals – may hold promise for predicting the fate of translocated animals.

The Time Local Convex Hull method as a tool for assessing responses of fauna to habitat restoration: a case study using the perentie (Varanus giganteus : Reptilia : Varanidae)

Understanding the behavioural responses of animals to habitat change is vital to their conservation in landscapes undergoing restoration. Studies of animal responses to habitat restoration typically assess species presence/absence; however, such studies may be restricted in their ability to show whether restoration is facilitating the return of self-sustaining and functional fauna populations. We present a case study using VHF/GPS tracking of a young adult perentie (Varanus giganteus), to demonstrate the range of applications of the Time Local Convex Hull method of home-range construction in analysing the behavioural responses of fauna to habitat change and restoration. Presence/absence studies provide single point locations of an animal, and the Minimum Convex Polygon method provides an invariant estimate of habitat use across the whole home range. However, the Time Local Convex Hull method provides a useful method for assessing movement and behavioural responses of fauna to habitat change and restoration, and the specific habitat requirements for the long-term support of populations. The breadth and multidimensionality of data generated indicates strongly that understanding the complex interactions between animals and their environment is fundamental to their conservation in the face of ever-increasing rates of human-induced habitat change and degradation.

Does urbanization influence the diet of a large snake?

Urbanization facilitates synanthropic species such as rodents, which benefit the diets of many predators in cities. We investigated how urbanization affects the feeding ecology of dugites Pseudonaja affinis, a common elapid snake in south-west Western Australia. We predicted that urban snakes: 1) more frequently contain prey and eat larger meals, 2) eat proportionally more non-native prey, 3) eat a lower diversity of prey species, and 4) are relatively heavier, than non-urban dugites. We analyzed the diet of 453 specimens obtained from the Western Australian Museum and opportunistic road-kill collections. Correcting for size, sex, season, and temporal biases, we tested whether location influenced diet for our 4 predictions. Body size was a strong predictor of diet (larger snakes had larger prey present, a greater number of prey items, and a greater diversity of prey). We identified potential collection biases: urban dugites were relatively smaller (snout-vent length) than non-urban specimens, and females were relatively lighter than males. Accounting for these effects, urban snakes were less likely to have prey present in their stomachs and were relatively lighter than non-urban snakes. Other urban-adapted carnivores appear to benefit from urbanization through increased food supplementation, but we found the opposite of this: urban dugites were less likely to contain a meal, and their meals were smaller, indicating they did not make greater use of synanthropic species than was evident for non-urban snakes. In contrast to other carnivores, snakes do not appear to fit a consistent directional pattern for size differences between urban and non-urban populations.

The pitfalls of short-range endemism: high vulnerability to ecological and landscape traps

Ecological traps attract biota to low-quality habitats. Landscape traps are zones caught in a vortex of spiralling degradation. Here, we demonstrate how short-range endemic (SRE) traits may make such taxa vulnerable to ecological and landscape traps. Three SRE species of mygalomorph spider were used in this study: Idiommata blackwalli, Idiosoma sigillatum and an undescribed Aganippe sp. Mygalomorphs can be long-lived (>43 years) and select sites for permanent burrows in their early dispersal phase. Spiderlings from two species, I. blackwalli (n = 20) and Aganippe sp. (n = 50), demonstrated choice for microhabitats under experimental conditions, that correspond to where adults typically occur in situ. An invasive veldt grass microhabitat was selected almost exclusively by spiderlings of I. sigillatum. At present, habitat dominated by veldt grass in Perth, Western Australia, has lower prey diversity and abundance than undisturbed habitats and therefore may act as an ecological trap for this species. Furthermore, as a homogenising force, veldt grass can spread to form a landscape trap in naturally heterogeneous ecosystems. Selection of specialised microhabitats of SREs may explain high extinction rates in old, stable landscapes undergoing (human-induced) rapid change.

Impacts of translocation on a large urban-adapted venomous snake

Context Translocation as a tool for management of nuisance or ‘problem’ snakes near urban areas is currently used worldwide with limited success. Translocated snakes experience modified behaviours, spatial use and survivorship, and few studies have investigated the impacts of translocation within a metropolitan area. Aims In the present study, we investigated the impacts of translocation on the most commonly encountered snake in Perth Western Australia, the dugite (Pseudonaja affinis, Elapidae), by comparing the space use of resident and translocated snakes. Methods We captured 10 dugites and attached telemetry packages, composed of a radio-telemetry transmitter and global positioning system (GPS) data-logger, externally to their tails. Snakes were either released within 200 m of their initial capture sites (residents, n = 6) or moved to new unconnected habitat at least 3 km away (translocated, n = 4). Spatial-use data were analysed using general linear models to identify differences between resident and translocated dugites. Key results Translocation influenced space use of dugites and detrimentally affected their survivorship. Translocated snakes had larger activity ranges than did residents, and there was a trend towards travelling greater distances over time. Mortality for all snakes was high: 100% for translocated snakes, and 50% for residents. Conclusions Urban dugites face many threats, and snakes were negatively affected by translocation. The GPS technology we used did not improve the quality of the data over traditional radio-telemetry methods, owing to the cryptic nature of the snakes that spent much of their time under cover or underground. Implications These findings support the growing body of evidence that translocating ‘problem’ snakes is a not a humane method of animal management, and alternatives such as public education, may be more appropriate.

Reduced efficacy of baiting programs for invasive species: some mechanisms and management implications

‘Bait-resistance’ is defined as progressive decreases in bait efficacy in controlled pest species populations. Understanding the mechanisms by which bait-resistance can develop is important for the sustainable control of pests worldwide, for both wildlife conservation programs and agricultural production. Bait-resistance is influenced by both behavioural (innate and learned bait-avoidance behaviour) and physiological aspects of the target pest species (its natural diet, its body mass, the mode of action of the toxin, and the animal’s ability to biochemically break down the toxin). In this review, we summarise the scientific literature, discuss factors that can lead to innate and learned aversion to baits, as well as physiological tolerance. We address the question of whether bait avoidance or tolerance to 1080 could develop in the red fox (Vulpes vulpes), an introduced predator of significant economic and environmental importance in Australia. Sublethal poisoning has been identified as the primary cause of both bait avoidance and increased toxin-tolerance, and so, finally, we provide examples of how management actions can minimise the risk of sublethal baits in pest species populations.

Stuck in a rut: Potential costs of sand roads to gopher tortoises Gopherus polyphemus

Roads affect wildlife significantly through direct mortality but also through behavioral change. We explored the effects of unsurfaced sand roads with a low traffic volume on the travelling behavior of gopher tortoises Gopherus polyphemus in scrub habitat in central Florida, as evidenced by the tracks left by tortoises on sand roads. Tortoises (and most other taxa leaving tracks on the roads) did not appear to make use of roads for travel but attempted to cross them, the success of which was influenced by the size of the individual. Smaller animals (presumably younger tortoises) were more challenged than larger animals by both sand road widths and depths of vehicle ruts in sand roads. Sand roads may present both physical and physiological challenges to gopher tortoises, particularly to small ones. This research provides further evidence that the negative influence of roads in fragmenting the environment is not limited to vehicle mortality.