Evaluating the success of wildlife crossing structures using genetic approaches and an experimental design: Lessons from a gliding mammal

Evaluating the genetic consequences of population subdivision as it unfolds and how to best mitigate them: A rare story about koalas

The genetic consequences of the subdivision of populations are regarded as significant to long-term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species which inhabit human-impacted landscapes. Here, we provide a rare and, to our knowledge, the first analysis of this process while it is happening and demonstrate a method of evaluating the effect of mitigation measures such as fauna crossings. We did this by using an extensive genetic data set collected from a koala population which was intensely monitored during the construction of linear transport infrastructure which resulted in the subdivision of their population. First, we found that both allelic richness and effective population size decreased through the process of population subdivision. Second, we predicted the extent to which genetic drift could impact genetic diversity over time and showed that after only 10 generations the resulting two subdivided populations could experience between 12% and 69% loss in genetic diversity. Lastly, using forward simulations we estimated that a minimum of eight koalas would need to disperse from each side of the subdivision per generation to maintain genetic connectivity close to zero but that 16 koalas would ensure that both genetic connectivity and diversity remained unchanged. These results have important consequences for the genetic management of species in human-impacted landscapes by showing which genetic metrics are best to identify immediate loss in genetic diversity and how to evaluate the effectiveness of any mitigation measures.

Informing Wildlife Corridor Creation through Population Genetics of an Arboreal Marsupial in a Fragmented Landscape

Habitat loss and fragmentation contribute significantly to the decline of arboreal mammal populations. As populations become fragmented and isolated, a reduction in gene flow can result in a loss of genetic diversity and have an overall impact upon long-term persistence. Creating wildlife corridors can mitigate such effects by increasing the movement and dispersal of animals, thus acting to reduce population isolation. To evaluate the success of a corridor, a before-after experimental research framework can be used. Here, we report the genetic diversity and structure of sugar glider (Petaurus breviceps) sampling locations within a fragmented landscape prior to the implementation of a wildlife corridor. This study used 5999 genome-wide SNPs from 94 sugar gliders caught from 8 locations in a fragmented landscape in south-eastern New South Wales, Australia. Overall genetic structure was limited, and gene flow was detected across the landscape. Our findings indicate that the study area contains one large population. A major highway dissecting the landscape did not act as a significant barrier to dispersal, though this may be because of its relatively new presence in the landscape (completed in 2018). Future studies may yet indicate its long-term impact as a barrier to gene flow. Future work should aim to repeat the methods of this study to examine the medium-to-long-term impacts of the wildlife corridor on sugar gliders, as well as examine the genetic structure of other native, specialist species in the landscape.

Use of road underpasses by mammals and a monitor lizard in eastern Australia and consideration of the prey‐trap hypothesis

Road networks continue to expand globally with predictable effects on ecological systems. Research into the effectiveness of road underpasses and overpasses for wildlife has been concentrated in North America and Europe. In Australia, most studies of underpasses have been of relatively short duration and without reference sites to give context to the measured rates of use. We studied 5–7 road underpasses at two locations in eastern Australia over 2–3 years, comparing camera trap detections of animals in underpasses with those at nearby forest sites. Three species of large macropod (wallabies and kangaroos) were frequently detected in the underpasses, with some underpasses traversed 1–4 times per week, and in many cases exceeded detections in the forest. The lace monitor (Varanus varius) was detected in all underpasses, often once per week during spring and summer, and infrequently in the forest. At each location, a different small macropod species, including one regionally threatened, showed a higher probability of detection in one underpass compared with several of the forest sites. The vulnerable koala (Phascolarctos cinereus) was detected infrequently in underpasses and in the adjoining forest. The short‐beaked echidna (Tachyglossus aculeatus) had a high probability of detection in a single underpass. The “prey‐trap hypothesis” postulates that predators will exhibit increased activity at underpasses as a consequence of prey being funneled. We found the red fox (Vulpes vulpes) had high activity in some underpasses. However, its activity coincided less than expected with the activity of the mammals most at risk to it. Our results provide no consistent support for the “prey‐trap hypothesis.” Instead, our study confirms the generic value of underpasses for a range of medium‐large mammals as well as one large reptile. Habitat adjoining underpasses exert a strong influence on their use and require greater consideration to maximize underpass use.

Identifying and mitigating the impacts on primates of transportation and service corridors

Most primate populations are declining; 60% of species face extinction. The expansion of transportation and service corridors (T&S) (i.e., roads and railways and utility and service lines) poses a significant yet underappreciated threat. With the development of T&S corridors predicted to increase across primates' ranges, it is necessary to understand the current extent of its impacts on primates, the available options to mitigate these effectively, and recognize research and knowledge gaps. By employing a systematic search approach to identify literature that described the relationship between primates and T&S corridors, we extracted information from 327 studies published between 1980 and 2020. Our results revealed that 218 species and subspecies across 62 genera are affected, significantly more than the 92 listed by the IUCN Red List of Threatened Species. The majority of studies took place in Asia (45%), followed by mainland Africa (31%), the Neotropics (22%), and Madagascar (2%). Brazil, Indonesia, Equatorial Guinea, Vietnam, and Madagascar contained the greatest number of affected primate species. Asia featured the highest number of species affected by roads, electrical transmission lines, and pipelines and the only studies addressing the impact of rail and aerial tramways on primates. The impact of seismic lines only emerged in the literature from Africa and the Neotropics. Impacts are diverse and multifaceted, for example, animal-vehicle collisions, electrocutions, habitat loss and fragmentation, impeded movement and genetic exchange, behavioral changes, exposure to pollution, and mortality associated with hunting. Although several mitigation measures were recommended, only 41% of studies focused on their implementation, whereas only 29% evaluated their effectiveness. Finally, there was a clear bias in the species and regions benefiting from research on this topic. We recommend that government and conservation bodies recognize T&S corridors as a serious and mounting threat to primates and that further research in this area is encouraged.

Reconnecting nature

The U.N. has declared 2021-2030 the 'decade of restoration' (https://www.decadeonrestoration.org). This initiative aspires to many actions, but its agenda must include 'reconnecting nature'. Even when natural habitats remain, they often come in fragments too small or isolated to sustain viable populations. Human activities surround habitats with unsuitable areas or constrict animals' movements with artificial barriers, such as roads or fences. The harm this fragmentation causes is evident. Here, we discuss various actions to mitigate its problems, seeking explicit evidence of their efficacy. These actions range from small-scale, controlled experiments to continent-wide programmes to allow species the freedom to roam. Even simple connections, such as highway overpasses or tunnels, usually allow movement such that the genetic and demographic problems that beset small, isolated populations may be diminished. Showing that species move when we give them the chance to do so may be a sufficient measure of success, even if we do not always understand the consequences in detail.

Comparison of sample types from white-tailed deer (Odocoileus virginianus) for DNA extraction and analyses

Collection of biological samples for DNA is necessary in a variety of disciplines including disease epidemiology, landscape genetics, and forensics. Quantity and quality of DNA varies depending on the method of collection or media available for collection (e.g., blood, tissue, fecal). Blood is the most common sample collected in vials or on Whatman Flinders Technology Associates (FTA) cards with short- and long-term storage providing adequate DNA for study objectives. The focus of this study was to determine if biological samples stored on Whatman FTA Elute cards were a reasonable alternative to traditional DNA sample collection, storage, and extraction. Tissue, nasal swabs, and ocular fluid were collected from white-tailed deer (Odocoileus virginianus). Tissue samples and nasal swabs acted as a control to compare extraction and DNA suitability for microsatellite analysis for nasal swabs and ocular fluid extracted from FTA Elute cards. We determined that FTA Elute cards improved the extraction time and storage of samples and that nasal swabs and ocular fluid containing pigmented fluid were reasonable alternatives to traditional tissue DNA extractions.

Urban Hedgehog Behavioural Responses to Temporary Habitat Disturbance versus Permanent Fragmentation

Anthropogenic activities can result in both transient and permanent changes in the environment. We studied spatial and temporal behavioural responses of European hedgehogs (Erinaceus europaeus) to a transient (open-air music festival) and a permanent (highly fragmented area) disturbance in the city of Berlin, Germany. Activity, foraging and movement patterns were observed in two distinct areas in 2016 and 2017 using a "Before & After" and "Control & Impact" study design. Confronted with a music festival, hedgehogs substantially changed their movement behaviour and nesting patterns and decreased the rhythmic synchronization (DFC) of their activity patterns with the environment. These findings suggest that a music festival is a substantial stressor influencing the trade-off between foraging and risk avoidance. Hedgehogs in a highly fragmented area used larger home ranges and moved faster than in low-fragmented and low-disturbed areas. They also showed behaviours and high DFCs similar to individuals in low-fragmented, low disturbed environment, suggesting that fragmentation posed a moderate challenge which they could accommodate. The acute but transient disturbance of a music festival, therefore, had more substantial and severe behavioural effects than the permanent disturbance through fragmentation. Our results are relevant for the welfare and conservation measure of urban wildlife and highlight the importance of allowing wildlife to avoid urban music festivals by facilitating avoidance behaviours.

Artificial lighting reduces the effectiveness of wildlife-crossing structures for insectivorous bats

In an attempt to improve cost-effectiveness, it has become increasingly popular to adapt wildlife crossing structures to enable people to also use them for safe passage across roads. However, the required needs of humans and wildlife may conflict, resulting in a structure that does not actually provide the perceived improvement in cost-effectiveness, but instead a reduction in conservation benefits. For example, lighting within crossing structures for human safety at night may reduce use of the structure by nocturnal wildlife, thus contributing to barrier and mortality effects of roads rather than mitigating them. In this study, we experimentally evaluated the impact of artificial light at night on the rate of use of wildlife crossing structures, specifically underpasses, by ten insectivorous bat species groups in south-eastern Australia. We monitored bat activity before, during and after artificially lighting the underpasses. We found that bats tended to avoided lit underpasses, and only one species consistently showed attraction to the light. Artificial light at night in underpasses hypothetically increases the vulnerability of bats to road-mortality or to the barrier effect of roads. The most likely outcomes of lighting underpasses were 1. an increase in crossing rate above the freeway and a decrease under the underpasses, or 2. a reduction in crossing rate both above freeways and under the underpasses, when structures were lit. Our results corroborate those of studies on terrestrial mammals, and thus we recommend that underpasses intended to facilitate the movement of wildlife across roads should not be lit.

Attraction and Avoidance between Predators and Prey at Wildlife Crossings on Roads

Wildlife passages are currently built at roads and railway lines to re-establish connectivity. However, little is known about whether predator-prey interactions may reduce the effectiveness of the crossing structures. We evaluated the co-occurrence patterns of predator-prey species-pairs at 113 crossing structures, noting their coincidence at the same structure and/or on the same day. We built occupancy models using presence-absence matrices for three prey and five predator types obtained during 2076 passage-days of monitoring. The results indicate that predators and prey do not use passages independently. Attraction or segregation effects occurred in 20% of predator-prey species-pairs and were detected in 67% of cases with respect to same-day use. Our results show that both predator and prey species used the same structures to cross fenced roads. However, the spatial and daily patterns of crossing suggest that there were predators that attended crossings to search for prey and that prey species avoided using crossings in the presence of predators. Our results support two recommendations to avoid crossing structures losing effectiveness or becoming prey traps: (i) increase the number of wider structures to reduce the risks of predator-prey encounters and (ii) include inside them structural heterogeneity and refuges, to reduce the likelihood for predator-prey interactions.

Landscape management of the mahogany glider (Petaurus gracilis) across its distribution: subpopulations and corridor priorities

Key threatening processes to biodiversity include habitat loss and fragmentation, with populations restricted to small fragments of habitat being more prone to extinction. The mahogany glider (Petaurus gracilis) is endemic to sclerophyll woodland forests between Tully and Ingham in north Queensland and is one of Australia’s most endangered arboreal mammals due to these processes. The aim of this study was to identify the degree of habitat fragmentation of the remaining remnant vegetation of the mahogany glider, identify subpopulations within its distribution and identify key wildlife corridors for restoration to facilitate the movement of this species within and between subpopulations. Ten glider subpopulations, spread over 998 habitat fragments, were identified, of which only five subpopulations may currently be considered to be viable. To assist in providing habitat connectivity between and within the subpopulations, 55 corridors were identified for restoration that had an average length of 8.25 km. The average number of gaps greater than 30 m was 3.4 per corridor, with the average length of these gaps being 523 m. This study confirmed a high degree of habitat fragmentation across the distribution of the mahogany glider and highlighted the need to strengthen the remaining subpopulations by restoring habitat connectivity between the remaining habitat fragments.

Mitigating Tropical Forest Fragmentation with Natural and Semi-Artificial Canopy Bridges

Fragmentation caused by linear infrastructures is a threat to forest-dwelling wildlife globally. Loss of canopy connectivity is particularly problematic for highly arboreal species such as those of the Neotropics. We explored the use of both natural canopy bridges (NCBs) and a semi-artificial one over a natural gas pipeline right-of-way (RoW) in the Peruvian Amazon to provide more information on both a proven and a novel solution to the problem of fragmentation. We monitored seven NCBs over 14 months and found crossing rates higher than previously recorded (57.70 crossings/100 trap nights by 16 species). We also constructed a semi-artificial canopy bridge (SACB) out of a liana and found it to be used quickly (seven days after installation) and frequently (90.23 crossings/100 trap nights—nearly nightly) by five species (two procyonids, one didelphid, one primate, and one rodent). This information contributes to our knowledge of mitigation solutions for fragmentation. As linear infrastructure grows globally, more solutions must be developed and tested.

Correcting common misconceptions to inspire conservation action in urban environments

Despite repeated calls to action, proposals for urban conservation are often met with surprise or scepticism. There remains a pervasive narrative in policy, practice, and the public psyche that urban environments, although useful for engaging people with nature or providing ecosystem services, are of little conservation value. We argue that the tendency to overlook the conservation value of urban environments stems from misconceptions about the ability of native species to persist within cities and towns and that this, in turn, hinders effective conservation action. However, recent scientific evidence shows that these assumptions do not always hold. Although it is generally true that increasing the size, quality, and connectivity of habitat patches will improve the probability that a species can persist, the inverse is not that small, degraded, or fragmented habitats found in urban environments are worthless. In light of these findings we propose updated messages that guide and inspire researchers, practitioners, and decision makers to undertake conservation action in urban environments: consider small spaces, recognize unconventional habitats, test creative solutions, and use science to minimize the impacts of future urban development.

Use of tall wooden poles by four species of gliding mammal provides further proof of concept for habitat restoration

Tall wooden poles (glide poles) and rope canopy-bridges are frequently installed along new highways in Australia to maintain population connectivity for gliding mammals. Knowledge of the use of these structures is rudimentary. We monitored two pairs of glide poles and a canopy-bridge over three years at Port Macquarie, New South Wales. The sugar glider (Petaurus breviceps) and the squirrel glider (Petaurus norfolcensis) were collectively detected on 12–18% of nights on the pole pairs compared with 1% on the rope-bridge. The feathertail glider (Acrobates frontalis) was detected on 3% of nights on the pole pairs compared with 0.2% on the rope-bridge. The yellow-bellied glider (Petaurus australis) was detected twice on one pole. Our results demonstrate that gliding mammals readily use glide poles. Further research is needed to resolve whether glide poles can mitigate the barrier effect of the road canopy gap.

Do we underestimate the impact of roads on arboreal animals? Roadkill as an important threat to Chaetomys subspinosus (Mammalia: Rodentia)

Abstract: The Thin-spined Porcupine (Chaetomys subspinosus) is a medium-sized and mainly arboreal rodent, endemic to the Brazilian Atlantic Forest, and threatened with extinction. Habitat loss, hunting, forest fires, agriculture and livestock are threats identified for the species. Here we raise the alert to the impact of roads on remaining populations of C. subspinosus based on roadkill records from the state of Espírito Santo, southeastern Brazil. Mortality due to roadkill is likely to impact C. subspinosus in different regions of the state, and is a widespread problem, not unique to a single location or population. The pattern of roadkills in the studied regions suggest that the species is more susceptible to collisions with vehicles in the breeding period. Additionally, concrete barriers that divide lanes on highways seens to increase the likelihood of roadkill for Thin-spined Porcupines. We recommend that roadkill should be included in the list of threats to C. subspinosus in the Espírito Santo. Mortality due to roadkill is probably relevant also for populations in the states of Bahia and Sergipe, and it should be evaluated locally. The installation of road-crossing structures for wildlife, such as arboreal overpasses, is recommended on roads crossing or close to protected areas with C. subspinosus presence in Espírito Santo and elsewhere.

Demographic and genetic viability of a medium-sized ground-dwelling mammal in a fire prone, rapidly urbanizing landscape

The rapid and large-scale urbanization of peri-urban areas poses major and complex challenges for wildlife conservation. We used population viability analysis (PVA) to evaluate the influence of urban encroachment, fire, and fauna crossing structures, with and without accounting for inbreeding effects, on the metapopulation viability of a medium-sized ground-dwelling mammal, the southern brown bandicoot (Isoodon obesulus), in the rapidly expanding city of Perth, Australia. We surveyed two metapopulations over one and a half years, and parameterized the PVA models using largely field-collected data. The models revealed that spatial isolation imposed by housing and road encroachment has major impacts on I. obesulus. Although the species is known to persist in small metapopulations at moderate levels of habitat fragmentation, the models indicate that these populations become highly vulnerable to demographic decline, genetic deterioration, and local extinction under increasing habitat connectivity loss. Isolated metapopulations were also predicted to be highly sensitive to fire, with large-scale fires having greater negative impacts on population abundance than small-scale ones. To reduce the risk of decline and local extirpation of I. obesulus and other small- to medium-sized ground-dwelling mammals in urbanizing, fire prone landscapes, we recommend that remnant vegetation and vegetated, structurally-complex corridors between habitat patches be retained. Well-designed road underpasses can be effective to connect habitat patches and reduce the probability of inbreeding and genetic differentiation; however, adjustment of fire management practices to limit the size of unplanned fires and ensure the retention of long unburnt vegetation will also be required to ensure persistence. Our study supports the evidence that in rapidly urbanizing landscapes, a pro-active conservation approach is required that manages species at the metapopulation level and that prioritizes metapopulations and habitat with greater long-term probability of persistence and conservation capacity, respectively. This strategy may help us prevent future declines and local extirpations, and currently relatively common species from becoming rare.