Using genetic techniques to quantify reinvasion, survival andin situbreeding rates during control operations

Using a Modeling Approach to Inform Progress Towards Stoat Eradication From the Orkney Islands

Invasive non-native species eradication attempts are typically large and expensive projects that benefit from the support of quantitative tools, such as population models, to be completed within the scheduled and funded time. Managed ecosystems are constantly changing due to population and ecosystem dynamics. Accordingly, any model predictions need to be updated, using different sources of data, to inform the project about the progress toward eradication. The stoat Mustela erminea was introduced to the hitherto predatory land mammal free Orkney archipelago around 2010. In 2016, a project aiming to eradicate stoats to preserve ecologically and economically important native wildlife was designed and implemented. It entailed a “knockdown” phase followed by a “mopping-up” phase to remove stoats that escaped capture. We used data from this project to iteratively predict the progress toward eradication. We applied spatially explicit individual-based models to estimate the proportion of stoats being exposed to capture, and then compared these simulation-based predictions with removal data, allowing us to estimate changes in the population size through time. We also used sighting data from members of the public to refine eradication probability. We were also able to demonstrate how the initially wide uncertainty gradually diminished as more evidence accumulated. The information derived from different types of data and quantitative models allowed us to track the effectiveness of current trapping approaches and to help to inform project managers about when the project achieved the knockdown phase milestone. Our analyses confirmed that the expected magnitude of the initial knockdown phase has been achieved in some areas, but also revealed spatial and temporal heterogeneity in the distribution of captures, most likely caused by the sequential trapping and stoat movement and trap shy stoats exposed to capture but not caught. This heterogeneity calls for additional data sources (e.g., from camera traps or detection dogs) to estimate the proportion of trap-shy individuals and the size of the untrapped population, and ultimately the feasibility of eradication.

Population Genetics of the Invasive Red Fox, Vulpes vulpes, in South-Eastern Australia

The use of genetic information in conservation biology has become more widespread with genetic information more readily available for non-model organisms. It has also been recognized that genetic information from invasive species can inform their management and control. The red fox poses a significant threat to Australian native fauna and the agricultural industry. Despite this, there are few recently published studies investigating the population genetics of foxes in Australia. This study investigated the population genetics of 94 foxes across the Illawarra and Shoalhaven regions of New South Wales, Australia. Diversity Array sequencing technology was used to genotype a large number of single nucleotide polymorphisms (N = 33,375). Moderate genetic diversity and relatedness were observed across the foxes sampled. Low to moderate levels of inbreeding, high-levels of identity-by-state values, as well as high identity-by-descent values were also found. There was limited evidence for population genetic structure among the foxes across the landscape sampled, supporting the presence of a single population across the study area. This indicates that there may be no barriers hindering fox dispersal across the landscape.

A population genetic study of feral cats on Christmas Island

Feral and stray cats are a major threat for endemic species on Christmas Island and have been contributing to their decline. Cats were introduced to Christmas Island in 1888 and are now distributed across the whole island. We analysed the genetic population structure and diversity of feral and stray cats on Christmas Island to evaluate connectivity across the island and the possibility of discernible populations that could be targeted separately. Results indicate no differentiated population structure across the island, with cats facing no habitat obstacles to reduce their dispersal abilities across the island. We found high kin structure, suggesting individuals breeding successfully on the whole island. With the management of domestic and feral/stray cats since 2010, removal efforts targeting the whole island have successfully reduced the effective population size of feral/stray cats in the last five years. We suggest the use of various management techniques to facilitate future removal efforts, especially in areas on the island that are difficult to access.

Using Genetics to Evaluate the Success of a Feral Cat (Felis catus) Control Program in North-Western Australia

Simple Summary

The management of invasive species is a major challenge for the conservation of biodiversity globally. One technique that has been widely used to control feral cats (Felis catus) and red foxes (Vulpes vulpes) in Western Australia is the aerial broadcast of toxic baits, but assessing its efficacy can be difficult. Here, we report on a method of evaluating the effectiveness of this method for the abatement of feral cats using genetic analysis techniques. However, our results were unable to provide robust evidence that, over a five-year program, baiting had a detrimental impact on both genetics and demography in this population, and the results were not significant. Monitoring the impact of control programs in this way may provide valuable information to managers on the effectiveness of their management strategy, but further refinement of the methodology is recommended.

Abstract

The feral cat has been implicated in the decline and extinction of many species worldwide and a range of strategies have been devised for its control. A five-year control program using the aerial broadcast of toxic Eradicat^® baits was undertaken at Fortescue Marsh in the Pilbara region of north-western Australia, for the protection of biodiversity in this important wetland area. This program has been shown to have had a significant detrimental effect on cats in this landscape, but the long-term impact is difficult to ascertain. We assessed population genetics across three cohorts of feral cats sampled as part of the control program. We also compared cat populations in natural habitats and around human infrastructure. A key challenge in any study of wild animal populations is small sample sizes and feral cats are particularly difficult to capture and sample. The results of this study superficially appear to suggest promising trends but were limited by sample size and many were not statistically significant. We find that the use of genetic techniques to monitor the impact of invasive species control programs is potentially useful, but ensuring adequate sample sizes over a long enough time-frame will be critical to the success of such studies.

Using fine-scale spatial genetics of Norway rats to improve control efforts and reduce leptospirosis risk in urban slum environments

The Norway rat (Rattus norvegicus) is a key pest species globally and responsible for seasonal outbreaks of the zoonotic bacterial disease leptospirosis in the tropics. The city of Salvador, Brazil, has seen recent and dramatic increases in human population residing in slums, where conditions foster high rat density and increasing leptospirosis infection rates. Intervention campaigns have been used to drastically reduce rat numbers. In planning these interventions, it is important to define the eradication units - the spatial scale at which rats constitute continuous populations and from where rats are likely recolonizing, post-intervention. To provide this information, we applied spatial genetic analyses to 706 rats collected across Salvador and genotyped at 16 microsatellite loci. We performed spatially explicit analyses and estimated migration levels to identify distinct genetic units and landscape features associated with genetic divergence at different spatial scales, ranging from valleys within a slum community to city-wide analyses. Clear genetic breaks exist between rats not only across Salvador but also between valleys of slums separated by <100 m-well within the dispersal capacity of rats. The genetic data indicate that valleys may be considered separate units and identified high-traffic roads as strong impediments to rat movement. Migration data suggest that most (71-90%) movement is contained within valleys, with no clear source population contributing to migrant rats. We use these data to recommend eradication units and discuss the importance of carrying out individual-based analyses at different spatial scales in urban landscapes.

Low genetic diversity but strong population structure reflects multiple introductions of western flower thrips (Thysanoptera: Thripidae) into China followed by human-mediated spread

Historical invasion scenarios based on observational records are usually incomplete and biased, but these can be supplemented by population genetic data. The western flower thrips (WFT), Frankliniella occidentalis, invaded China in the last 13 years and has rapidly become one of the most serious pests in the country. To assess whether this invasion involved a single event or multiple events, we examined patterns of genetic diversity and population structure of WFT across 12 Chinese populations and a native US population based on mitochondrial DNA and/or 18 microsatellite loci. The average allelic richness and haplotype diversity in Chinese populations were significantly lower than in a population from its native range. The distribution of mitochondrial haplotypes suggested multiple independent invasions of WFT into China, including two invasions into the Beijing region. Based on microsatellite data, two distinct clusters were identified, with both of them splitting further into two clusters; in the Beijing region, the microsatellite data also provided evidence for two introductions. Both the absence of isolation by distance and the fact that distant populations were similar genetically suggest patterns of WFT movement linked to human activities. Our study therefore suggests multiple introductions of WFT into China and human-assisted spread.

Capturing the cryptic: a comparison of detection methods for stoats (Mustela erminea) in alpine habitats

Context The ability to monitor the spatial distribution and abundance of species is essential for detecting population changes, and assessing the progress of conservation management programs. Stoats (Mustela erminea) are a serious conservation pest in New Zealand, but current monitoring methods are not sensitive enough to detect stoats in all situations. Aims We compare the effectiveness of the most commonly employed method for monitoring mustelids in New Zealand, footprint-tracking tunnels, with two alternative detection methods, camera traps and artificial nests. We were interested in determining whether alternative detection methods were more sensitive in detecting stoats than tracking tunnels. Methods We established a network of tracking tunnels, artificial nests and camera traps within alpine habitat. Devices were checked for stoat detections weekly across two seasons, in spring–early summer and autumn. Differences in detection rates and cost effectiveness among methods were analysed among seasons. Key results In spring–early summer, the time to first stoat detection using footprint-tracking tunnels was 61 days, compared with 7 days for camera traps and 8 days for artificial nests. The rate of stoat detection using artificial nests was significantly higher than it was using tracking tunnels (coef = 3.05 ± 1.29, P = 0.02), and moderately higher using camera traps (coef = 1.34 ± 1.09, P = 0.22). In autumn, when overall detectability of stoats was higher, there was no significant difference in detection rates among the three methods, although camera traps again recorded the earliest detection. Artificial nests were the most cost effective detection method in both seasons. Conclusions Artificial nests and camera traps were more efficient at detecting stoats during their spring breeding season (when they are known to be difficult to detect), compared with the more established footprint-tracking tunnel method. Artificial nests have potential to be developed into a monitoring index for small mammals, although further research is required. Both methods provide an important alternative to footprint tracking indices for monitoring stoats. Implications Our study demonstrated the importance of calibration among different monitoring methods, particularly when the target species is difficult to detect. We hypothesise that detection methods that do not rely on conspicuous, artificially constructed devices, may be more effective for monitoring small, cryptic mammals.

Inferential and forward projection modeling to evaluate options for controlling invasive mammals on islands

Successful pest-mammal eradications from remote islands have resulted in important biodiversity benefits. Near-shore islands can also serve as refuges for native biota but require ongoing effort to maintain low-pest or pest-free status. Three management options are available in the presence of reinvasion risk: (1) control-to-zero density, in which immigration may occur but reinvaders are removed; (2) sustained population suppression (to relatively low numbers); or (3) no action. Biodiversity benefits can result from options one and two. The management challenge is to make evidence-based decisions on the selection of an appropriate objective and to identify a financially feasible control strategy that has a high probability of success. This requires understanding the pest species population dynamics and how it will respond to a range of potential management strategies, each with an associated financial cost. We developed a two-stage modeling approach that consisted of (1) Bayesian inferential modeling to estimate parameters for a model of pest population dynamics and control, and (2) a forward projection model to simulate a range of plausible management scenarios and quantify the probability of obtaining zero density within four years. We applied the model to an ongoing, six-year trapping program to control stoats (Mustela erminea) on Resolution Island, New Zealand. Zero density has not yet been achieved. Results demonstrate that management objectives were impeded by a combination of a highly fecund population, insufficient trap attractiveness, and a substantial proportion of the population that did not enter traps. Immigration is known to occur because the founding population arrived on the island by swimming from the mainland. However, immigration rate during this study was indistinguishable from zero. The forward projection modeling showed that control-to-zero density was feasible but required greater than a two-fold budget increase to intensify the trapping rate relative to population growth. The two-stage modeling provides the foundation for a management program in which broad-scale trials of additional trapping effort or improved trap lures would test model predictions and increase our understanding of system dynamics.

Feral Cat Globetrotters: genetic traces of historical human-mediated dispersal

Endemic species on islands are highly susceptible to local extinction, in particular if they are exposed to invasive species. Invasive predators, such as feral cats, have been introduced to islands around the world, causing major losses in local biodiversity. In order to control and manage invasive species successfully, information about source populations and level of gene flow is essential. Here, we investigate the origin of feral cats of Hawaiian and Australian islands to verify their European ancestry and a potential pattern of isolation by distance. We analyzed the genetic structure and diversity of feral cats from eleven islands as well as samples from Malaysia and Europe using mitochondrial DNA (ND5 and ND6 regions) and microsatellite DNA data. Our results suggest an overall European origin of Hawaiian cats with no pattern of isolation by distance between Australian, Malaysian, and Hawaiian populations. Instead, we found low levels of genetic differentiation between samples from Tasman Island, Lana'i, Kaho'olawe, Cocos (Keeling) Island, and Asia. As these populations are separated by up to 10,000 kilometers, we assume an extensive passive dispersal event along global maritime trade routes in the beginning of the 19th century, connecting Australian, Asian, and Hawaiian islands. Thus, islands populations, which are characterized by low levels of current gene flow, represent valuable sources of information on historical, human‐mediated global dispersal patterns of feral cats.

Reduced Genetic Diversity and Increased Structure in American Mink on the Swedish Coast following Invasive Species Control

Eradication and population reductions are often used to mitigate the negative impacts of non-native invasive species on native biodiversity. However, monitoring the effectiveness of non-native species control programmes is necessary to evaluate the efficacy of these measures. Genetic monitoring could provide valuable insights into temporal changes in demographic, ecological, and evolutionary processes in invasive populations being subject to control programmes. Such programmes should cause a decrease in effective population size and/or in genetic diversity of the targeted non-native species and an increase in population genetic structuring over time. We used microsatellite DNA data from American mink (Neovison vison) to determine whether the removal of this predator on the Koster Islands archipelago and the nearby Swedish mainland affected genetic variation over six consecutive years of mink culling by trappers as part of a population control programme. We found that on Koster Islands allelic richness decreased (from on average 4.53 to 3.55), genetic structuring increased, and effective population size did not change. In contrast, the mink population from the Swedish coast showed no changes in genetic diversity or structure, suggesting the stability of this population over 6 years of culling. Effective population size did not change over time but was higher on the coast than on the islands across all years. Migration rates from the islands to the coast were almost two times higher than from the coast to the islands. Most migrants leaving the coast were localised on the southern edge of the archipelago, as expected from the direction of the sea current between the two sites. Genetic monitoring provided valuable information on temporal changes in the population of American mink suggesting that this approach can be used to evaluate and improve control programmes of invasive vertebrates.

Genetic evidence for ecological divergence in kokanee salmon

The evolution of locally adapted phenotypes among populations that experience divergent selective pressures is a central mechanism for generating and maintaining biodiversity. Recently, the advent of high-throughput DNA sequencing technology has provided tools for investigating the genetic basis of this process in natural populations of nonmodel organisms. Kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), occurs as two reproductive ecotypes, which differ in spawning habitat (tributaries vs. shorelines); however, outside of the spawning season the two ecotypes co-occur in many lakes and lack diagnostic morphological characteristics. We used restriction site-associated DNA (RAD) sequencing to identify 6145 SNPs and genotype kokanee from multiple spawning sites in Okanagan Lake (British Columbia, Canada). Outlier tests revealed 18 loci putatively under divergent selection between ecotypes, all of which exhibited temporally stable allele frequencies within ecotypes. Six outliers were annotated to sequences in the NCBI database, two of which matched genes associated with early development. There was no evidence for neutral genetic differentiation; however, outlier loci demonstrated significant structure with respect to ecotype and had high assignment accuracy in mixed composition simulations. The absence of neutral structure combined with a small number of highly divergent outlier loci is consistent with theoretical predictions for the early stages of ecological divergence. These outlier loci were then applied to a realistic fisheries scenario in which additional RAD sequencing was used to genotype kokanee collected by trawl in Okanagan Lake, providing preliminary evidence that this approach may be an effective tool for conservation and management.

Measuring connectivity of invasive stoat populations to inform conservation management

Context Effective design of conservation management programs for long-term population control requires an accurate definition of the spatial extent of populations, along with a proper understanding of the ways that landscape patchiness influences demography and dispersal within these populations. Aims In the present study, genetic techniques are used to describe the population genetic structure and connectivity of invasive stoats (Mustela erminea) across the Auckland region, New Zealand, so as to assist planning for mainland stoat control, and define potential future eradication units. Methods A sample of stoats from across the region (n = 120), was genotyped at 17 microsatellite loci, and a combination of clustering, genetic population assignment and various migration estimation methods were applied to these data. Key results Moderate population structure was observed (FST = 0.03–0.21), with five geographic populations defined by genetic clustering. Almost all individuals were correctly assigned to the location of origin, and recent migration rates among forest patches were found to be low. Conclusions It is possible to define the origin of stoats at this regional scale using genetic measures. From this, we show that the stoat incursion on Rangitoto Island that occurred post-eradication in 2010 probably came from East Auckland (P < 0.0001), whereas the 2014 stoat incursion on Motutapu Island probably originated from a population linked to the Waitakeres. Also, the Waiheke Island stoat population has minimal connection to all other populations and it is therefore a potential eradication unit. Implications The low migration rates among forest patches indicated that if thorough control is imposed on a discrete forest patch, reinvasion from other forest patches will be relatively low. Importantly, for stoat control in the region, the isolation of the Waiheke Island stoat population means that eradication here is likely to be feasible with low reinvasion pressure.