Targeted gene flow and rapid adaptation in an endangered marsupial

Analyzing captive breeding outcomes to inform reintroduction practice: lessons from the pookila (Pseudomys novaehollandiae)

Captive breeding is often used to produce individuals for reintroduction programs in order to reestablish a species in an area where it has become locally extinct. To maximize the likelihood of establishing a self-sustaining population in the wild, an analysis of data from captive breeding programs is commonly undertaken to (1) increase the quantity of individuals and rate at which they can be released, and (2) maintain or improve the genetic and phenotypic quality of individuals. Here we demonstrate how the knowledge gained from these analyses can also be applied to decision-making during the design of subsequent reintroductions to further advance a reintroduction program toward success. We conducted an analysis of data from a captive breeding program for the threatened pookila (Pseudomys novaehollandiae, New Holland mouse) spanning 6 years. We found evidence for relationships between the reproductive output of pookila and behavioral, demographic, experiential, health, and physiological predictors. Based on a biological interpretation of these results, and with reference to a checklist of all known translocation tactics, we recommend 11 specific design elements to maximize the probability of pookila reproduction postrelease (thereby improving the likelihood of reintroduction success). These recommendations should be interpreted as hypotheses to be evaluated and refined in future reintroduction trials for the pookila. The uncertainty around the postrelease survival and reproduction of a species that is common in reintroduction practice warrants the creative use of existing data to inform adaptive management. Indeed, there is a wealth information in well-kept captive breeding records that is currently underused by reintroduction practitioners. The direct integration of knowledge derived from captive breeding (where available) with decision-making for reintroductions, as described here, will help navigate these uncertainties, which would benefit the conservation of both understudied and well-known species around the world.

Addressing prey naivety in native mammals by accelerating selection for antipredator traits

Harnessing natural selection to improve conservation outcomes is a recent concept in ecology and evolutionary biology and a potentially powerful tool in species conservation. One possible application is the use of natural selection to improve antipredator responses of mammal species that are threatened by predation from novel predators. We investigated whether long-term exposure of an evolutionary naïve prey species to a novel predator would lead to phenotypic changes in a suite of physical and behavioral traits. We exposed a founder population of 353 burrowing bettongs (Bettongia lesueur) to feral cats (Felis catus) over 5 years and compared the physical and behavioral traits of this population (including offspring) to a control (non-predator exposed) population. We used selection analysis to investigate whether changes in the traits of bettongs were likely due to phenotypic plasticity or natural selection. We also quantified selection in both populations before and during major population crashes caused by drought (control) and high predation pressure (predator-exposed). Results showed that predator-exposed bettongs had longer flight initiation distances, larger hind feet, and larger heads than control bettongs. Trait divergence began soon after exposure and continued to intensify over time for flight initiation distance and hind foot length relative to control bettongs. Selection analysis found indicators of selection for larger hind feet and longer head length in predator-exposed populations. Results of a common garden experiment showed that the progeny of predator-exposed bettongs had larger feet than control bettongs. Results suggest that long-term, low-level exposure of naïve prey to novel predators can drive phenotypic changes that may assist with future conservation efforts.

Genomic health is dependent on long-term population demographic history

Current genetic methods of population assessment in conservation biology have been challenged by genome-scale analyses due to their quantitatively novel insights. These analyses include assessments of runs-of-homozygosity (ROH), genomic evolutionary rate profiling (GERP), and mutational load. Here, we aim to elucidate the relationships between these measures using three divergent ungulates: white-tailed deer, caribou, and mountain goat. The white-tailed deer is currently expanding, while caribou are in the midst of a significant decline. Mountain goats remain stable, having suffered a large historical bottleneck. We assessed genome-wide signatures of inbreeding using the inbreeding coefficient F and %ROH (F_ROH ) and identified evolutionarily constrained regions with GERP. Mutational load was estimated by identifying mutations in highly constrained elements (CEs) and sorting intolerant from tolerant (SIFT) mutations. Our results showed that F and F_ROH are higher in mountain goats than in caribou and white-tailed deer. Given the extended bottleneck and low N_e of the mountain goat, this supports the idea that the genome-wide effects of demographic change take time to accrue. Similarly, we found that mountain goats possess more highly constrained CEs and the lowest dN/dS values, both of which are indicative of greater purifying selection; this is also reflected by fewer mutations in CEs and deleterious mutations identified by SIFT. In contrast, white-tailed deer presented the highest mutational load with both metrics, in addition to dN/dS, while caribou were intermediate. Our results demonstrate that extended bottlenecks may lead to reduced diversity and increased F_ROH in ungulates, but not necessarily an increase in mutational load, probably due to the purging of deleterious alleles in small populations.

Affordable RFID loggers for monitoring animal movement, activity, and behaviour

Effective conservation management strategies require accurate information on the movement patterns and behaviour of wild animals. To collect these data, researchers are increasingly turning to remote sensing technology such as radio-frequency identification (RFID). RFID technology is a powerful tool that has been widely implemented in ecological research to identify and monitor unique individuals, but it bears a substantial price tag, restricting this technology to generously-funded disciplines and projects. To overcome this price hurdle, we provide detailed step-by-step instructions to source the components for, and construct portable RFID loggers in house, at a fraction of the cost (~5%) of commercial RFID units. Here, we assess the performance of these RFID loggers in the field and describe their application in two studies of Australian mammal species; monitoring nest-box use in the Northern quolls (Dasyurus hallucatus) and observing the foraging habits of quenda (Isoodon fusciventer) at feeding stations. The RFID loggers performed well, identifying quenda in >80% of visits, and facilitating the collection of individual-level behavioural data including common metrics such as emergence time, latency to approach, and foraging effort. While the technology itself is not novel, by lowering the cost per unit, our loggers enabled greater sample sizes, increasing statistical power from 0.09 to 0.75 in the quoll study. Further, we outline and provide solutions to the limitations of this design. Our RFID loggers proved an innovative method for collecting accurate behavioural and movement data. With their ability to successfully identify individuals, the RFID loggers described here can act as an alternative or complementary tool to camera traps. These RFID loggers can also be applied in a wide variety of projects which range from monitoring animal welfare or demographic traits to studies of anti-predator responses and animal personality, making them a valuable addition to the modern ecologists’ toolkit.

Impacts of invasive cane toads on an Endangered marsupial predator and its prey

Recent research has revealed that impacts of some invasive species are chronic. Invasive cane toads Rhinella marina have apparently caused rapid and severe population-level declines of the Endangered northern quoll Dasyurus hallucatus across tropical Australia; however, more targeted, quantitative impact data are needed to disentangle this from other threats such as fire regimes, disease, feral cats and dingos. Moreover, repeatable counts before, during, after and long after toad invasion are needed in order to determine if short-term impacts are chronic vs. transitory. We used game cameras to monitor 2 quoll populations and their prey over a 5 yr period spanning the invasion of the toxic cane toads in 2 gorges in northwestern Australia. We predicted severe declines in quolls with the toad invasion, and predatory release of 2 prey species of quolls, a rodent and a smaller marsupial. Quolls declined quickly upon arrival of toads, becoming undetectable in one gorge and barely detectable in the other. Identification of individuals via unique spot patterns confirmed that the declines in detection rates were due to changes in relative abundance rather than decreases in activity. Despite quoll declines we found no evidence of mesopredator release; small mammals generally declined as toads arrived. Our research confirmed rapid population-level declines of quolls, and possibly smaller mammals, associated with arrival of invasive cane toads. Importantly, our surveys provide a baseline for future surveys to determine whether these short-term impacts are chronic or transitory, and whether recovery requires assistance from managers.

Clair CC, Tobajas J. Conditioned Taste Aversion as a Tool for Mitigating Human-Wildlife Conflicts

Modern wildlife management has dual mandates to reduce human-wildlife conflict (HWC) for burgeoning populations of people while supporting conservation of biodiversity and the ecosystem functions it affords. These opposing goals can sometimes be achieved with non-lethal intervention tools that promote coexistence between people and wildlife. One such tool is conditioned taste aversion (CTA), the application of an evolutionary relevant learning paradigm in which an animal associates a transitory illness to the taste, odor or other characteristic of a particular food item, resulting in a long-term change in its perception of palatability. Despite extensive support for the power of CTA in laboratory studies, field studies have exhibited mixed results, which erodes manager confidence in using this tool. Here we review the literature on CTA in the context of wildlife conservation and management and discuss how success could be increased with more use of learning theory related to CTA, particularly selective association, stimulus salience, stimulus generalization, and extinction of behavior. We apply learning theory to the chronological stages of CTA application in the field and illustrate them by synthesizing and reviewing past applications of CTA in HWC situations. Specifically, we discuss (1) when CTA is suitable, (2) how aversion can be most effectively (and safely) established, (3) how generalization of aversion from treated to untreated food can be stimulated and (4) how extinction of aversion can be avoided. For each question, we offer specific implementation suggestions and methods for achieving them, which we summarize in a decision-support table that might be used by managers to guide their use of CTA across a range of contexts. Additionally, we highlight promising ideas that may further improve the effectiveness of CTA field applications in the future. With this review, we aspire to demonstrate the diverse past applications of CTA as a non-lethal tool in wildlife management and conservation and facilitate greater application and efficacy in the future.

Effects of learning and adaptation on population viability

Cultural adaptation is one means by which conservationists may help populations adapt to threats. A learned behavior may protect an individual from a threat, and the behavior can be transmitted horizontally (within generations) and vertically (between generations), rapidly conferring population-level protection. Although possible in theory, it remains unclear whether such manipulations work in a conservation setting; what conditions are required for them to work; and how they might affect the evolutionary process. We examined models in which a population can adapt through both genetic and cultural mechanisms. Our work was motivated by the invasion of highly toxic cane toads (Rhinella marina) across northern Australia and the resultant declines of endangered northern quolls (Dasyurus hallucatus), which attack and are fatally poisoned by the toxic toads. We examined whether a novel management strategy in which wild quolls are trained to avoid toads can reduce extinction probability. We used a simulation model tailored to quoll life history. Within simulations, individuals were trained and a continuous evolving trait determined innate tendency to attack toads. We applied this model in a population viability setting. The strategy reduced extinction probability only when heritability of innate aversion was low (<20%) and when trained mothers trained >70% of their young to avoid toads. When these conditions were met, genetic adaptation was slower, but rapid cultural adaptation kept the population extant while genetic adaptation was completed. To gain insight into the evolutionary dynamics (in which we saw a transitory peak in cultural adaptation over time), we also developed a simple analytical model of evolutionary dynamics. This model showed that the strength of natural selection declined as the cultural transmission rate increased and that adaptation proceeded only when the rate of cultural transmission was below a critical value determined by the relative levels of protection conferred by genetic versus cultural mechanisms. Together, our models showed that cultural adaptation can play a powerful role in preventing extinction, but that rates of cultural transmission need to be high for this to occur.

Genomic Approaches for Conservation Management in Australia under Climate Change

Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change.

Adaptive Divergence under Gene Flow along an Environmental Gradient in Two Coexisting Stickleback Species

There is a general and solid theoretical framework to explain how the interplay between natural selection and gene flow affects local adaptation. Yet, to what extent coexisting closely related species evolve collectively or show distinctive evolutionary responses remains a fundamental question. To address this, we studied the population genetic structure and morphological differentiation of sympatric three-spined and nine-spined stickleback. We conducted genotyping-by-sequencing and morphological trait characterisation using 24 individuals of each species from four lowland brackish water (LBW), four lowland freshwater (LFW) and three upland freshwater (UFW) sites in Belgium and the Netherlands. This combination of sites allowed us to contrast populations from isolated but environmentally similar locations (LFW vs. UFW), isolated but environmentally heterogeneous locations (LBW vs. UFW), and well-connected but environmentally heterogenous locations (LBW vs. LFW). Overall, both species showed comparable levels of genetic diversity and neutral genetic differentiation. However, for all three spatial scales, signatures of morphological and genomic adaptive divergence were substantially stronger among populations of the three-spined stickleback than among populations of the nine-spined stickleback. Furthermore, most outlier SNPs in the two species were associated with local freshwater sites. The few outlier SNPs that were associated with the split between brackish water and freshwater populations were located on one linkage group in three-spined stickleback and two linkage groups in nine-spined stickleback. We conclude that while both species show congruent evolutionary and genomic patterns of divergent selection, both species differ in the magnitude of their response to selection regardless of the geographical and environmental context.

Choose your meals carefully if you need to coexist with a toxic invader

Vulnerable native species may survive the impact of a lethally toxic invader by changes in behaviour, physiology and/or morphology. The roles of such mechanisms can be clarified by standardised testing. We recorded behavioural responses of monitor lizards (Varanus panoptes and V. varius) to legs of poisonous cane toads (Rhinella marina) and non-toxic control meals (chicken necks or chicken eggs and sardines) along 1300 and 2500 km transects, encompassing the toad's 85-year invasion trajectory across Australia as well as yet-to-be-invaded sites to the west and south of the currently colonised area. Patterns were identical in the two varanid species. Of monitors that consumed at least one prey type, 96% took control baits whereas toad legs were eaten by 60% of lizards in toad-free sites but 0% from toad-invaded sites. Our survey confirms that the ability to recognise and reject toads as prey enables monitor lizards to coexist with cane toads. As toxic invaders continue to impact ecosystems globally, it is vital to understand the mechanisms that allow some taxa to persist over long time-scales.

Learning in non-avian reptiles 40 years on: advances and promising new directions

Recently, there has been a surge in cognition research using non-avian reptile systems. As a diverse group of animals, non-avian reptiles [turtles, the tuatara, crocodylians, and squamates (lizards, snakes and amphisbaenids)] are good model systems for answering questions related to cognitive ecology, from the role of the environment on the brain, behaviour and learning, to how social and life-history factors correlate with learning ability. Furthermore, given their variable social structure and degree of sociality, studies on reptiles have shown that group living is not a pre-condition for social learning. Past research has demonstrated that non-avian reptiles are capable of more than just instinctive reactions and basic cognition. Despite their ability to provide answers to fundamental questions in cognitive ecology, and a growing literature, there have been no recent systematic syntheses of research in this group. Here, we systematically, and comprehensively review studies on reptile learning. We identify 92 new studies investigating learning in reptiles not included in previous reviews on this topic - affording a unique opportunity to provide a more in-depth synthesis of existing work, its taxonomic distribution, the types of cognitive domains tested and methodologies that have been used. Our review therefore provides a major update on our current state of knowledge and ties the collective evidence together under nine umbrella research areas: (i) habituation of behaviour, (ii) animal training through conditioning, (iii) avoiding aversive stimuli, (iv) spatial learning and memory, (v) learning during foraging, (vi) quality and quantity discrimination, (vii) responding to change, (viii) solving novel problems, and (ix) social learning. Importantly, we identify knowledge gaps and propose themes which offer important future research opportunities including how cognitive ability might influence fitness and survival, testing cognition in ecologically relevant situations, comparing cognition in invasive and non-invasive populations of species, and social learning. To move the field forward, it will be immensely important to build upon the descriptive approach of testing whether a species can learn a task with experimental studies elucidating causal reasons for cognitive variation within and among species. With the appropriate methodology, this young but rapidly growing field of research should advance greatly in the coming years providing significant opportunities for addressing general questions in cognitive ecology and beyond.

Skull shape of a widely distributed, endangered marsupial reveals little evidence of local adaptation between fragmented populations

The biogeographic distribution of diversity among populations of threatened mammalian species is generally investigated using population genetics. However, intraspecific phenotypic diversity is rarely assessed beyond taxonomy-focused linear measurements or qualitative descriptions. Here, we use a technique widely used in the evolutionary sciences-geometric morphometrics-to characterize shape diversity in the skull of an endangered marsupial, the northern quoll, across its 5,000 km distribution range along Northern Australia. Skull shape is a proxy for feeding, behavior, and phenotypic differentiation, allowing us to ask whether populations can be distinguished and whether patterns of variation indicate adaptability to changing environmental conditions. We analyzed skull shape in 101 individuals across four mainland populations and several islands. We assessed the contribution of population, size, sex, rainfall, temperature, and geography to skull shape variation using principal component analysis, Procrustes ANOVA, and variation partitioning analyses. The populations harbor similar amounts of broadly overlapping skull shape variation, with relatively low geographic effects. Size predicted skull shape best, coinciding with braincase size variation and differences in zygomatic arches. Size-adjusted differences in populations explained less variation with far smaller effect sizes, relating to changes in the insertion areas of masticatory muscles, as well as the upper muzzle and incisor region. Climatic and geographic variables contributed little. Strikingly, the vast majority of shape variation-76%-remained unexplained. Our results suggest a uniform intraspecific scope for shape variation, possibly due to allometric constraints or phenotypic plasticity beyond the relatively strong allometric effect. The lack of local adaptation indicates that cross-breeding between populations will not reduce local morphological skull (and probably general musculoskeletal) adaptation because none exists. However, the potential for heritable morphological variation (e.g., specialization to local diets) seems exceedingly limited. We conclude that 3D geometric morphometrics can provide a comprehensive, statistically rigorous phenomic contribution to genetic-based conservation studies.

Quantifying the efficacy of genetic shifting in control of mosquito-borne diseases

Many of the world's most prevalent diseases are transmitted by animal vectors such as dengue transmitted by mosquitoes. To reduce these vector-borne diseases, a promising approach is "genetic shifting": selective breeding of the vectors to be more resistant to pathogens and releasing them to the target populations to reduce their ability to transmit pathogens, that is, lower their vector competence. The efficacy of genetic shifting will depend on possible counterforces such as natural selection against low vector competence. To quantitatively evaluate the potential efficacy of genetic shifting, we developed a series of coupled genetic-demographic models that simulate the changes of vector competence during releases of individuals with low vector competence. We modeled vector competence using different genetic architectures, as a multilocus, one-locus, or two-locus trait. Using empirically determined estimates of model parameters, the model predicted a reduction of mean vector competence of at least three standard deviations after 20 releases, one release per generation, and 10% of the size of the target population released each time. Sensitivity analysis suggested that release efficacy depends mostly on the vector competence of the released population, release size, release frequency, and the survivorship of the released individuals, with duration of the release program less important. Natural processes such as density-dependent survival and immigration from external populations also strongly influence release efficacy. Among different sex-dependent release strategies, releasing blood-fed females together with males resulted in the highest release efficacy, as these females mate in captivity and reproduce when released, thus contributing a greater proportion of low-vector-competence offspring. Conclusions were generally consistent across three models assuming different genetic architectures of vector competence, suggesting that genetic shifting could generally apply to various vector systems and does not require detailed knowledge of the number of loci contributing to vector competence.

How many and when? Optimising targeted gene flow for a step change in the environment

Targeted gene flow is an emerging conservation strategy that involves introducing individuals with particular traits to places where these traits are of benefit. One obvious application is to adapt a recipient population to a known threat, but questions remain as to how best to achieve this. Here, we vary timing and size of the introduction to maximise our objective - survival of the recipient population's genome. We explore a generic population model as well as a specific example - the northern quoll, an Australian marsupial predator threatened by the toxic cane toad. We reveal a trade-off between preserving the recipient genome and reducing population extinction risk, but key management levers can often optimise this so that nearly 100% of the recipient population's genome is preserved. Any action was better than none but the size of the benefit was sensitive to outbreeding depression, recombination rate, and the timing and size of the introduction.