Genetic inference as a method for modelling occurrence: A viable alternative to visual surveys

Gaps and opportunities in modelling human influence on species distributions in the Anthropocene

Understanding species distributions is a global priority for mitigating environmental pressures from human activities. Ample studies have identified key environmental (climate and habitat) predictors and the spatial scales at which they influence species distributions. However, regarding human influence, such understandings are largely lacking. Here, to advance knowledge concerning human influence on species distributions, we systematically reviewed species distribution modelling (SDM) articles and assessed current modelling efforts. We searched 12,854 articles and found only 1,429 articles using human predictors within SDMs. Collectively, these studies of >58,000 species used 2,307 unique human predictors, suggesting that in contrast to environmental predictors, there is no 'rule of thumb' for human predictor selection in SDMs. The number of human predictors used across studies also varied (usually one to four per study). Moreover, nearly half the articles projecting to future climates held human predictors constant over time, risking false optimism about the effects of human activities compared with climate change. Advances in using human predictors in SDMs are paramount for accurately informing and advancing policy, conservation, management and ecology. We show considerable gaps in including human predictors to understand current and future species distributions in the Anthropocene, opening opportunities for new inquiries. We pose 15 questions to advance ecological theory, methods and real-world applications.

Noninvasive Genetic Assessment Is an Effective Wildlife Research Tool When Compared with Other Approaches

Wildlife research has been indispensable for increasing our insight into ecosystem functioning as well as for designing effective conservation measures under the currently high rates of biodiversity loss. Genetic and genomic analyses might be able to yield the same information on, e.g., population size, health, or diet composition as other wildlife research methods, and even provide additional data that would not be possible to obtain by alternative means. Moreover, if DNA is collected non-invasively, this technique has only minimal or no impact on animal welfare. Nevertheless, the implementation rate of noninvasive genetic assessment in wildlife studies has been rather low. This might be caused by the perceived inefficiency of DNA material obtained non-invasively in comparison with DNA obtained from blood or tissues, or poorer performance in comparison with other approaches used in wildlife research. Therefore, the aim of this review was to evaluate the performance of noninvasive genetic assessment in comparison with other methods across different types of wildlife studies. Through a search of three scientific databases, 113 relevant studies were identified, published between the years 1997 and 2020. Overall, most of the studies (94%) reported equivalent or superior performance of noninvasive genetic assessment when compared with either invasive genetic sampling or another research method. It might be also cheaper and more time-efficient than other techniques. In conclusion, noninvasive genetic assessment is a highly effective research approach, whose efficacy and performance are likely to improve even further in the future with the development of optimized protocols.

Multiplex PCRs for the specific identification of marsupial and deer species from faecal samples as a basis for non-invasive epidemiological studies of parasites

Background

The specific identification of animals through the analysis of faecal DNA is important in many areas of scientific endeavour, particularly in the field of parasitology.

Methods

Here, we designed and assessed two multiplex PCR assays using genetic markers in a mitochondrial cytochrome b (cytb) gene region for the unequivocal identification and discrimination of animal species based on the specific amplification of DNA from faecal samples collected from water catchment areas in Victoria, Australia. One of these assays differentiates three marsupial species (eastern grey kangaroo, swamp wallaby and common wombat) and the other distinguishes three deer species (fallow, red and sambar deer). We tested these two assays using a total of 669 faecal samples, collected as part of an ongoing programme to monitor parasites and microorganisms in these animals.

Results

These two PCR assays are entirely specific for these animal species and achieve analytical sensitivities of 0.1–1.0 picogram (pg). We tested 669 faecal samples and found that some previous inferences of species based on faecal morphology were erroneous. We were able to molecularly authenticate all of the 669 samples.

Conclusions

We have established PCR assays that accurately distinguish the faecal samples of some of the prominent large mammalian herbivores found within a water catchment system in the state of Victoria, Australia. The multiplex assays for marsupials and deer produce amplicons that are easily differentiable based on their size on an agarose gel, and can be readily sequenced for definitive species authentication. Although established for marsupials and deer, the methodology used here can be applied to other host-parasite study systems to ensure data integrity.

Modeling the distribution of a wide-ranging invasive species using the sampling efforts of expert and citizen scientists

In its invasive range in Australia, the European rabbit threatens the persistence of native flora and fauna and damages agricultural production. Understanding its distribution and ecological niche is critical for developing management plans to reduce populations and avoid further biodiversity and economic losses.We developed an ensemble of species distribution models (SDMs) to determine the geographic range limits and habitat suitability of the rabbit in Australia. We examined the advantage of incorporating data collected by citizens (separately and jointly with expert data) and explored issues of spatial biases in occurrence data by implementing different approaches to generate pseudo-absences. We evaluated the skill of our model using three approaches: cross-validation, out-of-region validation, and evaluation of the covariate response curves according to expert knowledge of rabbit ecology.Combining citizen and expert occurrence data improved model skill based on cross-validation, spatially reproduced important aspects of rabbit ecology, and reduced the need to extrapolate results beyond the studied areas.Our ensemble model projects that rabbits are distributed across approximately two thirds of Australia. Annual maximum temperatures >25°C and annual minimum temperatures >10°C define, respectively, the southern and northern most range limits of its distribution. In the arid and central regions, close access to permanent water (≤~ 0.4 km) and reduced clay soil composition (~20%-50%) were the major factors influencing the probability of occurrence of rabbits. Synthesis and applications. Our results show that citizen science data can play an important role in managing invasive species by providing missing information on occurrences in regions not surveyed by experts because of logistics or financial constraints. The additional sampling effort provided by citizens can improve the capacity of SDMs to capture important elements of a species ecological niche, improving the capacity of statistical models to accurately predict the geographic range of invasive species.