Genotyping-by-sequencing based SNP discovery in a non-model rodent, the endangered hazel dormouse

The hazel dormouse Muscardinus avellanarius presents an exemplary non-model species that is both locally threatened and whose genetic status is not fully understood owing to insufficient resolution of the currently available molecular tools. We performed normalized Genotyping-by-Sequencing (nGBS) on 48 hazel dormouse samples collected across the species European distribution, aiming at discovering useful single nucleotide polymorphism (SNP) markers for the assessment of population structure and genomic diversity. The analyses of > 24,000 SNPs showed a high divergence between the Eastern and Western lineage of the species with high rates of SNP allele fixation, consistent with previous studies suggesting the divergence of lineages occurred over 2 mya. These results indicate that investigating inter-lineage as well as within-lineage genetic composition will be a conclusive approach for identifying conservation strategies in the future. Results presented here indicate the highest genetic divergence in the Italian and Lithuanian populations. We document how nGBS allows the discovery of SNPs that can characterize patterns of genetic variation at multiple spatial scales in a non-model organism. We document how nGBS allows the discovery of SNPs that can characterize patterns of genetic variation at multiple spatial scales in a non-model organism, potentially informing monitoring and conservation strategies.

Different Species Requirements within a Heterogeneous Spring Complex Affects Patch Occupancy of Threatened Snails in Australian Desert Springs

(1) The distribution of organisms that inhabit patchy systems is dictated by their ability to move between patches, and the suitability of environmental conditions at patches to which they disperse. Understanding whether the species involved are identical to one another in their environmental requirements and their responses to variance in their environment is essential to understanding ecological processes in these systems, and to the management of species whose patchy and limited distributions present conservation risks. (2) Artesian springs in Australia’s arid interior are “islands” of hospitable wetland in uninhabitable “oceans” of dry land and are home to diverse and threatened assemblages of endemic species with severely restricted distributions. Many have strict environmental requirements, but the role of environmental heterogeneity amongst springs has rarely been considered alongside conventional patch characteristics (isolation and patch geometry). (3) We quantified environmental heterogeneity across springs, and the relationship between spring size, isolation (distances to neighbours) and environmental quality (depth, water chemistry), and patterns of occupancy and population persistence of six endemic spring snail species, all from different families, and with all restricted to a single <8000 ha system of springs in Australia. To do so, a survey was conducted for comparison against survey results of almost a decade before, and environmental variables of the springs were measured. Many of the snail species occupied few sites, and environmental variables strongly covaried, so an ordination-based approach was adopted to assess the relationship between environmental measures and the distribution of each species, and also whether springs that held a higher diversity of snails had specific characteristics. (4) Each snail species occupied a subset of springs (between 5% and 36% of the 85 sampled) and was associated with a particular set of conditions. Of the six species considered in further detail, most were restricted to the few springs that were large and deep. Species in family Tateidae were distinct in having colonised highly isolated springs (with >300 m to nearest neighbour). Springs with highest diversity were significantly larger, deeper and had more numerous neighbours within 300 m than those devoid of endemic snails, or those with low diversity. (5) Although spring size and isolation affect patterns of occupancy, the six snail species had significantly different environmental requirements from one another and these correlated with the distribution pattern of each. Approaches that ignore the role of environmental quality—and particularly depth in springs—are overlooking important processes outside of patch geometry that influence diversity. These organisms are highly susceptible to extinction, as most occupy less than 3 ha of habitat spread across few springs, and habitat degradation continues to compromise what little wetland area is needed for their persistence.

Gimme shelter: The effect of rocks and moonlight on occupancy and activity pattern of an endangered rodent, the garden dormouse Eliomys quercinus

Information on spatial behaviour and temporal activity patterns is paramount for the conservation of animal species. This is particularly true for endangered taxa that are threatened by ongoing climatic and environmental changes. The garden dormouse Eliomys quercinus is a native European rodent (family Gliridae), whose populations are declining throughout the Continent. Notwithstanding this, neither International nor National laws explicitly require mandatory monitoring of populations. As a result, compelling information on the spatiotemporal behaviour of dormouse is lacking. We aimed to fill this gap by investigating occupancy patterns in relation to environmental features and activity rhythms in relation to moonlit nights in an Alpine population of dormouse within the Stelvio National Park, northern Italy. Data were collected between May and October 2015. Twenty camera-traps were deployed in a 500 ha coniferous forest, using a random tessellation approach; camera trap data were analyzed with occupancy models and kernel smoothers. Camera-traps provided a reliable assessment of the presence of the garden dormouse, with only 1 % of false absence and a high detection probability (68 %). The occurrence of the garden dormouse was positively influenced by the percentage of rock coverage on the ground. The species showed a strictly nocturnal behaviour, with an activity peak before midnight, negatively related to moonlit nights. The use of rocky areas for nesting, shelter site and thigmotactic movements and moonlight avoidance may represent adaptations of the garden dormouse to avoid predation risk. Our results shed some light on the habitat requirement of a poorly known, near-threatened species, and provide baseline information for future monitoring and conservation activities.

Predation risk and patch size jointly determine perceived patch quality in ovipositing treefrogs, Hyla chrysoscelis

Two of the most important factors determining community structure and diversity within and among habitat patches are patch size and patch quality. Despite the importance of patch size in existing paradigms in island biogeography, metapopulation biology, landscape ecology, and metacommunity ecology, and growing conservation concerns with habitat fragmentation, there has been little investigation into how patch size interacts with patch quality. We crossed three levels of patch size (1.13 m² , 2.54 m² and 5.73 m² ) with two levels of patch quality (fish presence/absence, green sunfish [Lepomis cyanellus] and golden shiners [Notemigonus crysoleucus]) in six replicate experimental landscapes (3 × 2 × 6 = 36 patches). Both fish predators have been previously shown to elicit avoidance in ovipositing treefrogs. We examined how patch size and patch quality, as well as the interaction between size and quality, affected female oviposition preference and male calling site choice in a natural population of treefrogs (Hyla chrysoscelis). Females almost exclusively oviposited in the largest fishless patches, indicating that females use both risk, in the form of fish predators, and size itself, as components of patch quality. Females routinely use much smaller natural and experimental patches, suggesting that the responses to patch size are highly context dependent. Responses to fish were unaffected by patch size. Male responses largely mimicked those of females, but did not drive female oviposition. We suggest that patch size itself functions as another aspect of patch quality for H. chrysoscelis, and serves as another niche dimension across which species may behaviorally sort in natural systems. Because of strong, shared avoidance of fish (as well as other predators), among many colonizing taxa, patch size may be a critical factor in species sorting and processes of community assembly in freshwater habitats, allowing species to behaviorally segregate along gradients of patch size in fishless ponds. Conversely, lack of variation in patch size may concentrate colonization activity, leading to intensification of species interactions and/or increased use of lesser quality patches.

Locally dispersing populations in heterogeneous dynamic landscapes with spatiotemporal correlations. I. Block disturbance

Locally dispersing populations are generally favorably affected by increasing the scale of habitat heterogeneity because they can exploit contiguous patches of suitable habitat. Increasing the spatial scale of landscape disturbances (such as by applying a pesticide to control an unwanted species) drives down population density because of reasons including dispersal-limited recolonization and the resulting increase in temporal variability. Here, we examine how population density changes as the spatial scale of landscape disturbance increases: does it increase due to increases in spatial correlations in landscape habitat type, or does it decrease due to the various spatial and temporal effects of larger-scale disturbances? We use simulations, mean field approximations, pair approximations, landscape-improved pair approximations (LIPA), and block probabilities to investigate a model of a locally dispersing species on a dynamic landscape with spatiotemporally structured heterogeneous habitat. Pesticide is applied at a given spatial scale, leaving habitat unsuitable for some time before dissipating and allowing the habitat to revert to a suitable state. We found that increasing the spatial scale of disturbances (while keeping the overall disturbance rate fixed) can increase population density, but generally only when landscape turnover is slow relative to population dynamics and when the population is somewhat close to its extinction threshold. Applying control measures at larger spatial scales may allow them to be more effective with the same overall treatment rate. The optimal spatial strategy for applying disturbances depends on both habitat availability as well as the turnover rate of the control measure being used. For the large-scale habitat dynamics in our model, it is possible to analytically calculate spatial correlations in habitat types over arbitrary scales. However, including exact habitat correlations at the triplet scale but approximating population correlations at that scale still neglects information needed to accurately predict simulation results, showing that larger-scale correlations in the population distribution have an important effect on dynamics.