Occupancy in dynamic systems: accounting for multiple scales and false positives using environmental DNA to inform monitoring

Occupancy is an important metric to understand current and future trends in populations that have declined globally. In addition, occupancy can be an efficient tool for conducting landscape-scale and long-term monitoring. A challenge for occupancy monitoring programs is to determine the appropriate spatial scale of analysis and to obtain precise occupancy estimates for elusive species. We used a multi-scale occupancy model to assess occupancy of Columbia spotted frogs in the Great Basin, USA, based on environmental DNA (eDNA) detections. We collected three replicate eDNA samples at 220 sites across the Great Basin. We estimated and modeled ecological factors that described watershed and site occupancy at multiple spatial scales simultaneously while accounting for imperfect detection. Additionally, we conducted visual and dipnet surveys at all sites and used our paired detections to estimate the probability of a false positive detection for our eDNA sampling. We applied the estimated false positive rate to our multi-scale occupancy dataset and assessed changes in model selection. We had higher naïve occupancy estimates for eDNA (0.37) than for traditional survey methods (0.20). We estimated our false positive detection rate per qPCR replicate at 0.023 (95% CI: 0.016–0.033). When the false positive rate was applied to the multi-scale dataset, we did not observe substantial changes in model selection or parameter estimates. Conservation and resource managers have an increasing need to understand species occupancy in highly variable landscapes where the spatial distribution of habitat changes significantly over time due to climate change and human impact. A multi-scale occupancy approach can be used to obtain regional occupancy estimates that can account for spatially dynamic differences in availability over time, especially when assessing potential declines. Additionally, this study demonstrates how eDNA can be used as an effective tool for improved occupancy estimates across broad geographic scales for long-term monitoring.     

Transferring sediment containing intact seed banks: a method for studying plant community ecology

The experimental study of the ecology of natural plant communities is necessary to demonstrate the effects of environmental factors on plant growth. It allows one to make predictions of the likely effects of environmental changes on plant communities. Manipulating an entire ecosystem is complicated, and is rarely attempted. An alternative method is applied here for the submerged plant communities of the seasonally-flooded oligohaline marshes of the Camargue. It consists of collecting undisturbed sediment samples with their contained intact seed bank, and submitting them to different salinities. The study of total biomass and of the biomass of the more frequent species was carried out using parametric tests. The precision of the results depended on the frequency of the species in the replicates. When the frequency was low, non-parametric statistics were necessary. The method seems to be particularly suitable for the study of communities of annual species in aquatic environments.

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Résumé L'étude expérimentale de l'écologie des communautés naturelles de plantes est nécessaire pour démontrer les relations de cause à effet entre les facteurs environnementaux et l'abondance des plantes. Elle l'est également pour faire des prédictions réalistes sur les effets de modifications envisagées de l'environnement sur des communautés de plantes. La manipulation de l'écosystème complet est complexe, ce qui rend son utilisation rare. Une méthode alternative a été utilisée pour l'étude de la composition spécifique des communautés de plantes submergées des marais temporaires de Camargue. Elle consiste à prélever des échantillons non perturbés de sédiment, avec leur stock de semences intact, et à les soumettre à des conditions de salinité. L'étude de la biomasse totale et de la biomasse des espèces les plus fréquentes est faite au moyen de test paramétriques. La précision attendue des résultats dépend de la fréquence de l'espèce dans les réplicats. Lorsque la fréquence n'est pas élevée l'emploi de statistiques non paramétriques est indispensable. La méthode se révéle particulièrement bien adaptée à l'étude des communautés d'annuelles en milieu aquatique.

     

Landscape configuration and diversity hotspots in wintering sparrows

Community-level studies with finches have traditionally viewed local resources as the primary constrainst on local diversity. Patches have been considered to be self-contained and embedded in landscapes that were neutral with respect to the ecological processes under investigation. This study uses a factorial design to examine the relative roles of patch content and patch context in determining patterns of species richness. Sparrows were surveyed in small fallow patches that varied in both weed cover and the type of adjacent habitat. Species richness and total sparrow abundance were significantly influenced by both factors. Individual species were also influnced by both factors; however, responses were species-specific. Because occupation of particular plot types was conditional on their association with specific habitat types, the spatial patterning of species assemblages results from the configuration of patch types within the landscape.     

Population density,roads and altitude influences on spatial distribution of hares positive to EBHSV

Understanding of the ecology of infected animals facilitates disease risk assessment and is also crucial for wildlife conservation. Relatively little is known about the spatial distribution of infected wild mammals in relation to environmental factors. In neighboring Mediterranean ecosystems 250 European brown hares (Lepus europaeus) were collected and examined with RT-PCR to detect European Brown Hare Syndrome Virus (EBHSV). Multivariate statistics and Geographical Information System (GIS) analysis were applied to estimate spatial patterns of biotic and abiotic factors and human activities as determinants of EBHSV positivity. Hare population abundance was estimated using faeces counts and belt drive censuses. The study showed that EBHSV infected hares had widespread distribution even in isolated areas. However, EBHSV infection prevalence was higher in areas with higher hare abundance, closer to paved road networks and at lower altitudes. The risk map revealed the potential distribution of EBHSV-infected hares. This study shows that host abundance and landscape influence the ecology of the disease, a finding that should be taken into account in future studies. The management of harvest and restocking of hares is also discussed for population conservation.     

基于生态系统服务供需的景感尺度特征分析和应用

自然生态系统与人类感知的交互作用是景感生态学关注的焦点，与生态系统服务的供需紧密关联。生态系统、生态过程、生态系统服务以及人的需求均具有一定的时空尺度特征，因此，由这些过程产生的"景感"也具有时空尺度特征，并依赖于这个过程的尺度特征相互作用。梳理生态系统服务供需关系与景感营造规划的尺度特征，探索二者相互联系，进而提出基于景感生态学理论，通过景感营造实现生态系统服务供需平衡的多尺度实现路径。从空间维度，体现从"社区-城市-流域-区域"的多尺度景感规划框架，从应用维度，体现从生态系统服务需求探索-关键指标体系识别-多源谜码数据感知-景感营造与规划设计的具体流程。通过多尺度的联合景感营造，调整自然供给水平与人类不同尺度的生态系统服务需求以期达到平衡，从而实现人类生存环境福利与居民福祉提升的目标。在此基础上，结合雄安新区规划建设实例，从多尺度景感营造的角度为城市绿色生态建设与可持续发展提出优化建议。主要结论：（1）基于"社区-城市-流域-区域"的多尺度景感分析框架，将景感要素与生态系统服务供需思想融入城市规划，在不同尺度上趋善优化，对于实现可持续发展城市规划和管理具有重要指示意义；（2）雄安新区规划设计需更系统和细致地考虑人类感知需求，通过多尺度景感营造设计，共同实现雄安新区的可持续发展与人居环境提升。其中，在社区尺度，需重点关注社区植被配置和居民的休闲游憩；在新区尺度重点关注绿地系统网络构建；在大清河流域尺度重点关注河流健康与水文调节；在京津冀区域尺度需注重山体通风廊道与生态屏障的构建与优化。     

Twilight activity patterns and angling vulnerability of yellowmouth barracuda (Sphyraena viridensis Cuvier, 1829), a range-expanding thermophilic fish

Among the thermophilic fishes that have become established in the north-western Mediterranean as a consequence of sea warming, the yellowmouth barracuda (Sphyraena viridensis Cuvier, 1829) appears to be one of the most successful and abundant in the coastal rocky environment, having increasingly become the object of recreational and commercial exploitation in the study area. Lure-fishing sessions were carried out from May 2016 to November 2018 in the Catalan Sea (NE Spain) at dawn and dusk, with the aim of providing new insight into the behavioural, spatial and feeding ecology and vulnerability to angling of this poorly known species. Generalized mixed-effects linear models showed that S. viridensis is a crepuscular inshore dweller, whose vulnerability to angling is significantly influenced by solar and lunar light intensities, being highest in the pre-spawn and spawning periods. Asymmetries between dawn and dusk activity patterns were detected, evidently related to a drop in aggressiveness at dusk following the spawning period. The simple study design adopted may be applied to other contexts, aiming to the recognition of several levels of fish vulnerability to angling.     

Ontogeny of head and caudal fin shape of an apex marine predator: The tiger shark (Galeocerdo cuvier)

How morphology changes with size can have profound effects on the life history and ecology of an animal. For apex predators that can impact higher level ecosystem processes, such changes may have consequences for other species. Tiger sharks (Galeocerdo cuvier) are an apex predator in tropical seas, and, as adults, are highly migratory. However, little is known about ontogenetic changes in their body form, especially in relation to two aspects of shape that influence locomotion (caudal fin) and feeding (head shape). We captured digital images of the heads and caudal fins of live tiger sharks from Southern Florida and the Bahamas ranging in body size (hence age), and quantified shape of each using elliptical Fourier analysis. This revealed changes in the shape of the head and caudal fin of tiger sharks across ontogeny. Smaller juvenile tiger sharks show an asymmetrical tail with the dorsal (upper) lobe being substantially larger than the ventral (lower) lobe, and transition to more symmetrical tail in larger adults, although the upper lobe remains relatively larger in adults. The heads of juvenile tiger sharks are more conical, which transition to relatively broader heads over ontogeny. We interpret these changes as a result of two ecological transitions. First, adult tiger sharks can undertake extensive migrations and a more symmetrical tail could be more efficient for swimming longer distances, although we did not test this possibility. Second, adult tiger sharks expand their diet to consume larger and more diverse prey with age (turtles, mammals, and elasmobranchs), which requires substantially greater bite area and force to process. In contrast, juvenile tiger sharks consume smaller prey, such as fishes, crustaceans, and invertebrates. Our data reveal significant morphological shifts in an apex predator, which could have effects for other species that tiger sharks consume and interact with. J. Morphol. 277:556–564, 2016. © 2016 Wiley Periodicals, Inc.     

Food plant and herbivore host species affect the outcome of intrinsic competition among parasitoid larvae

1. In nature, several parasitoid species often exploit the same stages of a common herbivore host species and are able to coexist despite competitive interactions amongst them. Less is known about the direct effects of resource quality on intrinsic interactions between immature parasitoid stages. The present study is based on the hypothesis that variation in the quality or type of plant resources on which the parasitoids indirectly develop may be complementary and thus facilitate niche segregation favouring different parasitoids in intrinsic competition under different dietary regimes. 2. The present study investigated whether two herbivore species, the cabbage butterflies Pieris brassicae and Pieris rapae (Pieridae), and the quality of two important food plants, Brassica oleracea and Brassica nigra (Brassicaceae), affect the outcome of intrinsic competition between their primary larval endoparasitoids, the gregarious Cotesia glomerata (Braconidae) and the solitary Hyposoter ebeninus (Ichneumonidae). 3. Hyposoter ebeninus is generally an intrinsically superior competitor over C. glomerata. However, C. glomerata survived more antagonistic encounters with H. ebeninus when both developed in P. brassicae rather than in P. rapae caterpillars, and while its host was feeding on B. nigra rather than B. oleracea. Moreover, H. ebeninus benefitted from competition by its higher survival in multiparasitised hosts. 4. These results show that both plant and herbivore species mediate the battleground on which competitive interactions between parasitoids are played out and may affect the outcomes of these interactions in ways that enable parasitoids to segregate their niches. This in turn may promote coexistence among parasitoid species that are associated with the same herbivore host.