Estimating site occupancy rates for aquatic plants using spatial sub-sampling designs when detection probabilities are less than one

Estimation of site occupancy rates when detection probabilities are <1 is well established in wildlife science. Data from multiple visits to a sample of sites are used to estimate detection probabilities and the proportion of sites occupied by focal species. In this article we describe how site occupancy methods can be applied to estimate occupancy rates of plants and other sessile organisms. We illustrate this approach and the pitfalls of ignoring incomplete detection using spatial data for 2 aquatic vascular plants collected under the Upper Mississippi River's Long Term Resource Monitoring Program (LTRMP). Site occupancy models considered include: a naïve model that ignores incomplete detection, a simple site occupancy model assuming a constant occupancy rate and a constant probability of detection across sites, several models that allow site occupancy rates and probabilities of detection to vary with habitat characteristics, and mixture models that allow for unexplained variation in detection probabilities. We used information theoretic methods to rank competing models and bootstrapping to evaluate the goodness-of-fit of the final models. Results of our analysis confirm that ignoring incomplete detection can result in biased estimates of occupancy rates. Estimates of site occupancy rates for 2 aquatic plant species were 19–36% higher compared to naive estimates that ignored probabilities of detection <1. Simulations indicate that final models have little bias when 50 or more sites are sampled, and little gains in precision could be expected for sample sizes >300. We recommend applying site occupancy methods for monitoring presence of aquatic species.     

Development and field validation of a regional,management‐scale habitat model: A koala Phascolarctos cinereus case study

Species distribution models have great potential to efficiently guide management for threatened species, especially for those that are rare or cryptic. We used MaxEnt to develop a regional‐scale model for the koala Phascolarctos cinereus at a resolution (250 m) that could be used to guide management. To ensure the model was fit for purpose, we placed emphasis on validating the model using independently‐collected field data. We reduced substantial spatial clustering of records in coastal urban areas using a 2‐km spatial filter and by modeling separately two subregions separated by the 500‐m elevational contour. A bias file was prepared that accounted for variable survey effort. Frequency of wildfire, soil type, floristics and elevation had the highest relative contribution to the model, while a number of other variables made minor contributions. The model was effective in discriminating different habitat suitability classes when compared with koala records not used in modeling. We validated the MaxEnt model at 65 ground‐truth sites using independent data on koala occupancy (acoustic sampling) and habitat quality (browse tree availability). Koala bellows (n = 276) were analyzed in an occupancy modeling framework, while site habitat quality was indexed based on browse trees. Field validation demonstrated a linear increase in koala occupancy with higher modeled habitat suitability at ground‐truth sites. Similarly, a site habitat quality index at ground‐truth sites was correlated positively with modeled habitat suitability. The MaxEnt model provided a better fit to estimated koala occupancy than the site‐based habitat quality index, probably because many variables were considered simultaneously by the model rather than just browse species. The positive relationship of the model with both site occupancy and habitat quality indicates that the model is fit for application at relevant management scales. Field‐validated models of similar resolution would assist in guiding management of conservation‐dependent species.     

A Framework for Identifying Plant Species to Be Used as ‘Ecological Engineers’ for Fixing Soil on Unstable Slopes

Major reforestation programs have been initiated on hillsides prone to erosion and landslides in China, but no framework exists to guide managers in the choice of plant species. We developed such a framework based on the suitability of given plant traits for fixing soil on steep slopes in western Yunnan, China. We examined the utility of 55 native and exotic species with regard to the services they provided. We then chose nine species differing in life form. Plant root system architecture, root mechanical and physiological traits were then measured at two adjacent field sites. One site was highly unstable, with severe soil slippage and erosion. The second site had been replanted 8 years previously and appeared to be physically stable. How root traits differed between sites, season, depth in soil and distance from the plant stem were determined. Root system morphology was analysed by considering architectural traits (root angle, depth, diameter and volume) both up- and downslope. Significant differences between all factors were found, depending on species. We estimated the most useful architectural and mechanical traits for physically fixing soil in place. We then combined these results with those concerning root physiological traits, which were used as a proxy for root metabolic activity. Scores were assigned to each species based on traits. No one species possessed a suite of highly desirable traits, therefore mixtures of species should be used on vulnerable slopes. We also propose a conceptual model describing how to position plants on an unstable site, based on root system traits.     

Exploiting opportunistic observations to estimate changes in seasonal site use: An example with wetland birds

Nonsystematically collected, a.k.a. opportunistic, species observations are accumulating at a high rate in biodiversity databases. Occupancy models have arisen as the main tool to reduce effects of limited knowledge about effort in analyses of opportunistic data. These models are generally using long closure periods (e.g., breeding season) for the estimation of probability of detection and occurrence. Here, we use the fact that multiple opportunistic observations in biodiversity databases may be available even within days (e.g., at popular birding localities) to reduce the closure period to 1 day in order to estimate daily occupancies within the breeding season. We use a hierarchical dynamic occupancy model for daily visits to analyze opportunistic observations of 71 species from nine wetlands during 10 years. Our model derives measures of seasonal site use within seasons from estimates of daily occupancy. Comparing results from our “seasonal site use model” to results from a traditional annual occupancy model (using a closure criterion of 2 months or more) showed that our model provides more detailed biologically relevant information. For example, when the aim is to analyze occurrences of breeding species, an annual occupancy model will over‐estimate site use of species with temporary occurrences (e.g., migrants passing by, single itinerary prospecting individuals) as even a single observation during the closure period will be viewed as an occupancy. Alternatively, our model produces estimates of the extent to which sites are actually used. Model validation based on simulated data confirmed that our model is robust to changes and variability in sampling effort and species detectability. We conclude that more information can be gained from opportunistic data with multiple replicates (e.g., several reports per day almost every day) by reducing the time window of the closure criterion to acquire estimates of occupancies within seasons.     

Hydraulic redistribution of soil water in two old-growth coniferous forests: quantifying patterns and controls

Although hydraulic redistribution of soil water (HR) by roots is a widespread phenomenon, the processes governing spatial and temporal patterns of HR are not well understood. We incorporated soil/plant biophysical properties into a simple model based on Darcy's law to predict seasonal trajectories of HR. We investigated the spatial and temporal variability of HR across multiple years in two old-growth coniferous forest ecosystems with contrasting species and moisture regimes by measurement of soil water content (theta) and water potential (Psi) throughout the upper soil profile, root distribution and conductivity, and relevant climate variables. Large HR variability within sites (0-0.5 mm d(-1)) was attributed to spatial patterns of roots, soil moisture and depletion. HR accounted for 3-9% of estimated total site water depletion seasonally, peaking at 0.16 mm d(-1) (ponderosa pine; Pinus ponderosa) or 0.30 mm d(-1) (Douglas-fir; Pseudotsuga menziesii), then declining as modeled pathway conductance dropped with increasing root cavitation. While HR can vary tremendously within a site, among years and among ecosystems, this variability can be explained by natural variability in Psi gradients and seasonal courses of root conductivity.     

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.     

Conservation Assessments of Arboreal Mammals in Difficult Terrain: Occupancy Modeling of Pileated Gibbons (Hylobates pileatus)

Long-term monitoring programs, wildlife surveys, and other research involving species population assessment require reliable data on population status. Given the logistically challenging nature of some species’ habitats and cryptic behaviors, collecting these data can prove to be a considerable barrier. We used detection/nondetection data from pileated gibbons (Hylobates pileatus) in the Cardamom Mountains of southwest Cambodia to estimate their population occupancy and detectability. We modeled occupancy using elevation, tree height, tree density, tree diversity, and disturbance covariates. Modeling demonstrated that 83% of the sites are occupied by Hylobates pileatus and that the detectability of the species varies positively with elevation. No clear relationship between habitat quality covariates and occupancy of Hylobates pileatus emerged. Effort analysis based on model estimates demonstrated that at high elevations, less than half the number of site visits is needed to attain the same detectability estimate precision as across all elevations. We suggest that human activities at low elevations, which affect forest composition, are the central factors impacting the detectability and occupancy of Hylobates pileatus. Longer sampling durations and/or a higher number of site visits, especially at lower elevations, increase precision of the occupancy estimator for the least effort. For effective future monitoring and research for this and similar species, using this relatively simple method, applied with repeat site visits, would allow a longitudinal comparison of detection at sites in difficult terrain.     

Scale‐dependent occupancy patterns in reptiles across topographically different landscapes

Understanding what factors influence species occupancy in human‐modified landscapes is a central theme in ecology. We examined scale‐dependent habitat relationships and site occupancy in reptiles across three topographically different study areas in south‐eastern Australia. We collected presence–absence data on reptiles from 443 sites associated with three long‐term biodiversity monitoring programs, on four to seven occasions, between 2001 and 2013. We characterised sites by the following four variable domains: 1) field design, 2) topography, 3) local‐scale vegetation attributes and 4) landscape‐scale vegetation cover. We constructed occupancy models for 14 species and used an information‐theoretic approach to compare multiple alternative hypotheses to explain occupancy within and between study areas. We modelled detection probability and used the model with the lowest AIC in subsequent analyses. We then modelled occupancy probability against all subsets of the variable groups (field design, topography, local‐ and landscape‐scale vegetation), as well as a model that held occupancy constant (null model). We found that local‐scale vegetation attributes were important for explaining site occupancy in 12/19 possible models, although, in several cases model fit was improved by the addition of topographic variables or native vegetation cover in the surrounding landscape. Occupancy models for widespread species were broadly congruent across study areas. We demonstrate that topographic variables are important for explaining reptile occupancy in hilly landscapes, and local‐ and landscape‐scale variables are important for explaining reptile occupancy in flat or gently undulating landscapes. Management actions that improve habitat complexity at a site‐level, and encompass entire topographic gradients, will have greater benefit to woodland reptiles than simply increasing vegetation cover in the surrounding landscape.     

Towards meaningful monitoring: A case study of a threatened rodent

Detecting trends in species’ distribution and abundance are essential for conserving threatened species, and depend upon effective monitoring programmes. Despite this, monitoring programmes are often designed without explicit consideration of their ability to deliver the information required by managers, such as their power to detect population changes. Here, we demonstrate the use of existing data to support the design of monitoring programmes aimed at detecting declines in species occupancy. We used single‐season occupancy models and baseline data to gain information on variables affecting the occupancy and detectability of the threatened brush‐tailed rabbit‐rat Conilurus penicillatus (Gould 1842) on the Tiwi Islands, Australia. This information was then used to estimate the survey effort required to achieve sufficient power to detect changes in occupancy of different magnitudes. We found that occupancy varied spatially, driven primarily by habitat (canopy height and cover, distance to water) and fire history across the landscape. Detectability varied strongly among seasons, and was three times higher in the late dry season (July–September), compared to the early dry season (April–June). Evaluation of three monitoring scenarios showed that conducting surveys at times when detectability is highest can lead to a substantial improvement in our ability to detect declines, thus reducing the survey effort and costs. Our study highlights the need for careful consideration of survey design related to the ecology of a species, as it can lead to substantial cost savings and improved insight into species population change via monitoring.     

滨海泥质盐碱地衬膜造林技术

盐碱地造林是当今世界上许多国家面临的巨大难题,中国的滨海泥质盐碱地就是其中之一,盐分含量高至不适宜苗木生长的程度。研究目的在于检验衬膜在滨海泥质盐碱地造林中的成效。于2007—2009年,对使用衬膜的新造林模式和全面客土、穴状客土两种传统造林模式栽植穴内外土壤电导率值、含水量及苗木生长情况进行测定和分析。与传统造林模式相比,新造林模式在衬膜的作用下,其穴内客土土壤水分含量有明显提高,盐分含量也明显较低;2009年苗木的成活率、苗高和冠幅较全面客土传统造林模式同比高出150.00%,7.00%和12.00%,较穴状客土传统造林模式同比高出838.00%,12.00%和22.00%;选用的四种苗木中,香花槐效果最好,最适宜滨海泥质盐碱地这种新的造林体系,红叶杨不适宜滨海泥质盐碱地。结果表明,使用衬膜在滨海泥质盐碱地造林体系中效果明显,且成本低廉,宜于推广。     

Soil Ripping and Herbicides Enhance Tree and Shrub Restoration on Stripmines

I evaluated responses by 16 native woody species to differential soil compaction and density of ground cover. The trees and shrubs studied represent sites in southern Illinois that commonly have restrictions to root growth from soil or drainage conditions. The study site was a restored surface coal mine in southern Illinois with a rooting medium compacted by grading and a dense ground cover of pasture species. Soil compaction was alleviated in half the study area before tree planting by mechanically ripping the soil to a depth of 1.2 m. Roots of half the trees and shrubs were dipped in a Terra® slurry before planting, and the ground cover around all planting spots was afterwards sprayed with herbicide. In year 2 after planting the ground cover in half of the unripped and half of the ripped area was further controlled by repeated application of herbicides. Ripping significantly increased height growth of all trees combined and all species individually in each year of the study. Second-year control of ground cover increased height growth of all trees combined and of seven species individually. Some species were damaged by herbicides. Terra® had little evident effect on species performance. Animal damage reduced early survival and growth, especially of Acer (maple) and Cornus (dogwood) species, and later growth of Quercus rubra (red oak). Removal of ground cover with herbicides tended to increase deer browse. Soil ripping, herbicide application, and choosing tree species unattractive to deer can be recommended to increase success in planting trees for forest restoration.     

Modeling stream fish distributions using interval‐censored detection times

Controlling for imperfect detection is important for developing species distribution models (SDMs). Occupancy‐detection models based on the time needed to detect a species can be used to address this problem, but this is hindered when times to detection are not known precisely. Here, we extend the time‐to‐detection model to deal with detections recorded in time intervals and illustrate the method using a case study on stream fish distribution modeling. We collected electrofishing samples of six fish species across a Mediterranean watershed in Northeast Portugal. Based on a Bayesian hierarchical framework, we modeled the probability of water presence in stream channels, and the probability of species occupancy conditional on water presence, in relation to environmental and spatial variables. We also modeled time‐to‐first detection conditional on occupancy in relation to local factors, using modified interval‐censored exponential survival models. Posterior distributions of occupancy probabilities derived from the models were used to produce species distribution maps. Simulations indicated that the modified time‐to‐detection model provided unbiased parameter estimates despite interval‐censoring. There was a tendency for spatial variation in detection rates to be primarily influenced by depth and, to a lesser extent, stream width. Species occupancies were consistently affected by stream order, elevation, and annual precipitation. Bayesian P‐values and AUCs indicated that all models had adequate fit and high discrimination ability, respectively. Mapping of predicted occupancy probabilities showed widespread distribution by most species, but uncertainty was generally higher in tributaries and upper reaches. The interval‐censored time‐to‐detection model provides a practical solution to model occupancy‐detection when detections are recorded in time intervals. This modeling framework is useful for developing SDMs while controlling for variation in detection rates, as it uses simple data that can be readily collected by field ecologists.     

The influence of patch demographics on metapopulations, with particular reference to successional landscapes

The classical view of metapopulations relates the regional abundance of a species to the balance between the extinction and colonization dynamics of identical local populations. Species in successional landscapes may represent the most appropriate examples of classical metapopulations. However, Levins‐type metapopulation models do not explicitly separate population loss due to successional habitat change from other causes of extinction. A further complication is that the chance of population loss due to successional habitat change may be related to the age of a patch. I developed simple patch occupancy models to include succession and included consideration of patch age structure to address two related questions: what are the implications of changes in patch demographic rates and when is a move to a structured patch occupancy model justified? Age‐related variation in patch demography could increase or decrease the equilibrium fraction of the available habitat occupied by a species when compared to the predictions of an unstructured model. Metapopulation persistence was enhanced when the age class of patches with the highest species occupancy suffered relatively low losses to habitat succession. Conversely, when the age class of patches with the highest species occupancy also had relatively high successional loss rates, extinction thresholds were higher that would be predicted by a simple unstructured model. Hence age‐related variation in patch successional rate introduces biases into the predictions of simple unstructured models. Such biases can be detected from field surveys of the fraction of occupied and unoccupied patches in each age class. Where a bias is demonstrated, unstructured models will not be adequate for making predictions about the effects of changing parameters on metapopulation size. Thinking in successional terms emphasizes how landscapes might be managed to enhance or reduce the patch occupancy by any particular metapopulation     

Designing occupancy surveys and interpreting non‐detection when observations are imperfect

Aim Conservation practitioners use biological surveys to ascertain whether or not a site is occupied by a particular species. Widely used statistical methods estimate the probability that a species will be detected in a survey of an occupied site. However, these estimates of detection probability are alone not sufficient to calculate the probability that a species is present given that it was not detected. The aim of this paper is to demonstrate methods for correctly calculating (1) the probability a species occupies a site given one or more non‐detections, and (2) the number of sequential non‐detections necessary to assert, with a pre‐specified confidence, that a species is absent from a site. Location Occupancy data for a tree frog in eastern Australia serve to illustrate methods that may be applied anywhere species’ occupancy data are used and detection probabilities are < 1. Methods Building on Bayesian expressions for the probability that a site is occupied by a species when it is not detected, and the number of non‐detections necessary to assert absence with a pre‐specified confidence, we estimate occupancy probabilities across tree frog survey locations, drawing on information about where and when the species was detected during surveys. Results We show that the number of sequential non‐detections necessary to assert that a species is absent increases nonlinearly with the prior probability of occupancy, the probability of detection if present, and the desired level of confidence about absence. Main conclusions If used more widely, the Bayesian analytical approaches illustrated here would improve collection and interpretation of biological survey data, providing a coherent way to incorporate detection probability estimates in the design of minimum survey requirements for monitoring, impact assessment and distribution modelling.     

Observation and Simulation of Root Reinforcement on Abandoned Mediterranean Slopes

The mechanics of root reinforcement have been described satisfactorily for a single root or several roots passing a potential slip plane and verified by field experiments. Yet, precious little attempts have been made to apply these models to the hillslope scale pertinent to landsliding at which variations in soil and vegetation become important. On natural slopes positive pore pressures occur often at the weathering depth of the soil profile. At this critical depth root reinforcement is crucial to avert slope instability. This is particularly relevant for the abandoned slopes in the European part of the Mediterranean basin where root development has to balance the increasing infiltration capacity during re-vegetation. Detailed investigations related to root reinforcement were made at two abandoned slopes susceptible to landsliding located in the Alcoy basin (SE Spain). On these slopes semi-natural vegetation, consisting of a patchy herbaceous cover and dispersed Aleppo pine trees, has established itself. Soil and vegetation conditions were mapped in detail and large-scale, in-situ direct shear tests on the topsoil and pull-out tests performed in order to quantify root reinforcement under different vegetation conditions. These tests showed that root reinforcement was present but limited. Under herbaceous cover, the typical reinforcement was in the order of 0.6 kPa while values up to 18 kPa were observed under dense pine cover. The tests indicate that fine root content and vegetation conditions are important factors that explain the root reinforcement of the topsoil. These findings were confirmed by the simulation of the direct shear tests by means of an advanced root reinforcement model developed in FLAC 2D. Inclusion of the root distribution for the observed vegetation cover mimics root failure realistically but returns over-optimistic estimates of the root reinforcement. When the root reinforcement is applied with this information at the hillslope scale under fully saturated and critical hydrological conditions, root pull-out becomes the dominant root failure mechanism and the slip plane is located at the weathering depth of the soil profile where root reinforcement is negligible. The safety factors increase only slightly when roots are present but the changes in the surface velocity at failure are more substantial. Root reinforcement on these natural slopes therefore appears to be limited to a small range of critical hydrological conditions and its mitigating effect occurs mainly after failure.     

Root tensile strength and root distribution of typical Mediterranean plant species and their contribution to soil shear strength

In Mediterranean environments, gully erosion is responsible for large soil losses. It has since long been recognized that slopes under vegetation are much more resistant to soil erosion processes compared to bare soils and improve slope stability. Planting or preserving vegetation in areas vulnerable to erosion is therefore considered to be a very effective soil erosion control measure. Re-vegetation strategies for erosion control rely in most cases on the effects of the above-ground biomass in reducing water erosion rates, whereas the role of the below-ground biomass is often neglected or underestimated. While the above-ground biomass can temporally disappear in semi-arid environments, roots may still be present underground and play an important role in protecting the topsoil from being eroded. In order to evaluate the potential of plant species growing in Mediterranean environments to prevent shallow mass movements on gully or terrace walls, the root reinforcement effect of 25 typical Mediterranean matorral species (i.e. shrubs, grasses herbs, small trees) was assessed, using the simple perpendicular model of Wu et al. (Can Geotech J 16:19–33, 1979). As little information is available on Mediterranean plant root characteristics, root distribution data were collected in SE-Spain and root tensile strength tests were conducted in the laboratory. The power root tensile strength–root diameter relationships depend on plant species. The results show that the shrubs Salsola genistoides Juss. Ex Poir. and Atriplex halimus L. have the strongest roots, followed by the grass Brachypodium retusum (Pers.) Beauv. The shrubs Nerium oleander L. and the grass Avenula bromoides (Gouan) H. Scholz have the weakest roots in tension. Root area ratio for the 0–0.1 m topsoil ranges from 0.08% for the grass Piptatherum miliaceum (L.) Coss to 0.8% for the tree Tamarix canariensis Willd. The rush Juncus acutus L. provides the maximum soil reinforcement to the topsoil by its roots (i.e. 304 kPa). Grasses also increase soil shear strength significantly (up to 244 kPa in the 0–0.1 m topsoil for Brachypodium retusum (Pers.) Beauv.). The shrubs Retama sphaerocarpa (L.) Boiss. and Anthyllis cytisoides L. are increasing soil shear strength to a large extent as well (up to 134 and 160 kPa respectively in the 0–0.10 m topsoil). Whereas grasses and the rush Juncus acutus L. increase soil shear strength in the topsoil (0–0.10 m) to a large extent, the shrubs Anthyllis cytisoides (L.), Retama sphaerocarpa (L.) Boiss., Salsola genistoides Juss. Ex Poir. and Atriplex halimus L. strongly reinforce the soil to a greater depth (0–0.5 m). As other studies reported that Wu’s model overestimates root cohesion values, reported root cohesion values in this study are maximum values. Nevertheless, the calculated cohesion values are used to rank species according to their potential to reinforce the soil.     

川西不同树种人工林对土壤涵水能力的影响

为评价青藏高原东缘不同树种造林对土壤涵水能力的影响,选择立地条件与营林方式相同的4种人工林(连香树(Cercidiphyllum japonicum)、油松(Pinus tabulaeformis)、落叶松(Larix kaempferi)和华山松(Pinus armandii))为研究对象,以落叶阔叶灌丛为对照,比较造林恢复28 a后不同人工林土壤孔隙度及持水性的变化,结合林地凋落物贮量及细根生物量等参数,试图揭示造成不同人工林地土壤涵水能力及潜力差异化的因素。结果显示:营造油松和华山松纯林不仅没能有效改善土壤孔隙状况,反而加剧了土壤涵水功能的退化。相反,连香树和落叶松在代替次生落叶灌丛造林后,土壤容重显著下降,孔隙度增加且小孔隙比例升高,持蓄水能力提高。凋落物及细根特性是不同林地土壤持水性能差异的重要因素。综合分析表明,在对退化生态系统进行造林恢复时,应尽量避免营造高密度针叶纯林,应结合种植有助于土壤结构改良的落叶或阔叶树种。     

The relative contribution of local habitat and landscape context to metapopulation processes: a dynamic occupancy modeling approach

Changes in site occupancy across habitat patches have often been attributed to landscape features in fragmented systems, particularly when considering metapopulations. However, failure to include habitat quality of individual patches can mask the relative importance of local scale features in determining distributional changes. We employed dynamic occupancy modeling to compare the strength of local habitat variables and metrics of landscape patterns as drivers of metapopulation dynamics for a vulnerable, high‐elevation species in a naturally fragmented landscape. Repeat surveys of Bicknell's thrush Catharus bicknelli presence/non‐detection were conducted at 88 sites across Vermont, USA in 2006 and 2007. We used an organism‐based approach, such that at each site we measured important local‐scale habitat characteristics and quantified landscape‐scale features using a predictive habitat model for this species. We performed a principal component analysis on both the local and landscape features to reduce dimensionality. We estimated site occupancy, colonization, and extinction probabilities while accounting for imperfect detection. Univariate, additive, and interaction models of local habitat and landscape context were ranked using AICc scores. Both local and landscape scales were important in determining changes in occupancy patterns. An interaction between scales was detected for occupancy dynamics indicating that the relationship of the parameters to local‐scale habitat conditions can change depending on the landscape context and vice versa. An increase in both landscape‐ and local‐scale habitat quality increased occupancy and colonization probability while decreasing extinction risk. Colonization and extinction were both more strongly influenced by local habitat quality relative to landscape patterns. We also identified clear, qualitative thresholds for landscape‐scale features. Conservation of large habitat patches in high‐cover landscapes will help ensure persistence of Bicknell's thrushes, but only if local scale habitat quality is maintained. Our results highlight the importance of incorporating information beyond landscape characteristics when investigating patch occupancy patterns in metapopulations.     

Optimizing occupancy surveys by maximizing detection probability: application to amphibian monitoring in the Mediterranean region

• Setting up effective conservation strategies requires the precise determination of the targeted species’ distribution area and, if possible, its local abundance. However, detection issues make these objectives complex for most vertebrates. The detection probability is usually <1 and is highly dependent on species phenology and other environmental variables. The aim of this study was to define an optimized survey protocol for the Mediterranean amphibian community, that is, to determine the most favorable periods and the most effective sampling techniques for detecting all species present on a site in a minimum number of field sessions and a minimum amount of prospecting effort. We visited 49 ponds located in the Languedoc region of southern France on four occasions between February and June 2011. Amphibians were detected using three methods: nighttime call count, nighttime visual encounter, and daytime netting. The detection nondetection data obtained was then modeled using site‐occupancy models. The detection probability of amphibians sharply differed between species, the survey method used and the date of the survey. These three covariates also interacted. Thus, a minimum of three visits spread over the breeding season, using a combination of all three survey methods, is needed to reach a 95% detection level for all species in the Mediterranean region. Synthesis and applications: detection nondetection surveys combined to site occupancy modeling approach are powerful methods that can be used to estimate the detection probability and to determine the prospecting effort necessary to assert that a species is absent from a site.

     

Quantifying the role of vegetation in slope stability: A case study in Tuscany (Italy)

Vegetation significantly affects hillslope hydrological and mechanical properties related to shallow landslide triggering. In view of the complexity of soil plant hydrological interactions, the quantification of root mechanical reinforcement remains a challenge. Herein we present a back analysis of mechanical stability criteria related to a well-characterized vegetated shallow landslide in Italy, focusing on the quantification of lateral and basal root reinforcement. Lateral root reinforcement is included in slope stability estimates by adding a stabilizing force proportional to the scarp surface and root distribution. This stabilizing force is added to the force balance equation for the infinite slope model for different landslide shapes and dimensions. To quantify root reinforcement, we use the Wu model and the fiber bundle model (WM and FBM, respectively). Implementation of the latter model allows the quantification of the stress–strain behaviour of a bundle of roots for different root distributions and mechanical properties. Results of these models are compared highlighting key differences between the two approaches. Calculations using the FBM can explain the overestimation of lateral root reinforcement using WM and the commonly observed overestimation in the factor of safety. The model also quantifies the displacement-dependent behaviour of root reinforcement on vegetated slopes. Lateral root reinforcement can strongly influence the stability of slopes up to a certain area (1000–2000 m²). The magnitude of this stabilizing effect depends on parameters such as inclination, soil mechanical properties, and root distribution.