Species Occupancy Research Articles

Using public surveys to rapidly profile biological invasions in hard‐to‐monitor areas

AbstractUnderstanding the impact and dynamics of invasive alien species (IAS) is essential for tailoring appropriate management plans. This information can be difficult to obtain in the short term, and intrinsic difficulties of monitoring hard‐to‐reach areas may hamper prompt estimation of IAS distributions. Using the case of the invasive Asian common toad (Duttaphrynus melanostictus) in Madagascar, we show how public surveys coupled with a multi‐analytical approach can promptly provide accurate information on invasion dynamics and impacts. On the basis of key‐informant responses, we built polynomial regressions to investigate the spatiotemporal invasion patterns, false‐positive occupancy models to estimate species occupancy, and mixed‐effect models to evaluate the public perception and attitudes. The invasion followed a linear expansion of approx. 2 km year−1, with human‐mediated dispersal facilitating the spread of the species. Toad occupancy decreased towards the invasion front and increased in the southern portion of its range. Negative perception decreased in urban areas, where people were less concerned by toad impacts on ecosystems, and in recently invaded localities, suggesting density‐ or time‐dependent effects. We also identified 12 potential impacts, with “loss of domestic apiaries”, “poisoning of poultry” and “decline of snakes” standing out for prevalence and potential severity. Our results bring important insights into the invasion dynamics and the human‐toad interactions in Madagascar, highlighting the versatility of public surveys to obtain essential information for invasion science and management, which can be especially useful in hard‐to‐monitor regions of the world with a low in‐country capacity to counter invasive species.

Addressing Detection Uncertainty in Bombus affinis (Hymenoptera: Apidae) Surveys Can Improve Inferences Made From Monitoring.

The U.S. Fish and Wildlife Service developed national guidelines to track species recovery of the endangered rusty patched bumble bee [Bombus affinis Cresson (Hymenoptera: Apidae)] and to investigate changes in species occupancy across space and time. As with other native bee monitoring efforts, managers have specifically acknowledged the need to address species detection uncertainty and determine the sampling effort required to infer species absence within sites. We used single-season, single-species occupancy models fit to field data collected in four states to estimate imperfect detection of B. affinis and to determine the survey effort required to achieve high confidence of species detection. Our analysis revealed a precipitous, seasonal, decline in B. affinis detection probability throughout the July through September sampling window in 2021. We estimated that six, 30-min surveys conducted in early July are required to achieve a 95% cumulative detection probability, whereas >10 surveys would be required in early August to achieve the same level of confidence. Our analysis also showed B. affinis was less likely to be detected during hot and humid days and at patches of reduced habitat quality. Bombus affinis was frequently observed on Monarda fistulosa (Lamiales: Lamiaceae), followed by [Pycnanthemum virginianum Rob. and Fernald (Lamiales: Lamiaceae)], Eutrochium maculatum Lamont (Asterales: Asteraceae), and Veronicastrum virginicum Farw. (Lamiales: Plantaginaceae). Although our research is focused on B. affinis, it is relevant for monitoring other bumble bees of conservation concern, such as B. occidentalis Greene (Hymenoptera: Apidae) and B. terricola Kirby (Hymenoptera: Apidae) for which monitoring efforts have been recently initiated and occupancy is a variable of conservation interest.

Spatial and temporal overlap of domestic cats (Felis catus) and native urban wildlife

Free-roaming domestic cats (Felis catus) are known to pose threats to ecosystem health via transmission of zoonotic diseases and predation of native wildlife. Likewise, free-roaming cats are also susceptible to predation or disease transmission from native wildlife. Physical interactions are required for many of these risks to be manifested, necessitating spatial and temporal overlap between cats and wildlife species. Therefore, knowledge of the location and extent of shared habitat and activity periods would benefit management programs. We used data from a 3-year camera trap survey to model species-specific occupancy and identify landscape variables that contribute to the distribution of free-roaming domestic cats and eight native mammal species in Washington, DC. (USA). Our analysis includes five species that are common prey items of domestic cats, and three species that are potential disease vectors or are otherwise known to be a risk to cats. We then predicted the probability of occupancy and estimated the probability of spatial overlap between cats and each native wildlife species at multiple scales. We also used kernel density estimations to calculate temporal overlap between cats and each native wildlife species. Across spatial scales, occupancy for potential disease vector species was generally positively correlated with canopy cover and open water. Prey species were also generally positively correlated with canopy cover, but displayed negative associations with human population density and inconsistent associations with average per capita income. Domestic cat occupancy was negatively correlated with natural habitat characteristics and positively correlated with human population density. Predicted spatial overlap between domestic cats and native wildlife was greatest for potential disease vector species. Temporal overlap was high (>0.50) between cats and all but two native wildlife species, indicating that temporal overlap is probable wherever species overlap spatially. Our findings indicate that the risk to and from domestic cats varies across urban landscapes, but primarily arises from human activities. As such, humans are implicated in the negative outcomes that result from cats interacting with wildlife. Data-driven management to reduce such interactions can aid in cat population management, biodiversity conservation, and public health campaigns.

Impact of different invasion methods of invasive species on omnivorous food webs

Biological invasion results in a lot of problems about ecosystem and human life. To explore the mechanism of alien species invading a stable food web, a patch dynamic model is established to describe the patch occupancy of each species in the omnivorous food web. A species as invader will be introduced to the food web on different tropical level as predator or as prey. The impact of invasion on the persistence of all species in formed food webs under different habitat loss and habitat fragmentation is investigated. The results show: (1) Compared with invasive species being predators, invasive species being prey is easy to success in omnivorous food webs; Invasive species are much more tolerant of habitat loss and fragmentation when they invade an omnivorous food web in the role of prey than when they invade in the role of predator. (2) When invasive species is a predator in different trophic levels on omnivorous food webs, it shows different coexistence patterns varying with the role and habitat structure. The degree of habitat loss and habitat fragmentation also affects the habitat patch occupancy of the invasive species. On most habitat structure, the lower the trophic level of the invasion location, the more successful the invasion is. (3) When invasive species is a prey of species in omnivorous food webs, no matter what trophic level the invasive species is, it is easy to success. (4) The degree of habitat loss and fragmentation combined with colonization rate have certain impact on invasion result under different roles and trophic levels. The research gives some theoretical thinking of biological invasion, and it can be used as a guidance of biological control.

Developing cost-effective monitoring protocols for track-surveys: An empirical assessment using a Canada lynx Lynx canadensis dataset spanning 16 years

Management agencies need statistically robust, cost-effective monitoring programs to effectively conserve and manage wildlife. However, this requires pilot studies to assess the monitoring protocol's ability to detect meaningful changes in the state variable of interest. This is more challenging for elusive mammals due to low detection rates and the costs associated with fieldwork. A key knowledge gap concerns how spatio-temporal dynamics in species occupancy and detection rates alter the cost-effectiveness of sampling protocols. To fill this gap we used a dataset spanning 16 years on Canada lynx (Lynx canadensis) track surveys conducted in Maine, USA, and developed optimal monitoring protocols that empirically assess the cost-effectiveness of these protocols under different scenarios. We surveyed 96 townships and detected 949 track intercepts, which were converted to detection histories under a spatially-replicated occupancy design. By combining occupancy modeling and power analyses, we estimated the sampling effort required to detect declines in occupancy from 10 to 50 %. Calculating the monetary cost of these protocols indicated that detecting subtle changes in occupancy (<10 %) is very expensive even within high suitability habitats and may often be unrealistic. However, protocols that detected medium (30 %) to large (50 %) declines required similar budgets and were consistent with the observed shifts in occupancy during our study period (34 %), suggesting that a modest budget increase would pay large dividends in population assessment efficacy. Our results provide important guidance on how to implement robust and cost-effective monitoring programs with snow track surveys – a popular survey method used by many conservation agencies.

Using population monitoring programs to detect changes in mammalian communities

The global biodiversity crisis is escalating rapidly, with nearly a million species facing extinction risk in the near future. Monitoring of Essential Biodiversity Variables (EBV; key variables measured to detect changes in biodiversity) over time is important for biodiversity conservation, which in turn necessitates baseline estimates of EBVs. Using camera-trap data for six years (2013–2018) and a Bayesian multispecies occupancy model, we estimated species richness and species-specific occupancy of a mammalian community in Pakke Tiger Reserve, India. We detected 28 species of mammals in our camera traps. The model-based estimate of species richness during the study period was 41 (95 % CRI: 39–42) species, with no evidence of any substantial temporal variation. We found that carnivore and herbivore species richness was higher in greener habitats and that omnivore species richness was higher at lower-elevation sites. Annual average species occupancy probability (at the scale of 4-km2 sampling units) did not vary substantially between years but was lowest in 2014 (0.54, 95 % CRI: 0.20–0.84) and highest in 2013 (0.59, 95 % CRI: 0.27–0.87). Mean species-specific occupancy averaged across the years varied substantially among species, ranging from a low of 0.03 (95 % CRI: 0.00–0.08) for the masked palm civet Paguma larvata to a high of 0.94 (95 % CRI: 0.87–0.98) for the Asian elephant Elephas maximus. Mean occupancy probability was highest for herbivores followed by omnivores and carnivores. Species-specific detection probability (for a 30–60-day survey period) was not influenced by survey effort but increased with body mass for carnivores and decreased with body mass for herbivores and omnivores. We propose a framework for efficient monitoring of species and community-level EBV, utilizing data collected during the monitoring of high-profile species of conservation concern, such as tigers Panthera tigris in India.

A multifaceted field sampling approach for the management of extremely narrow endemic vascular plant species.

Extremely narrow endemic plant species (ENEs) are generally connected with microrefugia characterized by particular environmental conditions. In-depth knowledge of the ecological requirements of ENEs is fundamental to plan appropriate conservation measures. Using cross-cutting technology, this paper gives a multifaceted approach to collect on-site data on the ecology of ENEs, defines the protocols for a correct sampling design and describes the type of equipment, the time and expenditure needed. Our sampling approach is based on two orthogonal transects, long enough to extrapolate the whole ecological gradient across the area of occupancy of the target species. Microclimatic data are recorded all along the transects through iButton technology, plus a weather station installed at the intersection of the transects. Microtopographic data are recorded with high-resolution digital elevation model and sub-metric GPS. Edaphic data are recorded along the transects through standard soil analyses and on-site evaluation of the seasonal decomposition rate of organic matter. Additionally, vegetation sampling in 4m2 plots and on-site germination tests allow to collect data on auto- and synecological factors that regulate the life cycle of the target species. Our approach has proved to be cost-effective and efficient in terms of time spent in the field against the data collected. The most demanding activities were the establishment of the transects and the vegetation sampling. The time spent downloading microclimatic data and testing seed germination was relatively short. Our sampling design allows: (i) to catch as much micro-topographic variability as possible, both within and out of the tolerance range of the target species, (ii) to minimize the risk of recording identical micro-topographic conditions compared with a random sampling scheme, and (iii) to ensure quick and relatively easy retrieval of the plots and the equipment both on a multi-seasonal and multi-annual basis.

Environmental DNA metabarcoding effectively monitors terrestrial species by using urban green spaces

Ecological corridors and urban parks are created to connect habitats that become isolated due to urban development and integrate ecological, social, and cultural functions. Establishing and implementing the ecological function of urban green structures and conservation plans for urban terrestrial species requires prioritizing developing an understanding of the community structure of urban terrestrial species. However, understanding the appearance and distribution of terrestrial species in urban ecosystems is often neglected or lacking; furthermore, the inaccurate detection of species distribution can create biased estimates of species occupancy. Recently, an applied research method for detecting terrestrial species such as mammals and birds has been proposed based on molecular biology such as environmental DNA (eDNA) metabarcoding. We installed artificial water tanks (mesocosm) in urban green spaces (Urban forests; UFs, Urban ecological corridors; UECs, Urban parks; UPs), applying eDNA metabarcoding as a tool to detect wild terrestrial species, and camera traps (CTs) and field surveys were performed in parallel to verify the results. We detected 22 urban terrestrial species only by eDNA metabarcoding and identified 43 species in total by performing eDNA metabarcoding, CTs, and field surveys in parallel. In addition, we identified 31 species of UFs, 13 species of UECs, and 28 species of UPs of urban terrestrial species using the three species survey methods in parallel. We confirmed that eDNA metabarcoding is very useful for detecting small species that are difficult to detect with the naked eye and internal species vulnerable to disturbance. However, since some species were only detected by CTs or field surveys due to DNA false-negative errors or the species’ life-history characteristics, it was judged that the species inventory can be effectively collected using several monitoring techniques.

Interspecific variations in fish occupancy and abundance are driven by niche characteristics in a monsoon climate river basin

AbstractAimThe interspecific relationships between species occupancy and abundance have been broadly studied in terrestrial systems; however, the causes underlying this relationship in freshwater fishes remain poorly addressed. The main aims of this study were (a) to examine the occupancy–abundance relationship in 62 fish species in a monsoon climate river; (b) to determine the relative importance of species niche, functional traits and phylogenetic relatedness in shaping the occupancy–abundance relationship.LocationThe Chishui River, the Yunnan‐Guizhou Plateau and the Szechwan Basin, China.TaxonFreshwater fishes.MethodsA linear model was used to test the relationship between distribution and mean abundance across fish species. The outlying mean index analysis was performed to estimate niche breadth and niche position parameters for each fish species. In addition, using principal coordinates analysis, we created four trait vectors describing the similarity of species' traits. Fish phylogeny was obtained from a global molecular phylogenetic tree of actinopterygian fishes. We used a combination of linear models, commonality analyses and boosted regression trees to evaluate the relative effects of the niche metrics, traits and phylogenetic relatedness on occupancy and abundance.ResultsFish occupancy was strongly (R2 = 0.749) and positively correlated with mean abundance in the Chishui River. Niche parameters, especially niche position, were the main determinants of variation in occupancy (e.g. total contribution of niche position and breadth using commonality analyses: 0.587 and 0.318) and abundance (0.323 and 0.151) across species. Furthermore, traits and phylogeny had little to no effect on fish occupancy (0.034 and 0.037) and abundance (0.021 and 0.003).Main conclusionsFreshwater fishes in the Chishui River fit the common macroecological pattern of positive relationship between occupancy and abundance. Niche parameters, but not traits and phylogeny, are the primary correlates of riverine fish distribution and abundance.

Alien versus alien: spatiotemporal overlaps among introduced ungulates in a Mediterranean island ecosystem

Assessing the spatiotemporal behaviour of alien species is pivotal to designing effective management plans. Interspecific niche partitioning among ungulates is reported as a strategy to avoid direct interactions. The Mediterranean mouflon and wild boar are two ungulates introduced to Elba island for hunting and aesthetic purposes. We used intensive camera trapping to test whether species occupancy and temporal activity rhythms would vary in response to the presence or absence of the co-occurring species through multi-species occupancy modelling. Our findings report a lack of spatial and temporal segregation between the two species for the late spring–summer and late summer–autumn seasons. In contrast, results for the winter–early spring period suggest that spatial partitioning between wild boar and mouflon is present in areas with high artificial cover (e.g., paved roads). Animals may indeed exploit roads to move more rapidly in search of food; however, their occurrence in these areas seems to be influenced by the presence of the other species.

Where Land and Water Meet: Making Amphibian Breeding Sites Attractive for Amphibians

The protection of wetlands is a cornerstone in the conservation of pond-breeding amphibians. Because protected wetlands are rarely natural areas, but are often man-made, at least in Europe, it is important that they are well managed to fulfill their intended function. Appropriate management requires knowledge of the ecology of the species, particularly habitat requirements. Here, we combine species monitoring data and habitat mapping data in an analysis where our goal was to describe the factors that determine the occupancy of amphibian species in federally protected amphibian breeding sites. As expected, every species had its own habitat requirements, often a combination of both a terrestrial and aquatic habitat (i.e., landscape complementation). In most species, occupancy was strongly positively affected with the amount of aquatic habitat, but predicted occupancy probabilities were low because the amount of aquatic habitat was low in most sites. The area or proportion of ruderal vegetation also had positive effects on multiple species, while other types of terrestrial habitat (e.g., meadows) led to low occupancy probabilities. The total area of the protected breeding sites was never included in a final model and connectivity was important only for one species (Triturus cristatus). The latter finding implies that the quality of the landscape between breeding sizes is more important than distance per se, while the former implies that the area of some specific habitats within breeding sites is crucial for high occupancies. Thus, increasing the amount of aquatic habitats and likewise terrestrial habitats within protected areas would make them more likely to achieve their conservation objectives. Our study is an example of how the joint analysis of monitoring data and habitat data (based on mapping in the field) can lead to evidence-based suggestions on how to improve conservation practice.

Nesting associations and breeding output of Barn Owls Tyto alba and Red-billed Choughs Pyrrhocorax pyrrhocorax sharing nest boxes

ABSTRACT Capsule Barn Owls Tyto alba and Red-billed Choughs Pyrrhocorax pyrrhocorax show differential breeding outputs as a consequence of sharing nest boxes. Aims To describe for the first time a commensal relationship between the Red-billed Chough and the Barn Owl during the breeding period. Methods During systematic monitoring of 90 nest boxes installed for Barn Owls in Navarre, northern Spain, it was found that in some boxes, Barn Owls and Red-billed Choughs nested simultaneously (inside and on top of the box, respectively). The clutch size, breeding success, and the number of fledglings of each species were compared when nesting together versus separately during the breeding period of 2015 and 2017. Results About one-third of the nest boxes observed during the study were simultaneously used by both Barn Owls and Red-billed Choughs. No relationship was found between the composition of the habitat around the boxes and the degree of occupancy for either species. Nest box sharing had no significant effect on the breeding output of Barn Owls, but improved the breeding performance of Red-billed Choughs by increasing the number of fledglings in relation to clutch size. Conclusion Barn Owls can provide benefits to Red-billed Choughs by controlling the populations of rodents, which could act as nest predators. Given that Barn Owls apparently do not obtain benefits nor incur any costs by the association with Red-billed Choughs, this interaction may be defined as commensalism. To our knowledge, this is the first documented nesting association between a corvid and an owl species.

Conservation prioritization through combined approach of umbrella species selection, occupancy estimation, habitat suitability and connectivity analysis of kingfisher: A study from an internationally important wetland complex (Ramsar site) in India

Assessment of occupancy status, as well as projection of suitable habitats and connectivity of wetland indicator species, and thereby identification of potential conservation umbrella and projection of conservation priority areas are often considered important for wetland conservation. Kingfishers are wetland indicators and suffer from habitat degradation due to world-wide destruction of wetlands. Therefore, they can be considered potential candidates for conservation intervention. The present knowledge about the spatial distribution of suitable areas and habitat connectivity of kingfishers at a landscape level is non-existent. We conducted extensive surveys and recorded four kingfisher species in East Kolkata Wetlands (EKW; Ramsar site No. 1208; ∼125 km2). The occupancy estimates were highest for White-throated kingfisher (Halcyon smyrnensis, WTK), followed by common kingfisher (Alcedo atthis, CK), stork-billed kingfisher (Pelargopsis capensis, SBK) and lowest for pied kingfisher (Ceryle rudis, PK). WTK has the highest amount of suitable areas followed by CK, PK and SBK. The spatial overlap of suitable habitats showed that SBK is the potential umbrella species and therefore provides conservation benefits to other kingfisher species and eventually to the EKW. In addition to water areas, emergent vegetation, crop lands and tree cover are other important habitats for kingfishers. The connectivity analyses revealed that suitable habitats were disjunct and are under various anthropogenic threats. Therefore, we need to protect suitable habitats and connectivity between them. Finally, we identified conservation priority areas. Conservation intervention on these high priority zones will not only be beneficial for kingfishers, but also for other avifauna having similar resource requirements as well as the wetland parse.

Importance of AVIRIS-NG data in assessing the assemblage of guilds of tropical trees over a contrasting climate

Generating large-scale field-based guild data for assessing tree species sorting and distribution over tropical covers is difficult. In this study, we combined field, and the Airborne Visible-Infrared Imaging Spectrometer-Next Generation (AVIRIS-NG) datasets of tropical covers across a climate gradient to develop precision maps of abundant tree species. This assisted in the extraction of a large dataset of guilds with tree species assortment and occupancy. We observed parity in the distribution of local and regional species with an increase in the proportionate presence of local species over the climate gradient. We saw greater distribution of Fabaceae members in sites with relatively lesser rainfall. To address the impact of species sorting on the functional aspects of guilds, available R codes (Ackerly and Cornwell, 2007), and three vegetation indices (VIs) as functional traits (Photochemical Reflectance Index, PRI, Chlorophyll/Carotenoid Index, CCI, and Normalized Difference Water Index, NDWI) were tested. Species assortment and spread affected the guild's functional diversity, as noticed in the abundance weighted guild means of VIs. We also observed a consistent increase in the mean CCI of all species across the climate gradient correlating positively with rainfall and negatively with vapour pressure deficit (VPD). This shows that CCI could be an adequate measure for large-scale ecological observations of these tropical regions. Wider amplitudes in the measured VIs of deciduous species demonstrated their adaptability to the climate gradient. Gradient-driven species assembly dynamics and functional traits variability indicates of tropical tree biodiversity feedback to the climate dynamics.

Spatial drivers of wetland bird occupancy within an urbanized matrix in the Upper Midwestern United States

AbstractWetland birds are undergoing severe population declines in North America, with habitat degradation and wetland loss considered two of the primary causes. Due to the cryptic nature of many wetland bird species, the ecological conditions (e.g., matrix composition) that influence bird occupancy, and the relevant spatial scales at which to measure bird responses, remain unclear but may affect inference about wetland use and suitability. We conducted wetland bird surveys at 477 points across northeastern Illinois and northwestern Indiana within the highly urbanized landscape surrounding Chicago. Using remotely sensed land cover data, we built occupancy models for 10 wetland bird species (American Coot Fulica americana, Black‐crowned Night‐Heron Nycticorax nycticorax, Blue‐winged Teal Anas discors, Common Gallinule Gallinula galeata, Least Bittern Ixobrychus exilis, Marsh Wren Cistothorus palustris, Pied‐billed Grebe Podilymbus podiceps, Sora Porzana carolina, Swamp Sparrow Melospiza georgiana, and Virginia Rail Rallus limicola) to quantify their responses to wetland cover types (emergent wetland, forested wetland, riverine wetland, and freshwater pond) and urbanization at four spatial scales (200‐, 400‐, 800‐, and 2000‐m radial distances). We also included the distance to Lake Michigan as a covariate in occupancy models to account for ecological differences between coastal and inland wetlands. We found that relationships between land cover types and occupancy differed by species, as did the spatial scale of support. Generally, the presence of emergent wetlands or ponds at immediate (200 m) and local (400 m) spatial scales within the surrounding matrix was positively associated with wetland bird occupancy. Contrary to expectations, we did not find support for a negative relationship between urbanization and occupancy for most focal species, indicating that birds are using available wetland habitats despite surrounding development. While future research should evaluate management strategies at the watershed scale, our findings suggest that wetland conservation planning at immediate and local scales is likely to promote bird habitat use within highly modified landscapes of the Upper Midwestern United States.

Short-term responses of small mammal diversity to varying stand-scale patterns of retention tree patches.

Retention forestry is a common practice for biodiversity conservation in forests managed for wood production. Retention forestry often leaves unharvested patches of trees that vary in size and spatial pattern but experiments evaluating the effects of different retention patch configurations at a constant level of retention are lacking for many regions and taxonomic groups. We implemented an experimental study in clearcut conifer stands with retention across the U.S. Pacific Northwest region. The study consisted of five stand-level (11–55 ha) experimental treatments each replicated 10 times within a randomized complete block design, resulting in 50 treated stands. Retained tree density was comparable across treatments but size, number, and location (upland or riparian) of patches within stands varied among the five treatments. Within experimental treatments, we measured small mammal (<1kg) species and functional trait (i.e., body size, diet, activity stratum) richness in retention patches, surrounding harvested portions of stands, and nearby unharvested stands. We evaluated species and functional trait richness by treatment using generalized linear mixed-effects models and species-specific responses to retention placement using a community occupancy model. We obtained repeat captures of 21 species of small mammals but found limited evidence of a treatment effect on species richness, and no differences in functional trait richness. Species richness was highest where all retained trees were aggregated into one patch placed adjacent to a forested riparian buffer (mean = 6.6 species, 95% CI = 5.7–7.5), and lowest in the treatment containing one retention patch in the upland portion of a harvested stand (mean = 4.7 species, 95% CI = 3.8–5.6). Furthermore, estimates of species richness within retention patches of harvested stands (i.e., not considering species in harvested areas) did not differ among treatments, indicating that the slightly elevated species richness in riparian-associated retention results from 1–2 species in these patches that do not occur in adjacent harvested portions of each treated stand. Patch occupancy of several species was higher in riparian patches than harvested portions of the treated stands, and fewer species had higher occupancy in upland patches compared to harvested portions of treated stands. Our results indicated that at retention densities currently required in Oregon and Washington, the location of retention patches had a small influence on stand-scale measures of small mammal diversity, but local increases in species richness may be obtained by retaining trees adjacent to riparian buffers.

Wildlife 3D multi-object tracking

The study of wildlife populations and species has gained increased relevance due to significant endangerment, loss of habitats and world climate change. Using camera traps for monitoring is a common method to estimate species diversity, occupancy and relative abundance. We present a 3D multi-object tracking method for wildlife camera trapping using RGB-D cameras. We infer precise three-dimensional pose estimations of individual animals (i.e. locations and orientations) and also three-dimensional estimations of their observed movements, including velocity estimations. More precisely, we achieved a scaled Average Multi-Object Tracking Accuracy (sAMOTA) of 88.43%. The code is available athttps://github.com/m-klasen/3D_wildlife_tracking.

Rock Refuges Are Strongly Associated with Increased Urban Occupancy in the Western Fence Lizard, Sceloporus occidentalis

Urbanization has dramatically altered habitats for local species worldwide. While some species are unable to meet the challenges that these alterations bring, others are able to persist as long as a threshold for suitable habitat is met. For reptiles, a key feature for persistence in urban areas can be access to suitable refuges from predation, high temperatures, and/or other environmental challenges. We tested for effects of local and landscape variables affecting urban occupancy in the Western Fence Lizard, Sceloporus occidentalis, in transects across an urban–rural gradient, with a specific focus on the presence of rock, tree, and shrub refuges. We found that fence lizards were much more likely to be present in areas with more rock cover, and in parks or low-density residential areas. Occupancy was also positively related to canopy cover in the general vicinity, though negatively related to number of trees along the transects. Our results highlight the importance of assessing local habitat features to successfully predict the occupancy of reptile species in urban habitats, and present directions for future research with concrete conservation and management applications.

Logging intensity affects growth and lifespan trajectories for pioneer species in Central Amazonia

Management of tropical forest in the form of timber harvesting is a viable alternative to deforestation in Amazonia. Nevertheless, a significant challenge for timber management in the Amazon is the maintenance or establishment of commercial timber species, after logging operations are completed. This is because fast-growing non-commercial pioneer species outcompete the slower growing timber species. To determine the challenges posed to commercial species in the context of the cutting cycle in the Brazilian Amazon of 25–35 years, growth and cumulative survival rates of six abundant pioneer species were assessed. This was accomplished with 30 years of growth data from permanent plots established in the Central Amazon in the 1980′s and logged in 1987 and 1988 at various intensities. In terms of relative growth rates, pioneer species dominated the post-logging site by 2 to 5 times, when compared to commercial species, throughout the evaluation period. This was regardless of the various logging intensities of 5, 8 or 16 trees harvested per hectare. Two commercial pioneer species, Jacaranda copaia and Simarouba amara, presented rapid growth rates similar to non-commercial pioneer species. Three pioneer species survived beyond 30 years to continue into a potential 2nd cutting cycle. Therefore, to maintain or establish commercial timber species while there is a continued and expanding site occupancy of non-commercial pioneer species after logging presents numerous challenges for sustainable forest management.

Species richness, relative abundance and occupancy of ground-dwelling mammals denote the ineffectiveness of chimpanzee as flagship species

In conservation biology, flagship species are defined as species that can raise support for biodiversity conservation in a given place or social context. In the newly established Gishwati–Mukura National Park in Rwanda, the Eastern chimpanzee was considered such an ambassador. To test whether the flagship species concept was effective in the park, we studied species richness, relative abundance, and species distribution (occupancy) of medium- to large-sized, ground-dwelling mammals using camera trapping technology. The impact of three environmental and three anthropogenic variables on species distribution was investigated and the ecological diversity of the fauna in the national park assessed. Over a period of 9 months, two 4 × 4 camera trapping grids were deployed in Gishwati and Mukura Forest. Sampling effort in each forest equated to 32 and 29 camera trapping locations, yielding 258 and 242 independent photographic events of eight and six species, respectively. In both forests, the Emin's giant poached rat was the most frequently encountered species, while all other species showed high relative abundance only in Gishwati Forest. The relative abundance of the endangered Eastern chimpanzee in Gishwati Forest was 0.54, the estimated occupancy was 0.31. Single-species, single-season occupancy models revealed that forest cover, altitude and distance to forest edge influenced the detectability of L'Hoest's monkey and squirrel species, while no effect was found on their occupancy. Notably, no larger herbivore or carnivore species were observed in the park, while the flagship species, i.e., the Eastern chimpanzee, was relatively abundant. Moreover, in both forests, all detected carnivores were small- to medium-sized, suggesting a meso-predator release phenomenon, i.e., populations of medium-sized predators increased after the removal of larger, top carnivores, due to relaxed competition. It appears that the prioritization of the flagship species resulted in the neglect of other mammalian species, leading eventually into the demise of entire functional guilds. Based on these results, the Gishwati–Mukura NP was categorized as a ‘depleted forest’. We, therefore, strongly object chimpanzees as a suitable flagship species—at least in the Gishwati–Mukura NP—and recommend collating more knowledge on the release of meso-predators and the loss of forest ungulates to improve their future conservation in Afro-montane forest habitats.