Study area and protocol design
The Democratic Republic of the Congo (DRC) hosts three BRs (Lufira, Luki and Yangambi). These were established without adaptive partnerships between local communities and management bodies, making their management problematic (Sikuzani et al. 2020). The concept of a biosphere reserve or Man and Biosphere Reserve has not yet translated into legal texts, resulting in an unclear legal status of BRs as protected areas (Koy et al. 2019). This study focuses on the Yangambi Biosphere Reserve (YAB), an area in what had been the Yangambi Floristic Reserve since 1939 and was later declared a MAB reserve in 1977. There is no official management plan and the boundaries of the YAB remain controversial, with land use remains a challenging issue (Kipute et al. 2021). The YAB covers an area of about 2250 km² centered at 0.771°N, 24.527°E, including a proposed core area of about 375 km² (Fig. 1). The proposed zoning plan – as a spatial framework of three interrelated zones (one or more core areas, a buffer zone surrounding the core areas, and a transition zone) for achieving the three interconnected functions of a BR (Kratzer and Ammering 2019) – based solely on a floristic inventory was never clearly implemented. A continuum of closed evergreen forest dominates Yangambi region on the right bank of the Congo River, with scattered human-dominated areas (Van de Perre et al. 2018). The climate is characterised by two dry seasons, December-March and June-July, alternating with two wet seasons, April-May and August-November (van Vliet et al. 2019). Annual rainfall ranges from 1400 to 2000 mm, and the average temperature is around 26°C.
The sampling protocol is based on detection and non-detection data and is applicable to multiple taxa and contexts. The study design emphasised the status of bats as mobile link organisms that can facilitate within-community variation in species-specific traits such as mobility, home range, and habitat requirements (Kremen et al. 2007; Devarajan et al. 2020). The sampling design based on the assumption that the communities to be sampled are distributed over a spatial scale. Using different sampling methods in the same area illustrates the proper consideration of at finer spatial scales. We used camera traps for terrestrial and arboreal mammals and trapping techniques for volant mammals to account for the different spatial use patterns of forest mammals. To better study the forests adjacent to the YAB’s core area, the buffer zone was monitored longer than the transition zone. The transition zone was only surveyed on the ground to update a list of possible species. We monitored bats in both the buffer and transition zones with equal survey effort, which overlapped in time and space with the camera surveys. We used species-level attributes that could have a direct impact on detection estimates, e.g., nonvolant species-specific life-history traits (activity patterns, habitat use strategies, standing body mass, and social behaviour) and flight ability index (aspect ratio, Maximum range speed, wing loading) of volant mammals. Morphological trait estimators of uncaptured bats (i.e., species previously recorded in the same area) were compiled from the literature (Norberg and Rayner 1987; Patterson and Webala 2012). We described the forest characteristics where the traps were set. Building on published work (van Vliet et al. 2019), we outlined the number of hunters actively involved in the bushmeat market chain to support a broader interpretation of current trends in the standing body mass of mammal in the YAB.
Sampling And Covariates
We developed a comprehensive sampling design that may be representative for volant and nonvolant, arboreal and ground-dwelling mammals, including replication of sites. The bat surveys were based on approaches developed for Neotropical bat surveys (Farneda et al. 2015; Rocha et al. 2016; Ferreira et al. 2017), while camera design follows approaches developed in Rwanda (Moore et al. 2020). To capture local variation, the forest description, volant and nonvolant mammal surveys were conducted using a design based on a total of 36 plots (20 × 5 m), with 18 plots in the buffer zone and 18 in the transition zone. At each site, we recorded forest clutteredness and potential foraging/visitation area indicators. We recorded stem density, including lianas with diameter at breast height (dbh) ≥ 5 cm, and basal area of woody stems with dbh ≥ 10 cm (i.e., the sum of the cross-sectional area at 130 cm, or above the buttress, of all live trees). We determined the straight-line distance between each plot and the nearest waterways by combining public domain digital map data (RGC 2010) with our own field waypoints using QGIS 3.6.3 (QGIS Development Team 2019).
Each site (i.e., forest stand) was monitored by camera for six consecutive months at ground level, and for a further six consecutive months in the arboreal substrate at the same location (December 2019 to December 2020), concurrently with the bat surveys. One camera site corresponds to one plot. The ground cameras were placed at various heights ranging from 0.6 to 1 m (mean = 0.72 m ± 0.13 SD). Height variations were due to either the slope of the terrain or the need to record smaller to larger species dwelling on/near the ground. Arboreal cameras were placed below the canopy between 11 and 19 m (mean = 14.5 m ± 3.0 SD), with height variation depending on climbability. One camera was deployed per site, totalling 18 cameras for each substrate over six months, with monthly checks to ensure cameras had sufficient battery life and memory card space. Spatial schemes of camera distribution were designed to meet occupancy independence assumptions and exceed estimated home ranges of most small-bodied species, such as arboreal rodents (Kingdon 2015). The camera models (Bushnell Trophy Cam Essential HD and Victure HC200) were randomly selected for each site, both ground and arboreal, and were set to record a 32-second video each time they were triggered, with no delay between videos. We used expert knowledge to annotate camera recordings and then identified them using reliable sources (Kingdon et al. 2013a, b; Kingdon and Hoffmann 2013). The survey effort for each camera was set to 30 continuous recording days, i.e., one sampling occasion, henceforth event. A total of 6480 camera-days were carried out, i.e., 18 cameras × 30 days × (6 ground events + 6 arboreal events). A camera-day is defined as one camera used for one day.The bat sampling schedule covered the late rainy season and the early dry season. Each site was surveyed to ensure that sampling was continuous and not interrupted by heavy rains. We simultaneously used one set of six traps per site, namely four nylon mist nets (Ecotone, Poland) of three different mesh sizes (16 × 16 mm; 19 × 19 mm; 30 × 30 mm), shelves (5; 5; 4), dimensions (9 × 3 m; 9 × 3 m; 9 × 3.2 m), and two identical custom-made harp traps (Prince of Songkla University, Thailand) modified from (Francis 1989), iron and aluminum poles, four-bank 150 × 150 cm capture area, total weight 9 kg. The traps were randomly selected at each sampling point and placed near waterways and flyways. The height of the mist nets depended on available flyways and varied from 1 m to 7 m above the ground. To reduce the effects of time of night, observer, and trap shyness (Hoyle et al. 2001; MacKenzie and Royle 2005), we used a rotating survey scheme between sites. To fully standardise trapping effort, surveys were repeated at the same site seven days apart during different time periods. Because we were interested in studying bat flight activity, we used temporal events, as part of the night replication. We fixed the sampling time for the fly-out period so that the sampling duration (a 4-hour period corresponds to one event) was the same for the three replicate surveys, namely early evening (6:00pm-10:00pm), middle of the night (10:00pm-2:00am), and early morning (2:00am-6:00am) in Central Africa Time (UTC + 2:00). During each event, traps were checked at least 30 minutes apart.The total bat survey effort was 324 trap-nights (i.e., 6 traps × 3 consecutive nights × 3 replicates × 6 sites), with a trap-night defined as the simultaneous opening of a set of six traps for 4 hours after sunset. Captured bats were individually placed in cloth bags (30 × 40 cm) before measurements of taxonomically relevant external characters. We measured ear, tail (if possible) and tibia lengths with a caliper (± 0.01 mm), forearm and wingspan lengths with a ruler (± 0.1 mm), and body mass using spring balances (30g/0.2g, 50g/0.5g, 100g/1g, 300g/2g Pesola, Ecotone, Poland). We qualitatively differentiated juveniles from adults by transilluminating the wing of an individual with a headlamp and visualizing the cartilaginous zone of the long phalanges (Kunz and Anthony 1982). Individuals with a gap at the fourth metacarpal-phalangeal joint were defined as juveniles. Scrotal position was an additional indicator to distinguish adult males from juveniles. Reproductive status of adult females was categorised as pregnant (based on gentle palpation of the abdomen), lactating (enlarged nipples without surrounding fur and milk secretion when gently squeezed), or no reproductive signs (Lučan et al. 2014). Within 2 hours, captured bats were released unharmed at the capture point after being photographed for possible comparison with illustrated keys. We used reliable sources for bat identification in the DRC (Patterson and Webala 2012; Cakenberghe et al. 2017; Monadjem et al. 2020).
Index Estimates
Bat capture data were pooled for each bat trap site. Forest characteristics were averaged at the site scale into a single dataset. We calculated bat wing aspect ratio (AR), wing loading (WL) and predicted maximum range speed (Vmr) as potential species covariates according to the following allometric equations (Norberg and Rayner 1987; Rhodes 2002; Elangovan et al. 2004): AR = B2/S with B in metres and S in square metres; WL = M × g/S with M in kg, gravitational acceleration (g) equals 9.81 metres per square second, and WL is expressed in Newtons per square metre (N.m−²); Vmr = 8.71 × M0.423 × B− 0.498 × S− 0.144, with Vmr in metres per second (m/s).
The camera data recorded in the transition zone during 540 camera-days (18 cameras × 30 days) were not included in the analyses. Instead, they were used to update the list of potentially available species in the area. We combined ground and arboreal camera data from buffer zone and forest characteristics for each site into a single dataset. At the site level, we analysed the camera and bat detection datasets separately. We evaluated the distribution of camera success using quarterly pooled data (i.e., 18 cameras × 90 days), while keeping the bat trap data per the event design. We evaluated event-specific detection rates using the trap success index: (detections/trap-nights) × 100 (Miño et al. 2007). We replaced trap-night with camera-day for the three-event base to adapt the equation to camera data. We used the Kruskal-Wallis H-test to examine whether the camera trap success over four 3-month periods and the bat trap success over three event fell from the same distribution (Ostertagová et al. 2014). Once significant results were obtained (p < 0.05), Dunn's Kruskal-Wallis multiple comparisons with Holm's p-adjusted method and a correction to control for experimentwise error rates (\(\widehat{\epsilon }\)2) were applied to accurately determine the difference of trap success among events (Gelman and Tuerlinckx 2000).
Occupancy Modelling And Species Richness Estimates
We analysed repeated presence/absence data from a collection of spatial unit site over time event. This model was based on the assumption that non-detection (or non-capture) can be distinguished from absence through repeated sampling, and that using pooled data for all species observed during sampling can improve species-specific occupancy estimates (Zipkin et al. 2010). Indeed, the models built included two sub-models, namely an occupancy sub-model and a detection sub-model to estimate detection probability to account for imperfect species detection and sparse recording (Mackenzie et al. 2002; Royle and Kéry 2007). As this modelling approach requires a fixed list of possible species (S), we generated a species occurrence matrix containing the ‘true’ observation state at each site. We included previous unpublished data in the analyses to control for potential false-negative detections, where species may be present but not recorded (Miller et al. 2011). Each species observed at least once in both terrestrial and arboreal substrates was assigned a detection history of 1, otherwise 0 for unobserved but previously recorded species (as well as in the transition zone, specifically for nonvolant mammals). To control for false-positive errors in the estimates, we accounted for the fact that some nonvolant mammals may not be detectable on either ground or arboreal cameras. Thus, during the ground camera trapping (months one to six), arboreal species had a history of NA detection. The same was true during arboreal camera trapping (months seven to twelve), where ground-dwelling species had a history of NA detection.
We created separate matrices for mammal species characteristics and habitat descriptors, with each row of data relating to a particular site. Only average adult body mass and camera position height were scaled to a fixed range (0 to 1) before running the models to facilitate model convergence. Values were back-transformed into their original units when discussing model predictions. We fitted single-season occupancy models with multi-species data (camera records and bat captures separately) using the RPresence package (version 2.12.27). We included species covariates for detection probability and habitat covariates for occupancy probability (Table 1, Supplementary Information Table S1, and Table 2). We estimated psi or ψj: the occupancy probability at a given station j (i.e., the proportion of species present at each site), and pi: the detection probability for each species i (i.e., the probability of detecting species i given that it is present). We selected the most parsimonious model with a change in the corrected Akaike information criterion score (i.e., ΔAICc < 2) from a set of candidate models with the lowest AICc (Burnham et al. 2011). We checked whether the 95% confidence interval (95%CI) for the regression coefficient (β) included zero to evaluate the influence of covariates on model parameters. Estimates of species richness (SR) values were derived from occupancy probabilities (Mackenzie et al. 2002):
Table 1
Covariates for modelling detection (p) and occupancy (ψ) probabilities of volant and nonvolant mammals (see also Table 3, Supplementary Information Table S1, and Table S2)
Model component | Description |
Covariates of camera trap dataset |
Detection (p) | Activitya,b | Activity patterns, either 1 (diurnal) or 0 (nocturnal) species |
| Groupa,b | Social behaviour, either 1 (group-living), or 0 (solitary or pair-living) |
| Massa | Average adult body mass (kg) |
| Strataa,b | Forest strata use patterns, i.e., A (arboreal), G (ground), B (both) |
Occupancy (ψ) | BAb | Basal area of trees with dbh ≥ 10 cm measured on a 20 x 5 m plot (m².are − 1) |
| CHb | Camera height, i.e., the height above ground level at which each camera was placed (m) |
| LRb | Liana cover ratio, i.e., the proportion of lianas (≥ 5 cm) to total non-liana stems (≥ 5 cm) at 20 x 5 m plot |
| ORb | Forest stand growth ratio, i.e., the proportion of old-growth stems (≥ 30 cm) to undergrowth stems (< 30 cm to ≥ 5 cm) at 20 x 5 m plot |
| Siteb | Site location, i.e., a 100 m² area where forest characteristics were recorded (i.e., plot) and cameras were placed at ground and tree level. There is a possible co-variation effect with other uncontrolled conditions around the investigated forest stands. |
| STb | Stem density for all trees and lianas (dbh ≥ 5cm) at each site, scaled to m² level (stems.m− 2). |
| WDb | Straight-line distance between each site and the nearest water (km) |
Covariates of bat trap dataset |
Detection (p) | ARa,b | Wing aspect ratio |
| Vmrb | Maximum range speed of bat species (m/s) |
| WLa,b | Wing loading (N.m− 2) |
Occupancy (ψ) | BAb | Basal area of trees with dbh ≥ 10 cm measured at a set of six plots of 20 x 5 m |
| ORb | Forest stand growth ratio, i.e., the proportion of old-growth stems (≥ 30 cm) to undergrowth at a set of six plots |
| Siteb | Site location, i.e., a set of six 100 m² points where both forest characteristics were measured and six bat traps were set. There is a possible co-variation effect with other uncontrolled conditions around the investigated forest stands |
| STb | Stem density for all trees and lianas (dbh ≥ 5cm) at a set of six 100 m² points averaged at 100 m² level (stems.are − 1) |
| WDb | Average straight-line distance from bat site to the nearest water source (km) |
aValue from the literature, e.g., body mass range (Kingdon et al. 2013a, b; Kingdon and Hoffmann 2013) and wing morphology of non-captured species (Norberg and Rayner 1987; Patterson and Webala 2012; Cakenberghe et al. 2017) |
bOur own measurements or observations |
Table 2
Top model selection table for single-season occupancy models with multi-species data. Most parsimonious model for camera trap data (a) see also full models in Supplementary Information Table S3a. Top models for bat trap data (b) see also full models in Supplementary Information Table S3b. Model structure: effect of covariates on occupancy (ψ) and detection (p) probabilities, number of parameters (K), corrected Akaike information criterion (AICc), change in AICc between the top model and selected model (ΔAICc), AICc weight (wi), 95% confidence interval on beta coefficient on site occupancy (βψ) or species detection (βp) covariate with standard error measures (SE)
Model component | K | AICc | ∆AICc | wi | βψ(SE) | βp(SE) |
(a) | ψ(ST)p(mass + group) | 5 | 1182.544 | 0 | 0.46 | 9.06(3.16) | -39.08(7.53), -0.51(0.26) |
(b) | ψ(site)p(.) | 3 | 274.743 | 0 | 0.261 | -1.92(0.97) | . |
| ψ(site)p(Vmr) | 4 | 276.131 | 1.388 | 0.131 | -1.90(0.97) | 0.12(0.14) |
| ψ(site)p(AR) | 4 | 276.275 | 1.532 | 0.122 | -1.91(0.95) | 0.13(0.16) |
| ψ(site)p(WL) | 4 | 276.670 | 1.927 | 0.1 | -1.91(0.97) | 0.01(0.03) |
A dot indicates no variable |
Where S: total number of possible species, ψij: unconditional occupancy of each station j for each species i. The models were fitted in the R computing environment Rx64 4.0.4 (R Core Team 2021).