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Poaching is a pervasive threat to wildlife, yet quantifying the direct effect of poaching on wildlife is rarely possible because both wildlife and threat data are infrequently collected concurrently. In this study, we used poaching data collected through the Management Information System (MIST) and wildlife camera trap data collected by the Tropical Ecology Assessment and Monitoring (TEAM) network from 2014 to 2017 in Volcanoes National Park, Rwanda. We implemented co-occurrence multi-season occupancy models that accounted for imperfect detection to investigate the effect of poaching on initial occupancy, colonization, and extinction of five mammal species. Specifically, we focused on two species of conservation concern (mountain gorilla [Gorilla beringei beringei] and golden monkey [Cercopithecus mitis kandti]), and three species targeted by poachers (black-fronted duiker [Cephalophus nigrifrons], bushbuck [Tragelaphus scriptus], and African buffalo [Syncerus caffer]). We found that the probability of local extinction was highest in sites with poaching activity for golden monkey and bushbuck. In addition, the probability of initial occupancy for golden monkey was highest in sites without poaching activity. We only found weak evidence of effects of poaching on parameters governing the occupancy dynamics of the other species. All species showed evidence of poaching presence affecting the probability of detection of the wildlife species. This is the first study to our knowledge to combine direct threat observations from ranger-based monitoring data with camera trap wildlife observations to quantify the effect of poaching on wildlife. Given the widespread collection of ranger-based monitoring and camera trap data, our approach is broadly applicable to numerous protected areas and has the potential to significantly improve conservation management. Specifically, the relationship between poaching activity and wildlife population dynamics can be combined with information on the relationship between ranger patrols and poaching activity to develop models useful for making wise decisions about ranger patrol deployment.

In recent years, both depletion of wild animals and declining food supply have threatened the livelihoods of people inhabiting the forests of the Congo Basin, and rendered the bushmeat trade a national and global concern. Because initial approaches to wildlife management were criticized for lacking consideration of the customary rights of local people, a variety of projects have been proposed to ensure their active participation in management initiatives. However, unfamiliar with the concepts of conservation ecology, local people have found it difficult to contribute effectively. This paper proposes an approach to monitor the status of fauna, based on the ratio of blue duikers (Philantomba monticola) to medium-sized duikers (Cephalophusspp.) for the total number of hunting catches (the catch B/M). Analysis of changes in the composition of hunting catches across multiple sites in southeastern Cameroon revealed the following trends: (1) without substantive human intervention, i.e., hunting pressure and forest disturbance, medium-sized duikers were densely distributed while blue duikers were sparse, so that the catch B/M was low; (2) under moderate human intervention, blue duikers became more densely distributed while the original density of medium-sized duikers was maintained, so that the catch B/M increased; (3) with extensive human intervention in specific areas, medium-sized duikers became sparsely distributed while a relatively high density of blue duikers was maintained, so that the catch B/M increased significantly and a mosaic of different compositions of duikers was formed; and (4) with extensive human intervention extending over the specific extensive area, both medium-sized and blue duikers became sparse. It appears that the catch B/M predicts changes in the status of game animals and of the background wild fauna, and is both a sufficiently reliable variable for ecologists and perceptible for local people. Furthermore, this approach has the potential to cultivate a relationship of trust between ecologists and local people, which is indispensable in establishing effective collaborative wildlife management.

Background This study aims to assess the role that Pleistocene refugia, rivers and local habitat conditions may have played in the evolutionary diversification of three central African duiker species ( Cephalophus dorsalis, C. callipygus and Philantomba monticola ). Genetic data from geo-referenced feces were collected from a wide range of sites across Central Africa. Historical patterns of population genetic structure were assessed using a ~ 650 bp fragment of the mitochondrial control region and contemporary patterns of genetic differentiation were evaluated using 12 polymorphic microsatellite loci. Results Mitochondrial analyses revealed that populations of C. callipygus and P. monticola in the Gulf of Guinea refugium are distinct from other populations in west central Africa. All three species exhibit signatures of past population expansion across much of the study area consistent with a history of postglacial expansion. There was no strong evidence for a riverine barrier effect in any of the three species, suggesting that duikers can readily cross major rivers. Generalized dissimilarity models (GDM) showed that environmental variation explains most of the nuclear genetic differentiation in both C. callipygus and P. monticola . The forest-savanna transition across central Cameroon and the Plateaux Batéké region in southeastern Gabon show the highest environmentally-associated turnover in genetic variability. A pattern of genetic differentiation was also evident between the coast and forest interior that may reflect differences in precipitation and/or vegetation. Conclusions Findings from this study highlight the historical impact of Pleistocene fragmentation and current influence of environmental variation on genetic structure in duikers. Conservation efforts should therefore target areas that harbor as much environmentally-associated genetic variation as possible in order to maximize species’ capacity to adapt to environmental change.

The total mitogenome of the confiscated material of tufted deer, Elaphodus cephalophus cephalophus was sequenced and annotated. It is 16,351bp in length and contained 2 ribosomal RNAs, 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs) and, 1 control region (CR). Phylogenetic analyses showed the close relationship of Elaphodus and Muntiacus, and monophyletic clades of genera Elaphodus and Muntiacus.

Consumption and trade in bushmeat are entrenched in sub-Saharan Africa amid growing land degradation and environmental pollution that raise safety concerns, yet sustainability of bushmeat extraction and zoonoses considerations have been the focus of bushmeat research. Here, we evaluated the health risk of trace metals in the skeletal muscle, bone, liver, and skin of the black duiker ( Cephalophus niger ), brush-tailed porcupine ( Atherurus africanus ), bushbuck ( Tragelaphus scriptus ), cane rat ( Thryonomys swinderianus ), and Maxwell’s duiker ( Cephalophus maxwelli ) being the five most hunted and consumed species of bushmeat in Ghana. Sample tissues of the five species were analyzed for Cu, Zn, Se, Cd, As, Pb, and Hg. Targeted hazard quotient (THQ) of Se for black duiker, bushback, and Maxwell’s duiker as well as that of Pb for black duiker, Brush-tailed porcupine, and Maxwell’s duiker were concerning (> 1) for individuals foraging daily on bushmeat. Thus, cane rat was the only species that recorded both estimated daily intake (EDI) and THQ of Se and Pb within safe limits for daily consumption. In respect of Cu, Zn, Cd, As, and Hg, EDI and THQ values indicated no perceived risk to consumers for all five species. Lifetime cancer risk (CR) of As was negligible for all species. At the rate of bushmeat consumption in sub-Saharan Africa (0.104 kg per day), the cane rat was the only species considered safe for daily consumption among the five species.

1. Calibrating indices of animal abundance to true densities is critical in wildlife studies especially when direct density estimations are precluded by high costs, lack of required data or model parameters, elusiveness and rarity of target species. For studies deploying camera traps, the use of photographic rate (photographs per sampling time) as an index of abundance potentially applies to the majority of terrestrial mammals where individual recognition, and hence capture—recapture analysis, are unfeasible. The very few studies addressing this method have either been limited by lack of independence between trapping rates and density estimations, or because they combined different species, thus introducing potential bias in camera trap detection rates. This study uses a single model species from several sites to analyse calibration of trapping rates to independently derived estimations of density. The study also makes the first field test of the method by Rowcliffe et al. (2008) for density derivation from camera trapping rates based on modelling animal-camera contacts. 2. We deployed camera traps along line transects at six sites in the Udzungwa Mountains of Tanzania and correlated trapping rates of Harvey's duiker Cephalophus harveyi with densities estimated from counts made along the same transects. 3. We found a strong, linear relationship (R² = 0·90) between trapping rate and density. Sampling precision analysis indicates that camera trapping rates reach satisfactory precision when trapping effort amounts to 250-300 camera days. Density estimates using Rowcliffe et al.'s (2008) gas model conversion are higher than from transect censuses; we discuss the possible reasons and stress the need for more field tests. 4. Synthesis and applications. Subject to rigorous and periodic calibration, and standardization of sampling procedures in time and over different sites, camera trapping rate is shown to be, in this study, a valid index of density in the target species. Comparative data indicate that this may also apply to forest ungulates in general. The method has great potential for standardizing monitoring programmes and reducing the costs of wildlife surveys, especially in remote areas.

Aim Global warming is threatening species survival worldwide. Cold‐adapted montane ungulates may be among the first species to be affected by global warming. Here, we investigate the behavioural thermoregulation hypothesis that montane ungulates buffer the effects of warming climate through behavioural adjustment. Location Foping National Nature Reserve (FNNR) on the southern slopes of the Qinling Mountains, Shaanxi, China. Methods We used infrared camera traps over six consecutive years to monitor behavioural responses of montane ungulates to seasonal and diurnal changes in ambient temperature. We evaluated how seasonal altitudinal migration and changes to their daily activity budget may mitigate the effect of warming on montane ungulates. Results All four montane ungulate species examined here preferred ambient temperatures <22°C in summer. On this basis, we estimate that 27.9% (+2°C) and 46.7% (+3°C) of suitable summer habitats will become unsuitable under climate change. Chinese muntjac and tufted deer displayed behavioural changes to daily activity budgets, which may help them overcome global climate warming to a certain extent. By contrast, golden takin and wild boar did not display similar behavioural changes, and it may be because they are not affected by current shifts in climate due to larger body size and thus lower thermal stress. Main Conclusions These analyses demonstrate different species responses to warming are likely and are determined by specific tolerances to ambient temperature thresholds. However, it remains to be seen whether species interactions caused by behavioural shifts may affect species ability to respond to climate.

Livestock grazing occurs in many protected areas for wildlife and has become a threat to wildlife worldwide. Livestock grazing within protected areas causes negative effects to rare wildlife (e.g., giant panda [Ailuropoda melanoleuca]) and their habitat. We used the 2,000-km² Wolong National Nature Reserve, Sichuan Province, southwestern China, to document the effects of livestock on the giant panda and its habitat. We monitored arrow bamboo (Bashania fangiana), wildlife sign (i.e., feces and tracks), and characteristics of plant communities in intact habitat (IH; limited livestock grazing) and disturbed habitat (DH; with grazing disturbance) to assess the effects of livestock grazing and the responses of giant pandas and sympatric species across spatial and temporal scales. Bamboo coverage and the height and basal diameter of bamboo in IH were greater than those in DH, whereas the number of herbaceous species and herbaceous coverage in IH were lower than those in DH. Wildlife signs in IH were greater than those in DH; specifically, giant panda and red panda (Ailurus fulgens) signs were greater, whereas signs of sambar (Rusa unicolor) and tufted deer (Elaphodus cephalophus) in IH were similar to those in DH. Livestock grazing reduced bamboo, which may threaten the long-term survival of the giant panda. Our results have implications for understanding and management of livestock grazing in the Wolong National Nature Reserve and elsewhere.

The family Cervidae is the second most diverse in the infraorder Pecora and is characterized by variability in the diploid chromosome numbers among species. X chromosomes in Cervidae evolved through complex chromosomal rearrangements of conserved segments within the chromosome, changes in centromere position, heterochromatic variation, and X-autosomal translocations. The family Cervidae consists of two subfamilies: Cervinae and Capreolinae. Here we build a detailed X chromosome map with 29 cattle bacterial artificial chromosomes of representatives of both subfamilies: reindeer ( Rangifer tarandus ), gray brocket deer ( Mazama gouazoubira ), Chinese water deer ( Hydropotes inermis ) (Capreolinae); black muntjac ( Muntiacus crinifron s), tufted deer ( Elaphodus cephalophus ), sika deer ( Cervus nippon ) and red deer ( Cervus elaphus ) (Cervinae). To track chromosomal rearrangements during Cervidae evolution, we summarized new data, and compared them with available X chromosomal maps and chromosome level assemblies of other species. We demonstrate the types of rearrangements that may have underlined the variability of Cervidae X chromosomes. We detected two types of cervine X chromosome—acrocentric and submetacentric. The acrocentric type is found in three independent deer lineages (subfamily Cervinae and in two Capreolinae tribes—Odocoileini and Capreolini). We show that chromosomal rearrangements on the X-chromosome in Cervidae occur at a higher frequency than in the entire Ruminantia lineage: the rate of rearrangements is 2 per 10 million years.

Surveying and quantifying the bushmeat crisis in Africa requires up-front, reliable species-level identification. We conducted a comprehensive survey of 31 trading places where bushmeat are sold in Côte d’Ivoire (West Africa) and two seizures from Europe, using a multi-gene DNA-typing approach and a dedicated species-assignment pipeline (DNAbushmeat). We identified 47 wild and five domestic species-level taxa from 348 collected carcasses, including mammals (15 Cetartiodactyla, 10 Rodentia, seven Carnivora, seven Primates, two Pholidota, two Lagomorpha, one Hyracoidea, one Chiroptera), reptiles (two Squamata), birds (one Bucerotiformes, one Galliformes, one Otidiformes) and fish (one Perciformes). Our DNA-based approach allowed the detection of two separate lineages of red-flanked duikers (Cephalophus rufilatus), a yet unreferenced cane rat (but possibly Thryonomys gregorianus) and two cryptic species of Gambian rat (Cricetomys). We also observed important levels of intraspecific diversity in several mammals and squamates, suggesting additional cryptic diversity within bushmeat species from Côte d’Ivoire. More than half of the bushmeat carcasses were inaccurately identified, with European customs peaking at 100% inaccuracy. Our study also explored the use of diversity indices among bushmeat markets to identify ‘hotspot’ market places where biodiversity would be the most impacted. Overall, 12 protected species (including pangolins, crocodiles, primates and antelopes) were impacted by the bushmeat trade in Côte d’Ivoire, indicating weak law enforcement related to game protection. We suggest that the recognition of the bushmeat sector by the state and its DNA-based surveillance is necessary to reach a sustainable management of the bushmeat trade in Côte d’Ivoire.