Leibniz Institute for Zoo and Wildlife Research

Urbanisation is one of the biggest environmental challenges of our time, yet we still lack an integrative understanding of how cities affect behaviour, physiology and parasite susceptibility of free-living organisms. In this study, we focus on carotenoids, strictly dietary micronutrients that can either be used as yellow-red pigments, for integument colouration (signalling function), or as antioxidants, to strengthen the immune system (physiological function) in an urban predator, the Eurasian kestrel (Falco tinnunculus). Kestrels are specialised vole hunters but shift to avian prey in cities where diurnal rodents are not sufficiently available. This different foraging strategy might determine the quantity of carotenoids available. We measured integument colouration, circulating carotenoids in the blood and ectoparasite burden in kestrels along an urban gradient. Our results showed that nestlings that were raised in more urbanised areas displayed, unrelated to their ectoparasite burden, a paler integument colouration. Paler colours were furthermore associated with a lower concentration of circulating carotenoids. These findings support the hypothesis that the entire urban food web is carotenoid deprived and only prey of low quality with low carotenoid content is available (e.g. fewer carotenoids in urban trees, insects, small birds and finally kestrels). The alternative hypothesis that nestlings allocate carotenoids to reduce physiological stress and/or to cope with parasites rather than invest into colouration could not be supported. Our study adds to existing evidence that urban stressors negatively affect carotenoid production in urban areas, a deficiency that dissipate into higher trophic levels.

The present study was conducted in the isolated desert town of Oranjemund in the far south of Namibia. It is an extremely arid region where no livestock husbandry is practiced and only animals adapted to the desert can be found. However, in and around the city, artificial irrigation maintains lush green patches of grass that attract wild animals, in particular oryx antelopes ( Oryx gazella ). In 2015 four oryx antelopes were euthanised due to poor conditions and a post-mortem examination was conducted. Two were found positive for cystic echinococcosis and 16 cysts were collected for molecular analyses. In addition, faecal samples from black-backed jackals (n=5) and domestic dogs (n=9), which were regularly observed to feed on oryx carcasses, were collected and taeniid eggs isolated. Parasite species identification of the cysts and eggs was done by amplifying and sequencing the mitochondrial nad1 gene. Both oryx antelopes were found infected with E. ortleppi and one co-infected with E. canadensis G6/7. Both Echinococcus species were able to develop fertile cysts in oryx, making oryx antelopes competent hosts for these parasites. Therefore, the analysis of faecal samples was of high interest and although the numbers were quite small, taeniid eggs were found in three out of five faecal samples of jackals and in all nine dog samples. However, species determination was only successful with two jackal and one dog sample. All three were positive for E. canadensis G6/7. The absence of E. ortleppi may be due to the low number of faecal samples examined. In our small study, we discovered a rather unique lifecycle of Echinococcus spp. between jackals and domestic dogs as definitive hosts and oryx antelopes as intermediate hosts. Here, the presence of E. canadensis G6/7 is of particular concern, as it is the second most important causative agent of CE in humans.

Context Landscape composition and configuration, as well as seasonal landscape dynamics shape the behaviour, movement and energy expenditure of animals, i.e. foraging, hiding or fleeing, and ultimately survival. Especially in highly modified agricultural systems, it is crucial to understand how animal behaviour is influenced by landscape context to develop sustainable land management concepts. Objectives We show how landscape composition and configuration, together with seasonal dynamics affect animal behavioural types, accounting for the different life-history events in both sexes. Methods We investigated 34 European hares in two contrasting agricultural landscapes (a simple and a complex landscape) by using tri-axial accelerometer data to classify the animals’ behaviour into five categories: resting, foraging, moving, grooming and standing upright (i.e. vigilance behaviour). We tested whether the amount of behaviours per category changed with landscape composition and configuration, season and sex. Results During peak breeding, hares in areas of high habitat diversity rested more, moved less and spent less time searching for resources. During winter, hares moved more and rested less. Females rested less and foraged more in areas with large agricultural fields. Conclusions A complex landscape is particularly important during the breeding season, allowing animals to allocate enough energy into reproduction. In winter, hares in areas of low habitat diversity may not find enough thermal and anti-predator shelter to move as much as they would need to meet their requirements. Hence, high habitat diversity and small field sizes guarantee species persistence in human-altered agricultural areas throughout the year.

Previously unknown pathogens often emerge from primary ecosystems, but there is little knowledge on the mechanisms of emergence. Most studies analyzing the influence of land-use change on pathogen emergence focus on a single host-pathogen system and often observe contradictory effects. Here, we studied virus diversity and prevalence patterns in natural and disturbed ecosystems using a multi-host and multi-taxa approach. Mosquitoes sampled along a disturbance gradient in Côte d’Ivoire were tested by generic RT-PCR assays established for all major arbovirus and insect-specific virus taxa including novel viruses previously discovered in these samples based on cell culture isolates enabling an unbiased and comprehensive approach. The taxonomic composition of detected viruses was characterized and viral infection rates according to habitat and host were analyzed. We detected 331 viral sequences pertaining to 34 novel and 15 previously identified viruses of the families Flavi -, Rhabdo -, Reo -, Toga -, Mesoni - and Iflaviridae and the order Bunyavirales . Highest host and virus diversity was observed in pristine and intermediately disturbed habitats. The majority of the 49 viruses was detected with low prevalence. However, nine viruses were found frequently across different habitats of which five viruses increased in prevalence towards disturbed habitats, in congruence with the dilution effect hypothesis. These viruses were mainly associated with one specific mosquito species ( Culex nebulosus ), that increased in relative abundance from pristine (3%) to disturbed habitats (38%). Interestingly, the observed increased prevalence of these five viruses in disturbed habitats was not caused by higher host infection rates but by increased host abundance, an effect tentatively named abundance effect. Our data show that host species composition is critical for virus abundance. Environmental changes that lead to an uneven host community composition and to more individuals of a single species is a key driver of virus emergence.

The Annamite striped rabbit Nesolagus timminsi is an endangered lagomorph restricted to the Annamite mountains of Viet Nam and Lao P.D.R. Much remains unknown about the species, especially in its unexplored range in southern Lao P.D.R. Here, we report two market specimens from Dak Cheung district in Sekong province. Both animals were killed by firearms, and were reportedly hunted in the mountain range along the Viet Nam border. The specimens represent the southernmost records known from Lao P.D.R., and indicate that hunting with firearms may be a localized threat in some areas, along with the widespread threat of snares across the region.

An increasingly globalised world has facilitated the movement of non‐native species (NNS) via the poorly regulated international pet trade. While focus is increasingly being placed on preventative action to combat invasive NNS—often cheaper and less difficult than the management of established populations—successful prevention requires controlling potential pathways and obtaining baseline knowledge of species' availability. Here we performed an in‐depth analysis of the freshwater pet trade as one major vector of NNS, compiling its species inventory and deriving threats of NNS release and establishment in the wild. With Germany as our study region, we surveyed pet stores, websites and the country's largest online classified portal, eBay Kleinanzeigen, recording the taxa encountered. For each species, we determined the likelihood of release based on availability and price (cheaper and/or more readily available species have been shown to be of greater risk), and the likelihood of establishment based on ecological niche breadth and niche overlap with environmental conditions in Germany. The survey revealed 669 species, of which 651 were non‐native to Germany. Looking at release likelihood, more readily available species in pet stores and on websites proved to be cheaper. For websites, there was a significant effect of occurrence status (i.e. released, not released, native) on price, with released and native species being significantly cheaper. Species previously released in Germany and elsewhere demonstrated greater niche breadths and greater niche overlaps between their source regions and Germany; and for species released in Germany, there was a significantly positive relationship between the magnitude of niche overlap and the number of documented occurrences. Finally, we combined our release and establishment likelihood findings under ‘Release Risk’ metrics to highlight the species most worthy of prioritisation. We propose these metrics as proactive methods for screening species in the trade, which can inform future policy direction and intervention. Read the free Plain Language Summary for this article on the Journal blog.

Captive pandas are suffering from intestinal infection due to intestinal microbiota characterized by a high abundance of Enterobacteriaceae induced by long-term captivity. Probiotic supplements showed improvement in intestinal barrier function and inflammation. However, the effects of panda-derived probiotics on the intestinal epithelium and inflammation have not been elucidated. In the present study, lipopolysaccharide (LPS) impaired Caco-2 and RAW264.7 inflammatory models were applied to assess the protection of Lactiplantibacillus plantarum BSG201683 (L. plantarum G83) on barrier disruption and inflammation. The results showed that treatment with L. plantarum G83 significantly decreased the paracellular permeability to fluorescein isothiocyanate conjugated dextran (MW 4000, FITC-D4) after LPS induction. Meanwhile, L. plantarum G83 alleviated the reduction in tight junction (TJ) proteins and downregulated proinflammatory cytokines caused by LPS in Caco-2 cells. L. plantarum G83 also significantly decreased the expression and secretion of pro-inflammatory cytokines in LPS-induced RAW264.7 cells. In addition, the IL-10 increased in both Caco-2 and RAW264.7 cells after L. plantarum G83 treatment. The phagocytosis activity of RAW264.7 cells was significantly increased after L. plantarum G83 treatment. Toll-like receptor 4/ nuclear factor kappa-B (TLR4/NF-κB) signaling pathways were significantly down-regulated after L. plantarum G83 intervention, and the phosphorylation of NF-κB/p65 was consistent with this result. Our findings suggest that L. plantarum G83 improves intestinal inflammation and epithelial barrier disruption in vitro.

Urban ecology is a rapidly growing research field that has to keep pace with the pressing need to tackle the sustainability crisis. As an inherently multidisciplinary field with close ties to practitioners and administrators, research synthesis and knowledge transfer between those different stakeholders is crucial. Knowledge maps can enhance knowledge transfer and provide orientation to researchers as well as practitioners. A promising option for developing such knowledge maps is to create hypothesis networks, which structure existing hypotheses and aggregate them according to topics and research aims. Combining expert knowledge with information from the literature, we here identify 62 research hypotheses used in urban ecology and link them in such a network. Our network clusters hypotheses into four distinct themes: (i) Urban species traits & evolution, (ii) Urban biotic communities, (iii) Urban habitats and (iv) Urban ecosystems. We discuss the potentials and limitations of this approach. All information is openly provided as part of an extendable Wikidata project, and we invite researchers, practitioners and others interested in urban ecology to contribute additional hypotheses, as well as comment and add to the existing ones. The hypothesis network and Wikidata project form a first step towards a knowledge base for urban ecology, which can be expanded and curated to benefit both practitioners and researchers.

The Anthropocene is marked by a dramatic biodiversity decline, particularly affecting the family Rhinocerotidae. Three of five extant species are listed as Critically Endangered (Sumatran, Javan, Black rhinoceros), one as Vulnerable (Indian rhinoceros), and only one white rhino (WR) subspecies, the Southern white rhinoceros (SWR), after more than a century of successful protection is currently classified as Near Threatened by the IUCN, while numbers again are declining. Conversely, in 2008, the SWR’s northern counterpart and second WR subspecies, the Northern white rhinoceros (NWR), was declared extinct in the wild. Safeguarding these vanishing keystone species urgently requires new reproductive strategies. We here assess one such strategy, the novel in vitro fertilization program in SWR and – for the first time NWR – regarding health effects, donor-related, as well as procedural factors. Over the past 8 years, we performed 65 procedures in 22 white rhinoceros females (20 SWR and 2 NWR) comprising hormonal ovarian stimulation, ovum pick-up (OPU), in vitro oocyte maturation, fertilization, embryo culture, and blastocyst cryopreservation, at an efficiency of 1.0 ± 1.3 blastocysts per OPU, generating 22 NWR and 29 SWR blastocysts for the future generation of live offspring.

Genetic non-invasive sampling (gNIS) is a critical tool for population genetics studies, supporting conservation efforts while imposing minimal impacts on wildlife. However, gNIS often presents variable levels of DNA degradation and non-endogenous contamination, which can incur considerable processing costs. Furthermore, the use of restriction-site-associated DNA sequencing methods (RADseq) for assessing thousands of genetic markers introduces the challenge of obtaining large sets of shared loci with similar coverage across multiple individuals. Here, we present an approach to handling large-scale gNIS-based datasets using data from the spotted hyena population inhabiting the Ngorongoro Crater in Tanzania. We generated 3RADseq data for more than a thousand individuals, mostly from faecal mucus samples collected non-invasively and varying in DNA degradation and contamination level. Using small-scale sequencing, we screened samples for endogenous DNA content, removed highly contaminated samples, confirmed overlap fragment length between libraries, and balanced individual representation in a sequencing pool. We evaluated the impact of (1) DNA degradation and contamination of non-invasive samples, (2) PCR duplicates and (3) different SNP filters on genotype accuracy based on Mendelian error estimated for parent-offspring trio datasets. Our results showed that when balanced for sequencing depth, contaminated samples presented similar genotype error rates to those of non-contaminated samples. We also showed that PCR duplicates and different SNP filters impact genotype accuracy. In summary, we showed the potential of using gNIS for large-scale genetic monitoring based on SNPs and demonstrated how to improve control over library preparation by using a weighted re-pooling strategy that considers the endogenous DNA content.

The United Nations recently agreed to major expansions of global protected areas (PAs) to slow biodiversity declines1. However, although reserves often reduce habitat loss, their efficacy at preserving animal diversity and their influence on biodiversity in surrounding unprotected areas remain unclear2-5. Unregulated hunting can empty PAs of large animals6, illegal tree felling can degrade habitat quality7, and parks can simply displace disturbances such as logging and hunting to unprotected areas of the landscape8 (a phenomenon called leakage). Alternatively, well-functioning PAs could enhance animal diversity within reserves as well as in nearby unprotected sites9 (an effect called spillover). Here we test whether PAs across mega-diverse Southeast Asia contribute to vertebrate conservation inside and outside their boundaries. Reserves increased all facets of bird diversity. Large reserves were also associated with substantially enhanced mammal diversity in the adjacent unprotected landscape. Rather than PAs generating leakage that deteriorated ecological conditions elsewhere, our results are consistent with PAs inducing spillover that benefits biodiversity in surrounding areas. These findings support the United Nations goal of achieving 30% PA coverage by 2030 by demonstrating that PAs are associated with higher vertebrate diversity both inside their boundaries and in the broader landscape.

Coppice forests are socio-ecological systems especially rich in biodiversity. They have been transformed into high forest and abandoned across large areas of Europe over the past 200 years. Coppice loss is likely an important driver of insect declines. It is currently unclear whether habitat quality or decreasing connectivity of the remaining fragments is more important for the survival of insect populations. We related the abundance of two coppice-associated butterflies of conservation concern, Satyrium ilicis and Melitaea athalia, to indicators of habitat quality and habitat connectivity. We estimated butterfly densities using Distance Sampling along a successional gradient (time since last cut: 1–9 years; N = 130 plots) across one of the largest remaining simple oak-birch coppice landscapes in Central Europe. Both species reached abundance peaks within four to six years after the last cut, declining rapidly in abundance with subsequent succession. We found no evidence that coupe size, coppice availability and patch (= coupe) connectivity were related to the density of the species. Besides stand age, the cover of larval foodplants explained predicted butterfly densities well. Only Satyrium ilicis benefitted from high Red Deer densities. Implications for insect conservation: Our results suggest that habitat quality and sufficient availability of coppice of suitable age matters more than coupe size and fragmentation within a traditional managed coppice landscape. Coppice restoration aiming at the study species should ensure a shifting mosaic of successional habitat to provide a large availability of resprouting oak stools and bilberry vegetation that holds dense Melampyrum pratense stands.

Quantifying and monitoring the risk of defaunation and extinction require assessing and monitoring biodiversity in impacted regions. Camera traps that photograph animals as they pass sensors have revolutionized wildlife assessment and monitoring globally. We conducted a global review of camera trap research on terrestrial mammals over the last two decades. We assessed if the spatial distribution of 3395 camera trap research locations from 2324 studies overlapped areas with high defaunation risk. We used a geospatial distribution modeling approach to predict the spatial allocation of camera trap research on terrestrial mammals and to identify its key correlates. We show that camera trap research over the past two decades has not targeted areas where defaunation risk is highest and that 76.8% of the global research allocation can be attributed to country income, biome, terrestrial mammal richness, and accessibility. The lowest probabilities of camera trap research allocation occurred in low‐income countries. The Amazon and Congo Forest basins – two highly biodiverse ecosystems facing unprecedented anthropogenic alteration – received inadequate camera trap research attention. Even within the best covered regions, most of the research (64.2%) was located outside the top 20% areas where defaunation risk was greatest. To monitor terrestrial mammal populations and assess the risk of extinction, more research should be extended to regions with high defaunation risk but have received low camera trap research allocation.

Widely dispersed fragmented populations are a challenge to monitor because subpopulation sizes may be very small, difficult to access and time consuming to sample regularly. We use the coconut crab ( Birgus latro ) on Pemba, United Republic of Zanzibar as a case study for estimating highly fragmented populations and metapopulation sizes. The species is a very large terrestrial decapod threatened by exploitation and habitat alteration and now classified as vulnerable. We developed an integrated model to analyse capture‐mark‐recapture (CMR) data from five sites jointly with count data from 24 sites to estimate site‐level densities and population sizes, predicted total population size across the Pemba archipelago, and investigated the effect of six predictors of human influence on density. We fitted separate models to test the effect of the same predictors on raw counts and individual body mass. We estimate the total population of coconut crabs on the Pemba archipelago to be c . 6700 terrestrial individuals. We show that government protection generally affects crabs positively, whereas presence of agriculture negatively affects their densities. This study highlights that time‐consuming CMR data can be leveraged to estimate densities on less visited sites, and that fully protected islands are critical for maintaining relatively high population densities. Our overall population estimate suggests that Pemba still hosts a viable coconut crab population in a part of its range where the species is otherwise in steep decline.

Cities can host significant biological diversity. Yet, urbanisation leads to the loss of habitats, species, and functional groups. Understanding how multiple taxa respond to urbanisation globally is essential to promote and conserve biodiversity in cities. Using a dataset encompassing six terrestrial faunal taxa (amphibians, bats, bees, birds, carabid beetles and reptiles) across 379 cities on 6 continents, we show that urbanisation produces taxon-specific changes in trait composition, with traits related to reproductive strategy showing the strongest response. Our findings suggest that urbanisation results in four trait syndromes (mobile generalists, site specialists, central place foragers, and mobile specialists), with resources associated with reproduction and diet likely driving patterns in traits associated with mobility and body size. Functional diversity measures showed varied responses, leading to shifts in trait space likely driven by critical resource distribution and abundance, and taxon-specific trait syndromes. Maximising opportunities to support taxa with different urban trait syndromes should be pivotal in conservation and management programmes within and among cities. This will reduce the likelihood of biotic homogenisation and helps ensure that urban environments have the capacity to respond to future challenges. These actions are critical to reframe the role of cities in global biodiversity loss.

Assessing and predicting the persistence of populations is essential for the conservation and control of species. Here, we argue that local mechanisms require a better conceptual synthesis to facilitate a more holistic consideration along with regional mechanisms known from metapopulation theory. We summarise the evidence for local buffer mechanisms along with their capacities and emphasise the need to include multiple buffer mechanisms in studies of population persistence. We propose an accessible framework for local buffer mechanisms that distinguishes between damping (reducing fluctuations in population size) and repelling (reducing population declines) mechanisms. We highlight opportunities for empirical and modelling studies to investigate the interactions and capacities of buffer mechanisms to facilitate better ecological understanding in times of ecological upheaval.

Historically, reproductive health in wildlife species has been evaluated primarily via immunoassay detection of fecal and urinary steroid hormone metabolites. This combination of sample type, biomarker category, and assay has been preferred for decades due to the ease of assessing reproductive health through the evaluation of stable compounds in easily collected biological samples using a cost-effective method. Increasingly, beginning with high performance liquid chromatography (HPLC) and more recently with convergence chromatography and ultra HPLC coupled with mass spectrometry (MS), wildlife studies are incorporating more sensitive and specific high-throughput technologies for the assessment of not only steroid hormone metabolites but proteins as well. Of note, a comprehensive health evaluation requires the measurement of biological readouts that modulate reproduction such as: glucocorticoids, leptin, insulin, thyroid hormones, melatonin, the microbiome, and markers of inflammation. Emerging modulatory biomarkers of reproductive health include acute phase proteins, microRNAs, and reactive oxygen species. Several of these biomarkers require application of newer technologies such as LC-MS/MS and sequencing, which demonstrates the need for the field of wildlife reproductive biology to diversify from its reliance on immunoassays. Importantly, endocrine disrupting chemicals adversely affect many aspects of reproductive function and evaluation of these compounds requires high throughput technology such as LC-MS/MS. The application of sequencing, particularly Next Generation Sequencing of bulk RNA (RNA-Seq) and single cell RNA-Seq, is uncommon in studies of wildlife reproductive health. However, as the cost of these methods decreases and consortiums of wildlife researchers band together to raise funds in support of studies using these technologies, their use will become more routine. Future research should focus on integration of known biomarkers of related systems into comprehensive reproductive assessments and the development of new biomarkers which are sensitive, precise, and employ non-invasive methodologies for the assessment of reproductive health of wildlife species.

The evolution of endothermy in vertebrates is a major research topic in recent decades that has been tackled by a myriad of research disciplines including paleontology, anatomy, physiology, evolutionary and developmental biology. The ability of most mammals to maintain a relatively constant and high body temperature is considered a key adaptation, enabling them to successfully colonize new habitats and harsh environments. It has been proposed that in mammals the anterior nasal cavity, which houses the maxilloturbinal, plays a pivotal role in body temperature maintenance, via a bony system supporting an epithelium involved in heat and moisture conservation. The presence and the relative size of the maxilloturbinal has been proposed to reflect the endothermic conditions and basal metabolic rate in extinct vertebrates. We show that there is no evidence to relate the origin of endothermy and the development of some turbinal bones by using a comprehensive dataset of µCT-derived maxilloturbinals spanning most mammalian orders. Indeed, we demonstrate that neither corrected basal metabolic rate nor body temperature significantly correlate with the relative surface area of the maxilloturbinal. Instead, we identify important variations in the relative surface area, morpho-anatomy, and complexity of the maxilloturbinal across the mammalian phylogeny and species ecology.

Background Helminth infections are an important public health problem in humans and have an even greater impact on domestic animal and livestock welfare. Current readouts for anthelmintic drug screening assays are stage development, migration, or motility that can be subjective, laborious, and low in throughput. The aim of this study was to apply and optimize a fluorometric technique using resazurin for evaluating changes in the metabolic activity of Ascaris suum third-stage larvae (L3), a parasite of high economic relevance in swine. Methods Ascaris suum L3 were mechanically hatched from 6- to 8-week embryonated and sucrose-gradient-enriched eggs. Resazurin dye and A. suum L3 were titrated in 96-well microtiter plates, and resazurin reduction activity was assessed by fluorometry after 24 h of incubation. Fluorescence microscopy was used to localize the resazurin reduction site within the larvae. Finally, we exposed A. suum L3 to various stress conditions including heat, methanol, and anthelmintics, and investigated their impact on larval metabolism through resazurin reduction activity. Results We show that the non-fluorescent dye resazurin is reduced inside vital A. suum L3 to fluorescent resorufin and released into the culture media. Optimal assay parameters are 100–1000 L3 per well, a resazurin concentration of 7.5 µg/ml, and incubation at 37 °C/5% CO2 for 24 h. An intact L2 sheath around the L3 of A. suum completely prevents the uptake of resazurin, while in unsheathed L3, the most intense fluorescence signal is observed along the larval midgut. L3 exposed to methanol or heat show a gradually decreased resazurin reduction activity. In addition, 24 h exposure to ivermectin at 0.625 µM, mebendazole at 5 µM, and thiabendazole from 10 to 100 µM significantly decreased larval metabolic activity by 55%, 73%, and 70% to 89%, respectively. Conclusions Together, our results show that both metabolic stressors and anthelmintic drugs significantly and reproducibly reduce the resazurin reduction activity of A. suum L3, making the proposed assay a sensitive and easy-to-use method to evaluate metabolic activity of A. suum L3 in vitro. Graphical Abstract