Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard

Species of the family Felidae are thought to be obligate carnivores. However, detection of plants in their faeces raises questions about the role of plants in their diet. This is particularly true for the snow leopard (Panthera uncia). Our study aimed to comprehensively identify the prey and plants consumed by snow leopards. We applied DNA metabarcoding methods on 90 faecal samples of snow leopards collected in Kyrgyzstan, employing one vertebrate and four plant markers. We found that argali (Ovis ammon) was detected only from male snow leopards. Myricaraia sp. was the most consumed among 77 plant operational taxonomic units found in snow leopard samples. It frequently appeared in samples lacking any prey animal DNA, indicating that snow leopards might have consumed this plant especially when their digestive tracts were empty. We also observed differences in the patterns of plant consumption between male and female snow leopards. Our comprehensive overview of prey and plants detected in the faeces of snow leopards and other sympatric mammals will help in formulating hypotheses and guiding future research to understand the adaptive significance of plant-eating behaviour in felids. This knowledge supports the enhancement of their captive environments and the conservation planning of their natural habitats.

Seasonal diet partition among top predators of a small island, Iriomote Island in the Ryukyu Archipelago, Japan

Small islands tend to lack predators because species at higher trophic levels often cannot survive. However, two exceptional top predators-the Iriomote cat Prionailurus bengalensis iriomotensis, and the Crested Serpent Eagle Spilornis cheela perplexus-live on the small Iriomote Island in the Ryukyu Archipelago. To understand how these predators coexist with limited resources, we focused on their seasonal diets between which conflicts are considered to occur. To compare the diets, we used DNA metabarcoding analysis of faecal samples. In the summer, we identified 16 unique prey items from Iriomote cat faecal samples and 15 unique prey items from Crested Serpent Eagle faecal samples. In the winter, we identified 37 and 14, respectively. Using a non-metric multidimensional scaling and a permutational multivariate analysis of variance, our study reveals significant differences in the diet composition at the order level between the predators during both seasons. Furthermore, although some prey items at the species-to-order level overlapped between them, the frequency of occurrence of most prey items differed in both seasons. These results suggest that this difference in diets is one of the reasons why the Iriomote cat and the Crested Serpent Eagle are able to coexist on such a small island.

Food webs reveal coexistence mechanisms and community organization in carnivores

Globally, massive carnivore guild extirpations have led to trophic downgrading and compromised ecosystem services. However, the complexity of multi-carnivore food webs complicates accurate identification of species interactions and community organization. Here, we used fecal DNA metabarcoding to investigate three communities that together encompass eight large- and meso-carnivore species and their 44 prey taxa of the Qinghai-Tibet Plateau (QTP), one of the last places on Earth that still harbors intact carnivore assemblages. Quantitative food-web analyses revealed pronounced interspecific variations in the carnivores' prey compositions and dietary partitioning both between and within guilds. Additionally, body masses of the carnivores and their prey exhibited consistent hump-shaped correlations across communities. Overall, differences in prey diversity, size category, and proportional utilization among the carnivore species result in trophic niche segregation that likely promotes carnivore coexistence in the harsh QTP environment. Network structure analyses detected significant modularity in all food webs but nestedness in only one. Furthermore, network characterization identified pikas (Ochotona spp.), bharal (Pseudois nayaur), and domestic yak (Bos grunniens) as potential keystone prey across the areas. Our results paint a holistic and detailed picture of the QTP carnivore assemblages' trophic networks and demonstrate that the combined use of the molecular dietary approach and network analysis can generate structural insights into carnivore coexistence and can identify functionally important species in complex communities. Such knowledge can help safeguard carnivore guild integrity and enhance community resilience to environmental perturbations in the sensitive QTP ecosystems.

Domestic Cattle in a National Park Restricting the Sika Deer Due to Diet Overlap

Managers need to know the extent of the conflict between livestock and wild animals. Although many studies have reported the conflict between livestock and wild animals, few have checked the extent of the conflict. Cattle raising in the Northeast Tiger and Leopard National Park is considered one of the main driving forces behind the restricted distribution of sika deer. To understand whether foraging competition is contributing to avoidance patterns between sika deer and cattle, we investigated their feeding habits using DNA barcoding and high-throughput sequencing. Our study shows that although cattle are grazers in the traditional division of herbivores, their diet shifted to a predominance of dicotyledonous woody plants, and this diet shift resulted in a high degree of dietary overlap between sika deer and cattle. Moreover, compared to sika deer, cattle diets are more diverse at the species level with a wider ecological niche. Our results confirm that overlapping dietary niches and the superior competitive abilities of cattle contribute to the restricted distribution of the sika deer, which has critical implications for the conservation of their predators. Our study suggests that cattle grazing should be prohibited in the Park and effective measures should be taken for the benefit of sika deer.

The pikas of China: a review of current research priorities and challenges for conservation

Of the approximately 30 extant species of pika (Ochotona; Ochotonidae; Lagomorpha), at least 23 occur in China. Of these, 8 are endemic, and 3 are classified as Endangered by the IUCN. Research into most Chinese species is scarce, and there is much to learn about basic aspects of their ecology. We reviewed the literature on the 23 Chinese Ochotona species, with the aim of highlighting knowledge gaps and biases in research allocation. Specifically, we identify (1) which pika species receive the most attention from researchers, (2) which topics are the most frequently studied, and (3) how well research satisfies conservation priorities. We covered a total of 879 articles, most of which were written in English or Chinese. Around 75% of all publications focused on the plateau pika Ochotona curzoniae. Seven species were represented by 10 or fewer publications each. Endangered and endemic species were particularly poorly represented. 204 papers treated pikas as a pest, while 13 studied conservation issues. Nine species were considered possible targets for pest control, including some poorly known endemics. We make some recommendations on how research into Chinese Ochotona could be improved, including: (1) recognizing that the current species-level taxonomy may be an ineffective way to prioritize conservation research in Ochotona, (2) directing more research toward threatened and endemic species, subspecies, and populations, (3) researching the ecosystem engineering effects of pikas, (4) collecting basic data on natural history of the many understudied species, and (5) researching threats, including climate change and pest control campaigns.

Combining vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing to investigate the diet of the leopard cat (Prionailurus bengalensis) in Korea

The leopard cat (Prionailurus bengalensis), an endangered species in South Korea, is a small feline widely distributed in Asia. Here, we investigated the diet of leopard cats in the inland areas of Korea by examining their fecal contents using vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing. Shotgun metagenomic sequencing revealed that the feces were rich in DNA not only of vertebrates but also of arthropods and plants, but care should be taken when using shotgun metagenomic sequencing to identify vertebrates at low taxonomic levels (e.g., genus level), as it was often erroneous. Meanwhile, vertebrate mitochondrial 12S rRNA gene sequencing was found to be accurate in the genus-level identification, as the genera identified were consistent with the Korean fauna. We found that small mammals such as murids were their main prey. By using these two sequencing methods in combination, this study demonstrated that accurate information about the overall dietary content and vertebrate prey of leopard cats could be obtained. We expect that the continued community efforts to expand the genome database of wildlife, including vertebrates, will alleviate the problem of erroneous identification of prey at low taxonomic levels by shotgun metagenomic sequencing in the near future.

The Ecological Roles of Medium and Small Carnivores in the Terrestrial Animal Community in Liancheng National Nature Reserve, China

It is vitally important to understand the ecological roles of medium and small carnivores in the context of the massive decline in the number of large carnivores around the world. Based on a spatial association network of terrestrial birds and mammals, this study analyzed the ecological roles of medium and small carnivores in the community in Liancheng National Nature Reserve. From October 2019 to June 2020, we obtained 3559 independent detections of 20 terrestrial birds and mammals from 112 camera traps. There are seven species that are medium and small carnivores present in the study area, including red fox (Vulpes vulpes), leopard cat (Prionailurus bengalensis), Chinese mountain cat (Felis bieti), stone marten (Martes foina), Asian badger (Meles leucurus), Siberian weasel (Mustela sibirica) and mountain weasel (Mustela altaica). By calculating the Phi coefficient of all species pairs, a spatial association network composed of twelve species was constructed. We analyzed the characterization of spatial associations by the Shannon-Wiener index and Lambda statistic. The results showed that: (1) the status of the network reflects the changes of community composition and structure after the decline in large carnivores and other species; (2) with the exception of the Chinese mountain cat and stone marten, the other five medium and small carnivores were located in the network, which played an important role in the complexity of the network and the maintenance of the community; (3) the medium and small carnivores could not take the place of the large carnivores in order to control the population of herbivores, such as Siberian roe deer (Capreolus pygargus) and Himalayan marmot (Marmota himalayana). The results of this study provide guidance for determining the direction and focus of conservation efforts.

Investigation of Parasitic Nematodes Detected in the Feces of Wild Carnivores in the Eastern Qinghai-Tibet Plateau, China

Wildlife shares grazing areas with herders in the eastern Qinghai-Tibet Plateau, and humans can be infected by zoonotic nematodes through direct contact with animals or contaminated water. In this study, fecal samples (n = 296) from wild carnivores were collected to explore the infection rate and molecular genetic characteristics of nematodes by stratified random sampling in the survey areas. Host species and the nematodes they carried were then identified using 16S rRNA and 18S rRNA gene sequencing, respectively. Statistical analysis, neutrality tests, genetic diversity analysis and Bayesian inferred trees were performed to complete the study. In total, 10 species of nematodes were detected in 240 feces from six species of carnivores identified (including dominant Vulpes ferrilata and Vulpes vulpes), namely Uncinaria stenocephala, Toxascaris sp., Crenosoma vulpis, Parapharyngodon bainae, Oesophagostomum muntiacum, Aspiculuris tetraptera, Mastophorus muris, Nematodirus spathiger, Muellerius capillaris, and Molineus patens. Among these nematodes, U. stenocephala (35.83%, 86/240) and Toxascaris sp. (14.58%, 35/240) were detected at higher rates than the other nematodes (χ2 = 516.909, p < 0.05). Of 17 and 18 haplotypes were found based on the ITS1 gene for U. stenocephala and nad1 gene for Toxascaris sp., respectively. For the first time, using molecular methods, we report the infection of V. ferrilata by U. stenocephala, a potential zoonotic parasite, and suggest Toxascaris sp. may be a newly discovered nematode that lives within the fox intestine.

Molecular Dietary Analysis of Three Sympatric Mustelidae in Northeast China

Diet analysis is essential to fully understand the biology of a species and its function within the ecosystem, as well as being key in identifying food web interactions and the population dynamics of predators and prey. The understanding of the diet of small to mid-sized carnivores remains generally lacking or uninformative due to the inability for taxonomic resolution based on morphology. The yellow-throated marten (Martes flavigula), Eurasian river otter (Lutra lutra), and Siberian weasel (Mustela sibirica) are three important Mustelidae species in ecosystems of northeast China. Based on fecal DNA and a next-generation sequencing (NGS) approach, we analyzed the vertebrate prey of these three sympatric Mustelidae. Prey included 7 mammalian taxa, 10 fishes, 2 birds, and 2 amphibians, with 85% of the taxa assigned to the species level. In total, twenty-one vertebrate prey taxa were identified from seven yellow-throated martens, eight Eurasian river otters, and two Siberian weasels. Concerning identified dietary species, 10 taxa were consumed by yellow-throated martens, 14 by Eurasian river otters, and 4 by Siberian weasels. Some prey species were identified in more than one species. Amphibians and fishes were the most dominant Eurasian river otter prey categories, whereas Eurasian badger (Meles leucurus), birds, and rodents were the main yellow-throated marten prey; amphibians and rodents were largely contained in Siberian weasel prey. Among prey items, Dybowski's frog (Rana dybowskii) and Korean field mouse (Apodemus peninsulae) were identified in all three Mustelidae species but our analyses suggest potential diet preferences among Mustelidae species. Future studies should focus on understanding the trophic relationships of these three Mustelidae species, providing valuable information for their conservation planning.

Diet preferences based on sequence read count: the role of species interaction in tissue bias correction

High-throughput sequencing and metabarcoding techniques provide a unique opportunity to study predator-prey relationships. However, in animal dietary preference studies, how to properly correct tissue bias within the sequence read count and the role of interactions between co-occurring species in metabarcoding mixtures remain largely unknown. In this study, we proposed two categories of tissue bias correction indices: sequence read count number per unit tissue (SCN) and its ratio form (SCN ratio). By constructing plant mock communities with different numbers of co-occurring species in metabarcoding mixtures and conducting feeding trails on captive sika deer (Cervus nippon), we demonstrated the features of the SCN and SCN ratio, evaluated their correction effects, and assessed the role of species interactions during tissue bias correction. Tissue differences between species are defined as the differential ability in generating sequence counts. Our study suggests that pure tissue differences among species without species interaction is not an optimal correction index for many biomes with limited tissue differences among species. Species interactions in mixtures may amplify tissue differences, which is beneficial for tissue bias correction. However, caution must be taken because varied species interaction among communities may increase the risk of worse correction. Correction effects based on the SCN and SCN ratio are comparable, while the SCN is less influenced by control species than the SCN ratio. According to our study, several suggestions were provided for future animal diet studies or other high-throughput sequencing studies containing tissue bias.

Using DNA metabarcoding and a novel canid-specific blocking oligonucleotide to investigate the composition of animal diets of raccoon dogs (Nyctereutes procyonoides) inhabiting the waterside area in Korea

The raccoon dog (Nyctereutes procyonoides) is known to be an opportunistic generalist who feeds on a wide variety of foods. Historically, their diet has been investigated by morphological observation of undigested remains in feces, requiring specialized knowledge such as osteology, zoology, and phytology. Here, we used DNA metabarcoding of vertebrate 12S rRNA gene and invertebrate 16S rRNA gene to investigate their fecal contents. Additionally, we developed a blocking oligonucleotide that specifically inhibits the amplification of the canid 12S rRNA gene. We confirmed that the blocking oligonucleotide selectively inhibit the amplification of raccoon dog’s DNA without significantly changing the composition of the preys’ DNA. We found that the main foods of raccoon dogs in our study area, the waterside of paddy fields in Korea, were fishes such as Cyprinidae and insects such as mole crickets, which makes sense given the Korean fauna and their well-known opportunistic feeding behaviors. As a method to conveniently and objectively investigate feeding habits of raccoon dogs, this study provided baseline information on DNA metabarcoding. By using DNA metabarcoding, it is expected that the diet habits and ecology of raccoon dogs will be better understood by future research.

Density and occupancy of leopard cats across different forest types in Cambodia

The leopard cat (Prionailurus bengalensis) is the most common wild felid in Southeast Asia, yet little is known about the factors that affect their population density and occupancy in natural habitats. Although leopard cats are highly adaptable and reportedly can attain high densities in human-modified habitats, it is not clear which natural habitat is optimal for the species. Also, this felid has been preyed upon by large carnivores in Southeast Asia, yet the intra-guild effects of large carnivore presence on leopard cats are almost unknown. To shed light on these fundamental questions, we used data from camera trap surveys for felids to determine the leopard cat densities in three different forest types within Cambodia: continuous evergreen, mosaic dominated by evergreen (hereafter evergreen mosaic), and mosaic dominated by open dry deciduous forests (hereafter DDF mosaic). We also conducted occupancy analyses to evaluate the interactions of the leopard cats with three large carnivores: leopards (Panthera pardus), dholes (Cuon alpinus), and domestic dogs (Canis familiaris). The estimated density (individuals/100 km2 ± SE) was highest in the continuous evergreen (27.83 ± 7.68), followed by evergreen mosaic (22.06 ± 5.35) and DDF mosaic (13.53 ± 3.23). Densities in all three forest types were relatively high compared to previous studies. Domestic dogs were detected on all 3 sites, and leopards and dholes had sufficient records on only one site each. The occupancy probability of leopard cats was not affected by the presence or absence of any large carnivore, indicating that large carnivores and leopard cats occurred independently of each other. Our findings support the claim that leopard cats are habitat generalists, but we show that evergreen forest is the optimum natural habitat for this species in the region. The DDF mosaic appears to sustain lower densities of leopard cats, probably due to the harsh dry season and wildfires that led to reduced prey base, although this generalist felid was still able to occupy DDF in relatively moderate numbers. Overall, the adaptability of leopard cats to various forest types, and lack of negative interaction with large carnivores, helps to explain why this species is the most common and widespread felid in Southeast Asia.

Snow Leopard Dietary Preferences and Livestock Predation Revealed by Fecal DNA Metabarcoding: No Evidence for Apparent Competition Between Wild and Domestic Prey

Accurate assessments of the patterns and drivers of livestock depredation by wild carnivores are vital for designing effective mitigation strategies to reduce human-wildlife conflict. Snow leopard’s (Panthera uncia) range extensively overlaps pastoralist land-use and livestock predation there is widely reported, but the ecological determinants of livestock consumption by snow leopards remain obscure. We investigated snow leopard dietary habits at seven sites across the Sanjiangyuan region of the Qinghai–Tibetan Plateau (QTP), an area central to the species’ global range. Snow leopard abundance, wild prey composition, and livestock density varied among those sites, thus allowing us to test the effects of various factors on snow leopard diet and livestock predation. Using DNA metabarcoding, we obtained highly resolved dietary data from 351 genetically verified snow leopard fecal samples. We then analyzed the prey preferences of snow leopards and examined ecological factors related to their livestock consumption. Across the sites, snow leopard prey was composed mainly of wild ungulates (mean = 81.5% of dietary sequences), particularly bharal (Pseudois nayaur), and supplemented with livestock (7.62%) and smaller mammals (marmots, pikas, mice; 10.7%). Snow leopards showed a strong preference for bharal, relative to livestock, based on their densities. Interestingly, both proportional and total livestock consumption by snow leopards increased linearly with local livestock biomass, but not with livestock density. That, together with a slight negative relationship with bharal density, supports apparent facilitation between wild and domestic prey. We also found a significant positive correlation between population densities of snow leopard and bharal, yet those densities showed slight negative relationships with livestock density. Our results highlight the importance of sufficient wild ungulate abundance to the conservation of viable snow leopard populations. Additionally, livestock protection is critically needed to reduce losses to snow leopard depredation, especially where local livestock abundances are high.

Prey partitioning and livestock consumption in the world's richest large carnivore assemblage

Large mammalian carnivores have undergone catastrophic declines during the Anthropocene across the world. Despite their pivotal roles as apex predators in food webs and ecosystem dynamics, few detailed dietary datasets of large carnivores exist, prohibiting deep understanding of their coexistence and persistence in human-dominated landscapes. Here, we present fine-scaled, quantitative trophic interactions among sympatric carnivores from three assemblages in the Mountains of Southwest China, a global biodiversity hotspot harboring the world's richest large-carnivore diversity, derived from DNA metabarcoding of 1,097 fecal samples. These assemblages comprise a large-carnivore guild ranging from zero to five species along with two mesocarnivore species. We constructed predator-prey food webs for each assemblage and identified 95 vertebrate prey taxa and 260 feeding interactions in sum. Each carnivore species consumed 6-39 prey taxa, and dietary diversity decreased with increased carnivore body mass across guilds. Dietary partitioning was more evident between large-carnivore and mesocarnivore guilds, yet different large carnivores showed divergent proportional utilization of different-sized prey correlating with their own body masses. Large carnivores particularly selected livestock in Tibetan-dominated regions, where the indigenous people show high tolerance toward wild predators. Our results suggest that dietary niche partitioning and livestock subsidies facilitate large-carnivore sympatry and persistence and have key implications for sustainable conservation promoting human-carnivore coexistence.

Diet, parasites, and other pathogens of Sunda leopard cats (Prionailurus javanensis Desmarest 1816) in Aborlan, Palawan Island, Philippines

This study is the first investigation of parasites and other pathogens present in Sunda leopard cats (Prionailurus javanensis) in Aborlan, Palawan, Philippines. With the nature of wild carnivore sampling, four (4) wild Sunda leopard cats were captured in Aborlan, Palawan, Philippines for a period of nine (9) months. Of these, three (3) were considered for blood and fecal examination due to the poor condition of one animal. Rapid diagnostic kits were used to detect the presence of selected pathogens in blood samples while fecal samples were examined for parasite fauna and diet contents. Nine (9) parasite species were identified namely: Toxoplasma gondii, Ancylostoma sp., Capillaria hepatica, Echinostoma sp., Hymenolepis nana, Isospora felis, Physaloptera sp., Trichostrongylus sp., and a fasciolid. Chlamydophila felis, a bacterial pathogen was also detected in the blood. No individuals were found to be positive for feline immunodeficiency virus, feline infectious peritonitis virus, and feline leukemia virus antibodies. Six (6) small mammal prey species were identified from the feces of Sunda leopard cats namely: Palawan spiny rat (Maxomys panglima), Asian house rat (Rattus tanezumi), Polynesian rat (Rattus exulans), house mouse (Mus musculus), Southern Palawan tree squirrel (Sundasciurus steerii), and Palawan treeshrew (Tupaia palawanensis). Sunda leopard cats in Aborlan, Palawan, may be highly infected by parasites primarily due to their diet of small mammals such as rodents. Transmission is also possible through environmental contact with contaminated water or soil or direct physical contact with infected domestic animals. This paper contributes to the knowledge on host-parasite systems in wildlife ecosystem in the Philippines which is extremely poorly understood.

Issues of under-representation in quantitative DNA metabarcoding weaken the inference about diet of the tundra vole Microtus oeconomus

During the last decade, methods based on high-throughput sequencing such as DNA metabarcoding have opened up for a range of new questions in animal dietary studies. One of the major advantages of dietary metabarcoding resides in the potential to infer a quantitative relationship between sequence read proportions and biomass of ingested food. However, this relationship's robustness is highly dependent on the system under study, calling for case-specific assessments. Herbivorous small rodents often play important roles in the ecosystem, and the use of DNA metabarcoding for analyses of rodent diets is increasing. However, there has been no direct validation of the quantitative reliability of DNA metabarcoding for small rodents. Therefore, we used an experimental approach to assess the relationship between input plant biomass and sequence reads proportions from DNA metabarcoding in the tundra vole Microtus oeconomus. We found a weakly positive relationship between the number of high-throughput DNA sequences and the expected biomass proportions of food plants. The weak relationship was possibly caused by a systematic under-amplification of one of the three plant taxa fed. Generally, our results add to the growing evidence that case-specific validation studies are required to reliably make use of sequence read abundance as a proxy of relative food proportions in the diet.

Plant-eating carnivores: Multispecies analysis on factors influencing the frequency of plant occurrence in obligate carnivores

Plant-eating behavior is one of the greatest mysteries in obligate carnivores. Despite unsuitable morphological and physiological traits for plant consumption, the presence of plants in scat or stomach contents has been reported in various carnivorous species. However, researchers' interpretations of this subject are varied, and knowledge about it is scarce, without any multispecies studies. This study assessed the extent of variation in the frequency of plant occurrence in scat and stomach contents, as well as its relationship with various factors in 24 felid species using data from 213 published articles. Since the frequency of plant occurrence has not always been reported, we created two-part models and estimated parameters in a Bayesian framework. We found a significant negative relationship between the frequency of plant occurrence and body mass. This may be because plant-eating behavior reduces the energy loss caused by parasites and increases the efficiency of energy intake, which has a greater importance in smaller animals that have relatively high metabolic rates. This exploratory study highlights the importance of considering plant consumption in dietary studies on carnivorous species to understand the adaptive significance of this behavior and the relationship between obligate carnivores and plants.

Implementing a comprehensive approach to study the causes of human-bear (Ursus arctos pruinosus) conflicts in the Sanjiangyuan region, China

Personal injury and property loss caused by wildlife often deteriorates the relationship between humans and animals, prompting retaliatory killings that threaten species survival. Conflicts between humans and Tibetan brown bears (Ursus arctos pruinosus) (Human-Bear Conflicts, HBC) in the Sanjiangyuan region have recently dramatically increased, seriously affecting community enthusiasm for brown bears and the conservation of other species. In order to understand the driving mechanisms of HBC, we proposed six potential drivers leading to increased occurrences of HBC. We conducted field research in Zhiduo County of the Sanjiangyuan region from 2017 to 2019 to test hypotheses through semi-constructed interviews, marmot (Marmota himalayana) density surveys and brown bear diet analysis based on metagenomic sequencing. Analysis of herder perceptions revealed that the driving factors of HBC were related to changes in their settlement practice and living habits, changes in foraging behavior of brown bears and recovery of the brown bear population. Since the establishment of winter homes, brown bears have gradually learned to utilize the food in unattended homes. Although 91.4% (n = 285) of the respondents no longer store food in unattended homes, brown bears were reported to still frequently approach winter homes for food due to improper disposal of dead livestock and household garbage. The frequency and abundance of marmots were found to be high in brown bear diet, indicating that marmots were the bears' primary food. However, marmot density had no significant effect on brown bears utilizing human food (P = 0.329), and HBC appears to not be caused by natural food shortages. Distance to rocky outcrops (P = 0.022) and winter homes (P = 0.040) were the key factors linked to brown bears pursuing human food. The number of brown bears has increased over the past decade, and HBC is likely linked to its population recovery. Our findings will provide scientific basis for formulating effective mitigation measures and protection countermeasures for brown bears.

Influences of submerged plant collapse on diet composition, breadth, and overlap among four crane species at Poyang Lake, China

Background

Interannual variation in resource abundance has become more unpredictable, and food shortages have increasingly occurred in the recent decades. However, compared to seasonal fluctuations in resource abundance, the influences of interannual variation in resource abundance on the dietary niches of consumers remain poorly understood. Poyang Lake, China, is a very important wintering ground for the globally endangered Siberian Crane (Leucogeranus leucogeranus), White-naped Crane (Grus vipio), and Hooded Crane (G. monacha), as well as the non-endangered Eurasian Crane (G. grus). Tubers of Vallisneria spp., the dominant submerged macrophytes at Poyang Lake, is an important food for cranes. Nevertheless, submerged macrophytes have experienced serious degradation recently. In this study, we used metabarcoding technology to explore the consequences of Vallisneria tuber collapse on the diet compositions, breadths, and overlaps of the four crane species based on fecal samples collected in winter 2017 (a year with tuber collapse) and winter 2018 (a year with high tuber abundance).

Results

Compared to previous studies, our study elucidates crane diets in an unprecedented level of detail. Vallisneria tubers was confirmed as an important food source of cranes. Surprisingly, the grassland plant Polygonum criopolitanum was also found to be an important food source in the feces of cranes. Agricultural fields were important foraging sites for Siberian Cranes, White-naped Cranes, and Hooded Cranes, providing foods that allowed them to survive in winters with natural food shortages. However, the three crane species preferred natural wetlands to agricultural fields when the abundance of natural foods was high. The abundance of Vallisneria tubers, and probably P. criopolitanum, greatly influenced the dietary compositions, breadths and overlap of cranes. During periods of preferred resource shortage, White-naped Cranes and Hooded Cranes widened their dietary niches, while Siberian Cranes maintained a stable niche width. The dietary niche overlap among crane species increased substantially under conditions of plentiful preferred food resources.

Conclusions

Our study emphasizes the superior quality of natural wetlands compared to agricultural fields as foraging habitats for cranes. To provide safer and better foraging areas for cranes, it is urgent to restore the submerged plants at Poyang Lake. While high dietary niche overlap is often interpreted as intense interspecific competition, our study highlights the importance of taking food abundance into account.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12983-021-00411-2.

The relationship between plant-eating and hair evacuation in snow leopards (Panthera uncia)

Although most felids have an exclusive carnivore diet, the presence of plant matter in scat has been reported among various species. This indicates that there may be an adaptive significance to the conservation of plant-eating behavior in felid evolution. Some studies have hypothesized that felids consume plants for self-medication or as a source of nutrition. In addition, it is thought that plant intake helps them to excrete hairballs, however, no scientific work has confirmed these effects. Thus, the objective of this study is to investigate the relationship between plant intake and hair evacuation in felid species. We selected snow leopards (Panthera uncia) as the study species because they have longer and denser hair than other felids. The behavior of 11 captive snow leopards was observed and scat samples from eight of them and two other captive individuals were analyzed. Snow leopards evacuate hair possibly by vomiting and excreting in scats. The frequency of plant-eating and vomiting and the amount of hair and plant in scat were evaluated. We found that the frequency of vomiting was much lower than the frequency of plant-eating. In addition, there was no significant relationship between the amount of plant matter contained in scats and the amount of hair in scats. Contrary to the common assumption, our results indicate that plant intake has little effect on hair evacuation in felid species.

Vertebrate prey composition analysis of the Pallas’s cat (Otocolobus manul) in the Gongga Mountain Nature Reserve, based on fecal DNA

Diet analysis is essential to fully understanding the biology of a species and its function within the ecosystem, and is also key in identifying food web interactions and the population dynamics of predators and prey. There is currently little information on the diet of small to mid-sized carnivores due to their elusive behavior. We used a DNA-based method to analyze the vertebrate prey of the Pallas’s cat (Otocolobus manul) in the Gongga Mountain Nature Reserve of southwestern China, a global biodiversity hotspot region. We confirmed 14 scat samples containing the Pallas’s cat DNA from 100 small carnivore scats collected at altitudes between 3200 and 4900 m, and then performed polymerase chain reaction (PCR) amplifications using primers targeting the vertebrate mitochondrial 12S rRNA gene with a blocking oligonucleotide specific to the predator sequence. We identified a total of 18 prey taxa, including nine mammals, eight birds and one fish. Our results show that pikas (in 79% of the scats) and birds (in 50% of the scats) are the predominant prey consumed by the Pallas’s cat in our investigation area. The most important finding in our study is that Cypriniformes species were found in the Pallas’s cat’s diet, exhibiting dietary diversification consistent with the accessible fauna of the surrounding environment. In order to increase the detectability of both typical and rare vertebrate prey items, we constructed a blocking primer to inhibit the amplification of the Pallas’s cat DNA.

Challenges for assessing vertebrate diversity in turbid Saharan water-bodies using environmental DNA

The Sahara desert is the largest warm desert in the world and a poorly explored area. Small water-bodies occur across the desert and are crucial habitats for vertebrate biodiversity. Environmental DNA (eDNA) is a powerful tool for species detection and is being increasingly used to conduct biodiversity assessments. However, there are a number of difficulties with sampling eDNA from such turbid water-bodies and it is often not feasible to rely on electrical tools in remote desert environments. We trialled a manually powered filtering method in Mauritania, using pre-filtration to circumvent problems posed by turbid water in remote arid areas. From nine vertebrate species expected in the water-bodies, four were detected visually, two via metabarcoding, and one via both methods. Difficulties filtering turbid water led to severe constraints, limiting the sampling protocol to only one sampling point per study site, which alone may largely explain why many of the expected vertebrate species were not detected. The amplification of human DNA using general vertebrate primers is also likely to have contributed to the low number of taxa identified. Here we highlight a number of challenges that need to be overcome to successfully conduct metabarcoding eDNA studies for vertebrates in desert environments in Africa.

Molecular dietary analysis of two sympatric felids in the Mountains of Southwest China biodiversity hotspot and conservation implications

Dietary information is lacking in most of small to mid-sized carnivores due to their elusive predatory behaviour and versatile feeding habits. The leopard cat (LPC; Prionailurus bengalensis) and the Asiatic golden cat (AGC; Catopuma temminckii) are two important yet increasingly endangered carnivore species in the temperate mountain forest ecosystem in Southwest China, a global biodiversity hotspot and a significant reservoir of China's endemic species. We investigated the vertebrate prey of the two sympatric felids using faecal DNA and a next-generation sequencing (NGS)/metabarcoding approach. Forty vertebrate prey taxa were identified from 93 LPC and 10 AGC faecal samples; 37 taxa were found in the LPC diet, and 20 were detected in the AGC diet. Prey included 27 mammalian taxa, 11 birds, one lizard and one fish, with 73% (29/40) of the taxa assigned to the species level. Rodents and pikas were the most dominant LPC prey categories, whereas rodents, pheasant, fowl and ungulates were the main AGC prey. We also analysed the seasonal and altitudinal variations in the LPC diet. Our results provide the most comprehensive dietary data for these felids and valuable information for their conservation planning.