Prey preference of snow leopard (Panthera uncia) in South Gobi, Mongolia

Accurate information about the diet of large carnivores that are elusive and inhabit inaccessible terrain, is required to properly design conservation strategies. Predation on livestock and retaliatory killing of predators have become serious issues throughout the range of the snow leopard. Several feeding ecology studies of snow leopards have been conducted using classical approaches. These techniques have inherent limitations in their ability to properly identify both snow leopard feces and prey taxa. To examine the frequency of livestock prey and nearly-threatened argali in the diet of the snow leopard, we employed the recently developed DNA-based diet approach to study a snow leopard population located in the Tost Mountains, South Gobi, Mongolia. After DNA was extracted from the feces, a region of ～100 bp long from mitochondrial 12S rRNA gene was amplified, making use of universal primers for vertebrates and a blocking oligonucleotide specific to snow leopard DNA. The amplicons were then sequenced using a next-generation sequencing platform. We observed a total of five different prey items from 81 fecal samples. Siberian ibex predominated the diet (in 70.4% of the feces), followed by domestic goat (17.3%) and argali sheep (8.6%). The major part of the diet was comprised of large ungulates (in 98.8% of the feces) including wild ungulates (79%) and domestic livestock (19.7%). The findings of the present study will help to understand the feeding ecology of the snow leopard, as well as to address the conservation and management issues pertaining to this wild cat.     

Ecological and biogeographical inferences on two sympatric and enigmatic Andean cat species using genetic identification of faecal samples

The carnivore community of the altiplano ecosystem of the high Andes, including the Andean mountain cat (Leopardus jacobita) and pampas cat (Leopardus colocolo), is one of the least studied in the world. We determined the origin of 186 carnivore samples (184 faeces and two skulls) collected above 3000 m above sea level in northern Chile, including 33 from the Andean mountain cat and 75 from the pampas cat using diagnostic molecular genetic sequence variation. We determined for the first time food habits, habitat and physiographic associations, and general patterns of molecular genetic variation of the Andean mountain cat and the pampas cat in Chile. Both species had narrow dietary niches dominated by small rodents and there was a wide overlap in diet composition (0.82), suggesting low levels of prey partitioning between species. The mountain viscacha (Lagidium viscacia) made up a large proportion of the biomass of the diet of both species, especially for the Andean mountain cat (93.9% vs. 74.8% for the pampas cat), underscoring the importance of further research and conservation focus on this vanishing prey species. Although the probability of finding Andean mountain cat scats increased with altitude and slope, there was substantial geographical overlap in distribution between species, revealing that the pampas cat distribution includes high-altitude grassland habitats. The Andean mountain cat had relatively low levels of mitochondrial DNA (mtDNA) genetic variation (two mtDNA haplotypes) compared with the pampas cat (17 mtDNA haplotypes), suggestive of a distinct evolutionary history and relatively smaller historic populations. These insights will facilitate and provide tools and hypotheses for much-needed research and conservation efforts on these species and this ecosystem.     

New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach

The development of DNA barcoding (species identification using a standardized DNA sequence), and the availability of recent DNA sequencing techniques offer new possibilities in diet analysis. DNA fragments shorter than 100-150 bp remain in a much higher proportion in degraded DNA samples and can be recovered from faeces. As a consequence, by using universal primers that amplify a very short but informative DNA fragment, it is possible to reliably identify the plant taxon that has been eaten. According to our experience and using this identification system, about 50% of the taxa can be identified to species using the trnL approach, that is, using the P6 loop of the chloroplast trnL (UAA) intron. We demonstrated that this new method is fast, simple to implement, and very robust. It can be applied for diet analyses of a wide range of phytophagous species at large scales. We also demonstrated that our approach is efficient for mammals, birds, insects and molluscs. This method opens new perspectives in ecology, not only by allowing large-scale studies on diet, but also by enhancing studies on resource partitioning among competing species, and describing food webs in ecosystems.     

Fecal DNA analysis for identifying species and sex of sympatric carnivores: a noninvasive method for conservation on the Tsushima Islands, Japan

Fecal analysis is a useful tool for the investigation of food habits and species identity in mammals. However, it is generally difficult to identify the species based on the morphological features and contents of feces deposited by mammals of similar body size. Therefore we developed noninvasive DNA analysis methods using fecal samples for identification of the species and sex of four small sympatric carnivores living on the Tsushima Islands of Japan: the leopard cat (Felis bengalensis), Japanese marten (Martes melampus), Siberian weasel (Mustela sibirica), and feral cat (Felis catus). Based on DNA sequence data from previous phylogenetic studies, we designed species-specific primers for polymerase chain reaction (PCR) amplification of the partial mitochondrial cytochrome b gene (112-347 bp) to identify the species and primers for the partial SRY gene (135 bp) to determine the sex. Due to the adjustment of PCR conditions, those specific DNA fragments were successfully amplified and then applied for species and sex identification. Nucleotide sequences obtained from the PCR products corresponded with cytochrome b sequences of the carnivore species expected. The protocol developed could be a valuable tool in the management and conservation of the four carnivore species occurring on the Tsushima Islands.     

Predator-prey size relationships in an African large-mammal food web

1. Size relationships are central in structuring trophic linkages within food webs, leading to suggestions that the dietary niche of smaller carnivores is nested within that of larger species. However, past analyses have not taken into account the differing selection shown by carnivores for specific size ranges of prey, nor the extent to which the greater carcass mass of larger prey outweighs the greater numerical representation of smaller prey species in the predator diet. Furthermore, the top-down impact that predation has on prey abundance cannot be assessed simply in terms of the number of predator species involved. 2. Records of found carcasses and cause of death assembled over 46 years in the Kruger National Park, South Africa, corrected for under-recording of smaller species, enabled a definitive assessment of size relationships between large mammalian carnivores and their ungulate prey. Five carnivore species were considered, including lion (Panthera leo), leopard (Panthera pardus), cheetah (Acinonyx jubatus), African wild dog (Lycaon pictus) and spotted hyena (Crocuta crocuta), and 22 herbivore prey species larger than 10 kg in adult body mass. 3. These carnivores selectively favoured prey species approximately half to twice their mass, within a total prey size range from an order of magnitude below to an order of magnitude above the body mass of the predator. The three smallest carnivores, i.e. leopard, cheetah and wild dog, showed high similarity in prey species favoured. Despite overlap in prey size range, each carnivore showed a distinct dietary preference. 4. Almost all mortality was through the agency of a predator for ungulate species up to the size of a giraffe (800-1200 kg). Ungulates larger than twice the mass of the predator contributed substantially to the dietary intake of lions, despite the low proportional mortality inflicted by predation on these species. Only for megaherbivores substantially exceeding 1000 kg in adult body mass did predation become a negligible cause of mortality. 5. Hence, the relative size of predators and prey had a pervasive structuring influence on biomass fluxes within this large-mammal food web. Nevertheless, the large carnivore assemblage was dominated overwhelmingly by the largest predator, which contributed the major share of animals killed across a wide size range.     

Feeding ecological knowledge: the underutilised power of faecal DNA approaches for carnivore diet analysis

相似文献   

Seasonal variation in prey preference,diet partitioning and niche breadth in a rich large carnivore guild

Large carnivore community structure is affected by direct and indirect interactions between intra-guild members. Co-existence between different species within a carnivore guild may occur through diet, habitat or temporal partitioning. Since carnivore species are highly dependent on availability and accessibility of prey, diet partitioning is potentially one of the most important mechanisms in allowing carnivores to co-exist. Intra-guild interactions may vary over time as carnivore prey preference and diet overlap can change due to seasonal changes in resource availability. We conducted scat analysis to compare the seasonal changes in prey preference, diet partitioning and niche breadth of four large carnivore species, namely leopard Panthera pardus, spotted hyena Crocuta crocuta, brown hyena Parahyaena brunnea and wild dog Lycaon pictus in central Tuli, Botswana. Large carnivores in central Tuli display a high dietary overlap, with spotted hyena and brown hyena displaying almost complete dietary overlap and the other carnivore species displaying slightly lower but still significant dietary overlap. Dietary niche breadth for both hyena species was high possibly due to their flexible foraging strategies, including scavenging, while leopard and wild dog showed a relatively low niche breadth, suggesting a more specialised diet. High dietary overlap in central Tuli is possibly explained by the high abundance of prey species in the area thereby reducing competition pressure between carnivore species. Our research highlights the need to assess the influence of diet partitioning in structuring large carnivore communities across multiple study sites, by demonstrating that in prey rich environments, the need for diet partitioning by carnivores to avoid competition may be limited.     

Diversity and occupancy of small carnivores within oil palm plantations in central Sumatra,Indonesia

In Southeast Asia, the conversion of native forests to oil palm plantations threatens tropical biodiversity, but very little is known about the impacts of oil palm cultivation on small carnivore species. To determine the diversity and occupancy of small carnivores within oil palm plantations and to investigate possible factors that might affect their presence within oil palm, we used camera-traps within two oil palm plantations in central Sumatra, analysed the data using occupancy modelling and tested whether two covariates (distance to the edge of the oil palm habitat and distance from extensive areas of lowland forest) affected the model parameters for each small carnivore species. From 3164 camera-trap days, we detected only three small carnivores: leopard cat (Prionailurus bengalensis), common palm civet (Paradoxurus hermaphroditus) and Malay civet (Viverra tangalunga), which indicates that there was a low diversity of small carnivores within the oil palm plantations. Both the leopard cat and common palm civet were found deep within the oil palm, whereas the Malay civet was only detected near the edge in one of the plantations. The leopard cat and common palm civet had very high occupancy values, whereas the Malay civet had low values for both occupancy and detection probability. Neither covariate affected occupancy of the leopard cat and common palm civet, but distance from the edge of the oil palm habitat did influence their detection probabilities. Malay civet occupancy decreased with distance from the oil palm edge, and detection probability was affected by distance from extensive areas of lowland forest. Forests and rest/den site availability are suggested to be important features for small carnivores with oil palm-dominated landscapes.     

基于分子宏条形码分析四川卧龙国家级自然保护区雪豹的食性

作为中亚和青藏高原山地生态系统中的顶级捕食者, 雪豹(Panthera uncia)对于维持食物网结构和生态系统稳定性有重要作用。了解雪豹的食性组成和变化对于理解其生态系统功能和物种间相互作用有重要意义。以往的雪豹食性分析多基于对其粪便中食物残渣的形态学鉴定, 但准确度受人员经验和主观因素影响较大。邛崃山脉位于雪豹分布区东南缘, 该区域的雪豹种群规模小且相对孤立, 研究匮乏。本研究基于非损伤性取样, 在邛崃山脉的卧龙国家级保护区采集疑似雪豹粪便样品38份, 首先提取粪便DNA, 并扩增线粒体DNA 16S rRNA基因片段进行分子物种鉴定, 确定其中22份为雪豹粪便样品。随后, 利用脊椎动物通用引物和雪豹特异性阻抑引物扩增粪便DNA中的食物成分, 并进行高通量测序, 分析雪豹食性构成。食性分析结果显示岩羊(Pseudois nayaur)是卧龙地区雪豹最主要的食物, 在67%的样品中均有检出。家牦牛(Bos grunniens)在33%的样品中出现, 也在雪豹食性中占较高比例。此外, 鼠兔(Ochotona spp.)和鸟类也在少量样品中发现。可见, 野生猎物是卧龙地区雪豹的主要食物资源; 与大世界大多数其他地区的雪豹食性相同, 野生大型有蹄类是雪豹最重要的食物。然而家畜(牦牛)在卧龙雪豹食谱中有相当高的占比, 显示该区域内可能存在较为严重的由雪豹捕食散养家畜引起的人兽冲突问题。     

两种分析方法在豹猫食物构成中的应用比较

豹猫(Prionailurus bengalensis)作为北京地区的顶级食肉动物,对于维持食物网结构和生态系统稳定性起到重要的生态作用。对于捕食动物食物构成研究,较为简便的方法是粪样内容物检视法,而粪样残余物DNA鉴定技术具有更为准确细致的优势,但也存在不足,探索不同方法的优势互补,将有助于提高技术应用成效。本研究利用DNA宏条形码技术与粪样内容物分析法,对采集自北京市4个自然保护区的71份豹猫粪样进行食物构成分析,比较两种分析方法的特点,了解豹猫的食物资源利用状况。结果显示,DNA宏条形码技术共鉴别出36种猎物,来自10目22科,4个保护区的豹猫食性具有显著差异,百花山、松山、云蒙山保护区的豹猫食物种类的出现比率均以小型哺乳类为主,其中对鼠类的捕食比例最高,对鸟类的捕食次之,而分布于云峰山保护区的豹猫对鸟类捕食比例最高,对鼠类的捕食次之。粪样内容物分析法鉴别出9类猎物,其中包括昆虫和植物两种DNA宏条形码技术未检出的食物,4个保护区的豹猫食物均以鼠类和鸟类为主,且最多检测出鼠类数量为3只、鸟类2只,次要食物则为植物和昆虫。两种方法均显示北社鼠(Niviventer confucia...     

DNA metabarcoding reveals that African leopard diet varies between habitats

Understanding carnivores’ diet is key to understanding their adaptability in a rapidly changing world. However, studying diet of large carnivores is difficult due to their elusive nature. In this study, we performed DNA metabarcoding analyses of 82 putative leopard scats collected from two distinct, but connected, habitat types (rainforest and grassland) in the Udzungwa Mountains, Tanzania. Two mitochondrial markers were used to identify predator and prey. Metabarcoding confirmed that 60 of the collected scats (73%) originated from leopards, and nineteen mammalian prey DNA sequences were identified to species. Using prey size correction factors for leopards, and covariates on habitat type and prey ecology, we investigated whether differences in leopard dietary composition were detectable between habitats. We found that leopards in grassland consumed a larger mean prey size compared with leopards in rainforest. Small prey (<19 kg) constituted >70% of the biomass consumed by leopards in rainforest, while large prey (≥80 kg) were only eaten in grassland. Arboreal species constituted 50% of the biomass consumed by rainforest leopards. Our results highlight the importance of arboreal species in their diet. From a management perspective, we suggest continued protection of all prey species in the protected areas to prevent human–wildlife conflicts.     

Comparative analyses on food habits of Japanese marten,Siberian weasel and leopard cat in the Tsushima islands,Japan

Food habits of three sympatric carnivore mammals in the Tsushima islands of Japan were studied during 1986–91. Scats of the Tsushima marten (n=1236), the Siberian weasel (n=218) and the Tsushima leopard cat (n=350) were collected monthly and the food items were determined by scat contents analysis. Marten was omnivorous showing a high level of diversity of food throughout the year. The important foods for marten were fruits and berries from spring to autumn, insects in summer and autumn and small mammals all year round. Leopard cat preferred to hunt wood/mice and birds, and remained a flesh meat specialist throughout the year. Weasel was intermediate between marten and leopard cat, but was slightly biased towards the flesh meat eater. The three carnivores do not compete against one another for food, except for small rodents. A conflict for food between leopard cat and weasel was suggested to be more intense than that of other combinations based on diet overlapping. Marten may be characterized as an opportunistic generalist. When interspecific competitors existed, or human disturbance to the habitat occurred, the preferential flexibility of the marten to alternative food resources might become more advantageous than the other two species.     

Coprolites as a source of information on the genome and diet of the cave hyena

We performed high-throughput sequencing of DNA from fossilized faeces to evaluate this material as a source of information on the genome and diet of Pleistocene carnivores. We analysed coprolites derived from the extinct cave hyena (Crocuta crocuta spelaea), and sequenced 90 million DNA fragments from two specimens. The DNA reads enabled a reconstruction of the cave hyena mitochondrial genome with up to a 158-fold coverage. This genome, and those sequenced from extant spotted (Crocuta crocuta) and striped (Hyaena hyaena) hyena specimens, allows for the establishment of a robust phylogeny that supports a close relationship between the cave and the spotted hyena. We also demonstrate that high-throughput sequencing yields data for cave hyena multi-copy and single-copy nuclear genes, and that about 50 per cent of the coprolite DNA can be ascribed to this species. Analysing the data for additional species to indicate the cave hyena diet, we retrieved abundant sequences for the red deer (Cervus elaphus), and characterized its mitochondrial genome with up to a 3.8-fold coverage. In conclusion, we have demonstrated the presence of abundant ancient DNA in the coprolites surveyed. Shotgun sequencing of this material yielded a wealth of DNA sequences for a Pleistocene carnivore and allowed unbiased identification of diet.     

A pragmatic approach to the analysis of diets of generalist predators: the use of next‐generation sequencing with no blocking probes

Predicting whether a predator is capable of affecting the dynamics of a prey species in the field implies the analysis of the complete diet of the predator, not simply rates of predation on a target taxon. Here, we employed the Ion Torrent next‐generation sequencing technology to investigate the diet of a generalist arthropod predator. A complete dietary analysis requires the use of general primers, but these will also amplify the predator unless suppressed using a blocking probe. However, blocking probes can potentially block other species, particularly if they are phylogenetically close. Here, we aimed to demonstrate that enough prey sequence could be obtained without blocking probes. In communities with many predators, this approach obviates the need to design and test numerous blocking primers, thus making analysis of complex community food webs a viable proposition. We applied this approach to the analysis of predation by the linyphiid spider Oedothorax fuscus in an arable field. We obtained over two million raw reads. After discarding the low‐quality and predator reads, the libraries still contained over 61 000 prey reads (3% of the raw reads; 6% of reads passing quality control). The libraries were rich in Collembola, Lepidoptera, Diptera and Nematoda. They also contained sequences derived from several spider species and from horticultural pests (aphids). Oedothorax fuscus is common in UK cereal fields, and the results showed that it is exploiting a wide range of prey. Next‐generation sequencing using general primers but without blocking probes provided ample sequences for analysis of the prey range of this spider and proved to be a simple and inexpensive approach.     

Predator‐Naïve Brown Trout (Salmo trutta) Show Antipredator Behaviours to Scent from an Introduced Piscivorous Mammalian Predator Fed Conspecifics

Introduced mammalian predators may pose a high risk for native and naïve prey populations, but little is known about how native fish species may recognize and respond to scents from introduced mammalian predators. We investigated the role of diet‐released chemical cues in facilitating predator recognition, hypothesizing that native brown trout (Salmo trutta) would exhibit antipredator behaviours to faeces scents from the introduced American mink (Neovision vison) fed conspecifics, but not to non‐trout diets. In treatments‐control and replicate stream tank experiments, brown trout showed significant antipredator responses to faeces scent from mink fed conspecifics, but not to faeces scent from mink fed a non‐trout diet (chicken), or the non‐predator food control, Eurasian beaver (Castor fiber). We conclude that native and naïve brown trout show relevant antipredator behaviours to an introduced mammalian predator, presumably based on diet‐released conspecific alarm cues and thereby estimate the predation risk.     

Universal and blocking primer mismatches limit the use of high‐throughput DNA sequencing for the quantitative metabarcoding of arthropods

The quantification of the biological diversity in environmental samples using high‐throughput DNA sequencing is hindered by the PCR bias caused by variable primer–template mismatches of the individual species. In some dietary studies, there is the added problem that samples are enriched with predator DNA, so often a predator‐specific blocking oligonucleotide is used to alleviate the problem. However, specific blocking oligonucleotides could coblock nontarget species to some degree. Here, we accurately estimate the extent of the PCR biases induced by universal and blocking primers on a mock community prepared with DNA of twelve species of terrestrial arthropods. We also compare universal and blocking primer biases with those induced by variable annealing temperature and number of PCR cycles. The results show that reads of all species were recovered after PCR enrichment at our control conditions (no blocking oligonucleotide, 45 °C annealing temperature and 40 cycles) and high‐throughput sequencing. They also show that the four factors considered biased the final proportions of the species to some degree. Among these factors, the number of primer–template mismatches of each species had a disproportionate effect (up to five orders of magnitude) on the amplification efficiency. In particular, the number of primer–template mismatches explained most of the variation (~3/4) in the amplification efficiency of the species. The effect of blocking oligonucleotide concentration on nontarget species relative abundance was also significant, but less important (below one order of magnitude). Considering the results reported here, the quantitative potential of the technique is limited, and only qualitative results (the species list) are reliable, at least when targeting the barcoding COI region.     

Directional selection in the evolution of elongated upper canines in clouded leopards and sabre‐toothed cats

Extremely developed or specialized traits such as the elongated upper canines of extinct sabre‐toothed cats are often not analogous to those of any extant species, which limits our understanding of their evolutionary cause. However, an extant species may have undergone directional selection for a similar extreme phenotype. Among living felids, the clouded leopard, Neofelis nebulosa, has exceptionally long upper canines for its body size. We hypothesized that directional selection generated the elongated upper canines of clouded leopards in a manner similar to the process in extinct sabre‐toothed cats. To test this, we developed an approach that compared the effect of directional selection among lineages in a phylogeny using a simulation of trait evolution and approximate Bayesian computation. This approach was applied to analyse the evolution of upper canine length in the Felidae phylogeny. Our analyses consistently showed directional selection favouring longer upper canines in the clouded leopard lineage and a lineage leading to the sabre‐toothed cat with the longest upper canines, Smilodon. Most of our analyses detected an effect of directional selection for longer upper canines in the lineage leading to another sabre‐toothed cat, Homotherium, although this selection may have occurred exclusively in the primitive species. In all the analyses, the clouded leopard and Smilodon lineages showed comparable directional selection. This implies that clouded leopards share a selection advantage with sabre‐toothed cats in having elongated upper canines.     

Building food networks from molecular data: Bayesian or fixed-number thresholds for including links

DNA metabarcoding of faeces or gut contents has greatly increased our ability to construct networks of predators and prey (food webs) by reducing the need to observe predation events directly. The possibility of both false positives and false negatives in DNA sequences, however, means that constructing food networks using DNA requires researchers to make many choices as to which DNA sequences indicate true prey for a particular predator. To date, DNA-based food networks are usually constructed by including any DNA sequence with more than a threshold number of reads. The logic used to select this threshold is often not explained, leading to somewhat arbitrary-seeming networks. As an alternative strategy, we demonstrate how to construct food networks using a simple Bayesian model to suggest which sequences correspond to true prey. The networks obtained using a well-chosen fixed cutoff and our Bayesian approach are very similar, especially when links are resolved to prey families rather than species. We therefore recommend that researchers reconstruct diet data using a Bayesian approach with well-specified assumptions rather than continuing with arbitrary fixed cutoffs. Explicitly stating assumptions within a Bayesian framework will lead to better-informed comparisons between networks constructed by different groups and facilitate drawing together individual case studies into more coherent ecological theory. Note that our approach can easily be extended to other types of ecological networks constructed by DNA metabarcoding of pollen loads, identification of parasite DNA in faeces, etc.