Non-invasive multi-species monitoring: real-time PCR detection of small mammal and squirrel prey DNA in pine marten (Martes martes) scats

DNA identification of mammal species occurring in the diet of a predator is potentially a useful approach to remotely monitor the distribution of multiple species. This is important in Ireland, where it has been shown that the combined presence of the introduced bank vole and greater white-toothed shrew impact the distribution of the indigenous small mammals, the wood mouse and pygmy shrew. Direct monitoring of these species and their interactions requires trapping, a labour-intensive and costly approach. In this study, we applied an indirect method by genetically testing the presence of small mammals in pine marten scats collected during the National Pine Marten Survey (2005–2007) to map their distribution. We also included additional scats to investigate if less common prey items, the red squirrel and grey squirrel, could also be detected. This study demonstrates that all target species were genetically detected from pine marten scats. This strategy could be implemented as a monitoring programme for indigenous and introduced mammal species.     

Structure of parasitic arthropod communities in forest small mammals

Species composition and structure of ectoparasite arthropod communities were examined all year round six years in the bank vole Clethrionomys glareolus, Ural wood mouse Apodemus uralensis and the common shrew Sorex araneus in forests of the Ilmen'-Volkhov depression. In total, 4500 host samples have been examined and all ectoparasites have been collected. The species composition of ectoparasite community in small mammal species are as follows: the bank vole--29 insect, tick and mite species, the common shrew--23 species, the Ural wood mouse--16 species. In forest biotopes, many temporary ectoparasitic species occur on several host species living in the same habitats under a forest canopy and contacting each other. A parasitic supracommunity in the ecosystem examined has a pool of temporary ectoparasites, which is available for all the community of small mammals. A role of different rodent and shrew species are hosts of insects and ticks changes depending on a density of potential host populations and numerous other environment factors.     

Life on high: the diversity of small mammals at high altitude in South Africa

The Great Escarpment is the major mountain system in South Africa, yet very few biological surveys have been conducted outside of the well-known Drakensberg section. This is surprising given the important role that mountains play in local and global biodiversity patterns. In this study, small mammal diversity and community composition were estimated at three high altitude (>1,700?m) sites within the Sneeuberg Mountain Complex (SMC) of the Great Escarpment, South Africa from June 2009 to May 2010. The influences of selected environmental variables on diversity were also tested. Of 423 live-captures, a total of 292 unique individuals of 12 small mammal species (one shrew, one elephant shrew and 10 rodents) were identified during 5,280 trap nights. No single environmental variable could account for the variation observed in diversity measurements but vegetation height appeared to be the most important factor to influence the number of individuals captured. It is hypothesised that the high species richness and diversity of small mammals observed in the SMC compared to other parts of the Great Escarpment is due to the SMC being located in a transition zone of the Grassland and Nama-Karoo biomes. Our results suggest that the SMC could be important in conserving small mammal species from western and eastern assemblages across South Africa.     

四川南充市郊区鼠型小兽群落组成研究

2005年3月～2006年2月对四川省南充市郊区的鼠型小兽进行了调查。共捕获鼠型小兽1499只,隶属于2目2科7种,根据优势种分为两个群落:微尾鼩 黑线姬鼠群落中除优势种外,还捕到少量大足鼠、社鼠、褐家鼠和灰麝鼩,主要分布于住宅区以外的农田林地;褐家鼠 黄胸鼠群落,有少量微尾鼩,分布于住宅区。采用Shannon-Weiner多样性指数、均匀性指数、Hurlbert生态优势度和物种数对沟谷地、半坡地、坡顶地以及住宅区4种微生境中捕获的小兽进行了分析。住宅区的多样性指数、均匀性指数最高,其次为沟谷地。     

Comparative mitochondrial and nuclear quantitative PCR of historical marine mammal tissue,bone, baleen,and tooth samples

The use of historical and ancient tissue samples for genetic analysis is increasing, with ever greater numbers of samples proving to contain sufficient mitochondrial and even nuclear DNA for multilocus analysis. DNA yield, however, remains highly variable and largely unpredictable based solely on sample morphology or age. Quantification of DNA from historical and degraded samples can greatly improve efficiency of screening DNA extracts prior to attempting sequencing or genotyping, but requires sequence‐specific quantitative polymerase chain reaction (qPCR) based assays to detect such minute quantities of degraded DNA. We present two qPCR assays for marine mammal DNA quantification, and results from analysis of DNA extracted from preserved soft tissues, bone, baleen, and tooth from several cetacean species. These two assays have been shown to amplify DNA from 26 marine mammal species representing 12 families of pinnipeds and cetaceans. Our results indicate that different tissues retain different ratios of mitochondrial to nuclear DNA, and may be more or less suitable for analysis of nuclear loci. Specifically, historical bone and tooth samples average 60‐fold higher ratio of mitochondrial DNA to nuclear DNA than preserved fresh soft tissue, and the ratio is almost 8000‐fold higher in baleen.     

Structure and seasonal dynamics of an ectoparasite community on the common shrew (Sorex araneus) in the Il'men'-Volkhov lowland

Species composition, seasonal dynamics, and a load of ectoparasites per individual and population of the common shrew Sorex araneus have been examined in coniferous and mixed forests of the Ilmen'-Volkhov lowland (a neighbourhood of Oskuy village, Chudovo district, Novgorod Province) during the period 1999-2003. Trapping of mammals was carried monthly, with exception of few accidental gaps. The Gero traps were used for catching micromammalian hosts. The lines of trap were checked 2 times a day, places of lines changed each 3-5 day. Total number of micromammalians collected during the period of study is 3215, including 1115 specimens of the common shrew S. araneus and 246 ones of the pigmy shrew S. minutus. Parasite fauna on the common shrew included 23 ectoparasite species: fleas--12, ixodid ticks--2, gamasid mites--7, and myobiid mites--2 species. Among recorded species, 9 fleas species and some gamasid species are accidental parasites. These accidental ectoparasite species are common to the bank vole Clethrionomys glareolus in the territory investigated. Species composition, occurrence and abundance indices of parasites changed during the year. In total, about 55% shrew specimens are infected with ectoparasites. The infracommunity of ectoparasites on the common shrew usually consists of 6 species or less. Mean number of all ectoparasite individuals per one host specimens varies from 4 to 83. The greatest number of parasites (50 and 83) was recorded on the shrews, which carried 5 and 4 parasites species, respectively. Biodiversity of parasite species in the ectoparasite community on the common shrew and the load of parasites per one host specimen are lower than those in the bank vole. In forest biotopes explored, the most part of temporary ectoparasite species found on the common shrew was also recorded on other small mammals, which could have contacts with this host. It is possible to conclude that among the parasite supracommunity in the explored ecosystem, the temporary ectoparasites represent a "fond" of temporary parasites, which are common for most small mammal species. A role of different shrew and rodent species as main of additional hosts changes depending on a population density of potential mammalian hosts and other environment factors.     

Species richness,relative abundances and habitat use in local assemblages ofSorex shrews in Eurasian boreal forests

Using a large body of observational data on the occurrence ofSorex shrews in boreal forests, we test two models that predict the structure of small mammal communities along a gradient of increasing habitat productivity. Tilman’s (1982) model predicts a humped curve of species richness along productivity gradients. In contrast, we found a linear increase in species richness with increasing logarithm of the pooled density of shrews, which we use as a measure of habitat productivity for shrews. The model of Hanski and Kaikusalo (1989) assumes a trade-off between exploitative and interference competitive abilities, and it predicts that the size structure of small mammal communities should shift from the dominance of small species (superior in exploitative competition) in unproductive habitats to the dominance of large species (superior in interference competition) in productive habitats. Shrew assemblages show such a shift. Though it is not possible to draw definite conclusions about the role of interspecific competition from our observational data, the changing size structure of local shrew assemblages with increasing habitat productivity is a predictable feature of their community structure.     

Diversity of rodent and shrew assemblages in different vegetation types of the savannah biome in South Africa: no evidence for nested subsets or competition

Identifying nonrandom species composition patterns predicted by assembly rules has been a central theme in community ecology. Few studies have investigated the prevalence of multiple drivers on species composition patterns in small mammal assemblages in the Old World. This study investigated seasonal changes in rodent and shrew diversity in eleven savannah vegetation types in South Africa. We tested whether species composition patterns are nonrandom with respect to predictions from Diamond's assembly rules, niche limitation hypothesis and nestedness hypothesis. Species richness estimators indicated that inventories for the rodents (80%) and shrews (100%) were relatively complete. Rodent (n = 11 species) diversity and shrew (n = 5 species) diversity were highest in summer and lowest in autumn. Rodent richness was highest in the Terminalia sericea bushveld and woodlands and lowest in the Drypetes arguta sand forest, whilst shrew richness was highest in the T. sericea bushveld and woodlands and lowest in the Acacia nilotica/Dichrostachys cinerea open shrub savannah. We found no support for the predictions of competition and nestedness hypotheses and suggest that this was probably due to the high seasonal and annual variability in rodent and shrew diversity.     

Cyclic voles and shrews and non-cyclic mice in a marginal grassland within European temperate forest

Cyclic population dynamics of small mammals are not restricted to the boreal and arctic zones of Eurasia and North America, but long-term data series from lower latitudes are still less common. We demonstrated here the presence of periodic oscillations in small mammal populations in eastern Poland using 22-year (1986–2007) trapping data from marginal meadow and river valley grasslands located in the extensive temperate woodland of Białowieża Primeval Forest. The two most common species inhabiting meadows and river valleys, root vole Microtus oeconomus and common shrew Sorex araneus, exhibited synchronous periodic changes, characterised by a 3-year time lag as indicated by an autocorrelation function. Moreover, the cycles of these two species were synchronous within both habitats. Population dynamics of the striped field mouse Apodemus agrarius was not cyclic. However, this species regularly reached maximum density 1 year before the synchronized peak of root voles and common shrews, which may suggest the existence of interspecific competition. Dynamics of all three species was dominated by direct density-dependent process, whereas delayed density dependent feedback was significant only in the root vole and common shrew. Climatic factors acting in winter and spring (affecting mainly survival and initial reproduction rates) were more important than those acting in summer and autumn and affected significantly only the common shrew. High temperatures in winter and spring had positive effects on autumn-to-autumn changes in abundance of this species, whereas deep snow in combination with high rainfall in spring negatively affected population increase rates in common shrew.     

Structure of populations and ecological nishes of ectoparasites in the parasite communities of small forest mammals

The paper reports the results of eight-year investigations on the ectoparasites of rodents and insectivores carried out in southern taiga of the Ilmen-Volkhov lowland (Novgorod Region) and Kurgolovsky reserve (Leningrad Region). Twelve species of small mammals were captured including three dominate species--bank vole Clethrionomys glareolus (2722 specimens), common shrew Sorex araneus (1658 specimens), and wood mouse Apodemus uralensis (367 specimens). Parasite community of the bank vole comprises 34 species of mites, ticks, and insects, the community of common shrew comprises 25 species, and the community of A. uralensis includes 28 species. Taxonomic diversity of the ectoparasite communities was shown to be based on the diversity of types of parasitism and ecological nishes of the host body. Permanent ectoparasites are found to be represented by 2 species of lie and 14 species of acariform mites. The group of temporary parasites includes 13 species of fleas, 10 species of gamasid mites. 3 ixodid species and 1 Trombiculidae. There is a common pool of temporary parasites of small mammals in the ecological system of taiga. Significance of different shrew and rodent species as hosts were found to be dependent on the population density in possible hosts and many other factors. Species diversity in the parasite communities of different small mammal species is dependent on the number of possible ecological nishes in the host body. Actual infill of these nishes by ectoparasites is usually lesser than potential one. Species composition of temporary parasites, their occurrence and abundance changes according to season. Interspecific competition in the temporary parasite species can decrease because of the seasonal disjunction of their population peaks. Diversification of the ecological niches of ectoparasites allow simultaneous feeding of more parasite individuals on one host, than in the case of parasitising of single species or several species with similar ecological nishes. The distribution of parasites on their hosts was also studied. The aggregative distribution has been found in ixodid larvae only, and the distribution of fleas was close to the Poisson distribution. Deviations from the aggregative distribution can be an effect of several independent factors, including limited ability of small mammals for providing numerous parasites with food. On the most part of hosts simultaneous parasitizing of no more than 1-3 individuals of each tick, mite, and flea species was registered. Excessive infestation by ectoparasites may probably be limited by effective reactions of self-purification in the mammal hosts.     

Trophic Niche Differentiation and Microhabitat Utilization in a Species‐rich Montane Forest Small Mammal Community of Eastern Madagascar

Unraveling the mechanisms facilitating species coexistence in communities is a central theme in ecology. Species‐rich tropical mammal communities provide excellent settings to explore such mechanisms as they often harbor numerous congeneric species with close phylogenetic relationships. Explicit tests for the mechanisms that allow syntopic occurrence in these assemblages, however, is often hampered because of the difficulty in obtaining detailed ecological data on the organisms making up the community. Using stable nitrogen and carbon ratios of hair samples, we examine whether trophic niche differentiation and microhabitat segregation explain the coexistence of 21 small mammal species at a montane humid forest site in eastern Madagascar. Overall, the community was trophically diverse and covered wide isotopic space. This diversity was based on: (1) a multi‐layered trophic community structure with mainly frugivorous‐granivorous rodents (subfamily Nesomyinae) as primary consumers and insectivorous tenrecs (family Tenrecidae) as secondary and tertiary consumers; (2) trophic segregation of rodents and tenrecs with the latter occupying different microhabitats; and (3) a dense and regular packing of species in the community. The 12 locally occurring Microgale shrew tenrecs (subfamily Oryzorictinae) showed high trophic redundancy, but were maximally spaced from each other within the trophic space covered by the genus. Results of stable isotope analysis suggest that in combination the differentiation of microhabitats and trophic niches explain the coexistence of small mammals in this community. Congeneric species appeared to be under more intense competition compared with non‐congeneric species and their coexistence can only partly be explained by trophic and microhabitat niche segregation.     

Discovery of novel DNA viruses in small mammals from Kenya

Emergence and re-emergence of infectious diseases of wildlife origin have led pre-emptive pathogen surveillances in animals to be a public health priority. Rodents and shrews are among the most numerically abundant vertebrate taxa and are known as natural hosts of important zoonotic viruses. Many surveillance programs focused more on RNA viruses. In comparison, much less is known about DNA viruses harbored by these small mammals. To fill this knowledge gap, tissue specimens of 232 animals including 226 rodents, five shrews and one hedgehog were collected from 5 counties in Kenya and tested for the presence of DNA viruses belonging to 7 viral families by PCR. Diverse DNA sequences of adenoviruses, adeno-associated viruses, herpesviruses and polyomaviruses were detected. Phylogenetic analyses revealed that most of these viruses showed distinction from previously described viruses and formed new clusters. Furthermore, this is the first report of the discovery and full-length genome characterization of a polyomavirus in Lemniscomys species. This novel polyomavirus, named LsPyV KY187, has less than 60% amino acid sequence identity to the most related Glis glis polyomavirus 1 and Sciurus carolinensis polyomavirus 1 in both large and small T-antigen proteins and thus can be putatively allocated to a novel species within Betapolyomavirus. Our findings help us better understand the genetic diversity of DNA viruses in rodent and shrew populations in Kenya and provide new insights into the evolution of those DNA viruses in their small mammal reservoirs. It demonstrates the necessity of ongoing pathogen discovery studies targeting rodent-borne viruses in East Africa.     

实验树鼩肠道螺杆菌属细菌特征分析

近年来,树鼩(Tupaia belangeri)作为一种新型的实验动物被广泛应用于生物医学研究的各个领域。本研究组前期的研究结果显示,螺杆菌属(Helicobacter)是树鼩肠道微生物群落中相对丰度最高的一类细菌,但其具体的细菌种类和结构特征仍然不清楚。因此,本研究将开展实验树鼩肠道中螺杆菌属细菌的分布种类和特征分析,为后续实验研究工作提供资料。通过系统采集72只树鼩的粪便样本,提取核酸后采用巢氏PCR法应用属特异性引物扩增螺杆菌属特异性片段,再分别采用7个种特异性引物对属特异性阳性样本扩增螺杆菌种特异性片段,包括肝螺杆菌(H.hepaticus)、家鼠螺杆菌(H.muridarum)、胆汁螺杆菌(H. bilis)、啮齿类螺杆菌(H. rodentium)、弯曲螺杆菌(Flexispira rappini)、鼩螺杆菌(H. suncus)和盲肠螺杆菌(H. typhlonius)。属特异性引物扩增阳性但种引物扩增阴性的样本进行核酸序列测定和BLAST比对分析,确认其最终所属的螺杆菌种类。结果显示,72份树鼩粪便样本中,属特异性引物扩增阳性有18份,总体阳性率为25.0%。其中,盲肠...     

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA‐based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water‐limited ecosystem where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for noninvasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment and water filtered through glass fibre filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus‐specific PCRs were tested on environmental samples for two genera producing fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non‐African mammals showed that baits covering 30% of nontarget mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over‐representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100‐fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.     

Shifts from native to invasive small mammals across gradients from tropical forest to urban habitat in Borneo

Urbanization has paved the way for the spread of commensal rodents at global scale. However, it is largely unknown how these species use tropical anthropogenic landscapes originally covered with forests and inhabited by diverse small mammal assemblages. We surveyed non-flying small mammals in various urban and suburban habitat types and adjacent forest in the tropical town of Kota Kinabalu in Borneo. We used occupancy and polynomial regression models to determine variation in species occurrences along gradients of land-use intensity. Müller’s sundamys (Sundamys muelleri) was the only native small mammal species found in urban and suburban landscapes with a continuous decrease in occurrence probability from forests to urban habitats. The invasive Asian black rat (Rattus rattus species complex) and the invasive Asian house shrew (Suncus murinus) had the highest occurrence probabilities in habitats of intermediate land-use intensity, but Asian black rats are also likely to occasionally invade forested habitats and occupied urban habitats in sympatry with the Norway rat (Rattus norvegicus). In urban and suburban habitats, fallow land possibly favoured the occurrence of S. muelleri and S. murinus. Other native small mammal species (Muridae, Sciuridae, Tupaiidae) were found only in forested areas. Our study shows that native small mammals found in forest are largely replaced by invasive species in urban and suburban habitats. Due to their occurrence in habitats of various land use intensities, S. muelleri and R. rattus comprise central links between forest wildlife and urban species, an association that is important to consider in studies of parasite and disease transmission dynamics.     

Resource partitioning confirmed by isotopic signatures allows small mammals to share seasonally flooded meadows

Meadows in river deltas are characterized by a high diversity and abundance of small mammals. However, neither their spatial arrangement nor differences in their use of microhabitat can necessarily explain the dense co‐occurrence of sympatric species. We investigated how several small mammal species share a seasonally flooded meadow of limited size, testing predictions (P1) that herbivore, granivore, insectivore, and omnivore species are separated in time (dominant in different years), (P2) that sympatric species undergo isotopic partitioning, and (P3) that there are intraspecific differences in diet. Stable carbon and nitrogen isotope signatures in the hair of seven synantropic shrew, vole, and mice species were used as a proxy for their diet. We found that the three most abundant species in eight of the nine years were from different diet groups. However, based on the number of species in the functional groups, the state of small mammal community was considered unfavored in five out of the nine investigation years. In years with the greatest dominance of Apodemus agrarius, the small mammal community was characterized by decreased diversity and Micromys minutus was either in low abundance or absent. In 2014 and 2016, years of low abundance or absence of M. oeconomus, M. agrestis, and M. glareolus were both recorded in high numbers. Differences in the isotopic signatures of the three most abundant small mammal species in the community were clearly expressed and core areas in the isotopic space were separated, showing their dependence on different dietary resources. Intraspecific dietary separation between young and adult animals was observed only in M. oeconomus. Thus, the high species diversity of small mammals and the formation of their community in this investigated flooded meadow are maintained by isotopic partitioning (segregation in dietary space) and by changes in their number over time (shifting dominance).     

峨眉山夏季小型兽类垂直空间生态位的初步研究

正空间生态位研究是群落生态学研究中的一个非常重要的领域。它能反映一定空间内生物群落中物种对环境资源的综合利用状况和种间的竞争关系(史作民和程瑞梅,1999;Ibarra et al.,2014)。小型兽类生态位的研究在国内外已有不少报道(Churchfield et al.,1999;Patrick,2000;王艳妮等,2005;付和平等,2005;申跃武等,2008;马     

红外相机技术监测喀斯特生兽类和鸟类多样性及活动节律

2012年8月至2013年11月,在15 hm2弄岗森林动态监测样地及其周边地区以1台/2 hm2密度布设了35台红外相机,对研究区域内大中型兽类和林下鸟类资源进行连续监测。共记录到20种兽类和26种鸟类,包括2种国家I级、8种国家II级重点保护野生动物。其中,小泡巨鼠（Leopoldamys edwardsi）、帚尾豪猪（Atherurus macrourus）、赤腹松鼠（Callosciurus erythraeus）、北树鼩（Tupaia belangeri）、赤麂（Muntiacus muntjak）等5种动物拍摄率和相对丰富度均居于兽类的前5位;白鹇（Lophura nycthemera）、橙头地鸫（Zoothera citrina）和蓝背八色鸫（Pitta soror）的相对丰富度居于鸟类的前3位。虽然每月监测的鸟兽种数、多样性指数和均匀度指数均不存在显著的季节性差异,但不同季节记录到的兽类和鸟类种类存在一定差异：黑叶猴（Trachypithecus francoisi）、野猪（Sus scrofa）2种兽类和斑头鸺鹠（Glaucidium cuculoides）、长尾阔嘴鸟（Psarisomus dalhousiae）、红胁蓝尾鸲（Tarsiger cyanurus）3种鸟类仅在旱季记录到;而仙八色鸫（Pitta nympha）和凤头鹰（Accipiter trivirgatus）2种鸟类仅在雨季记录到。活动节律分析结果表明赤麂、北树鼩、赤腹松鼠和白鹇为昼行性动物,帚尾豪猪与小泡巨鼠为夜行性动物。以上研究结果有助于监测喀斯特生境大中型兽类和林下鸟类种群的变化,为保护区有效管理提供数据支持。     

DNA条形码技术在青海海东地区小型兽类鉴定中的应用

为弥补传统形态分类方法的不足,探究应用DNA条形码技术进行分子生物学鉴定的可行性,本研究用DNA条形码技术检测了青海省海东地区3目6科14属18种110只小型兽类的COI基因部分序列。分析所测COI基因序列可知:种内遗传距离≤3%,种间遗传距离5-10%,属间遗传距离12-19%,种间遗传距离显著大于种内遗传距离。NJ树显示同种个体聚为有很高支持度的单一分支。有6个个体(4只黄胸鼠、2只小家鼠)在现场鉴定中被误定为其他种类。研究结果表明使用条形码技术能纠正形态学鉴定中的错误,也说明动物线粒体COI基因是一个有效的DNA条形码标准基因。