Combined genomic-metabolomic approach for the differentiation of geographical origins of natural products: deer antlers as an example

The correct identification of the geographical origin of deer antlers is essential to quality control, as its positive physiological effects correlate with chemical components. In this study, we applied both genomics and metabolomics to the origin-identification of 101 samples from Canada, New Zealand, and Korea. The genomics identified deer species in each country but failed to categorize all the samples, due to the presence of identical species in different countries. For identical species, NMR-based metabolomics gave clean separations, compounds specific to each country were identified, and the validity was confirmed by prediction analysis. As the genomics provided unambiguous read-outs for different species, and the metabolomics cleanly distinguished among identical species from different countries, their combined use could be a robust method for origin-identification even in difficult cases. We believe the method to be generally applicable to many herbal medicinal products for which various species are grown internationally.     

Effects of Key deer herbivory on forest communities in the lower Florida Keys

Ungulate herbivory can have strong impacts on plant communities, but these impacts are rarely considered in recovery plans of endangered species. This study examined the effects of the endangered Key deer (Odocoileus virginianus clavium) on its environment in the lower Florida Keys. The Key deer population has increased to over 700 deer from approximately 50 deer in the 1950s; however, approximately 75% of the population resides on only a few islands (Big Pine, No Name, Big Munson) where Key deer herbivory on forest communities may be substantial. Effects of deer herbivory on plant densities were estimated on these islands using vegetation quadrats in hardwood hammock, buttonwood transition, and mangrove wetlands and compared to nine other islands with intermediate or low deer densities. On islands with high deer density, densities of preferred woody plant species <1.2 m tall (within Key deer reach) were significantly lower than islands with lower deer densities, while densities of some nonpreferred species were significantly higher. Deer exclosures established in hardwood hammock on a high-density deer island revealed a mean increase in abundance/height of preferred woody species inside exclosures, while nonpreferred species significantly increased in open plots. We conclude that on high deer density islands, highly preferred plant species might eventually fail to regenerate and unpalatable plant species may become dominant. Careful criteria need to be developed to maintain Key deer numbers above an endangered species status yet below levels that are destructive to local forest species.     

Identification of the clam species Ruditapes decussatus (Grooved carpet shell), Venerupis pullastra (Pullet carpet shell), and Ruditapes philippinarum (Japanese carpet shell)by PCR-RFLP

PCR-RFLP analysis has been applied to the identification of three clam species: Ruditapes decussatus (grooved carpet shell), Venerupis pullastra (pullet carpet shell), and Ruditapes philippinarum (Japanese carpet shell). PCR amplification was carried out using a set of primers designed from the DNA nucleotide sequences reported for alpha-actins from humans and various animals. Restriction endonuclease analysis based on sequence data of the PCR products of each clam species revealed the presence of species-specific polymorphic sites for MaeIII and RsaI endonucleases. Electrophoretic analysis of the amplicons digested with MaeIII and RsaI produced species-specific profiles that allowed the genetic identification of the three clam species.     

Impacts of urbanization on Florida Key deer behavior and population dynamics

Rapid human population growth and urbanization have had a negative impact on species biodiversity. As competition for resources between man and wildlife continues, it is important to understand the effects of urbanization on species. Endangered Key deer (Odocoileus virginianus clavium) are endemic to the Florida Keys which have undergone rapid human population growth and development over the past 30 years. Our study objectives were to evaluate the impacts of urban development on Key deer habitat use, population dynamics, behavior, and body mass. We used data from two comprehensive studies on Key deer spanning 30 years to evaluate these changes. Our results suggest that Key deer have become more urbanized, using urban areas more today than they did 30 years ago. Contrary to our predictions, survival was higher for more urban deer than for less urban deer. Problems still exist with mortality factors heavily impacting some portions of the deer population including lower survival associated with less urban male deer. Analysis of Key deer body mass also was converse to our predictions as deer weights appear to have increased over time. Collectively, our results suggest that over the past 30 years Key deer have become more urbanized and that deer plasticity has allowed them to adapt and persist in an urbanizing environment. However, the future ability of Key deer to persist in an environment with continued urban development is unknown. At some threshold, urban development would become unsustainable and unlike other forms of habitat change or environmental disturbances, urban development is in most cases irreversible requiring careful planning in habitat conservation strategies.     

Conservation status and causes of decline of musk deer (Moschus spp.) in China

Five species of musk deer (Forest musk deer Moschus berezovskii, Alpine musk deer M. sifanicus, Black musk deer M. fuscus, Himalayan musk deer M. chrysogaster and Siberian musk deer M. moschiferus) occur throughout 17 provinces in China, and all were listed in the second category of the Chinese State Key Protected Wildlife List in 1998. Among these species, the Forest musk deer has the widest distribution, and its population is estimated at about 100,000-200,000 individuals in the wild. Additionally, there are about 100,000 Alpine musk deer and 2000 Siberian musk deer. As for the Black musk deer and Himalayan musk deer, which occur only in parts of Yunnan Province and Tibet, their populations remain unknown but they can be estimated to be rare due to their narrow and limited distribution. Furthermore, there are some 1900 musk deer kept in farms in China. Generally, the musk deer population has been declining due to over-hunting for musk and to loss of habitats. However, the Chinese government is greatly concerned with wildlife protection today. A series of laws and regulations have been launched and many natural reserves and national parks have been established as refuges for this animal, most of which, are within the musk deer's range, and should have positive effects for musk deer conservation.     

A natural experiment on the effects of high deer densities on the native flora of coastal temperate rain forests

The introduction of Sitka black-tailed deer (Odocoileus hemionus sitkensis Merriam) to Haida Gwaii (Queen Charlotte Islands, BC, Canada) in the late 19th century, provided an opportunity to understand the long-term effects of deer populations on the vegetation of temperate rain forests in the absence of their natural predators wolves (Canis lupus L.), and cougars (Puma concolor L.). Using seven small islands with different browsing histories (no deer, deer for <20 years, deer for >50 years), we tested the long-term effects of high deer densities on plant cover and species richness in the understorey of forest interior and forest edge habitats. Overall vegetation cover exceeded 80% in the lower vegetation layers on islands without deer and was less than 10% on the islands with deer for more than 50 years. Although overall plant species richness was similar on islands with or without deer, plant species richness at the plot scale (314 m²) was reduced by 20-50% on islands with deer for >50 years. The differences were most pronounced for the species-rich edge communities and among herb and shrub species. These results suggest that in the absence of predators, deer have the potential to greatly simplify the forest ecosystem.     

Assessing the sustainability of brocket deer hunting in the Tamshiyacu-Tahuayo Communal Reserve, northeastern Peru

Since the 1800s, brocket deer have been an important source of meat and income for subsistence and professional hunters in the Peruvian Amazon. Today, local people continue to hunt brocket deer for subsistence meat and for sale in local meat markets. Although brocket deer are not hunted as frequently as peccaries, they make a significant contribution to rural household economies. This study assessed the sustainability of hunting of brocket deer by local communities in the Tamshiyacu Tahuayo Communal Reserve (TTCR), northeastern Peru. We analyzed data from 1991 to 1999 using density comparisons, hunting pressures, an age structure model, and a harvest model comparing results between heavily hunted, slightly hunted, and non-hunted sites. The four approaches agreed that brocket deer are harvested sustainably. The sustainability of brocket deer hunting will depend on the continued presence of other valuable wildlife species (e.g. peccaries and large rodents), which are more preferred due to their ease of hunting and higher rates of encounters. Gross productivity indicates that brocket deer are showing resilience in the form of density dependent reproductive adjustments in the TTCR, but they may still be vulnerable to overhunting. Consequently, current levels of harvesting may be continued until further ecological and biological information on the species' population trends assist in defining more reliable sustainable offtake levels.     

Roe deer (Capreolus capreolus) browsing pressure affects yew (Taxus baccata) recruitment within nature reserves in Norway

Grazing and browsing by large herbivores is known to affect patterns of biodiversity. Still much remains to be done to assess the specific role of browsing on single, red listed plant species. In Norway, the yew (Taxus baccata) is a threatened species and several nature reserves have been established. We show, that within two nature reserves between 1988 and 2003, yew recruitment was strongly dependent on variation in roe deer (Capreolus capreolus) browsing pressure. Our study emphasized that establishing nature reserves for yew is not enough to conserve this species unless control over browsing roe deer population is also taken. We argue that roe deer, being the most abundant large herbivore in Europe, may have a larger effect on conservation than currently realized.     

Long-term response of spring flora to chronic herbivory and deer exclusion in Great Smoky Mountains National Park, USA

Chronic herbivory by white-tailed deer (Odocoileus virginianus Zimmerman) can have profound impacts on the function and structure of forest ecosystems. We examined the combined influence of intense herbivory associated with a deer population eruption and chronic herbivory by the post eruption population on the spring flora of Cades Cove, Great Smoky Mountains National Park. During the 1970s the deer population reached a peak of 43 deer per km², from which it has slowly declined in recent decades. To examine the influence of intense herbivory, we compared the abundance and flowering rates of early flowering plants in Cades Cove to a nearby reference site with similar bedrock geology, vegetation, and disturbance history but contrasting history of deer abundance. Our results suggest that significant changes (p ? 0.05) in the diversity, evenness, and species richness of the spring flora occurred during the eruptive phase. Trillium spp. and other liliaceous species appeared to be disproportionately impacted. Comparisons between control and exclosure plots established after the deer population eruption indicate that recovery has been largely restricted to species that were able to persist under intense herbivory. These species have increased in number in exclosures, suggesting continued impacts by deer on the plant community outside the exclosures. Little to no recolonization by browse sensitive species was observed. Consequently, to restore the natural diversity of early flowering plants once present in Cades Cove, active restoration may be necessary in addition to maintaining deer densities below current levels.     

Long-term effects of deer browsing and trampling on the vegetation of peatlands

Overabundance of wild ungulates, especially exotic species, is a major threat to several ecosystems worldwide. While the response of forest vegetation to high density of herbivores has been well studied, far less is known about peatland vegetation. In this paper, we assessed the long term impact of white-tailed deer (Odocoileus virginianus) on plant communities of ombrotrophic (bog) and minerotrophic (fen) peatlands in eastern North America. Vegetation of five peatlands that have experienced high deer densities for at least 75 years was compared with that of five peatlands situated at proximity but on deer-free islands. We investigated deer impacts on plant species composition and cover, shrub height and cloudberry (Rubus chamaemorus) fruit/flower production and morphology. In bogs, white-tailed deer had no long-term impact on plant species assemblages, but reduced lichen cover and increased sedges and grasses cover as well as the surface area of bare peat. On the other hand, the floristic composition of fens differed significantly between sites where deer were present or absent. Plant diversity was greater in undisturbed fens than in disturbed fens, especially for shrubs, sedges and liverworts. No detrimental effects of browsing on shrub height were observed. Conversely, deer browsing seemed to have deleterious impacts on cloudberry fruit/flower production as well as on the number of leaves per individual. Overall, our results suggest that white-tailed deer had some important impacts on the vegetation of peatlands that could be harmful for the long-term conservation of peatland plant diversity.     

Finding a needle in the haystack: Regional analysis of suitable Eld’s deer (Cervus eldi) forest in Southeast Asia

For species whose decline preceded the modern era and whose distribution is in the developing world, it is difficult to map suitable habitat across its former range. Eld’s deer (Cervus eldi) is an endangered cervid whose range across Southeast Asia was reduced during the last century to disjoint populations in Myanmar and Cambodia. We used ecological data from the present populations to determine landscape and habitat parameters that would help us predict the occurrence of the species in forests not yet surveyed. The suitable-forest GIS model was created using four readily available datasets for elevation, forest type, canopy closure, and human density. Comparison of the GIS model with 24 verified sightings of Eld’s deer during recent large mammal surveys in Cambodia, found 22 sightings (92%) within predicted suitable forest. Use the suitable-forest GIS model to survey a province in southern Lao People’s Democratic Republic, located a single, previously unreported population from 9 patches surveyed. In a separate analysis, a logistic regression model to predict Eld’s deer habitat in Northern Cambodia found percent tree cover, presence of wetlands, and distance to villages as the best predictors of deer, similar to variables used in the GIS model, with the exception of the importance of wetlands. Using mean annual rainfall to rank suitable-forest patches identified in the GIS model indicated dry dipterocarp forests in Northeastern Cambodia and Northern Myanmar have the highest potential to conserve eld’s deer. Examination of the suitable-forest GIS map and current protected areas indicated only Cambodia, with 11% suitable forest protected, has placed sufficient dry dipterocarp forest under protected status. Other Southeast Asia countries have not recognized dry dipterocarp forest as a significant ecotype worthy of conservation status.     

Effects of white-tailed deer on the native earthworm,Eisenoides carolinensis,in the southern Appalachian Mountains,USA

Research on earthworms in North America has focused on the effects of invasive earthworms, with few studies examining the ecology of native earthworm species. Deer have been shown to influence belowground processes through grazing, trampling, and fecal pellet deposition. We proposed that native earthworms in an oak-dominated forest in Virginia might benefit from increased organic matter provided by deer fecal material. We examined potential interactions between a common aboveground herbivore, the white-tailed deer (Odocoileus virginianus), and earthworms using laboratory and field experiments. In our laboratory experiment, we found that a native earthworm, Eisenoides carolinensis, and an invasive earthworm, Lumbricus terrestris both fared better in treatments with deer pellets compared with the treatment with leaf litter alone. In our field experiment, we used fences to exclude deer from six plots and left twelve plots unfenced to explore the effects of deer activity on earthworm biomass and density. We also examined the effects of deer on soil and vegetation characteristics. After three years, the amount of herbaceous cover was higher on fenced plots compared with unfenced plots. Although we found no other differences for vegetation and soil characteristics between fenced and unfenced plots, many of these variables were important as covariates in our models examining the effect of deer exclusion on earthworms, indicating plot-level (as opposed to treatment-level) variation in these variables. All identifiable earthworms were either E. carolinensis or Diplocardia spp. (both native species), with E. carolinensis making up 90% of the specimens. The total biomass of earthworms, as well as the biomass and density of adult and small juvenile earthworms, was greater on unfenced plots with deer activity compared with fenced plots. This study highlights the importance of above- and below-ground interactions in forest ecosystems by showing that E. carolinensis appears to benefit from the presence of deer and adds to our sparse knowledge of the ecology of this native earthworm.     

A genetic fingerprinting test for identifying carcasses of protected deer species in China

State governments in China have laid down laws for protecting rare and endangered species. This study develops a genetic test using ‘southern hybridization’ to identify carcases of Chinese water deer (Hydropotes inermis Swinhoe) to provide forensic evidence of poaching. The method uses pta₂ oligonucleotide probe, which is quite distinct from PCR amplification and sequencing of Cytb gene or ribosomal sequences. It could be extended to identify other species of protected deer.     

Population demise and extinction threat of the Angel de la Guarda deer mouse (Peromyscus guardia)

We analyze the status of the Angel de la Guarda deer mouse (Peromyscus guardia), a species endemic to Mexico, based on our own fieldwork, bibliographic records and information from colleagues. This species, with different subspecies on three islands and a population of an undetermined subspecies on a fourth, was apparently common until the mid-1960s. Currently the species is critically endangered, if not already extinct. One of the subspecies and the undetermined population are presumed extinct. Of the two other subspecies, one is at least in critical condition, and the other at least reduced. The demise of the species can be attributed to the introduction of domestic cats. The case of P. guardia is a good example of the vulnerability of other taxa of endemic rodents on islands in the Gulf of California.     

Breeding and post-breeding responses of woodland birds to modification of habitat structure by deer

Birds in woodland can be affected by increasing deer populations through changes to vegetation structure and potential impacts on foraging resources; these effects need to be better understood. Effects of deer browsing are reported from a replicated split-plot exclusion experiment in English coppiced woodland. All stages of growth were examined up to eight years after felling. We used standardised mist-netting (totaling 1920 h) to sample birds in breeding and post-breeding periods. Deer browsing strongly altered vegetation structure by reducing canopy cover and shrub layer foliage density. However deer did not affect invertebrate density per unit of foliage, providing no evidence of an ungulate-mediated plant chemical response affecting forage quality for invertebrate herbivores. At avian guild level, significantly more ground and understorey foraging birds were captured where deer were excluded, and negative responses to browsing were more marked for pooled migrants than pooled residents. At the species level, especially pronounced negative effects were evident for dunnock (Prunella modularis) and garden warbler (Sylvia borin); approximately five times more dunnocks were captured in deer exclosures than in browsed vegetation. We also detected negative responses to browsing by nightingale (Luscinia megarhynchos) and long-tailed tit (Aegithalos caudatus). No significant positive responses to browsing were detected. For some species the use of young re-growth increased post breeding relative to the breeding period, including a marked shift by pooled residents that involved a disproportionate number of juveniles. Previous studies in North America have shown that, through vegetation modification, ungulate activity can alter woodland bird assemblages; as far as we are aware this is the first experimental demonstration of effects in Europe, and at low to moderate browsing intensity typical of the wider landscape scale.     

PCR-RFLP analysis of mitochondrial DNA: a reliable method for species identification

A method for identification of game species has been developed on the basis of the amplification of a specific part of the mitochondrial genome (tRNA(Glu)/cytochrome b) using the polymerase chain reaction (PCR). To distinguish between several game species, the obtained 464-bp-long PCR products were cut with different restriction endonucleases (RE) resulting in species-specific restriction fragment length polymorphism (RFLP). Even closely related deer species could be distinguished by application of one or two RE. Natural polymorphisms of the target sequence within one species were examined for red deer (Cervus elaphus), and base pair substitutions were identified affecting the RFLP pattern.     

Trophic cascades involving cougar, mule deer, and black oaks in Yosemite National Park

Using a historical reconstruction, we discovered a potential trophic cascade involving cougar (Puma concolor), mule deer (Odocoileus hemionus), and California black oak (Quercus kelloggii) in the Yosemite Valley of Yosemite National Park in California. Our objective was to determine whether large deer populations in the absence of a top-level carnivore were suppressing tree regeneration. As human visitation increased in the early 1900s and cougar became increasingly scarce, the mule deer population irrupted in the 1920s. In August 2006, we undertook a retrospective study of black oak recruitment (i.e., growth of seedling/sprouts into tall saplings and trees) by inventorying all black oaks in stands accessible to deer and greater than 0.5 ha in size (18 stands, 2921 trees). We similarly inventoried oaks within sites representing refugia from deer browsing (4 stands, 481 trees). While significantly diminished oak recruitment has occurred since the 1920s in stands accessible to deer (p < 0.01), continuous recruitment of oaks was found in refugia sites. We also found less oak recruitment in areas of high human activity near the park’s visitor center (p < 0.01), possibly due to behaviorally-mediated effects of lower cougar and higher deer densities. Overall our results are consistent with trophic cascade theory involving large predators, herbivores, and plants. The long-term lack of oak recruitment is also an indicator of a probable loss of biodiversity.     

Sexual dimorphism,survival and dispersal in red deer

A detailed and extensive mark-recapture-recovery study of red deer on the island of Rum forms the basis of the modeling of this article. We analyze male and female deer separately, and report results for both in this article, but use the female data to demonstrate our modeling approach. We provide a model-selection procedure that allows us to describe the survival by a combination of age-classes, with common survival within each class, and senility, which is modeled continuously as a parametric function of age. Dispersal out of the study area is modeled separately. Survival and dispersal probabilities are examined for the possible influence of both environmental and individual covariates, including a range of alternative measures of population density. The resulting model is succinct and biologically realistic. We compare and contrast survival rates of male and female deer of different ages and compare the factors that affect their survival. We demonstrate large differences in the rate of senescence between males and females even though their senescence begins at the same age. The differences between the sexes suggest that, in population modeling of sexually size-dimorphic species, it is important to identify sex-specific survival functions.     

Identification of grouper (Epinephelus guaza), wreck fish (Polyprion americanus), and Nile perch (Lates niloticus) fillets by polyclonal antibody-based enzyme-linked immunosorbent assay

An indirect enzyme-linked immunosorbent assay (ELISA) has been developed for the species identification of grouper (Epinephelus guaza), wreck fish (Polyprion americanus), and Nile perch (Lates niloticus) fillets. The assay was performed in two different formats, microtiter plates and immunostick tubes, and uses polyclonal antibodies raised in rabbits against muscle-soluble proteins of grouper (anti-GSP), wreck fish (anti-WSP), and Nile perch (anti-PSP). The antibodies were made species-specific by blocking them with the heterologous soluble muscle proteins. Immunorecognition of polyclonal antibodies adsorbed to their specific fish samples was made with swine antirabbit immunoglobulins conjugated to the enzyme horseradish peroxidase. Subsequent enzymatic conversion of the substrate allowed unequivocal identification of the species studied.     

Two genetically distinct units of the Chinese sika deer (cervus nippon): analyses of mitochondrial DNA variation

Chinese sika deer, Cervus nippon, are currently threatened by habitat loss, fragmentation and human hunting, which has led to the extinction of three subspecies in the wild. The remaining subspecies subsist in the narrow regions of Jilin, Heilongjiang, Sichuan, Gansu, Jiangxi, Anhui, and Zhejiang provinces. In order to design effective conservation strategies for the Chinese sika deer, we have investigated genetic diversity, population structure and gene flow in the Chinese sika deer populations by analyzing ≈995 base pairs of the mitochondrial DNA (mtDNA) control region in 59 individuals sampled from the northeast of China, Sichuan, Jiangxi and Zhejiang. Chinese sika deer exhibited low mtDNA diversity and high gene flow among the four populations, and showed no strong geographical structure. The analyses of mtDNA variation among individuals of sika deer identified only two main phylogenetic groups even though three subspecies were sampled. These data singles out the Zhejiang population as being highly genetically distinct and worthy of separate conservation consideration. Therefore, it is recommended that a breeding program for the Zhejiang population be established.