Characterization of Genotypes of Enterocytozoon bieneusi in Immunosuppressed and Immunocompetent Patient Groups

ABSTRACT. A retrospective phylogenetic analysis was performed on isolates of Enterocytozoon bieneusi to characterize the genotypes in different patient cohorts. Fifty-seven isolates, collected from patients living in Malawi and the Netherlands, were classified by age and immune status of the hosts. Sequence analysis of the internal transcribed spacer (ITS) region identified 16 genotypes; nine have not previously been described. Genotypes K and D were most prevalent among patient groups, whereas genotype C was restricted to transplantation patients receiving immunosupressives and genotype B showed a predisposition toward patients living with HIV/AIDS. Different genotypes showed more dispersion among isolates from Malawi compared with those from the Netherlands. A constructed map estimating the genealogy of the ITS region reveals a dynamic evolutionary process between the genotypes.     

Submerged macrophytes, zooplankton and the predominance of low- over high-chlorophyll states in western boreal, shallow-water wetlands

1. Shallow‐water (<2 m deep) wetlands in northern Alberta's western boreal forest tend to have either extremely high‐chlorophyll, pea‐green water or water that is low in chlorophyll and clear. The relative importance of top‐down processes (e.g. zooplankton grazing) compared with bottom‐up processes (e.g. nutrient limitation) for regulating the existence of these alternate states has yet to be explicitly investigated in these poorly studied waterbodies. 2. To assess the relationship between chemical and biological factors and the predominance of low‐chlorophyll over high‐chlorophyll states, a survey of 24 shallow‐water wetlands in northern Alberta was conducted over the summers of 2001 and 2002. 3. In wetlands without fish, statistical analysis indicated that high‐ and low‐chlorophyll sites could be differentiated with 82% accuracy based solely on whether submerged aquatic vegetation (SAV) coverage was greater or less than 25%. Further, high‐SAV lakes with zooplankton communities dominated by large cladocerans were clear 96% of the time. 4. In the few wetlands that supported stickleback populations, large cladocerans were absent. However, the development of zooplankton communities dominated by small cladocera (Bosmina) with calanoid copepods in fish‐containing wetlands corresponded with a shift from high‐ to low‐chlorophyll states. 5. Results suggest that in fishless wetlands high‐SAV coverage and grazing by large, SAV‐associated cladocerans promotes low‐chlorophyll states. Results also suggest that suppression of macroinvertebrate predators by sticklebacks allowing Bosmina to flourish may also promote low‐chlorophyll, clear‐water conditions.     

Effects of grazing and ant/beetle interaction on seed production in the legume Vicia sepium in a seminatural grassland

Abstract.  1. Seed production can be affected by cattle grazing, insect herbivores, and seed predators. Bush vetch, Vicia sepium L. (Fabaceae), possess extra floral nectaries (EFNs), which can attract ants that act as plant defenders.
2. In this field study, four different manipulations were used to investigate interactions between V. sepium , ants, aphids, and seed predators, mainly Bruchus atomarius. The experiment was set up in grazed and non-grazed plots in a semi-natural grassland in south-central Sweden.
3. Grazing negatively affected number of V. sepium buds, flowers, and pods. Seed set, defined as the number of developed seeds per number of ovules in a pod, was higher in grazed plots. Ant abundance, however, was not affected by grazing. Ten different ant species were found on V. sepium and the number of ants was positively correlated with the presence of EFNs. Aphids were found only when ants were excluded from the plants. Pod and seed production of V. sepium plants was not affected by the presence of ants. The seed predator B. atomarius was not affected by the presence of ants. No support was found for the supposition that V. sepium benefited from attracting ants by producing extra floral nectar.
4. A small observational study of V. sepium plants in shrub ( Rosa dumalis ) plots compared with grassland plots was added to the experimental study . Vicia sepium plants were longer and had higher seed-set (seeds/ovules) in shrub plots than in grassland plots.     

Efficient,Noninvasive Genetic Sampling for Monitoring Reintroduced Wolves

ABSTRACT Traditional methods of monitoring gray wolves (Canis lupus) are expensive and invasive and require extensive efforts to capture individual animals. Noninvasive genetic sampling (NGS) is an alternative method that can provide data to answer management questions and complement already-existing methods. In a 2-year study, we tested this approach for Idaho gray wolves in areas of known high and low wolf density. To focus sampling efforts across a large study area and increase our chances of detecting reproductive packs, we visited 964 areas with landscape characteristics similar to known wolf rendezvous sites. We collected scat or hair samples from 20% of sites and identified 122 wolves, using 8–9 microsatellite loci. We used the minimum count of wolves to accurately detect known differences in wolf density. Maximum likelihood and Bayesian single-session population estimators performed similarly and accurately estimated the population size, compared with a radiotelemetry population estimate, in both years, and an average of 1.7 captures per individual were necessary for achieving accurate population estimates. Subsampling scenarios revealed that both scat and hair samples were important for achieving accurate population estimates, but visiting 75% and 50% of the sites still gave reasonable estimates and reduced costs. Our research provides managers with an efficient and accurate method for monitoring high-density and low-density wolf populations in remote areas.     

Noninvasive genetic tracking of the endangered Pyrenean brown bear population

Pyrenean brown bears Ursus arctos are threatened with extinction. Management efforts to preserve this population require a comprehensive knowledge of the number and sex of the remaining individuals and their respective home ranges. This goal has been achieved using a combination of noninvasive genetic sampling of hair and faeces collected in the field and corresponding track size data. Genotypic data were collected at 24 microsatellite loci using a rigorous multiple-tubes approach to avoid genotyping errors associated with low quantities of DNA. Based on field and genetic data, the Pyrenean population was shown to be composed at least of one yearling, three adult males, and one adult female. These data indicate that extinction of the Pyrenean brown bear population is imminent without population augmentation. To preserve the remaining Pyrenean gene pool and increase genetic diversity, we suggest that managers consider population augmentation using only females. This study demonstrates that comprehensive knowledge of endangered small populations of mammals can be obtained using noninvasive genetic sampling.     

Plucked hair samples as a source of DNA: reliability of dinucleotide microsatellite genotyping

To test whether plucked hairs are a reliable source of DNA for genotyping microsatellite loci, we carried out experiments using one, three, or 10 hairs per extract for 50 alpine marmots. For each extract, seven independent genotypings were performed for the same locus (multiple-tubes approach). Two types of genotyping errors were recorded: a false homozygote defined as the detection of only one allele of a true heterozygote, and a false allele defined as a PCR-generated allele that was not one of the alleles of the true genotype. Using DNA extracted from one, three, or 10 hairs, the overall error rate was 14.00%, 4.86%, and 0.29%, respectively. Based on our results, we conclude that 10 hairs should be used to obtain consistently reliable genotypings using the single-tube approach, and that a single plucked hair could represent a reliable source of DNA if the multiple-tubes approach is used. For future studies of dinucleotide repeat diversity using DNA extracted from one to three shed or plucked hairs, we strongly recommend initiating an appropriate pilot study to quantify the error rate and to determine the reliability of the single-tube approach.     

A select panel of polymorphic microsatellite loci for individual identification of snow leopards (Panthera uncia)

Snow leopards (Panthera uncia) are elusive endangered carnivores found in remote mountain regions of Central Asia. New methods for identifying and counting snow leopards are needed for conservation and management efforts. To develop molecular genetic tools for individual identification of hair and faecal samples, we screened 50 microsatellite loci developed for the domestic cat (Felis catus) in 19 captive snow leopards. Forty‐eight loci were polymorphic with numbers of alleles per locus ranging from two to 11. The probability of observing matching genotypes for unrelated individuals (2.1 × 10^?11) and siblings (7.5 × 10^?5) using the 10 most polymorphic loci was low, suggesting that this panel would easily discriminate among individuals in the wild.     

Assessing Estimators of Snow Leopard Abundance

Abstract: The secretive nature of snow leopards (Uncia uncia) makes them difficult to monitor, yet conservation efforts require accurate and precise methods to estimate abundance. We assessed accuracy of Snow Leopard Information Management System (SLIMS) sign surveys by comparing them with 4 methods for estimating snow leopard abundance: predator:prey biomass ratios, capture-recapture density estimation, photo-capture rate, and individual identification through genetic analysis. We recorded snow leopard sign during standardized surveys in the SaryChat Zapovednik, the Jangart hunting reserve, and the Tomur Strictly Protected Area, in the Tien Shan Mountains of Kyrgyzstan and China. During June-December 2005, adjusted sign averaged 46.3 (SaryChat), 94.6 (Jangart), and 150.8 (Tomur) occurrences/km. We used counts of ibex (Capra ibex) and argali (Ovis ammon) to estimate available prey biomass and subsequent potential snow leopard densities of 8.7 (SaryChat), 1.0 (Jangart), and 1.1 (Tomur) snow leopards/100 km². Photo capture-recapture density estimates were 0.15 (n = 1 identified individual/1 photo), 0.87 (n = 4/13), and 0.74 (n = 5/6) individuals/100 km² in SaryChat, Jangart, and Tomur, respectively. Photo-capture rates (photos/100 trap-nights) were 0.09 (SaryChat), 0.93 (Jangart), and 2.37 (Tomur). Genetic analysis of snow leopard fecal samples provided minimum population sizes of 3 (SaryChat), 5 (Jangart), and 9 (Tomur) snow leopards. These results suggest SLIMS sign surveys may be affected by observer bias and environmental variance. However, when such bias and variation are accounted for, sign surveys indicate relative abundances similar to photo rates and genetic individual identification results. Density or abundance estimates based on capture-recapture or ungulate biomass did not agree with other indices of abundance. Confidence in estimated densities, or even detection of significant changes in abundance of snow leopard, will require more effort and better documentation.