79 research outputs found
A spatial fingerprint of land-water linkage of biodiversity uncovered by remote sensing and environmental DNA
Aquatic and terrestrial ecosystems are tightly connected via spatial flows of organisms and resources. Such land-water linkages integrate biodiversity across ecosystems and suggest a spatial association of aquatic and terrestrial biodiversity. However, knowledge about the extent of this spatial association is limited. By combining satellite remote sensing (RS) and environmental DNA (eDNA) extraction from river water across a 740-km2 mountainous catchment, we identify a characteristic spatial land-water fingerprint. Specifically, we find a spatial association of riverine eDNA diversity with RS spectral diversity of terrestrial ecosystems upstream, peaking at a 400 m distance yet still detectable up to a 2.0 km radius. Our findings show that biodiversity patterns in rivers can be linked to the functional diversity of surrounding terrestrial ecosystems and provide a dominant scale at which these linkages are strongest. Such spatially explicit information is necessary for a functional understanding of land-water linkages
Diversity and distribution of freshwater amphipod species in Switzerland (Crustacea: Amphipoda).
Amphipods are key organisms in many freshwater systems and contribute substantially to the diversity and functioning of macroinvertebrate communities. Furthermore, they are commonly used as bioindicators and for ecotoxicological tests. For many areas, however, diversity and distribution of amphipods is inadequately known, which limits their use in ecological and ecotoxicological studies and handicaps conservation initiatives. We studied the diversity and distribution of amphipods in Switzerland (Central Europe), covering four major drainage basins, an altitudinal gradient of>2,500 m, and various habitats (rivers, streams, lakes and groundwater). We provide the first provisional checklist and detailed information on the distribution and diversity of all amphipod species from Switzerland. In total, we found 29 amphipod species. This includes 16 native and 13 non-native species, one of the latter (Orchestia cavimana) reported here for the first time for Switzerland. The diversity is compared to neighboring countries. We specifically discuss species of the genus Niphargus, which are often receiving less attention. We also found evidence of an even higher level of hidden diversity, and the potential occurrence of further cryptic species. This diversity reflects the biogeographic past of Switzerland, and suggests that amphipods are ideally suited to address questions on endemism and adaptive radiations, post-glaciation re-colonization and invasion dynamics as well as biodiversity-ecosystem functioning relationships in aquatic systems
Environmental DNA metabarcoding:Transforming how we survey animal and plant communities
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing (?HTS?) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed ?environmental DNA? or ?eDNA?). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called ?eDNA metabarcoding? and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity educationpublishersversionPeer reviewe
Mapping biodiversity hotspots of fish communities in subtropical streams through environmental DNA.
Large tropical and subtropical rivers are among the most biodiverse ecosystems worldwide, but also suffer from high anthropogenic pressures. These rivers are hitherto subject to little or no routine biomonitoring, which would be essential for identification of conservation areas of high importance. Here, we use a single environmental DNA multi-site sampling campaign across the 200,000 km2 Chao Phraya river basin, Thailand, to provide key information on fish diversity. We found a total of 108 fish taxa and identified key biodiversity patterns within the river network. By using hierarchical clustering, we grouped the fish communities of all sites across the catchment into distinct clusters. The clusters not only accurately matched the topology of the river network, but also revealed distinct groups of sites enabling informed conservation measures. Our study reveals novel opportunities of large-scale monitoring via eDNA to identify relevant areas within whole river catchments for conservation and habitat protection
Non-parametric foreground subtraction for 21cm epoch of reionization experiments
An obstacle to the detection of redshifted 21cm emission from the epoch of
reionization (EoR) is the presence of foregrounds which exceed the cosmological
signal in intensity by orders of magnitude. We argue that in principle it would
be better to fit the foregrounds non-parametrically - allowing the data to
determine their shape - rather than selecting some functional form in advance
and then fitting its parameters. Non-parametric fits often suffer from other
problems, however. We discuss these before suggesting a non-parametric method,
Wp smoothing, which seems to avoid some of them. After outlining the principles
of Wp smoothing we describe an algorithm used to implement it. We then apply Wp
smoothing to a synthetic data cube for the LOFAR EoR experiment. The
performance of Wp smoothing, measured by the extent to which it is able to
recover the variance of the cosmological signal and to which it avoids leakage
of power from the foregrounds, is compared to that of a parametric fit, and to
another non-parametric method (smoothing splines). We find that Wp smoothing is
superior to smoothing splines for our application, and is competitive with
parametric methods even though in the latter case we may choose the functional
form of the fit with advance knowledge of the simulated foregrounds. Finally,
we discuss how the quality of the fit is affected by the frequency resolution
and range, by the characteristics of the cosmological signal and by edge
effects.Comment: 15 pages, 12 figures; lengthened and two figures added, to match
version accepted by MNRA
Using eDNA to detect the distribution and density of invasive crayfish in the Honghe-Hani rice terrace World Heritage site
The Honghe-Hani landscape in China is a UNESCO World Natural Heritage site due to the beauty of its thousands of rice terraces, but these structures are in danger from the invasive crayfish Procambarus clarkii. Crayfish dig nest holes, which collapse terrace walls and destroy rice production. Under the current control strategy, farmers self-report crayfish and are issued pesticide, but this strategy is not expected to eradicate the crayfish nor to prevent their spread since farmers are not able to detect small numbers of crayfish. Thus, we tested whether environmental DNA (eDNA) from paddy-water samples could provide a sensitive detection method. In an aquarium experiment, Real-time Quantitative polymerase chain reaction (qPCR) successfully detected crayfish, even at a simulated density of one crayfish per average-sized paddy (with one false negative). In a field test, we tested eDNA and bottle traps against direct counts of crayfish. eDNA successfully detected crayfish in all 25 paddies where crayfish were observed and in none of the 7 paddies where crayfish were absent. Bottle-trapping was successful in only 68% of the crayfish-present paddies. eDNA concentrations also correlated positively with crayfish counts. In sum, these results suggest that single samples of eDNA are able to detect small crayfish populations, but not perfectly. Thus, we conclude that a program of repeated eDNA sampling is now feasible and likely reliable for measuring crayfish geographic range and for detecting new invasion fronts in the Honghe Hani landscape, which would inform regional control efforts and help to prevent the further spread of this invasive crayfish
Imaging neutral hydrogen on large-scales during the Epoch of Reionization with LOFAR
The first generation of redshifted 21 cm detection experiments, carried out
with arrays like LOFAR, MWA and GMRT, will have a very low signal-to-noise
ratio per resolution element (\sim 0.2). In addition, whereas the variance of
the cosmological signal decreases on scales larger than the typical size of
ionization bubbles, the variance of the formidable galactic foregrounds
increases, making it hard to disentangle the two on such large scales. The poor
sensitivity on small scales on the one hand, and the foregrounds effect on
large scales on the other hand, make direct imaging of the Epoch of
Reionization of the Universe very difficult, and detection of the signal
therefore is expected to be statistical.Despite these hurdles, in this paper we
argue that for many reionization scenarios low resolution images could be
obtained from the expected data. This is because at the later stages of the
process one still finds very large pockets of neutral regions in the IGM,
reflecting the clustering of the large-scale structure, which stays strong up
to scales of \sim 120 comoving Mpc/h (\sim 1 degree). The coherence of the
emission on those scales allows us to reach sufficient S/N (\sim 3) so as to
obtain reionization 21 cm images. Such images will be extremely valuable for
answering many cosmological questions but above all they will be a very
powerful tool to test our control of the systematics in the data. The existence
of this typical scale (\sim 120 comoving Mpc/h) also argues for designing
future EoR experiments, e.g., with SKA, with a field of view of at least 4
degree.Comment: Replaced with final version (minor changes), 9 figures, 11 pages,
accepted for publication in MNRA
Optimising sampling and analysis protocols in environmental DNA studies
Ecological surveys risk incurring false negative and false positive detections of the target species. With indirect survey methods, such as environmental DNA, such error can occur at two stages: sample collection and laboratory analysis. Here we analyse a large qPCR based eDNA data set using two occupancy models, one of which accounts for false positive error by Griffin et al. (2020), and a second that assumes no false positive error by Stratton et al. (2020). Additionally, we apply the Griffin et al. (2020) model to simulated data to determine optimal levels of replication at both sampling stages. The Stratton et al. (2020) model, which assumes no false positive results, consistently overestimated both overall and individual site occupancy compared to both the Griffin et al. (2020) model and to previous estimates of pond occupancy for the target species. The inclusion of replication at both stages of eDNA analysis (sample collection and in the laboratory) reduces both bias and credible interval width in estimates of both occupancy and detectability. Even the collection of >1 sample from a site can improve parameter estimates more than having a high number of replicates only within the laboratory analysis
Malariaprophylaxe und Selbsttherapie 1990 - Probleme und aktuelle Lösungen
For successful malaria prophylaxis, future travelers need to be informed about the risks of infection and about systematic measures to be taken against mosquito bites. For visits in areas of high transmission, continuous chemoprophylaxis is recommended, whereas in regions with low transmission a stand-by medication for self-therapy is sufficient. Each of these four measures has some problems which are discussed here in addition to the recently published recommendations by the Swiss Working Group for Medical Advice to Travelers
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