Find research datasets worth reusing

Data from: Immunoglobulin detection in wild birds: effectiveness of three secondary anti-avian IgY antibodies in direct ELISAs in 41 avian species

1.Immunological reagents for wild, non-model species are limited or often non-existent for many species. 2. In this study, we compare the reactivity of a new anti-passerine IgY secondary antibody with existing secondary antibodies developed for use with birds. Samples from 41 species from the following six avian orders were analysed: Anseriformes (1 family, 1 species), Columbiformes (1 family, 2 species), Galliformes (1 family, 1 species), Passeriformes (16 families, 34 species), Piciformes (1 family, 2 species) and Suliformes (1 family, 1 species). Direct ELISAs were performed to detect total IgY using goat anti-passerine IgY, goat anti-chicken IgY or goat anti-bird IgY secondary antibodies. 3.The anti-passerine antibody exhibited significantly higher IgY reactivity compared to the anti-chicken and/or anti-bird antibodies in 80% of the passerine families tested. Birds in the order Piciformes (woodpeckers) and order Suliformes (cormorants) were poorly detected by all three secondary antibodies. A comparison of serum and plasma IgY levels was made within the same individuals for two passerine species (house finch and white-crowned sparrow), and serum exhibited significantly more IgY than the plasma for all three secondary antibodies. This result indicates that serum may be preferred to plasma when measuring total antibody levels in blood. 4.This study indicates that the anti-passerine IgY secondary antibody can effectively be used in immunological assays to detect passerine IgY for species in most passerine families and is preferred over anti-chicken and anti-bird secondary antibodies for the majority of passerine species. This anti-passerine antibody will allow for more accurate detection and quantification of IgY in more wild bird species than was possible with previously available secondary antibodies.

Data from: Development and validation of a score to detect paroxysmal atrial fibrillation after stroke

Objective: Prolonged monitoring times (72h) are recommended to detect paroxysmal atrial fibrillation (pAF) after ischemic stroke, but not yet clinical practice; therefore, an individual patient selection for prolonged ECG monitoring might increase the diagnostic yield of pAF in a resource-saving manner. Methods: We used individual patient data from three prospective studies (ntotal=1556) performing prolonged Holter ECG monitoring (at least 72h) and centralized data evaluation after TIA or stroke in patients with sinus rhythm. Based on the TRIPOD guideline, a clinical score was developed on one cohort, internally validated by bootstrapping and externally validated on two other studies. Results: pAF was detected in 77 (4.9%) of 1556 patients during 72h-Holter monitoring. After logistic regression analysis with variable selection, age and the qualifying stroke event (categorised as stroke severity with NIH-SS≤5 (OR 2.4 vs. TIA; 95%CI0.8-6.9,p=0.112) or stroke with NIH-SS>5 (OR 7.2 vs. TIA; 95%CI 2.4-21.8,p<0.001)) were found to be predictive for the detection of pAF within 72h-Holter monitoring and included in the final score (Age: 0.76 points/year, Stroke Severity NIH-SS≤5 = 9 points, NIH-SS>5 = 21 points; to Find AF, AS5F). The high risk group defined by AS5F is characterized by a predicted risk between 5.2% and 40.8% for detection of pAF with a number needed to screen of 3 for the highest observed AS5F points within the study population. Regarding the low number of outcomes before generalization of AS5F the results need replication. Conclusion: The AS5F score can select patients for prolonged ECG monitoring after ischemic stroke to detect pAF.

Data from: High-throughput adaptive sampling for whole-slide histopathology image analysis (HASHI) via convolutional neural networks: application to invasive breast cancer detection

Precise detection of invasive cancer on whole-slide images (WSI) is a critical first step in digital pathology tasks of diagnosis and grading. Convolutional neural network (CNN) is the most popular representation learning method for computer vision tasks, which have been successfully applied in digital pathology, including tumor and mitosis detection. However, CNNs are typically only tenable with relatively small image sizes (200x200 pixels). Only recently, Fully convolutional networks (FCN) are able to deal with larger image sizes (500x500 pixels) for semantic segmentation. Hence, the direct application of CNNs to WSI is not computationally feasible because for a WSI, a CNN would require billions or trillions of parameters. To alleviate this issue, this paper presents a novel method, High-throughput Adaptive Sampling for whole-slide Histopathology Image analysis (HASHI), which involves: i) a new efficient adaptive sampling method based on probability gradient and quasi-Monte Carlo sampling, and, ii) a powerful representation learning classifier based on CNNs. We applied HASHI to automated detection of invasive breast cancer on WSI. HASHI was trained and validated using three different data cohorts involving near 500 cases and then independently tested on 195 studies from The Cancer Genome Atlas. The results show that (1) the adaptive sampling method is an effective strategy to deal with WSI without compromising prediction accuracy by obtaining comparative results of a dense sampling (~6 million of samples in 24 hours) with far fewer samples (~2,000 samples in 1 minute), and (2) on an independent test dataset, HASHI is effective and robust to data from multiple sites, scanners, and platforms, achieving an average Dice coefficient of 76%.

opencc-zeroDec 2014View details →

Data from: The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

Although genome scans have become a popular approach towards understanding the genetic basis of local adaptation, the field still does not have a firm grasp on how sampling design and demographic history affect the performance of genome scans on complex landscapes. To explore these issues, we compared 20 different sampling designs in equilibrium (i.e. island model and isolation by distance) and nonequilibrium (i.e. range expansion from one or two refugia) demographic histories in spatially heterogeneous environments. We simulated spatially complex landscapes, which allowed us to exploit local maxima and minima in the environment in 'pair' and 'transect' sampling strategies. We compared FST outlier and genetic–environment association (GEA) methods for each of two approaches that control for population structure: with a covariance matrix or with latent factors. We show that while the relative power of two methods in the same category (FST or GEA) depended largely on the number of individuals sampled, overall GEA tests had higher power in the island model and FST had higher power under isolation by distance. In the refugia models, however, these methods varied in their power to detect local adaptation at weakly selected loci. At weakly selected loci, paired sampling designs had equal or higher power than transect or random designs to detect local adaptation. Our results can inform sampling designs for studies of local adaptation and have important implications for the interpretation of genome scans based on landscape data.

opencc-zeroDec 2009View details →

Data from: Transgenes in Mexican maize: molecular evidence and methodological considerations for GMO detection in landrace populations

A possible consequence of planting GMOs in centers of crop origin is unintended gene flow into traditional landraces. In 2001, a study reported the presence of the transgenic 35S promoter in maize landraces sampled in 2000 from the Sierra Juarez of Oaxaca, Mexico. Analysis of a large sample taken from the same region in 2003 and 2004 could not confirm the existence of transgenes, thereby casting doubt on the earlier results. These two studies were based on different sampling and analytical procedures and are thus hard to compare. Here we present new molecular data for this region that confirm the presence of transgenes in three of 23 localities sampled in 2001. Transgene sequences were not detected in samples taken in 2002 from nine localities, while directed samples taken in 2004 from two of the positive 2001 localities were again found to contain transgenic sequences. These findings suggest the persistence or re-introduction of transgenes up until 2004 in this area. We address variability in recombinant sequence detection by analyzing the consistency of current molecular assays. We also present theoretical results on the limitations of estimating the probability of transgene detection in samples taken from landraces. The inclusion of a limited number of female gametes, but more importantly, aggregated transgene distributions may significantly lower detection probabilities. Our analytical and sampling considerations help explain discrepancies among different detection efforts, including the one presented here, and provide considerations for the establishment of monitoring protocols to detect the presence of transgenes among structured populations of landraces.

Data from: Detecting evolutionarily significant units above the species level using the Generalized Mixed Yule Coalescent method

1. There is renewed interest in inferring evolutionary history by modelling diversification rates using phylogenies. Understanding the performance of the methods used under different scenarios is essential for assessing empirical results. Recently we introduced a new approach for analysing broadscale diversity patterns, using the Generalized Mixed Yule Coalescent (GMYC) method to test for the existence of evolutionarily significant units above the species (higher ESUs). This approach focuses on identifying clades as well as estimating rates and we refer to it as clade-dependent. However, the ability of the GMYC to detect the phylogenetic signature of higher ESUs has not been fully explored, nor has it been placed in the context of other, clade-independent approaches. 2. We simulated >32,000 trees under two clade-independent models: constant-rate birth-death (CRBD) and variable-rate birth-death (VRBD), using parameter estimates from nine empirical trees and more general parameter values. The simulated trees were used to evaluate scenarios under which GMYC might incorrectly detect the presence of higher ESUs. 3. The GMYC null model was rejected at a high rate on CRBD-simulated trees. This would lead to spurious inference of higher ESUs. However, the support for the GMYC model was significantly greater in most of the empirical clades than expected under a CRBD process. Simulations with empirically derived parameter values could therefore be used to exclude CRBD as an explanation for diversification patterns. In contrast, a VRBD process could not be ruled out as an alternative explanation for the apparent signature of hESUs in the empirical clades, based on the GMYC method alone. Other metrics of tree shape, however, differed notably between the empirical and VRBD-simulated trees. These metrics could be used in future to distinguish clade-dependent and clade-independent models. 4. In conclusion, detection of higher ESUs using the GMYC is robust against some clade-independent models, as long as simulations are used to evaluate these alternatives, but not against others. The differences between clade-dependent and clade-independent processes are biologically interesting, but most current models focus on the latter. We advocate more research into clade-dependent models for broad diversity patterns.

opencc-zeroDec 2018View details →

Data from: Two-step pyrolysis-gas chromatography method with mass spectrometric detection for identification of tattoo ink ingredients and counterfeit products

Tattoo inks are complex mixtures of ingredients. Each of them possesses different chemical properties which have to be addressed upon chemical analysis. In this method for two-step pyrolysis online coupled to gas chromatography mass spectrometry (py-GC-MS) volatile compounds are analyzed during a first desorption run. In the second run, the same dried sample is pyrolyzed for analysis of non-volatile compounds such as pigments and polymers. These can be identified by their specific decomposition patterns. Additionally, this method can be used to differentiate original from counterfeit inks. Easy screening methods for data evaluation using the average mass spectra and self-made pyrolysis libraries are applied to speed up substance identification. Using specialized evaluation software for pyrolysis GS-MS data, a fast and reliable comparison of the full chromatogram can be achieved. Since GC-MS is used as separation technique, the method is limited to volatile substances upon desorption and after pyrolysis of the sample. The method can be applied for quick substance screening in market control surveys since it requires no sample preparation steps.

opencc-zeroDec 2010View details →

Data from: Environmental effects on the detection of adaptation

Detecting adaptation involves comparing the performance of populations evolving in different environments. This detection may be confounded by effects due to the environment experienced by organisms prior to the test. We tested whether such confounding effects occur, using spider-mite selection lines on two novel hosts and one ancestral host, after 15 generations of selection. Mites were either sampled directly from the selection lines, or subjected to a common juvenile or to a common maternal environment, mimicking the most frequent environmental manipulations. These environments strongly affected all life-history traits. Moreover, the detection of adaptation and of correlated responses on the ancestral host was inconsistent among environments in almost 20% of the cases. Indeed, we did not detect responses unambiguously for any life-history trait. This inconsistency was due to differential environmental effects on lines from different selection regimes. Therefore the detection of adaptation requires a careful control of these environmental effects.

Data from: Color pattern facilitates species recognition but not signal detection: a field test using robots

There are many factors that affect signal design, including the need for rapid signal detection and the ability to identify the signal as conspecific. Understanding these different sources of selection on signal design is essential to explain the evolution of both signal complexity and signal diversity. We assessed the relative importance of detection and recognition for signal design in the black-bearded gliding lizard, Draco melanopogon, which uses the extension and retraction of a large, black-and-white dewlap (or throat fan) in territorial communication. We presented free-living lizards with robots displaying dewlaps of different designs that varied in the proportion of the black and white components. We found no effect of dewlap brightness or design on the time it took for a lizard to detect the robot, consistent with the view that initial detection is likely to be primarily elicited by movement rather than specific color or pattern. However, males (but not females) responded with a greater intensity to the dewlap treatment that most resembled the natural dewlap color and design of the species. Furthermore, males were more likely to display to any dewlap color in the presence of a neighbor. These results suggest that dewlap pattern may play an important role in species recognition but has minimal influence on the initial detection of the signal. Importantly, our results also highlight that factors unrelated to discrimination, such as social cues and individual motivational state, may affect responses to species identity cues.

opencc-zeroDec 2018View details →

Data from: Optical coherence tomography is highly sensitive in detecting prior optic neuritis

Objective: To explore sensitivity of optical coherence tomography (OCT) in detecting prior unilateral optic neuritis. Methods: Retrospective, observational clinical study of all patients who presented from 1/1/14 to 6/1/17 with unilateral optic neuritis and OCT available at least three months after the attack. We compared OCT retinal nerve fiber layer (RNFL) and ganglion cell inner plexiform layer (GCIPL) thicknesses between affected and unaffected contralateral eyes. We excluded patients with concomitant glaucoma or other optic neuropathies. Based on analysis of normal controls, thinning was considered significant if RNFL was at least 9-µm or GCIPL was at least 6-µm less in affected eye compared to unaffected eye. Results: Fifty-one patients (18 male and 33 female) were included in the study. RNFL and GCIPL thicknesses were significantly lower in eyes with optic neuritis compared to unaffected eyes (p<0.001). RNFL was thinner by ≥9-µm in 73% of optic neuritis eyes compared to the unaffected eye. GCIPL was thinner by ≥6-µm in 96% of optic neuritis eyes. The sensitivity of OCT in detecting prior optic neuritis was 96% when using both average RNFL and GCIPL thicknesses. When using a threshold ≤1st percentile of age-matched controls, sensitivities were 37% for RNFL, 76% for GCIPL, and 78% for either GCIPL or RNFL thicknesses, each of which was lower than those calculated using the inter-eye difference as the threshold (p<0.05). Conclusions: OCT, especially in GCIPL, is a highly sensitive modality in detecting prior optic neuritis, which is made more robust by using inter-eye differences to approximate change.

Data from: Detection of SNPs based on transcriptome sequencing in Norway spruce (Picea abies (L.) Karst)

A novel set of SNPs was derived from transcriptome data of ten Norway spruce (Picea abies) trees from the Bavarian Forest National Park in Germany (BaFoNP). SNPs were identified by mapping against a de-novo transcriptome assembly and against pre-mRNAs of predicted genes of the reference genome assembly. This resulted in 111,849 and 366,577 SNPs, respectively. Out of these, 311 were either randomly selected or chosen because of their pronounced divergence between sampling sites and genotyped in 218 trees with an Illumina Infinium HD iSelect BeadChip.

Data from: Both trait-neutrality and filtering effects are validated by the vegetation patterns detected in the functional recovery of sand grasslands

Neutral theory of species assembly means that species assembly is governed by stochastic dispersal processes and fluctuations in established populations. An alternative theory suggests that assembly is strongly determined by functional trait filtering governed by abiotic and biotic filtering selecting species from the local species pool. To test these assumptions, in the current paper we analysed vegetation changes in the first 12 years of succession after heavy goose grazing on acidic sand. With trait-based analyses using permanent plots we addressed the following hypotheses: (i) High fluctuations in the trait values are typical in the first years; later a temporally divergent change in the trait patterns of sites with different vertical position became characteristic. (ii) In the functional diversity of regenerative and vegetative traits we expected different temporal patterns. We confirmed the first hypothesis, as in the first few years most traits displayed high fluctuations with no clear patterns. Our findings weakly supported the second hypothesis; while there were distinct patterns detected in the functional richness of traits, functional divergence and evenness displayed no clear distinctive patterns. We can conclude that both trait neutrality and filtering effects operate in the vegetation changes of the first period of secondary succession.

opencc-zeroDec 2016View details →

Data from: Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honeybee genome

Context-dependent gene expression in eukaryotes is controlled by several mechanisms including cytosine methylation that primarily occurs in the CG dinucleotides (CpGs). However, less frequent non-CpG asymmetric methylation has been found in various cell types, such as mammalian neurons, and recent results suggest that these sites can repress transcription independently of CpG contexts. In addition, an emerging view is that CpG hemimethylation may arise not only from deregulation of cellular processes but also be a standard feature of the methylome. Here, we have applied a novel approach to examine whether asymmetric CpG methylation is present in a sparsely methylated genome of the honeybee, a social insect with a high level of epigenetically driven phenotypic plasticity. By combining strand-specific ultra-deep amplicon sequencing of illustrator genes with whole-genome methylomics and bioinformatics, we show that rare asymmetrically methylated CpGs can be unambiguously detected in the honeybee genome. Additionally, we confirm differential methylation between two phenotypically and reproductively distinct castes, queens and workers, and offer new insight into the heterogeneity of brain methylation patterns. In particular, we challenge the assumption that symmetrical methylation levels reflect symmetry in the underlying methylation patterns and conclude that hemimethylation may occur more frequently than indicated by methylation levels. Finally, we question the validity of a prior study in which most of cytosine methylation in this species was reported to be asymmetric.

Data from: Detecting copper toxicity in sediments: from the sub-individual level to the population level

1.Sediments accumulate chemicals that can be toxic to biota and often contribute to aquatic ecosystem decline. Measuring mortality in laboratory-bred organisms is a common way to assess sediment toxicity. However, mortality-based responses of resilient laboratory organisms may not reflect indigenous macroinvertebrate responses, which can be relatively more sensitive to sediment toxicants. A possible solution is to also measure responses at the sub-individual level. 2.Several organism responses to sediment copper toxicity were assessed in a field-based microcosm. Responses of laboratory-bred chironomids and snails deployed in microcosms were compared at sub-individual (metabolomic and gene expression), individual (survival and dry weight) and population (reproduction) levels, and contrasted to the abundance of colonizing macroinvertebrates in the microcosms. 3.Colonizing macroinvertebrate abundance showed a range of sensitivities based on EC50 (effect dose 50% change). Chironomidae made up 94.5% of the microcosm macroinvertebrates, with Paratanytarsus the most sensitive genus (EC50: 89 mg/kg copper) and Procladius the least sensitive (EC50: 681 mg/kg). 4.Survival of laboratory-bred organisms was the least sensitive response, comparable to decreased abundance of the least sensitive macroinvertebrate. Juvenile production in the snail, Potamopyrgus antipodarum, was the most sensitive population level response (EC50: 121 mg/kg), in contrast the snail Physella acuta was relatively more tolerant (EC50: 298 mg/kg). 5.Changes in sub-individual responses (gene expression and metabolite abundance) in laboratory-bred chironomid, Chironomus tepperi, were evident at 60 mg/kg. These changes likely reflect the direct effects of copper exposure and represent metal-specific responses. 6.Synthesis and applications. We showed that copper toxicity in sediments could be readily detected through changes in gene expression and metabolites in laboratory-bred chironomids exposed in field-based microcosms. These responses were more sensitive than mortality, and detected copper levels that caused microcosm chironomid populations to decline. These novel approaches will provide managers with new tools to better assess sediment toxicity.

Data from: Detecting local diversity-dependence in diversification

Whether there are ecological limits to species diversification is a hotly debated topic. Molecular phylogenies show slowdowns in lineage accumulation, suggesting that speciation rates decline with increasing diversity. A maximum likelihood method to detect diversity-dependent diversification from phylogenetic branching times exists, but it assumes that diversity-dependence is a global phenomenon and therefore ignores that the underlying species interactions are mostly local, and not all species in the phylogeny co-occur locally. Here, we explore whether this maximum likelihood method based on the non-spatial diversity-dependence model can detect local diversity-dependence, by applying it to phylogenies, simulated with a spatial stochastic model of local-diversity-dependent speciation, extinction and dispersal between two local communities. We find that type I errors (falsely detecting diversity-dependence) are low, and the power to detect diversity-dependence is high when dispersal rates are not too low. Interestingly, when dispersal is high the power to detect diversity-dependence is even higher than in the non-spatial model. Moreover, estimates of intrinsic speciation rate, extinction rate and ecological limit strongly depend on dispersal rate. We conclude that the non-spatial diversity-dependent approach can be used to detect diversity-dependence in clades of species that live in not too disconnected areas, but parameter estimates must be interpreted cautiously.

opencc-zeroDec 2010View details →

Data from: More than meets the eye: detecting cryptic microgeographic population structure in a parasite with a complex life cycle

Nonrandom recruitment of parasites among hosts can lead to genetic differentiation among hosts and mating dynamics that promote inbreeding. It has been hypothesized that strictly aquatic parasites with intermediate hosts will behave as panmictic populations among hosts because ample opportunity exists for random mixing of unrelated individuals during transmission to the definitive host. A previous allozyme study on the marine trematode Lecithochirium fusiforme did not support this hypothesis in that there was genetic differentiation among, and significant heterozygote deficiencies within, definitive hosts. We revisit this system and use microsatellites to obtain multilocus genotypes. Our goal was to determine if cryptic subgroups and/or the presence of clones could account for the apparent deviation from 'panmixia'. We find strong evidence for cryptic subdivision (three genetic clusters) that causes the Wahlund effect and differentiation among definitive hosts. After accounting for these cryptic groups, we see panmictic genetic structure among definitive hosts that is consistent with the "high mixing in aquatic habitats" hypothesis. We see evidence for co-transmission of clones in all three clusters, but this level of clonal structure did not have a major impact in causing deviations from Hardy-Weinberg equilibrium, and only affected genetic differentiation among hosts in one cluster. A cursory examination of the data may have led to incorrect conclusions about non-random transmission. However, it is obvious in this system that there is more than meets the eye in relation to the actual makeup of parasite populations. In general, the methods we employ will be useful for elucidating hidden patterns in other organisms where cryptic structure may be common (e.g., those with limited morphology or complex life histories).

Data from: A lateral flow immunochromatographic strip test for rapid detection of hexoestrol in fish samples

A lateral flow immunochromatographic test strip was developed for on-site rapid and sensitive detection of Hexoestrol (HES) residues in fish samples with colloidal gold labeled the anti-HES monoclonal antibody (mAb). The strip is composed of a sample pad, a conjugate reagent pad, an absorbent pad, and a test membrane containing a control line and a test line. The sensitivity (half inhibitory concentration, IC50) of the strip in the detection of fish extract samples was confirmed to be 1.86 μg/kg, and the limit detection (LOD) value was 0.62 μg/kg. For intra-assay and inter-assay reproducibility, recoveries of HES spiked samples were ranged from 86.3% to 92.3% and 85.8% to 93.4%, coefficients of variation were 2.91-4.64% and 4.24-5.17% respectively. High-performance liquid chromatography (HPLC) was employed to confirm the performance of the strip. The strip test only took less than 10 minutes, and thus provides a repaid method for on-site detection of HES residues.

Data from: Identification and validation of single nucleotide polymorphisms as tools to detect hybridization and population structure in freshwater stingrays

Single nucleotide polymorphism (SNP) markers were identified and validated for two stingrays species, Potamotrygon motoro and Potamotrygon falkneri, using double digest restriction-site associated DNA (ddRAD) reads using 454-Roche technology. A total of 226 774 reads (65.5 Mb) were obtained (mean read length 289 ± 183 bp) detecting a total of 5399 contigs (mean contig length: 396 ± 91 bp). Mining this data set, a panel of 143 in silico SNPs was selected. Eighty-two of these SNPs were successfully validated and 61 were polymorphic: 14 in P. falkneri, 21 in P. motoro, 3 in both species and 26 fixed for alternative variants in both species, thus being useful for population analyses and hybrid detection.

opencc-zeroDec 2016View details →

Data from: Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill

Biomonitoring underpins the environmental assessment of freshwater ecosystems and guides management and conservation. Current methodology for surveys of (macro)invertebrates uses coarse taxonomic identification where species-level resolution is difficult to obtain. Next-generation sequencing of entire assemblages (metabarcoding) provides a new approach for species detection, but requires further validation. We used metabarcoding of invertebrate assemblages with two fragments of the cox1 "barcode" and partial nuclear ribosomal (SSU) genes, to assess the effects of a pesticide spill in the River Kennet (Southern England). Operational Taxonomic Unit (OTU) recovery was tested under72 parameters (read denoising, filtering, pair merging and clustering). Similar taxonomic profiles were obtained under a broad range of parameters. The SSU marker recovered Platyhelminthes and Nematoda, missed by cox1,while Rotifera were only amplified with cox1. A reference set was created from all available barcode entries for Arthropoda in the BOLD database and clustered into OTUs. The River Kennet metabarcoding produced matches to 207 of these reference OTUs, five times the number of species recognised with morphological monitoring. The increase was due to: greater taxonomic resolution (e.g. splitting a single morphotaxon 'Chironomidae' into 55 named OTUs); splitting of binomial species names into multiple molecular OTUs in species complexes; and the use of a filtration-flotation protocol for extraction of minute specimens (meiofauna). Community analyses revealed strong differences between "impacted" vs. "control" samples, detectable with each gene marker, for each major taxonomic group, and for meio- and macro-faunal samples separately. Thus, highly resolved taxonomic data can be extracted at a fraction of the time and cost of traditional non-molecular methods, opening new avenues for freshwater invertebrate biodiversity monitoring and molecular ecology.