Responses of multiple structural and functional indicators along three contrasting disturbance gradients

Ecosystem functioning and community structure are recognized as key components of ecosystem integrity, but comprehensive, standardized studies of the responses of both structural and functional indicators to different types of anthropogenic pressures remain rare. Consequently, we lack an empirical basis for (i) identifying when monitoring ecosystem structure alone misses important changes in ecosystem functioning, (ii) recommending sets of structural and functional metrics best suited for detecting ecological change driven by different anthropogenic pressures, and (iii) understanding the cumulative effects of multiple, co-occurring stressors on structure and function. We investigated variation in community structure and ecosystem functioning of stream ecosystems along three gradients (10-16 independent stream sites each) of increasing impact arising from agriculture, forestry and river regulation for hydropower, respectively. For each stream, we quantified variation in (i) the abiotic environment, (ii) community composition of four organism groups and (iii) three basal ecosystem processes underpinning carbon and nutrient cycling in streams. We assessed the responsiveness of multiple biodiversity, community structure and ecosystem functioning indicators based on variance explained and effect size metrics. Along a gradient of increasing agricultural impact, diatoms and fish were the most responsive groups overall, but significant variation was detected in at least one aspect of community composition, abundance and/ or biodiversity of every organism group . In contrast, most of our functional metrics did not vary significantly along the agricultural gradient, possibly due to contrasting, antagonistic effects of increasing nutrient concentrations and turbidity on ecosystem process rates. The exception was detritivore-mediated litter decomposition which increased up to moderate levels of nutrient. Impacts of river regulation were most marked for diatoms, which were responsive to both increasingly frequent hydropeaking and to increasing seasonal river regulation. Among functional indicators, both litter decomposition and algal biomass accrual declined significantly with increasing hydropeaking. Few structural or functional metrics varied with forest management, with macroinvertebrate diversity increasing along the forestry gradient, as did algal and fungal biomass accrual. Together, these findings highlight the challenges of making inferences about the impacts of anthropogenic disturbances at the ecosystem level based on community data alone, and pinpoint the need to identify optimal sets of functional and structural indicators best suited for detecting ecological changes associated with different human activities

Responses of multiple structural and functional indicators along three contrasting disturbance gradients

Ecosystem functioning and community structure are recognized as key components of ecosystem integrity, but comprehensive, standardized studies of the responses of both structural and functional indicators to different types of anthropogenic pressures remain rare. Consequently, we lack an empirical basis for (i) identifying when monitoring ecosystem structure alone misses important changes in ecosystem functioning, (ii) recommending sets of structural and functional metrics best suited for detecting ecological change driven by different anthropogenic pressures, and (iii) understanding the cumulative effects of multiple, co-occurring stressors on structure and function. We investigated variation in community structure and ecosystem functioning of stream ecosystems along three gradients (10–16 independent stream sites each) of increasing impact arising from agriculture, forestry and river regulation for hydropower, respectively. For each stream, we quantified variation in (i) the abiotic environment, (ii) community composition of four organism groups and (iii) three basal ecosystem processes underpinning carbon and nutrient cycling in streams. We assessed the responsiveness of multiple biodiversity, community structure and ecosystem functioning indicators based on variance explained and effect size metrics. Along a gradient of increasing agricultural impact, diatoms and fish were the most responsive groups overall, but significant variation was detected in at least one aspect of community composition, abundance and/ or biodiversity of every organism group . In contrast, most of our functional metrics did not vary significantly along the agricultural gradient, possibly due to contrasting, antagonistic effects of increasing nutrient concentrations and turbidity on ecosystem process rates. The exception was detritivore-mediated litter decomposition which increased up to moderate levels of nutrient. Impacts of river regulation were most marked for diatoms, which were responsive to both increasingly frequent hydropeaking and to increasing seasonal river regulation. Among functional indicators, both litter decomposition and algal biomass accrual declined significantly with increasing hydropeaking. Few structural or functional metrics varied with forest management, with macroinvertebrate diversity increasing along the forestry gradient, as did algal and fungal biomass accrual. Together, these findings highlight the challenges of making inferences about the impacts of anthropogenic disturbances at the ecosystem level based on community data alone, and pinpoint the need to identify optimal sets of functional and structural indicators best suited for detecting ecological changes associated with different human activities

Evolutionary Relationships of Ljungan Virus Variants Circulating in Multi-Host Systems across Europe

The picornavirus named ‘Ljungan virus’ (LV, species Parechovirus B) has been detected in a dozen small mammal species from across Europe, but detailed information on its genetic diversity and host specificity is lacking. Here, we analyze the evolutionary relationships of LV variants circulating in free-living mammal populations by comparing the phylogenetics of the VP1 region (encoding the capsid protein and associated with LV serotype) and the 3Dpol region (encoding the RNA polymerase) from 24 LV RNA-positive animals and a fragment of the 5′ untranslated region (UTR) sequence (used for defining strains) in sympatric small mammals. We define three new VP1 genotypes: two in bank voles (Myodes glareolus) (genotype 8 from Finland, Sweden, France, and Italy, and genotype 9 from France and Italy) and one in field voles (Microtus arvalis) (genotype 7 from Finland). There are several other indications that LV variants are host-specific, at least in parts of their range. Our results suggest that LV evolution is rapid, ongoing and affected by genetic drift, purifying selection, spillover and host evolutionary history. Although recent studies suggest that LV does not have zoonotic potential, its widespread geographical and host distribution in natural populations of well-characterized small mammals could make it useful as a model for studying RNA virus evolution and transmission

Evolutionary Relationships of Ljungan Virus Variants Circulating in Multi-Host Systems across Europe

The picornavirus named ‘Ljungan virus’ (LV, species Parechovirus B) has been detected in a dozen small mammal species from across Europe, but detailed information on its genetic diversity and host specificity is lacking. Here, we analyze the evolutionary relationships of LV variants circulating in free-living mammal populations by comparing the phylogenetics of the VP1 region (encoding the capsid protein and associated with LV serotype) and the 3Dpol region (encoding the RNA polymerase) from 24 LV RNA-positive animals and a fragment of the 5′ untranslated region (UTR) sequence (used for defining strains) in sympatric small mammals. We define three new VP1 genotypes: two in bank voles (Myodes glareolus) (genotype 8 from Finland, Sweden, France, and Italy, and genotype 9 from France and Italy) and one in field voles (Microtus arvalis) (genotype 7 from Finland). There are several other indications that LV variants are host-specific, at least in parts of their range. Our results suggest that LV evolution is rapid, ongoing and affected by genetic drift, purifying selection, spillover and host evolutionary history. Although recent studies suggest that LV does not have zoonotic potential, its widespread geographical and host distribution in natural populations of well-characterized small mammals could make it useful as a model for studying RNA virus evolution and transmission

Geographical Distribution and Genetic Diversity of Bank Vole Hepaciviruses in Europe

The development of new diagnostic methods resulted in the discovery of novel hepaciviruses in wild populations of the bank vole (Myodes glareolus, syn. Clethrionomys glareolus). The naturally infected voles demonstrate signs of hepatitis similar to those induced by hepatitis C virus (HCV) in humans. The aim of the present research was to investigate the geographical distribution of bank vole-associated hepaciviruses (BvHVs) and their genetic diversity in Europe. Real-time reverse transcription polymerase chain reaction (RT-qPCR) screening revealed BvHV RNA in 442 out of 1838 (24.0%) bank voles from nine European countries and in one of seven northern red-backed voles (Myodes rutilus, syn. Clethrionomys rutilus). BvHV RNA was not found in any other small mammal species (n = 23) tested here. Phylogenetic and isolation-by-distance analyses confirmed the occurrence of both BvHV species (Hepacivirus F and Hepacivirus J) and their sympatric occurrence at several trapping sites in two countries. The broad geographical distribution of BvHVs across Europe was associated with their presence in bank voles of different evolutionary lineages. The extensive geographical distribution and high levels of genetic diversity of BvHVs, as well as the high population fluctuations of bank voles and occasional commensalism in some parts of Europe warrant future studies on the zoonotic potential of BvHVs.Peer reviewe

Genetic analysis of global faba bean diversity, agronomic traits and selection signatures

Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for sustainable protein production. However, little is known about the genetics underlying trait diversity. In this study, we used 21,345 high-quality SNP markers to genetically characterize 2678 faba bean genotypes. We performed genome-wide association studies of key agronomic traits using a seven-parent-MAGIC population and detected 238 significant marker-trait associations linked to 12 traits of agronomic importance. Sixty-five of these were stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identified three subpopulations differentiated by geographical origin and 33 genomic regions subjected to strong diversifying selection between subpopulations. We found that SNP markers associated with the differentiation of northern and southern accessions explained a significant proportion of agronomic trait variance in the seven-parent-MAGIC population, suggesting that some of these traits were targets of selection during breeding. Our findings point to genomic regions associated with important agronomic traits and selection, facilitating faba bean genomics-based breeding

Cancer Biomarker Discovery: The Entropic Hallmark

Background: It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings: Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance: We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-throughput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe