sam is a Windows program designed to detect candidate loci for selection in whole-genome scans. It also gives valuable clues as regards the ecological factors at stake in the selection process. The ...method used is based on multiple univariate logistic regression models to test for association between allelic frequencies at marker loci and environmental variables. The software reads matrices constituted of presence/absence of molecular markers, and of the corresponding environmental parameters at sampling locations. It provides dynamic analysis tables to process the results. The tool is freely available for download at http://www.econogene.eu/software/sam/.
Life history changes may change resource use. Such shifts are not well understood in the dung beetles, despite recognised differences in larval and adult feeding ability. We use the flightless dung ...beetle Circellium bacchus to explore such shifts, identifying dung sources of adults using DNA metabarcoding, and comparing these with published accounts of larval dung sources. C. bacchus is traditionally considered to specialise on the dung of large herbivores for both larval and adult feeding. We successfully extracted mammal DNA from 151 adult C. bacchus fecal samples, representing 16 mammal species (ranging from elephants to small rodents), many of which are hitherto undescribed in the diet. Adult C. bacchus showed clear dung source preferences, especially for large herbivores inhabiting dense-cover vegetation. Our approach also confirmed the presence of cryptic taxa in the study area, and we propose that this may be used for biodiversity survey and monitoring purposes. Murid rodent feces were the most commonly fed-upon dung source (77.5 %) for adult C. bacchus, differing markedly from the large and megaherbivore dung sources used for larval rearing. These findings support the hypothesis of life history-specific shifts in resource use in dung beetles, and reveal a hitherto unsuspected, but ecologically important, role of these dung beetles in consuming rodent feces. The differences in feeding abilities of the larval and adult life history stages have profound consequences for their resource use and foraging strategies, and hence the ecological role of dung beetles. This principle and its ecological consequences should be explored in other scarabaeids.
Primary biogenic organic aerosols (PBOAs) represent a
major fraction of coarse organic matter (OM) in air. Despite their
implication in many atmospheric processes and human health problems, we
...surprisingly know little about PBOA characteristics (i.e., composition,
dominant sources, and contribution to airborne particles). In addition,
specific primary sugar compounds (SCs) are generally used as markers of PBOAs
associated with bacteria and fungi, but our knowledge of microbial
communities associated with atmospheric particulate matter (PM) remains
incomplete. This work aimed at providing a comprehensive understanding of
the microbial fingerprints associated with SCs in PM10 (particles
smaller than 10 µm) and their main sources in the surrounding
environment (soils and vegetation). An intensive study was conducted on
PM10 collected at a rural background site located in an agricultural area
in France. We combined high-throughput sequencing of bacteria and fungi with
detailed physicochemical characterizations of PM10, soil, and plant
samples and monitored meteorological and agricultural activities throughout
the sampling period. Results show that in summer SCs in PM10 are a
major contributor of OM in air, representing 0.8 % to 13.5 % of OM mass. SC
concentrations are clearly determined by the abundance of only a few
specific airborne fungal and bacterial taxa. The temporal fluctuations in the
abundance of only four predominant fungal genera, namely Cladosporium, Alternaria,
Sporobolomyces, and Dioszegia, reflect the
temporal dynamics in SC concentrations. Among bacterial taxa, the abundance
of only Massilia, Pseudomonas, Frigoribacterium, and Sphingomonas
is positively correlated with SC species. These
microbes
are significantly enhanced in leaf over soil samples. Interestingly, the
overall community structure of bacteria and fungi are similar within
PM10 and leaf samples and significantly distinct between PM10 and
soil samples, indicating that surrounding vegetation is the major source of
SC-associated microbial taxa in PM10 in this rural area of France.
Freshwater macroinvertebrates provide valuable indicators for biomonitoring ecosystem change in relation to natural and anthropogenic drivers. DNA metabarcoding is an efficient approach for ...estimating such indicators, but its results may differ from morphotaxonomic approaches traditionally used in biomonitoring. Here we test the hypothesis that despite differences in the number and identity of taxa recorded, both approaches may retrieve comparable patterns of community change, and detect similar ecological gradients influencing such changes. We compared results obtained with morphological identification at family level of macroinvertebrates collected at 80 streams under a Water Framework Directive biomonitoring program in Portugal, with results obtained with metabarcoding from the ethanol preserving the bulk samples, using either single (COI-M19BR2, 16S-Inse01, 18S-Euka02) or multiple markers. Metabarcoding recorded less families and different communities compared to morphotaxonomy, but community sensitivities to disturbance estimated with the IASPT index were more similar across approaches. Spatial variation in local community metrics and the factors influencing such variation were significantly correlated between morphotaxonomy and metabarcoding. After reducing random noise in the dissimilarity matrices, the spatial variation in community composition was also significantly correlated across methods. A dominant gradient of community change was consistently retrieved, and all methods identified a largely similar set of anthropogenic stressors strongly influencing such gradient. Overall, results confirm our initial hypothesis, suggesting that morphotaxonomy and metabarcoding can estimate consistent spatial patterns of community variation and their main drivers. These results are encouraging for macroinvertebrate biomonitoring using metabarcoding approaches, suggesting that they can be intercalibrated with morphotaxonomic approaches to recover equivalent spatial and temporal gradients of ecological change.
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•We described freshwater macroinvertebrate communities using morphotaxonomy and metabarcoding.•Local community metrics differed significantly between morphotaxonomy and metabarcoding.•Patterns of spatial variation in local community metrics were correlated between approaches.•Dominant community gradients and their ecological drivers were consistently estimated.•Morphotaxonomy and metabarcoding can be intercalibrated to detect equivalent ecological changes.
Summary
The development of terrestrial ecosystems depends greatly on plant mutualists such as mycorrhizal fungi. The global retreat of glaciers exposes nutrient‐poor substrates in extreme ...environments and provides a unique opportunity to study early successions of mycorrhizal fungi by assessing their dynamics and drivers.
We combined environmental DNA metabarcoding and measurements of local conditions to assess the succession of mycorrhizal communities during soil development in 46 glacier forelands around the globe, testing whether dynamics and drivers differ between mycorrhizal types.
Mycorrhizal fungi colonized deglaciated areas very quickly (< 10 yr), with arbuscular mycorrhizal fungi tending to become more diverse through time compared to ectomycorrhizal fungi. Both alpha‐ and beta‐diversity of arbuscular mycorrhizal fungi were significantly related to time since glacier retreat and plant communities, while microclimate and primary productivity were more important for ectomycorrhizal fungi. The richness and composition of mycorrhizal communities were also significantly explained by soil chemistry, highlighting the importance of microhabitat for community dynamics.
The acceleration of ice melt and the modifications of microclimate forecasted by climate change scenarios are expected to impact the diversity of mycorrhizal partners. These changes could alter the interactions underlying biotic colonization and belowground–aboveground linkages, with multifaceted impacts on soil development and associated ecological processes.
Primary Biogenic Organic Aerosols (PBOA) were recently shown to be produced by only a few types of microorganisms, emitted by the surrounding vegetation in the case of a regionally homogeneous field ...site. This study presents the first comprehensive description of the structure and main sources of airborne microbial communities associated with temporal trends in Sugar Compounds (SC) concentrations of PM
10
in 3 sites under a climatic gradient in France. By combining sugar chemistry and DNA Metabarcoding approaches, we intended to identify PM
10
-associated microbial communities and their main sources at three sampling-sites in France, under different climates, during the summer of 2018. This study accounted also for the interannual variability in summer airborne microbial community structure (bacteria and fungi only) associated with PM
10
-SC concentrations during a 2 consecutive years’ survey at one site. Our results showed that temporal changes in PM
10
-SC in the three sites are associated with the abundance of only a few specific taxa of airborne fungi and bacterial. These taxa differ significantly between the 3 climatic regions studied. The microbial communities structure associated with SC concentrations of PM
10
during a consecutive 2-year study remained stable in the rural area. Atmospheric concentration levels of PM
10
-SC species varied significantly between the 3 study sites, but with no clear difference according to site typology (rural vs. urban), suggesting that SC emissions are related to regional rather than local climatic characteristics. The overall microbial beta diversity in PM
10
samples is significantly different from that of the main vegetation around the urban sites studied. This indicates that the airborne microorganisms at these urban sites are not solely from the immediate surrounding vegetation, which contrasts with observations at the scale of a regionally homogeneous rural site in 2017. These results improve our understanding of the spatial behavior of tracers of PBOA emission sources, which need to be better characterized to further implement this important mass fraction of Organic Matter (OM) in Chemical Transport models (CTM).
The worldwide retreat of glaciers is causing a faster than ever increase in ice‐free areas that are leading to the emergence of new ecosystems. Understanding the dynamics of these environments is ...critical to predicting the consequences of climate change on mountains and at high latitudes. Climatic differences between regions of the world could modulate the emergence of biodiversity and functionality after glacier retreat, yet global tests of this hypothesis are lacking. Nematodes are the most abundant soil animals, with keystone roles in ecosystem functioning, but the lack of global‐scale studies limits our understanding of how the taxonomic and functional diversity of nematodes changes during the colonization of proglacial landscapes. We used environmental DNA metabarcoding to characterize nematode communities of 48 glacier forelands from five continents. We assessed how different facets of biodiversity change with the age of deglaciated terrains and tested the hypothesis that colonization patterns are different across forelands with different climatic conditions. Nematodes colonized ice‐free areas almost immediately. Both taxonomic and functional richness quickly increased over time, but the increase in nematode diversity was modulated by climate, so that colonization started earlier in forelands with mild summer temperatures. Colder forelands initially hosted poor communities, but the colonization rate then accelerated, eventually leveling biodiversity differences between climatic regimes in the long term. Immediately after glacier retreat, communities were dominated by colonizer taxa with short generation time and r‐ecological strategy but community composition shifted through time, with increased frequency of more persister taxa with K‐ecological strategy. These changes mostly occurred through the addition of new traits instead of their replacement during succession. The effects of local climate on nematode colonization led to heterogeneous but predictable patterns around the world that likely affect soil communities and overall ecosystem development.
The worldwide retreat of glaciers is expanding ice‐free areas, creating new ecosystems. Our global‐scale study reveals that deglaciation is followed by heterogeneous but predictable soil colonization dynamics by nematodes, depending on local climates. Cold forelands initially hosted limited biodiversity, but here the colonization rate was higher, so that in the long term (after ~150 years) biodiversity equalized that of mild climates, where the colonization started earlier. Nematode communities experienced functional changes involving a shift from communities dominated by fast‐reproducing taxa (r‐ecological strategy) to an increased frequency of more persister taxa (K‐strategy) during colonization.
Despite numerous studies suggesting that amphibians are highly sensitive to cumulative anthropogenic stresses, the role pollutants play in the decline of amphibian populations remains unclear. ...Amongst the most common aquatic contaminants, polycyclic aromatic hydrocarbons (PAHs) have been shown to induce several adverse effects on amphibian species in the larval stages. Conversely, adults exposed to high concentrations of the ubiquitous PAH, benzoapyrene (BaP), tolerate the compound thanks to their highly efficient hepatic detoxification mechanisms. Due to this apparent lack of toxic effect on adults, no studies have examined in depth the potential toxicological impact of PAH on the physiology of adult amphibian livers. This study sheds light on the hepatic responses of Xenopus tropicalis when exposed to high environmentally relevant concentrations of BaP, by combining a high throughput transcriptomic approach (mRNA deep sequencing) and a characterization of cellular and physiological modifications to the amphibian liver.
Transcriptomic changes observed in BaP-exposed Xenopus were further characterized using a time-dependent enrichment analysis, which revealed the pollutant-dependent gene regulation of important biochemical pathways, such as cholesterol biosynthesis, insulin signaling, adipocytokines signaling, glycolysis/gluconeogenesis and MAPK signaling. These results were substantiated at the physiological level with the detection of a pronounced metabolic disorder resulting in a possible insulin resistance-like syndrome phenotype. Hepatotoxicity induced by lipid and cholesterol metabolism impairments was clearly identified in BaP-exposed individuals.
Our data suggested that BaP may disrupt overall liver physiology, and carbohydrate and cholesterol metabolism in particular, even after short-term exposure. These results are further discussed in terms of how this deregulation of liver physiology can lead to general metabolic impairment in amphibians chronically exposed to contaminants, thereby illustrating the role xenobiotics might play in the global decline in amphibian populations.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Despite the intensive use of Bacillus thuringiensis israelensis (Bti) toxins for mosquito control, little is known about the long term effect of exposure to this cocktail of toxins on target mosquito ...populations. In contrast to the many cases of resistance to Bacillus thuringiensis Cry toxins observed in other insects, there is no evidence so far for Bti resistance evolution in field mosquito populations. High fitness costs measured in a Bti selected mosquito laboratory strain suggest that evolving resistance to Bti is costly. The aim of the present study was to identify transcription level and polymorphism variations associated with resistance to Bti toxins in the dengue vector Aedes aegypti. We used RNA sequencing (RNA-seq) for comparing a laboratory-selected strain showing elevated resistance to Bti toxins and its parental non-selected susceptible strain. As the resistant strain displayed two marked larval development phenotypes (slow and normal), each phenotype was analyzed separately in order to evidence potential links between resistance mechanisms and mosquito life-history traits.
A total of 12,458 genes were detected of which 844 were differentially transcribed between the resistant and susceptible strains. Polymorphism analysis revealed a total of 68,541 SNPs of which 12,571 SNPs exhibited more than 40% frequency difference between the resistant and susceptible strains, affecting 2,953 genes. Bti resistance is associated with changes in the transcription level of enzymes involved in detoxification and chitin metabolism. Among previously described Bti-toxin receptors, four alkaline phosphatases (ALPs) were differentially transcribed between resistant and susceptible larvae, and non-synonymous changes affected the protein sequence of one cadherin, six aminopeptidases (APNs) and four α-amylases. Other putative Cry receptors located in lipid rafts, such as flotillin and glycoside hydrolases, were under-transcribed and/or contained non-synonymous substitutions. Finally, immunity-related genes showed contrasted transcription and polymorphisms patterns between the two developmental resistant phenotypes, suggesting the existence of trade-offs between Bti-resistance, life-history traits and immunity.
The present study is the first to analyze the whole transcriptome of Bti-resistant mosquitoes by RNA-seq, shedding light on the importance of studying both transcription levels and sequence polymorphism variations to get a comprehensive view of insecticide resistance.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, ...empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, with high levels of adaptive evolution in Drosophila, bacteria, and viruses but very little evidence of widespread adaptive evolution in hominids. Although estimates in plants are more limited, some recent work has suggested that rates of adaptive evolution in a range of plant taxa are surprisingly low and that there is little association between adaptive evolution and effective population size in contrast to patterns seen in other taxa. Here, we analyze data from 35 loci for six sunflower species that vary dramatically in effective population size. We find that rates of adaptive evolution are positively correlated with effective population size in these species, with a significant fraction of amino acid substitutions driven by positive selection in the species with the largest effective population sizes but little or no evidence of adaptive evolution in species with smaller effective population sizes. Although other factors likely contribute as well, in sunflowers effective population size appears to be an important determinant of rates of adaptive evolution.
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