Miracle-dz/UniFAR-FTUs huggingface dataset:
Lost in Translation: population genomics of porcini (Boletus edulis) challenges use of ITS for DNA barcoding in Fungi

Abstract The internal transcribed spacers (ITS) of the rDNA cistron are the most commonly used DNA barcoding region in Fungi [1]. rDNA genes are repeated dozens to hundreds of times in the eukaryotic genome [2] and it is believed that these arrays are homogenized through concerted evolution [3, 4] preventing the accumulation of intragenomic, and intraspecific, variation. However, numerous studies have reported rampant intragenomic and intraspecific ITS variation [5–11], contradicting our current understanding of concerted evolution. Here we show that in Boletus edulis Bull., ITS intragenomic variation persists at low allele frequencies throughout the rDNA array, this variation does not correlate with genomic relatedness between populations, and rDNA genes may not evolve in a strictly concerted fashion despite the presence of unequal recombination and gene conversion. Under normal assumptions, heterozygous positions found in ITS sequences represent hybridization between populations, yet through allelic mapping of the rDNA array we found numerous heterozygous alleles to be stochastically introgressed throughout, presenting a dishonest signal of gene flow. Moreover, despite the signal of gene flow in ITS, our organisms were highly inbred, indicating a disconnect between true gene flow and barcoding signals. In addition, we showed that the mechanisms of concerted evolution are ongoing in pseudo-heterozygous individuals, yet are not homogenizing the ITS array. Concerted evolution of the rDNA array may insufficiently homogenize the ITS gene, allowing for misleading signals of gene flow to persist, vastly complicating the use of the ITS locus for DNA barcoding in Fungi.
Role of the α5β1 Integrin Receptor in the Proliferative Response of Quiescent Human Melanoma Cells to Fibronectin

The possible mitogenic activity of fibronectin (FN) in human primary and metastatic melanoma lines and clones and the involvement of integrins in mediating this effect were evaluated. Quiescent human melanoma cells cultured in serum-free medium proliferated in a dose- and time-dependent fashion to immobilized FN as indicated by [3H]thymidine incorporation, increment of cell number, and cell cycle analysis. This response to FN was observed with tumor clones isolated from a subcutaneous metastasis and with primary or metastatic melanomas from different patients, but only when tumor cells expressed the α5 subunit of the FN receptor ( i.e. , VLA-5). Proliferation to FN by a primary tumor (Me4405) expressing all FN receptors and by a tumor clone (2/60) lacking only the α4 subunit was inhibited by monoclonal antibodies to the α5 and β1 but not by monoclonal antibodies to other subunits of FN receptors. Mapping of FN regions responsible for the proliferative signal was performed by stimulating melanoma cells with different FN proteolytic fragments and indicated that a significant mitogenic signal was provided by the M r 120,000 α-chymotrypsin fragment containing the Arg-Gly-Asp sequence. The proliferation of melanoma cells to FN and to FN fragments was also significantly inhibited by peptides containing the Arg-Gly-Asp sequence. These data indicate that FN can stimulate the proliferation of quiescent melanoma cells and that integrins as α5β1 are involved in the response of tumor cells to this extracellular matrix protein.
Taxonomy and Geography of Sphagnum tundrae With a Description of S. mirum, sp. nov. (Sphagnaceae, sect. Squarrosa)

Abstract Sphagnum tundrae (sect. Squarrosa) is reported new to arctic North America and eastern Russia. This species was recently described from Svalbard, arctic Norway, and has until now not been reported from other areas. It is argued, that it reached Svalbard in early/middle Holocene by long distance chance dispersal through icerafting diaspores following main Arctic Ocean currents from arctic Eurasian sources. Supposedly closely related to S. teres, the distinctness of the gene pools of those two species is evaluated through isozyme analysis of a mixed population, as well as small samples from three other S. tundrae sites and two sites with S. teres populations from Svalbard. Fifteen putative enzyme loci were screened. Very little intraspecific genetic diversity was detected. Sphagnum tundrae was monomorphic throughout the four populations studied, whereas S. teres had three haplotypes. The mean genetic identity (Nei 1978) among populations of S. tundrae and S. teres in this sample from Svalbard was calculated as 0.525, which is in concordance with values obtained among other Sphagnum species. Sphagnum mirum is described as a new species from subarctic Alaska, differing in essential morphological characteristics from the related S. teres and S. tundrae. Morphological variation in mixed stands of S. mirum and S. teres from the type locality clearly demonstrates its specific distinctness in qualitative as well as quantitative characteristics.
Isolation of microsatellite loci and cross‐species amplifications in three gobiid fish of the genus Pomatoschistus

Gobiids of the genus Pomatoschistus are increasingly being investigated as models for adaptation to coastal environments and for mating system studies. Among the dozen currently analysed species, microsatellite primers have been characterized only for Pomatoschistus minutus. This paper describes seven new polymorphic loci isolated from Pomatoschistus marmoratus and Pomatoschistus microps, two species that hybridize. Cross-species amplification was tested for these new loci, together with seven already published P. minutus loci. Systematic amplification of samples of each of the three species provided a first indication of their polymorphism.
DNA Relatedness among Verticil-Forming Streptomyces Species (Formerly Streptoverticillium Species)

Levels of DNA relatedness among 35 strains of Streptomyces species originally classified in the genus Streptoverticillium were determined spectrophotometrically. These strains represent eight of the phenotypic cluster groups described for the genus Streptoverticillium in Bergey's Manual of Systematic Bacteriology. Average linkage clustering of the DNA relatedness data resulted in 20 clusters including 13 single-member clusters, at a level of relatedness of >70%. Several species could be reduced to synonymy on the basis of DNA homology data, but these taxa were not generally equivalent to the clusters suggested by phenotypic numerical taxonomy data.
Effects of a Visual Barrier Fence on Behavior and Movements of Black-Tailed Prairie Dogs

Abstract Prairie dogs (Cynomys spp.) prefer an open view of their surroundings and may abandon areas with visual obstructions. Wildlife managers have attempted to capitalize on this innate behavior by using visual barriers, with varying degrees of success, to induce black-tailed prairie dogs (C. ludovicianus) to emigrate from or abandon a colony or preclude them from colonizing a valued area. We examined the behavior and movements of adult female black-tailed prairie dogs in response to both a visual barrier (SB Tensar® snowfence, Tensar Polytechnologies, Morrow, Georgia) that had a see-through visibility of 60% and no visual barrier on 4 6- to 15-ha colonies in central Nebraska, USA. We applied visual barriers to the centerline of 2 colonies after depopulation of half of each colony. Prairie dogs did not respond to the visual barriers as expected. They did not consistently increase the frequency of vigilant or aggressive behavior, the size of use-areas, or the distance of their use-areas from the visual barriers. The number of prairie dogs within 50 m of visual barrier fences did not decline over a 2-month period. Surprisingly, frequency of foraging behavior increased for prairie dogs in the vicinity of a visual barrier. The SB Tensar snowfence was durable but was not effective as a visual barrier for controlling the behavior, movements, and population of black-tailed prairie dogs.
Climate change predicted to cause severe increase of organic carbon in lakes

Riverine transport of organic carbon (OC) to the ocean is a significant component in the global carbon (C) cycle and the concentration of total organic carbon (TOC) in rivers and lakes is vital for ecosystem properties and water quality for human use. By use of a large dataset comprising chemical variables and detailed catchment information in ∼1000 Norwegian pristine lakes covering a wide climatic range, we were able to predict TOC concentrations with high accuracy. We further predict, using a ‘space‐for‐time’ approach and a downscaled, moderate, climate change scenario, that northern, boreal regions likely will experience strong increases in OC export from catchments to surface waters. Median concentrations of OC in these lakes will increase by 65%, from the current median of 2.0–3.3 mg C L−1. This is a long‐term effect, primarily mediated by increased terrestrial vegetation cover in response to climate change. This increase OC will have severe impacts on food‐webs, productivity and human use. Given the robustness of the estimates and the general applicability of the parameters, we suggest that these findings would be relevant to boreal areas in general.
Sequence Differentiation Among Inversion Rearrangement are Revealed by Random Amplified Polymorphic DNA Markers in the Grasshopper Trimerotropis pallidipennis (Orthoptera: Acrididae: Oedipodinae)

Abstract South American populations of Trimerotropis pallidipennis Burmeister are polymorphic for pericentric inversions. In this species, rearrangement frequencies follow repetitive patterns of distributions along different geographic areas, which are determined by altitude, minimum temperature, and humidity variables. The current article reports the analysis of random amplified polymorphic DNA (RAPDs) in five populations of T. pallidipennis and shows the possible relationships of this kind of molecular variability with inversion and enzyme polymorphisms. Both comparisons of RAPDs versus chromosome and RAPDs versus enzyme genetic distances yielded significant results, indicating that the degree of differentiation between pairs of populations is significantly similar when all three types of variability are compared with each other. Specifically, the differentiation for loci amplified by some of the primers is significantly correlated with the differentiation in humidity conditions. Therefore, RAPD loci frequencies tend to follow similar patterns of variations as chromosome and enzymatic variability. Inversions are of evolutionary significance because they can generate supergenes that preserve special genetic sequences. A population of T. pallidipennis at high altitudes, which is monomorphic for basic sequences at all chromosomes, will not have the same allele sequence as a population at low altitudes with fixed inverted chromosomes. Because all seven inversions involve a good portion of the genome, a variation between supergenes that differentiate populations is expected to be observed when many random fragments of DNA are amplified, because an eventual recognition sequence of the primers sited into the inversion may be altered. The significance of the congruence between enzymatic and RAPD variability is also discussed.
Miscanthus × giganteus leaf senescence, decomposition and C and N inputs to soil

Energy crops are currently promoted as potential sources of alternative energy that can help mitigate the climate change caused by greenhouse gases (GHGs). The perennial crop Miscanthus × giganteus is considered promising due to its high potential for biomass production under conditions of low input. However, to assess its potential for GHG mitigation, a better quantification of the crop's contribution to soil organic matter recycling under various management systems is needed. The aim of this work was to study the effect of abscised leaves on carbon (C) and nitrogen (N) recycling in a Miscanthus plantation. The dynamics of senescent leaf fall, the rate of leaf decomposition (using a litter bag approach) and the leaf accumulation at the soil surface were tracked over two 1‐year periods under field conditions in Northern France. The fallen leaves represented an average yearly input of 1.40 Mg C ha−1 and 16 kg N ha−1. The abscised leaves lost approximately 54% of their initial mass in 1 year due to decomposition; the remaining mass, accumulated as a mulch layer at the soil surface, was equivalent to 7 Mg dry matter (DM) ha−1 5 years after planting. Based on the estimated annual leaf‐C recycling rate and a stabilization rate of 35% of the added C, the annual contribution of the senescent leaves to the soil C was estimated to be approximately 0.50 Mg C ha−1yr−1 or 10 Mg C ha−1 total over the 20‐year lifespan of a Miscanthus crop. This finding suggested that for Miscanthus, the abscised leaves contribute more to the soil C accumulation than do the rhizomes or roots. In contrast, the recycling of the leaf N to the soil was less than for the other N fluxes, particularly for those involving the transfer of N from the tops of the plant to the rhizome.
DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population

ABSTRACT Background: With the improved life expectancy of people living with HIV (PLWH), identifying vulnerable subpopulations at high mortality risk is important. Evidences showed that DNA methylation (DNAm) is associated with mortality in non-HIV populations. Here, we established a panel of DNAm biomarkers that can predict mortality risk among PLWH. Methods: 1,081 HIV-positive participants from the Veterans Ageing Cohort Study (VACS) were divided into training (N = 460), validation (N = 114), and testing (N = 507) sets. VACS index was used as a measure of mortality risk among PLWH. Model training and fine-tuning were conducted using the ensemble method in the training and validation sets and prediction performance was assessed in the testing set. The survival analysis comparing the predicted high and low mortality risk groups and the Gene Ontology enrichment analysis of the predictive CpG sites were performed. Results: We selected a panel of 393 CpGs for the ensemble prediction model that showed excellent performance in predicting high mortality risk with an auROC of 0.809 (95%CI: 0.767,0.851) and a balanced accuracy of 0.653 (95%CI: 0.611, 0.693) in the testing set. The high mortality risk group was significantly associated with 10-year mortality (hazard ratio = 1.79, p = 4E-05) compared with low risk group. These 393 CpGs were located in 280 genes enriched in immune and inflammation response pathways. Conclusions: We identified a panel of DNAm features associated with mortality risk in PLWH. These DNAm features may serve as predictive biomarkers for mortality risk among PLWH. Abbreviations: AUC: Area Under Curve; CI: Confidence interval; DMR: differentially methylated region; DNA: Deoxyribonucleic acid; DNAm: DNA methylation; DAVID: Database for Annotation, Visualization, and Integrated Discovery; EWA: epigenome-wide association; FDR: False discovery rate; FWER: Family-wise error rate; GLMNET: elastic-net-regularized generalized linear models; GO: Gene ontology; HIV: Human immunodeficiency virus; HM450K: Human Methylation 450 K BeadChip; k-NN: k-nearest neighbours; NK: Natural killer; PC: Principal component; PLWH: people living with HIV; QC: Quality control; SVM: Support Vector Machines; VACS: Veterans Ageing Cohort Study; XGBoost: Extreme Gradient Boosting Tree
WHEAT YIELDS FOR 50 YEARS AT SWIFT CURRENT, SASKATCHEWAN IN RELATION TO WEATHER

Half a century of wheat yield and weather records at Swift Current in southwestern Saskatchewan were analyzed to determine the response of wheat (Triticum aestivum L.) to changing weather patterns. Weather at Swift Current has undergone subtle but significant changes over the past 50 yr. Earlier years had disturbed conditions: hot, dry periods alternating with cool, wet ones resulting in yield fluctuations ranging from crop failures to maximum values. More recently the weather has been quiet: dry and cool but less variable from year to year. The resulting conditions were more favorable for near-normal but less variable yields. Simple precipitation-based yield–weather models developed two decades ago no longer apply, because temperature and precipitation patterns are currently out of phase relative to earlier conditions. A factorial yield–weather model was used to explain the complex relationship. This involved the summation of the product of several quadratic functions of various weather elements. Those e.
How might marbling begin

Marbling is an important meat quality trait, in that it contributes directly to the value of beef on international markets. The development of marbling is not well understood, though there have been some significant recent discoveries regarding adipogenesis in general. This article describes a working hypothesis around the early events of marbling. It attempts to rationalise findings from several mammalian experimental systems on hyperplastic growth of adipocyte precursor cells.
Genetic Stock Structure of Terapon jarbua in Taiwanese Waters

Abstract Over the past century, stock identification, which is crucial for fisheries stock assessments, has relied heavily on intraspecies variations to differentiate management units. In recent years, however, DNA approaches have shed additional light on some aspects of the natural history and ecology of species and stocks. The Crescent Grunter Terapon jarbua is widely distributed across the Indo-Pacific region. It inhabits coastal waters with sandy substrates and tends to aggregate in estuaries. In the present study, we collected 96 individuals of T. jarbua from 10 locations around the shoreline of Taiwan as well as near Guangdong, China. A concatenated sequence (1,753 bp) of mtDNA (cytochrome c oxidase I and cytochrome b) was obtained from all individuals. We discovered two genetically distinct clades (lineages A and B) with different historical demographies occurring sympatrically except at the Yilan collection site, which was dominated by lineage A haplotypes. Connectivity within this region is high according to FST and AMOVA tests. The genetic variation between the two clades is far below the interspecies threshold for the genus Terapon (0.007 versus 0.3156). Therefore, we suggest that they be considered different genetic stocks from a fisheries management point of view and that future stock reassessment should be conducted based on the genetic information provided in this study. Further large-scale sampling is needed to understand the mechanisms that drive genetic partitioning on regional (Northwest Pacific) and global (Indo-Pacific) scales.
Macroevolution and climate change influence phylogenetic community assembly of North American hoofed mammals

Animal richness, community composition, and phylogenetic community structure (PCS) vary across the modern landscape. Animal communities vary from phylogenetically clustered (i.e. higher relatedness amongst co-occurring species than is expected by chance) to phylogenetically even (i.e. co-occurring taxa are more distantly related than expected by chance), which is explained by abiotic or climatic filtering and competitive exclusion, respectively. Under this model, the contribution of historical origination and extinction events to modern animal PCS remains relatively unknown. Because origination and extinction determine the make-up of the terrestrial community, the study of historical changes in animal PCS is tantamount to understanding formation of modern communities. In the present study, we test the effects of macroevolution and climate changes on ‘hoofed mammals’ (i.e. perissodactyl and artiodactyl) PCS from the late Cenozoic of North America because they experience large, phylogenetically dispersed extinctions of browsing species and phylogenetically dispersed originations of grazing species associated with the evolution of grassland ecosystems during the late Miocene. We show that the loss of numerically dominant nonhypsodont (putatively browsing and mixed feeding) clades and phylogenetically dispersed origination of less speciose clades following the mid Miocene climatic optimum led to an increase in phylogenetic evenness at the regional scale that is well explained by global climate changes. Phylogenetic evenness and a reduced richness during the late Cenozoic may have facilitated reduced niche overlap among co-occurring hoofed mammal species as global climates cooled. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114, 485–494.
Sexual Dimorphism, Female-Female Pairs, and Test for Assortative Mating in Common Terns

Abstract We trapped 656 Common Terns (Sterna hirundo) and measured five body dimensions and body mass for each bird; 313 birds were of known age, and 229 were sexed by DNA. Males were larger than females in all five dimensions, but were smaller in body mass. Early-nesting birds were larger than late-nesting birds in all five dimensions: at least for wing length, this difference was related to both laying date and age. Head length (from back of skull to tip of bill) was the most useful measure for sexing Common Terns in the field. Discriminant functions indicated that 75.9% of single birds and 84.5% of pairs could be sexed correctly by head length alone. We present rules and nomograms for field sexing of Common Terns; these provide trade-offs between sensitivity (proportion of birds classified) and specificity (proportion of birds correctly sexed). Three of 80 pairs (4%) included two females: these pairs nested early and were at least as successful as male-female pairs. Within pairs, tarsus lengths were negatively correlated; we found no evidence for positive assortative mating by linear dimensions or body mass. This study confirms some previous reports of sexual dimorphism in this species based on less reliable methods of sexing, but fails to confirm other reports of sexual dimorphism and assortative mating.
Interactions Between Weedy Rice and Cultivated Rice in Italy

Field studies were carried out in 1997 and 1998 in northwest Italy with the aim of determining the effects of weedy rice competition on rice growth dynamics and yield. ‘Arborio’ (medium-high tall size, high early vigour) and ‘Thaibonnet’ (semi-dwarf size, low early vigour) rice cultivars were grown in competition with weedy rice at four densities (0, 10, 20, and 40 plants m-2). For both cultivars the plant height, the aboveground biomass and the number of tillers were determined at different intervals. With some exceptions, all the measured rice growth parameters were not remarkably affected by weedy rice interference. Weedy rice plants grown in competition with ‘Arborio’ were generally taller and produced more biomass. Weedy rice competition resulted in up to 50% (in ‘Thaibonnet’) and 48% (in ‘Arborio’) yield losses. The yield losses observed in both varieties were primarily related to the reduction of yield components, and of panicle density and number of filled grains per panicle, in particular.
Approaches for studying fish production: Do river and lake researchers have different perspectives?

Biased perspectives of fisheries researchers may hinder scientific progress and effective management if limiting factors controlling productivity go unrecognized. We investigated whether river and lake researchers used different approaches when studying salmonid production and whether any differences were ecologically supported. We assessed 564 peer-reviewed papers published between 1966 and 2012 that studied salmonid production or surrogate variables (e.g., abundance, growth, biomass, population) and classified them into five major predictor variable categories: physical habitat, fertility (i.e., nutrients, bottom-up), biotic, temperature, and pollution. The review demonstrated that river researchers primarily analyzed physical habitat (65% of studies) and lake researchers primarily analyzed fertility (45%) and biotic (51%) variables. Nevertheless, understudied variables were often statistically significant predictors of production for lake and river systems and, combined with other evidence, suggests th.