Miracle-dz/UniFAR-FTUs huggingface dataset:
Determinants of native and non-native plant community structure on an oceanic island

Understanding the relative importance of environmental and anthropogenic factors in driving plant community structure, including relative dominance of native and non-native species, helps predict community responses to biological invasions. To assess factors influencing plant communities on San Clemente Island, USA, we conducted an islandwide vegetation survey in which we measured plant species richness and percent cover of native and non-native plants, as well as physical environmental variables, soil chemical properties, abundance of soil microbial functional groups (e.g., arbuscular mycorrhizal fungi [AMF]), and a human disturbance variable (distance to road). We found that total plant species richness decreased with increasing non-native plant cover, soil pH, and AMF abundance. Native plant cover increased with increasing distance to a major paved road and decreased with increasing soil moisture and pH. Non-native plant cover decreased with increasing distance to a major paved road and increased with increasing soil moisture, AMF abundance, and from southwest to northeast, a geographic/climatic gradient that represents increasing moisture. Nonmetric multidimensional scaling ordination further illustrated that trends in plant community composition were correlated with elevation, distance to a major paved road, and soil moisture, organic matter, and ammonium. These results suggest complex effects of physical environmental, soil chemical, and human-related factors on plant community structure on an oceanic island, and moreover, that different factors affect cover of native and non-native plants. Notably, our observation of apparent moisture limitation of non-native plants suggests that, in some contexts, drought conditions can limit plant invasions and may even represent an opportunity for efficient control or eradication of invasive plants. The apparent negative effect of non-native plants on native plant cover and overall plant species richness represents a conservation concern for native biodiversity on oceanic islands and suggests the potential for community reassembly as invasive species increasingly dominate due to anthropogenic disturbances.
The ‘Hutchinsonian niche’ as an assemblage of demographic niches: implications for species geographic ranges

Hutchinson (1957) defined the ecological niche as a hypervolume shaped by the environmental conditions under which a species can “exist indefinitely”. Although several authors further discussed the need to adopt a demographic perspective of the ecological niche theory, very few have investigated the environmental requirements of different components of species’ life cycles (i.e. vital rates) in order to examine their internal niche structures. It therefore remains unclear how species’ demography, niches and distributions are interrelated. Using comprehensive demographic data for two well-studied, short-lived plants (Plantago coronopus, Clarkia xantiana), we show that the arrangement of species’ demographic niches reveals key features of their environmental niches and geographic distributions. In Plantago coronopus, opposing geographic trends in some individual vital rates, through different responses to environmental gradients (demographic compensation), stabilize population growth across the range. In Clarkia xantiana, a lack of demographic compensation underlies a gradient in population growth, which could translate in a directional geographic range shift. Overall, our results highlight that occurrence and performance niches cannot be assumed to be the same, and that studying their relationship is essential for a better understanding of species’ ecological niches. Finally, we argue for the value of considering the assemblage of species’ demographic niches when studying ecological systems, and predicting the dynamics of species geographical ranges. This article is protected by copyright. All rights reserved.
The Nucleolus and Nucleolar Proteins of Dictyostelium

Dictyostelium is a model eukaryote for the study of a multitude of fundamental cellular processes as well as several human diseases. Despite its extensive study relatively little is known about its nucleolus. Only three nucleolar proteins have been identified. The nucleolus in Dictyostelium is different than that of other eukaryotes since it is neither bipartite nor tripartite, possessing no visible subcompartments at the ultrastructural level. Moreover, it exists as two to four patches adjacent to the inner nuclear envelope instead of within the nucleoplasm. The aim of this study was thus to identify and characterize novel nucleolar proteins in Dictyostelium in order to better understand the structure and function of its nucleolus. Previous work had shown that NumA1, a protein linked to cell cycle in Dictyostelium, localizes to similar intranuclear patches suggesting it may be nucleolar. NumA1-binding partners Ca 2+ -binding protein (CBP) 4a and puromycinsensitive aminopeptidase A may therefore also reside in the nucleolus. Based on the function of a potential NumA1 homologue in other organisms, BRG1-associated factor 60a homologue Snf12 and checkpoint kinase 2 (Rad53 in yeast) homologue forkhead-associated kinase (Fhk) A were chosen as potential nucleolar proteins in Dictyostelium that may also be involved in cell cycle events. Using a diversity of approaches, this study found that NumA1, CBP4a, Snf12, and FhkA are nucleolar proteins in Dictyostelium while puromycin-sensitive aminopeptidase A is iii nucleoplasmic. Several nuclear localization signals (NLSs) were identified in these proteins some of which also act as nucleolar localization signals (NoLSs). These NLS/NoLSs (within NumA1 and Snf12) represent the first NoLSs and first NLS/NoLSs identified in Dictyostelium. Treatment with the rDNA transcription inhibitor AM-D led to the budding of nucleolar CBP4a, Snf12, and FhkA from the nucleus to the cytoplasm, a phenomenon not previously observed in any organism. This study also examined for the first time the redistribution of nucleolar proteins during mitosis, a time when the nucleolus disassembles into its component parts. The nuclear envelope was also shown to become permeable at this time. Finally, multiple nucleolar subcompartments were identified suggesting compartmentalization of different functions in the Dictyostelium nucleolus.
A Protocol for Callus Induction in Chilli Genotypes from Hypocotyls as Explant

Chilli (Capsicum annuum L.) commonly known as pepper is one of the most important spice crop grown in the world. There are about 25–30 species of Capsicum out of which five species are most common and currently cultivated Csilléry, (2006). C. annuum is the most widespread and widely cultivated species in subtropics and temperate countries Belletti et al., (1998). It is a native of tropical America and widely grown in India, China, Peru, Bangladesh, Pakistan and other European countries. India is the largest producer, consumer and exporter of chilli in the world. In India highest area under chilli (26%) is in Andhra Pradesh as well as maximum production (53%) comes from this state only. The yield potential, quality as well as nutritional value of chilli is affected by a number of biotic and abiotic stresses. However, genetic improvement of this crop, especially for characters like resistance to biotic and abiotic stresses using conventional breeding methods are laborious, time taking and also needs a large experimental area. So, different biotechnology techniques like plant tissue culture and recombinant DNA technologies are powerful tools that can complement conventional breeding and The yield potential as well as quality of chilli is affected by a number of biotic and abiotic stresses. The genetic improvement of this crop, especially for characters like resistance to biotic and abiotic stresses using conventional breeding methods are laborious, time taking and also needs a large experimental area. So, an attempt was made to study callus induction in chilli genotypes by using hypocotyls as explant to complement conventional breeding and expedite capsicum improvement. The study was carried out on callogenic response of chilli species with different hormones revealed that MS medium supplemented with NAA 2.5 mg/1+ BAP 2.5 mg/1 was found most suitable for callus induction to both the genotypes viz., Capsicum annuum and Capsicum frutescens. When NAA and BAP were used in combination early initiation of the callus was observed with fragile and pale yellow colour in both the genotypes of chilli. Among the chilli genotypes evaluated, the average callus formation was (77.24%) in case of C. annuum, whereas (79.20%) in C. frutescens. Hence, callus induction was significantly better in C. frutescens as compared to C. annuum. K e y w o r d s
Combining underwater video methods improves effectiveness of demersal fish assemblage surveys across habitats

: Knowledge of the biases and advantages of various methods can inform and create more efficient sampling of either whole fish assemblages or targeted species. Comparisons of stereo baited remote underwater video (stereo-BRUV) and stereo-towed video, a new and relatively un common methodology of assessing fish assemblages, were made for assessing fish assemblages beyond diveable depths (>30 m). Stereo-BRUV and towed video footage were analysed for species composition and functional feeding groups in structure-forming macroalgae and sponge-dominated benthic habitats in temperate waters off Warrnambool, Victoria, Australia. Multibeam echosounder (MBES) data, light attenuation and temperature recordings were gathered for each deployment in order to characterise the seafloor structure and oceanographic parameters at each stereo-BRUV location and towed transect. A more abundant and diverse fish assemblage was ob served in stereo-BRUV compared to towed video. The fish assemblage observed using the 2 methods was relatively similar in canopy forming algae habitat, but clearly distinct in sponge habitats. Power analysis also showed stereo-BRUV to have greater statistical power when observing total individuals, species richness and functional group richness across both habitats, with the exception of functional group richness in the sponge habitat. Stereo-BRUVs observed higher abundances of elasmobranches, Meuschenia spp. , snapper Chrysophrys auratus , demersal invertivores and pelagic planktivores, whilst towed video observed more cryptic and territorial species such as Olisthops cyanomelas and Pempheris multiradiata . Using a combination of stereo baited and towed video sampling techniques records a more detailed description of the fish assemblage on temperate reefs than using either method alone.
Ruffed grouse population declines after introduction of West Nile virus

The abundance of ruffed grouse (Bonasa umbellus) has declined over a broad region in the Appalachian Mountains in the last 3 decades. We determined empirical support for different hypothesized causes of declines: habitat loss, forest maturation, and the introduction of West Nile virus (WNV) in the early 2000s. We examined how these factors relate to declines observed in 2 data sets: changes between 2 Breeding Bird Atlas (BBA) surveys in Pennsylvania conducted in the 1980s and 2000s and a 48-year time series of flush rate data. Initial occupancy of BBA blocks was positively related to the amount of available forested habitat, and persistence and colonization probabilities were negatively related to WNV intensity and positively related to available forest and to increasing trends in early successional habitat. Flush rates dropped in most regions after the arrival of WNV, but trend estimates were imprecisely estimated, and there was considerable uncertainty about whether or how the slope of annual trends in flush rates changed. Our results provide support for the importance of forest and early successional forest, but taken together with other supporting evidence for the presence of WNV in wild ruffed grouse populations and mortality in ruffed grouse chicks caused by WNV infection, our results also suggest that ruffed grouse populations might have been affected by mortality from WNV. In the face of WNV, managing habitat may be insufficient to sustain ruffed grouse populations. © 2017 The Wildlife Society.
Host specificity, infrequent major host switching and the diversification of highly host-specific symbionts: The case of vane-dwelling feather mites

Aim Highly host-specific symbionts are very rarely found except with their typical host species. Although switches to new hosts are rare and difficult to detect, a switch to a host phylogenetically distant from the original one (a ‘major host switch’) could allow diversification of the symbionts onto the new host lineage. The consequences of such major host switches on the diversification of highly host-specific symbionts of animals have rarely been explored. Here, we examine the host specificity of vane-dwelling feather mites, a group that shows strong specificity, together with their host-switching dynamics and the consequences of major host switches for their diversification. Location Global. Time period From 1882 to 2015. Major taxa studied Feather mites and birds. Methods Using the largest published dataset of feather mite–bird associations, we analysed raw, phylogenetic and geographical host specificity of feather mites. We studied host-switching dynamics by describing the sharing by feather mites of bird species with different phylogenetic distances. For three of the most species-rich feather mite families, we quantified the consequences of major host switches for feather mite diversification. Results Most feather mite species (84%) inhabit one to three very closely related host species. Assemblages of feather mites on birds do not show a geographical signature, but rather show strong host-driven structuring. The probability that a mite species occurs on two host species decays sharply with host phylogenetic distance, with only one instance of a feather mite species occupying distantly related hosts from different orders. However, results suggest that despite the strong host specificity, a few major host switches triggered the origin of 21% of the species and 38% of the genera of the mite families studied. Main conclusions We show that feather mites are highly host-specific symbionts, whose assemblages do not show geographical structure, even at a continental scale. We conclude that major host switches are very rare events with strong macroevolutionary consequences for feather mite diversity.
Distribution and Abundance of Introduced Seal Salamanders (Desmognathus monticola) in Northwest Arkansas, USA

Many reptiles and amphibians are gaining recognition as harmful invaders, highlighted by well-known examples such as the Brown Tree Snake (Boiga irregularis), Cane Toad (Rhinella marina), American Bullfrog (Lithobates catesbeianus), and Burmese Python (Python molurus bivittatus). In 2003, an introduced population of Seal Salamanders (Desmognathus monticola) was found in Spavinaw Creek, within the Ozark Plateau of northwest Arkansas. Genetic evidence confirmed an introduction from northern Georgia. Very little is known about the status of this non-native population; thus, the objective of this study was to assess the current distribution and abundance of non-native D. monticola along Spavinaw Creek. We conducted repeated, low-intensity visual surveys along the 30 km extent of Spavinaw Creek in Arkansas and used a hierarchical Bayesian analysis to model the occupancy response of D. monticola and five native salamander species relative to river mile and habitat covariates. We also conducted a short-term closed capture-mark-recapture study to estimate abundance of D. monticola at the original collection site on Spavinaw Creek. We found a clear geographic pattern of distribution of D. monticola, with individuals found throughout the upper 10 km of Spavinaw Creek headwaters, but no clear habitat associations. Estimated abundance of D. monticola was extremely high—14.5 individuals and 50 g wet biomass per m2. Our results reveal that introduced D. monticola are much more widely distributed than previously recognized and occur at high densities, suggesting that this recent invader could negatively affect ecosystems of Spavinaw Creek and surrounding watersheds in the Ozark highlands.
Traits and impacts of invasive species: Myths and evidences from the perspective of introduced freshwater mussels

While invasion success is usually associated with the biological fitness of the invader and environmental similarity between the area of origin and the invaded range, some of the most notorious aquatic invasions involve species with traits that for millions of years were a burden, rather than an advantage, for their survival. These odd characteristics became major assets after man started reshaping the surface of the earth, facilitating their spread. Invasion risk-assessment models, chiefly based on environmental match parameters, are unlikely to predict the dispersion of these (and probably many other) species, whose invasive nature involves subtle and intricate mechanisms that operate at levels normally ignored by (and often unknown to) the models. Much of the literature on introduced species is focused on demonstrating their negative impacts on the ecosystems invaded. While the fact that invasive organisms can, and very often do, have enormous negative impacts, is beyond doubt, and all efforts possible for keeping biological invasions at bay should be made, once the introduction happens and the eradication of the invader is unfeasible, research efforts should be centered on objective analyses of how the invader interacts with the new ecosystem, untainted by efforts to forcibly demonstrate its negative impact.
Increasing detection sensitivity of low copy number transcripts through preamplification of cDNA molecules

With the advances in the field of molecular biology and its applications in the clinical practice during the recent years, it has become crucial to perform molecular analyses on limited amount of tissue obtained through biopsies. Additionally, tissue is fixed in formalin and further embedded in paraffin (FFPE), a procedure which causes extensive degradation of nucleic acids, mainly RNAs. Furthermore, when studying gene expression profiles of a set of genes, which present physiologically low expression, the number of transcripts is low and cannot be detected. In this study we focus on amplifying effectively cDNA molecules synthesized from small amounts of initial RNA before analyzing the expression levels through quantitative polymerase chain reaction (qPCR). By introducing the preamplification step in the procedure, we achieved highly effi-cacious detection and quantification of expression levels of low-expression genes.
Ecology of the Sand Roller (Percopsis transmontana) In A Lower Snake River Reservoir, Washington

Abstract The Sand Roller (Percopsis transmontana), has not been abundant in the Snake River since it was first found in the system in the 1950s, but its population has apparently increased in recent years. As a result, we initiated a study to better understand its ecology in habitats of Lower Granite Reservoir. From November 2014 to October 2015, Sand Rollers were present along shorelines, with peak abundance being observed during spring months. Logistic regression analyses showed that Sand Rollers were more likely to be present in shoreline habitats at temperatures ≤18.4°C. Fish were found over a range of substrates, with the lowest odds of fish presence being associated with riprap, which is common in hydropower reservoirs. From length-frequency analysis, we suggest that Sand Roller spawning occurs primarily in May and early June. Assessment of Sand Roller diets found dipteran (chironomid) larvae and pupae were the most important prey consumed by all sizes of Sand Rollers, but Opossum Shrimp (Neomysis mercedis) were also prominent in diets of larger fish in shoreline and offshore habitats. At a time when the populations of so many native species are in decline, the increase of the Sand Roller population in the lower Snake River represents a positive, yet curious occurrence.
Role of Bark Color on Stem Temperature and Carbohydrate Management during Dormancy Break in Persian Walnut

A BSTRACT . Temperature is assumed to be the principal regulatory signal that determines the end of dormancy and resumption of growth. Indirect evidence that stem temperature interferes with phenology comes from the common orchard practice of painting stems to protect them from disease. This work studies the effects of application of white paint to the stems of persian walnut ( Juglans regia ) trees on winter stem temperature, carbohydrate content, and spring phenology. Painting bark resulted in the delay of budbreak by several days, higher nonstructural carbohydrate (NSC) concentrations in the bark and wood of painted extension shoots and changes in the spatial gradients of NSC during budbreak. The demands of maintenance respiration exceeded mobilization from local carbon pools during bud development suggesting a potential role of carbohydrate transport during spring budbreak in persian walnut. Painting provides an exciting perspective for mitigating effects of milder winter in orchards. The effect of reducing diurnal and spatial temperature variability limits early budbreak, NSC depletion associated with intense maintenance respiration, freeze–thaw cycles and frost dehardening.