Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species

Ecologists are increasingly adopting an evolutionary perspective, and in recent years, the idea that closely related species are ecologically similar has become widespread. In this regard, phylogenetic signal must be distinguished from phylogenetic niche conservatism. Phylogenetic niche conservatism results when closely related species are more ecologically similar that would be expected based on their phylogenetic relationships; its occurrence suggests that some process is constraining divergence among closely related species. In contrast, phylogenetic signal refers to the situation in which ecological similarity between species is related to phylogenetic relatedness; this is the expected outcome of Brownian motion divergence and thus is necessary, but not sufficient, evidence for the existence of phylogenetic niche conservatism. Although many workers consider phylogenetic niche conservatism to be common, a review of case studies indicates that ecological and phylogenetic similarities often are not related. Consequently, ecologists should not assume that phylogenetic niche conservatism exists, but rather should empirically examine the extent to which it occurs.     

Lentic and lotic habitats as templets for fungal communities: traits,adaptations, and their significance to litter decomposition within freshwater ecosystems

Decomposition of plant matter is a key ecosystem process and considerable research has examined plant litter decay processes in freshwater habitats. Fungi are common inhabitants of the decomposer microbial community and representatives of all major fungal phyla have been identified within freshwater systems. Development and application of quantitative methods over the last several decades have firmly established that fungi are central players in the decomposition of plant litter in freshwaters and are important mediators of energy and nutrient transfer to higher trophic levels. Despite the critical roles that fungi play in carbon and nutrient cycling in freshwater ecosystems, there are notable differences in the types and adaptations of fungal communities between lotic and lentic habitats. These differences can be explained by the wide range of hydrologic, physical, chemical and biological conditions within freshwater systems, all of which can influence the presence, type, and activity of fungal decomposers and their impact on litter decomposition. This paper seeks to provide a brief overview of the types, adaptations, and role of fungi within lotic and lentic freshwater ecosystems, with a particular emphasis on their importance to litter decomposition and the key environmental conditions that impact their growth and decay activities. This discussion will specifically focus on fungal dynamics occurring on plant litter in forested headwater streams and emergent freshwater marshes, since published data concerning their role in these systems is considerably more abundant in comparison to other freshwater habitats.     

From fundamental biology to the search for innovation: The story of fungal extracellular vesicles

Fungal extracellular vesicles (EVs) have attracted increased attention in recent years. Originated from a serendipitous discovery, the initial observation of fungal EVs resulted in a set of data repetitively rejected by several scientific journals, which raised questions about their authenticity. However, after the most fundamental experimental issues related to their observation were addressed, fungal EVs were characterized in dozens of species and became an emerging field. In this essay, we will discuss these fundamental findings and the potential of fungal EVs for the development of vaccines and antifungals.     

Allocation of extracellular enzymatic activity in relation to litter composition, N deposition, and mass loss

Decomposition of plant material is a complex process that requiresinteraction among a diversity of microorganisms whose presence and activity issubject to regulation by a wide range of environmental factors. Analysis ofextracellular enzyme activity (EEA) provides a way to relate the functionalorganization of microdecomposer communities to environmental variables. In thisstudy, we examined EEA in relation to litter composition and nitrogendeposition. Mesh bags containing senescent leaves of Quercusborealis (red oak), Acer rubrum (red maple) andCornus florida (flowering dogwood) were placed on forestfloor plots in southeastern New York. One-third of the plots were sprayedmonthly with distilled water. The other plots were sprayed monthly withNH₄NO₃ solution at dose rates equivalent to 2 or 8 g N m^–2 y^–1. Mass loss, litter composition, fungal mass, and the activities ofeight enzymes were measured on 13 dates for each litter type. Dogwood wasfollowed for one year, maple for two, oak for three. For each litter type andtreatment, enzymatic turnover activities were calculated from regressions of LN(%mass remaining) vs. cumulative activity. The decomposition of dogwood litterwas more efficient than that of maple and oak. Maple litter had the lowestfungal mass and required the most enzymatic work to decompose, even though itsmass loss rate was twice that of oak. Across litter types, N amendment reducedapparent enzymatic efficiencies and shifted EEA away from N acquisition andtoward P acquisition, and away from polyphenol oxidation and towardpolysaccharide hydrolysis. The effect of these shifts on decomposition ratevaried with litter composition: dogwood was stimulated, oak was inhibited andmaple showed mixed effects. The results show that relatively small shifts intheactivity of one or two critical enzymes can significantly alter decompositionrates.     

Proteome analysis of fungal and bacterial involvement in leaf litter decomposition

Fungi and bacteria are key players in the decomposition of leaf litter, but their individual contributions to the process and their interactions are still poorly known. We combined semi‐quantitative proteome analyses (1‐D PAGE‐LC‐MS/MS) with qualitative and quantitative analyses of extracellular degradative enzyme activities to unravel the respective roles of a fungus and a bacterium during litter decomposition. Two model organisms, a mesophilic Gram‐negative bacterium (Pectobacterium carotovorum) and an ascomycete (Aspergillus nidulans), were grown in both, pure culture and co‐culture on minimal medium containing either glucose or beech leaf litter as sole carbon source. P. carotovorum grew best in co‐culture with the fungus, whereas growth of A. nidulans was significantly reduced when the bacterium was present. This observation suggests that P. carotovorum has only limited capabilities to degrade leaf litter and profits from the degradation products of A. nidulans at the expense of fungal growth. In accordance with this interpretation, our proteome analysis revealed that most of the extracellular biodegradative enzymes (i.e. proteases, pectinases, and cellulases) in the cultures with beech litter were expressed by the fungus, the bacterium producing only low levels of pectinases.     

Current patterns of plant diversity and phylogenetic structure on the Kunlun Mountains

Large-scale patterns of biodiversity and the underlying mechanisms that regulate these patterns are central topics in biogeography and macroecology. The Qinghai-Tibet Plateau serves as a natural laboratory for studying these issues. However, most previous studies have focused on the entire Qinghai-Tibet Plateau, leaving independent physical geographic subunits in the region less well understood. We studied the current plant diversity of the Kunlun Mountains, an independent physical geographic subunit located in northwestern China on the northern edge of the Qinghai-Tibet Plateau. We integrated measures of species distribution, geological history, and phylogeography, and analyzed the taxonomic richness, phylogenetic diversity, and community phylogenetic structure of the current plant diversity in the area. The distribution patterns of 1911 seed plants showed that species were distributed mainly in the eastern regions of the Kunlun Mountains. The taxonomic richness, phylogenetic diversity, and genera richness showed that the eastern regions of the Kunlun Mountains should be the priority area of biodiversity conservation, particularly the southeastern regions. The proportion of Chinese endemic species inhabiting the Kunlun Mountains and their floristic similarity may indicate that the current patterns of species diversity were favored via species colonization. The Hengduan Mountains, a biodiversity hotspot, is likely the largest source of species colonization of the Kunlun Mountains after the Quaternary. The net relatedness index indicated that 20 of the 28 communities examined were phylogenetically dispersed, while the remaining communities were phylogenetically clustered. The nearest taxon index indicated that 27 of the 28 communities were phylogenetically clustered. These results suggest that species colonization and habitat filtering may have contributed to the current plant diversity of the Kunlun Mountains via ecological and evolutionary processes, and habitat filtering may play an important role in this ecological process.     

On the origin of high growth rates in archosaurs and their ancient relatives: Complementary histological studies on Triassic archosauriforms and the problem of a “phylogenetic signal” in bone histology

Three possible hypotheses could explain the polarity of the histological features of basal archosauriform and archosauromorph reptiles: either, the fibrolamellar complex is basal; or, the lamellar-zonal complex is basal or finally, the condition varied, and each complex evolved more than once in these early groups. The answer to this question would have broad implications for our understanding of the physiological, ecological, and behavioral features of the first archosaurs. To this end, we sampled the bone histology of various archosauriforms and basal archosaurs from the Triassic and Lower Jurassic: erythrosuchids, proterochampsids, euparkeriids, and basal ornithischian dinosaurs, including forms close to the origin of archosaurs but poorly assessed phylogenetically. The new data suggest that the possibility of reaching and maintaining very high growth rates through ontogeny could have been a basal characteristic of archosauriforms. This was partly retained (at least during early ontogeny) in most lineages of Triassic pseudosuchians, which nevertheless generally relied on lower growth rates to reach large body sizes. This trend to slower growth seems to have been further emphasized among Crocodylomorpha, which may thus have secondarily reverted toward more generalized reptilian growth strategies. Accordingly, their “typical ectothermic reptilian condition” may be a derived condition within archosauriforms, homoplastic to the generalized physiological condition of basal amniotes. On the other hand, ornithosuchians apparently retained and even enhanced the high growth rates of many basal archosauriforms during most of their ontogenetic trajectories. The Triassic may have been a time of “experimentation” in growth strategies for several archosauriform lineages, only one of which (ornithodirans) eventually stayed with the higher investment strategy successfully.     

Independent gene evolution in the potato actin gene family demonstrated by phylogenetic procedures for resolving gene conversions and the phylogeny of angiosperm actin genes

Summary Nine different actin DNA sequences were isolated from the common potato,Solanum tuberosum, and the nucleotide sequence of five actin loci and of two allelic variants are presented. Unlike the wide variation in intron position among animal actin genes, the potato actin genes have three introns situated in the same positions as reported for all other angiosperm actin genes. Using a novel combination of analytical procedures (G-test and compatibility analysis), we could not find evidence of frequent large or small nonreciprocal exchanges of genetic material between the sequenced loci, although there were a few candidates. Resolution of such gene conversion events and the quantification of independence of gene evolution in multigene families is critical to the inference of phylogenetic relationships. Comparison with actin genes in other angiosperm species suggests that the actin multigene family can be divided into a number of subfamilies, evolved by descent rather than gene conversion, which are of possible functional origin, with one major subfamily diversification occurring before the divergence of monocots and dicots. The silent rate of nucleotide substitution was estimated to be similar to that suggested for a number of other plant nuclear genes, whereas the replacement rate was extremely slow, suggestive of selective constraints.     

Oxygen uptake rate measurements to monitor the activity of terpene transforming fungi

The application of a simple system for measuring the oxygen uptake rate (OUR) to determine the activity of pellet-forming fungi is described. A non-invasive easy-to-use respirometric system was used to measure the OUR as an activity parameter. The model sensor system was optimized in shake flask experiments with Pleurotus sapidus (DSMZ 8266) and Chaetomium globosum (DSMZ 1962). The toxicity of (+)-limonene and (+)-valencene to submerged fungal cultures and the influence of solvents on C. globosum were investigated. Finally, the new respirometric method was used for the determination of oxygen uptake rates in small scale bioreactors to control the activity of terpene transforming fungi.     

phylosignal: an R package to measure,test, and explore the phylogenetic signal

Phylogenetic signal is the tendency for closely related species to display similar trait values as a consequence of their phylogenetic proximity. Ecologists and evolutionary biologists are becoming increasingly interested in studying the phylogenetic signal and the processes which drive patterns of trait values in the phylogeny. Here, we present a new R package, phylosignal which provides a collection of tools to explore the phylogenetic signal for continuous biological traits. These tools are mainly based on the concept of autocorrelation and have been first developed in the field of spatial statistics. To illustrate the use of the package, we analyze the phylogenetic signal in pollution sensitivity for 17 species of diatoms.     

Prediction of the Diplocarpon rosae secretome reveals candidate genes for effectors and virulence factors

Rose black spot is one of the most severe diseases of field-grown roses. Though R-genes have been characterised, little information is known about the molecular details of the interaction between pathogen and host. Based on the recently published genome sequence of the black spot fungus, we analysed gene models with various bioinformatic tools utilising the expression data of infected host tissues, which led to the prediction of 827 secreted proteins. A significant proportion of the predicted secretome comprises enzymes for the degradation of cell wall components, several of which were highly expressed during the first infection stages. As the secretome comprises major factors determining the ability of the fungus to colonise its host, we focused our further analyses on predicted effector candidates. In total, 52 sequences of 251 effector candidates matched several bioinformatic criteria of effectors, contained a Y/F/WxC motif, and did not match annotated proteins from other fungi. Additional sequences were identified based on their high expression levels during the penetration/haustorium formation phase and/or by matching known effectors from other fungi. Several host genotypes that are resistant to the sequenced isolate but differ in the R-genes responsible for this resistance are available. The combination of these genotypes with functional studies of the identified candidate effectors will allow the mechanisms of the rose black spot interaction to be dissected.     

A simple method for measuring fungal metabolic quotient and comparing carbon use efficiency of different isolates: Application to Mediterranean leaf litter fungi

The metabolic efficiency of different microbial groups in carbon source uses and single species storage efficiency is poorly characterised and not adequately represented in most biogeochemical models. It is proposed here a simple approach for an estimation of the metabolic quotient of fungal isolates. The method is based on the values of substrate use (respiration) and growth (biomass production) obtainable for single fungal isolates in vitro using the Phenotype MicroArray? system to test the metabolic performance of fungi on different substrates. As a case study, this carbon-use efficiency method was used to compare a group of leaf litter fungi. The metabolic efforts of single fungal species were measured on 95 different substrates of different complexity. The respiration to biomass ratio showed a high reliability and the possibility of being used as a measurable property of the micro-organisms and an indicator of organism’s performance or fitness.     

Bioengineering plant resistance to abiotic stresses by the global calcium signal system

Considerable progresses have taken place both in the methodology available to study changes in intracellular cytosolic calcium and in our understanding of calcium signaling cascades. It is generally accepted that the global calcium signal system functions importantly in coping with plant abiotic stresses, especially drought stress, which has been proved further by the recent transgenic and molecular breeding reports under soil water deficits. In plant cells, calcium plays roles as a universal transducer coupling a wide range of extracellular stimuli with intracellular responses. Different extracellular stimuli trigger specific calcium signatures: dynamics, amplitude and duration of calcium transients specify the nature, implication and intensity of stimuli. Calcium-binding proteins (sensors) play a critical role in decoding calcium signatures and transducing signals by activating specific targets and corresponding metabolic pathways. Calmodulin (CAM) is a calcium sensor known to regulate the activity of many mammalian proteins, whose targets in plants are now being identified. Higher plants possess a rapidly growing list of CAM targets with a variety of cellular functions. Nevertheless, many targets appear to be unique to higher plant cells and remain characterized, calling for a concerted effort from plant and animal scientists to elucidate their functions. To date, three major classes of plant calcium signals encoding elements in the calcium signal system, including calcium-permeable ion channels,Ca(2)+/ H(+) antiporters and Ca(2)+-ATPases, are responsible for drought stress signal transduction directly or indirectly. This review summarizes the current knowledge of calcium signals involved in plant abiotic stresses and presents suggestions for future focus areas of study.     

Antioxidant enzyme activity and growth responses of Huangguogan citrus cultivar to nitrogen supplementation

ABSTRACT

This study examined the physiological effects of different amounts of nitrogen (N) supplementation (0 to 2.72 kg/year) on the citrus cultivar Huangguogan (Citrus reticulata × Citrus sinensis). Root activity, chlorophyll content, and fruit quality were measured, and the activities of the antioxidant enzymes superoxide dismutase (SOD), guaiacol peroxidase (POD), and catalase (CAT), and the contents of malondialdehyde (MDA) and soluble protein in root, leaf, and fruit tissues were examined at different developmental stages. Root activity, chlorophyll content, fruit quality, antioxidant enzyme activity, MDA content, and soluble protein content increased in plants treated with an appropriate amount of N. Both excessive N and N deficiency decreased the content of MDA and the activities of antioxidant enzymes. Application of 1.36–1.81 kg N/year is suggested for citrus fertilization and the lower end of this range is recommended for minimizing environmental impact and production cost.     

Analyses of factors influencing the birth weight and neonatal growth rate of Cheetah (Acinonyx jubatus) cubs

Birth weight and the neonatal growth rate are reliable indicators of neonatal survival prospects. Data on weight at birth and consecutive weights until 40 days of age were recorded for cheetah cubs in 16 litters. Growth was found to be linear during the first 40 days of life. Weight data were used to evaluate the influence of several factors on birth weight and neonatal growth. The factors used in these analyses were sex, litter identity, litter size, average litter size over the first 40 days, birth weight, parents, gestation length, parity of the dam, and inbreeding. For birth weight and neonatal growth, litter identity was the major explanatory factor (81.8 and 85.3%). For birth weight, a significant influence of gestation length was found (p < 0.05), whereas inbreeding coefficient tended to decrease the birth weight (p = 0.09). Together, gestation length and inbreeding coefficient account for 57.5% of the between‐litter variation for birth weight. Factors with significant influences on neonatal growth are gestation length and parity (p < 0.05). The average litter size over the first 40 days tended to influence neonatal growth (p = 0.07). These three variables together account for 99.9% of the between‐litter variation for neonatal growth during the first 40 days of life. A comparison of neonatal growth between mother‐raised and hand‐raised cubs revealed a lower growth rate in hand‐raised cubs (45 vs. 27 g/day). Zoo Biol 18:129–139, 1999. © 1999 Wiley‐Liss, Inc.     

Species delimitation in the European species of Clavulina (Cantharellales, Basidiomycota) inferred from phylogenetic analyses of ITS region and morphological data

The identification of the conventionally accepted species of Clavulina (Cantharellales, Basidiomycota) in Europe (Clavulina amethystina, Clavulina cinerea, Clavulina cristata, and Clavulina rugosa) is often difficult and many specimens are not straightforwardly assignable to any of those four species, which is why some authors have questioned their identity. In order to assess the status of those species, a morphological examination was combined with the molecular analysis of the ITS region. The same six major clades were obtained in the Bayesian and parsimony phylogenetic analyses, and all six clades were well-supported at least by one of the analyses. Morphological characters, such as the overall branching pattern, the presence and intensity of grey colour, the cristation of the apices, and basidiospore size and shape were to various extents correlated with the phylogenetic signal obtained from the ITS region. The congruence between the molecular analyses and morphology, rather than geographical origin, suggests the existence of several species that can be delimited using a combined phylogenetic and morphological species recognition. The analyses revealed that C. cristata and C. rugosa are well-delimited species. In contrast, more than one taxa could be subsumed under the names C. amethystina and C. cinerea, the taxonomical complexity of which is discussed. The ITS region is proved to be adequate to separate phylogenetic species of Clavulina.     

Cell geometry,signal dampening,and a bimodal transcriptional response underlie the spatial precision of an ERK-mediated embryonic induction

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