Seeing networks for what they are in mycorrhizal ecology

Networks tools are being increasingly used in the study of plant-fungus interactions and likely to provide new insights in the way plant-fungus interactions are structured. At the same time, they raise new questions and challenges. Here, I highlight the most important problems and outline how network tools can be effectively used in mycorrhizal ecology. Network-based tools can be used to explore and visualize mycorrhizal interaction patterns: this can pave the way towards further empirical work and hypothesis testing. However, network-based tools cannot, by themselves alone, provide much insight about the ecological mechanisms driving the establishment of mycorrhizal interactions, because many mechanisms can yield a given network-level pattern. They also cannot help predicting the future dynamics of mycorrhizal communities, because modelling studies need to be conducted using parameters and rules that are relevant to the mycorrhizal symbiosis, which is not currently done. Also, drawing analogies between mycorrhizal networks and other types of networks must be made with caution, taking into account all the potential similarities, but also discrepancies, between these kinds of unrelated networks. I think that keeping the above issues in mind will be critical to keep the network-based approach viable and useful in mycorrhizal ecology.     

Synthetic fuels: what are they and where do they come from?

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T‐lymphoid progenitors – we know what they are,but know not what they may be

An improved understanding of the biology underlying leukemogenesis, including the determination of the cells of leukemia origin, is of great importance as it can have immediate implications on patient treatment and management. The article by Riemke et al ( 2016 ) provides further evidence that a subgroup of acute myeloid leukemia (AML), the most common acute leukemia in adults, might arise from T‐lymphoid progenitor cells. This study not only supports that the lymphoid fate of early T‐cell progenitors is not yet fully stabilized but also shows that under oncogenic conditions, this multilineage plasticity potential of T‐lymphoid progenitors can lead to transdifferentiation into myeloid leukemia. While gene expression profiles suggest that approximately 5% of all AML cases originate from T‐lymphoid progenitors, novel treatment strategies targeting JAK2/STAT3 signaling might open new avenues for this AML cohort.     

‘Old-forest fungi’ are not always what they seem: the case of Antrodia crassa

Putatively old-forest dependent fungi have acquired a distinct position in biodiversity conservation, acting both as management targets and indicators for other nature values in the forest. Establishing old-forest dependency, however, requires rigorous sampling, taxonomy and identification approaches as exemplified here by a case study on Antrodia crassa. This rarely recorded polypore is considered indicative of old conifer forests in Northern Europe. We demonstrate that the material labelled as A. crassa includes not only frequent misidentifications, but it represents two genetically and ecologically distinct cryptic lineages with partly overlapping distributions. A balanced survey of different successional stages in Estonia indicated that one of those lineages prefers deadwood-rich disturbed habitats, notably clear-cuts, which have been previously undersampled. Because similar problems with cryptic lineages and biased surveys are common in mycological research, lists of ‘old-forest fungi’ should be considered as high-priority working hypotheses for taxonomic and ecological research, rather than well-established management tools.     

The bright side of parasitic plants: what are they good for?

Parasitic plants are mostly viewed as pests. This is caused by several species causing serious damage to agriculture and forestry. There is however much more to parasitic plants than presumed weeds. Many parasitic plans exert even positive effects on natural ecosystems and human society, which we review in this paper. Plant parasitism generally reduces the growth and fitness of the hosts. The network created by a parasitic plant attached to multiple host plant individuals may however trigger transferring systemic signals among these. Parasitic plants have repeatedly been documented to play the role of keystone species in the ecosystems. Harmful effects on community dominants, including invasive species, may facilitate species coexistence and thus increase biodiversity. Many parasitic plants enhance nutrient cycling and provide resources to other organisms like herbivores or pollinators, which contributes to facilitation cascades in the ecosystems. There is also a long tradition of human use of parasitic plants for medicinal and cultural purposes worldwide. Few species provide edible fruits. Several parasitic plants are even cultivated by agriculture/forestry for efficient harvesting of their products. Horticultural use of some parasitic plant species has also been considered. While providing multiple benefits, parasitic plants should always be used with care. In particular, parasitic plant species should not be cultivated outside their native geographical range to avoid the risk of their uncontrolled spread and the resulting damage to ecosystems.

Advances

• Parasitic plants may act as highways for transferring systemic signals among host plants.
• Harmful effects of parasitic plants on individual hosts suppress community dominants including invasive species, reduce competitive pressure, and may increase biodiversity.
• Parasitic plants enhance nutrient cycling and provide resources for other organisms thus contributing to facilitation cascades in ecosystems.
• Many parasitic plants are recorded to have medicinal values against a broad range of diseases.
• There is a long tradition of worldwide human use of parasitic plants, which have been cultivated for their products and aesthetic values.

     

DNA methylation studies using twins: what are they telling us?

Recent studies have identified both heritable DNA methylation effects and differential methylation in disease-discordant identical twins. Larger sample sizes, replication, genetic-epigenetic analyses and longitudinal assays are now needed to establish the role of epigenetic variants in disease.     

Career choices in the biosciences: what companies are looking for when they are filling a position

Holding a Ph.D. or other doctoral degree in the biological sciences used to allow for only one main career path. Faculty positions at either research-intensive universities or at predominantly teaching institutions defined the career path very well. The situation is considerably more complex now. Many individuals decide to pursue careers in for-profit organizations, either by personal preference, geographic needs, or simply as an expedient way to continue in biology in a meaningful way. This article arises from the need to define a better understanding of the nature of corporate job seeking for potential job applicants. The author draws upon his experience over a thirty-year scientific career in industry and academics. The distinctions he makes are helpful for job-seekers in this new environment.     

Alternatives to hospital care: what are they and who should decide?

OBJECTIVE--To examine potential for alternatives to care in hospitals for acute admissions, and to compare the decisions about these alternatives made by clinicians with different backgrounds. DESIGN--Standardised tool was used to identify patients who could potentially be treated in an alternative form of care. Information about such patients was assessed by three panels of clinicians: general practitioners without experience of general practitioner beds, general practitioners with experience of general practitioner beds, and consultants. SETTING--One hospital for acute admissions in a rural area of the South and West region of England. SUBJECTS--Of 620 patients admitted to specialties of general medicine and care of the elderly, details of 112 were assessed by panels. MAIN OUTCOME MEASURES--Proportion of hospitalised patients who could have received alternative care and identification of most appropriate alternative form of care. RESULTS--Both general practitioner panels estimated that between 51 and 89 of the hospitalised patients could have received alternative care (equivalent to 8-14% of all admissions). Consultants estimated that between 25 and 55 patients could have had alternative care (5.5-9% of all admissions). General practitioner bed and urgent outpatient appointment were the main alternatives chosen by all three panels. CONCLUSION--About 10% of admissions to general hospital might be suitable for alternative forms of care. Doctors with different backgrounds made similar overall assessments of most appropriate forms of care.     

Ecological laws: what would they be and why would they matter?

There remains considerable debate over the existence of ecological laws. However, this debate has not made use of an adequate account of what a relationship would have to be like in order for it to qualify as an ecological law. As a result, confusions have persisted not only over how to show that ecological laws do (or do not) exist, but also regarding why their existence would matter – other than to whether ecology looks like physics. I argue that ecological laws would have to possess collectively a distinctive kind of invariance under counterfactual perturbations. I call this invariance "stability." A law of physics, such as the law that all bodies travel no faster than the speed of light, is not only true, but also necessary in a physically significant sense. (A body must travel no faster than light; it couldn't do otherwise, even if it were subjected to a greater force.) Likewise, the stability of ecological laws would render them necessary in an ecologically relevant sense. Furthermore, ecological laws would differ from fundamental laws of physics in the range of counterfactual perturbations under which they are invariant. Therefore, I argue, the existence of ecological laws would make ecological explanations irreducible to even the most complete possible physical explanations of the same phenomena. Ecological laws would make ecology genuinely autonomous from physics.     

Predators are rare even when they are small

A recent review of published studies revealed that predators generally have lower population densities than non-predators in a variety of communities. We report here similar results for a highly replicated study of macroinvertebrates that colonized very uniform detrital microcosms in an old field. This pattern persisted even though predators usually were smaller than non-predators, as determined by body length and volume.     

Leaf structural dynamics associated with adaptation of two Ebenus cretica ecotypes

Morphological and anatomical features of Ebenus cretica leaflet, such as lanceolate shape, reduced size, dense cover with non-glandular hairs, epidermis of small cells, compact mesophyll, amphipleurous presence of palisade parenchyma, thick cuticle, development of numerous mesophyll phenol-storing cells and the amphistomatic type, disclose the xeromorphic character of the plant. In the island of Crete two ecotypes of E. cretica, ecotype A and ecotype C, are greatly extended. In ecotype A leaflets, the above features are more prominent than in ecotype C. This fact accomplished by physiological data favours the suggestion that plants of ecotype A are better adapted to the xerothermic environment of the island of Crete. This may be the reason that ecotype A occupies the major portion of the island and is predominant in the western and central regions. The distinction of ecotypes A and C, by evaluating the strategies these plants used in order to better adapt and the characteristics of their inflorescences may be used as a criterion for the selection of the most appropriate ecotype for application in floriculture and ornamental horticulture.     

Quantitative traits in relation to population structure: why and how are they used and what do they imply?

I describe the basic ingredients of a population structure analysis and the rationale for using polygenic quantitative traits in such analyses. The complexity of inheritance and the population dynamics of quantitative traits, however, imply that inferences regarding population structure based on such traits must be evaluated with appropriate cautions. Although many studies of quantitative traits in relation to population structure analysis underscore the importance of gene flow between subpopulations, I show that the role of selection in the evolution of a quantitative trait and its relationship to the inferred population structure cannot be overlooked. Finally, I review some recent advances in human quantitative genetic methodologies that can be used profitably in population structure analysis.