Host preferences and differential contributions of deciduous tree species shape mycorrhizal species richness in a mixed Central European forest

Mycorrhizal species richness and host ranges were investigated in mixed deciduous stands composed of Fagus sylvatica, Tilia spp., Carpinus betulus, Acer spp., and Fraxinus excelsior. Acer and Fraxinus were colonized by arbuscular mycorrhizas and contributed 5% to total stand mycorrhizal fungal species richness. Tilia hosted similar and Carpinus half the number of ectomycorrhizal (EM) fungal taxa compared with Fagus (75 putative taxa). The relative abundance of the host tree the EM fungal richness decreased in the order Fagus > Tilia >> Carpinus. After correction for similar sampling intensities, EM fungal species richness of Carpinus was still about 30–40% lower than that of Fagus and Tilia. About 10% of the mycorrhizal species were shared among the EM forming trees; 29% were associated with two host tree species and 61% with only one of the hosts. The latter group consisted mainly of rare EM fungal species colonizing about 20% of the root tips and included known specialists but also putative non-host associations such as conifer or shrub mycorrhizas. Our data indicate that EM fungal species richness was associated with tree identity and suggest that Fagus secures EM fungal diversity in an ecosystem since it shared more common EM fungi with Tilia and Carpinus than the latter two among each other

Use of brain MRI atlases to determine boundaries of age-related pathology: the importance of statistical method

Neurodegenerative disease diagnoses may be supported by the comparison of an individual patient's brain magnetic resonance image (MRI) with a voxel-based atlas of normal brain MRI. Most current brain MRI atlases are of young to middle-aged adults and parametric, e.g., mean ± standard deviation (SD); these atlases require data to be Gaussian. Brain MRI data, e.g., grey matter (GM) proportion images, from normal older subjects are apparently not Gaussian. We created a nonparametric and a parametric atlas of the normal limits of GM proportions in older subjects and compared their classifications of GM proportions in Alzheimer's disease (AD) patients.Using publicly available brain MRI from 138 normal subjects and 138 subjects diagnosed with AD (all 55-90 years), we created: a mean ± SD atlas to estimate parametrically the percentile ranks and limits of normal ageing GM; and, separately, a nonparametric, rank order-based GM atlas from the same normal ageing subjects. GM images from AD patients were then classified with respect to each atlas to determine the effect statistical distributions had on classifications of proportions of GM in AD patients.The parametric atlas often defined the lower normal limit of the proportion of GM to be negative (which does not make sense physiologically as the lowest possible proportion is zero). Because of this, for approximately half of the AD subjects, 25-45% of voxels were classified as normal when compared to the parametric atlas; but were classified as abnormal when compared to the nonparametric atlas. These voxels were mainly concentrated in the frontal and occipital lobes.To our knowledge, we have presented the first nonparametric brain MRI atlas. In conditions where there is increasing variability in brain structure, such as in old age, nonparametric brain MRI atlases may represent the limits of normal brain structure more accurately than parametric approaches. Therefore, we conclude that the statistical method used for construction of brain MRI atlases should be selected taking into account the population and aim under study. Parametric methods are generally robust for defining central tendencies, e.g., means, of brain structure. Nonparametric methods are advisable when studying the limits of brain structure in ageing and neurodegenerative disease

CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

<p>Abstract</p> <p>Background</p> <p>The implementation of high throughput sequencing for exploring biodiversity poses high demands on bioinformatics applications for automated data processing. Here we introduce <smcaps>CLOTU</smcaps>, an online and open access pipeline for processing 454 amplicon reads. C<smcaps>LOTU</smcaps> has been constructed to be highly user-friendly and flexible, since different types of analyses are needed for different datasets.</p> <p>Results</p> <p>In <smcaps>CLOTU</smcaps>, the user can filter out low quality sequences, trim tags, primers, adaptors, perform clustering of sequence reads, and run <smcaps>BLAST</smcaps> against NCBInr or a customized database in a high performance computing environment. The resulting data may be browsed in a user-friendly manner and easily forwarded to downstream analyses. Although <smcaps>CLOTU</smcaps> is specifically designed for analyzing 454 amplicon reads, other types of DNA sequence data can also be processed. A fungal ITS sequence dataset generated by 454 sequencing of environmental samples is used to demonstrate the utility of <smcaps>CLOTU</smcaps>.</p> <p>Conclusions</p> <p>C<smcaps>LOTU</smcaps> is a flexible and easy to use bioinformatics pipeline that includes different options for filtering, trimming, clustering and taxonomic annotation of high throughput sequence reads. Some of these options are not included in comparable pipelines. C<smcaps>LOTU</smcaps> is implemented in a Linux computer cluster and is freely accessible to academic users through the Bioportal web-based bioinformatics service (<url>http://www.bioportal.uio.no</url>).</p

What Goes in Must Come out: Testing for Biases in Molecular Analysis of Arbuscular Mycorrhizal Fungal Communities

Arbuscular mycorrhizal (AM) fungi are widely distributed microbes that form obligate symbioses with the majority of terrestrial plants, altering nutrient transfers between soils and plants, thereby profoundly affecting plant growth and ecosystem properties. Molecular methods are commonly used in the study of AM fungal communities. However, the biases associated with PCR amplification of these organisms and their ability to be utilized quantitatively has never been fully tested. We used Terminal Restriction Fragment Length Polymorphism (TRFLP) analysis to characterise artificial community templates containing known quantities of defined AM fungal genotypes. This was compared to a parallel in silico analysis that predicted the results of this experiment in the absence of bias. The data suggest that when used quantitatively the TRFLP protocol tested is a powerful, repeatable method for AM fungal community analysis. However, we suggest some limitations to its use for population-level analyses. We found no evidence of PCR bias, supporting the quantitative use of other PCR-based methods for the study of AM fungi such as next generation amplicon sequencing. This finding greatly improves our confidence in methods that quantitatively examine AM fungal communities, providing a greater understanding of the ecology of these important fungi

Fear of predation drives stable and differentiated social relationships in guppies

This is the author accepted manuscript. The final version is available from Springer Nature via the DOI in this record.Social relationships can have important consequences for fitness in animals. Whilst numerous studies have shown that individuals often join larger groups in response to perceived predation risk (i.e. fear of predation), the importance of predation risk in driving the formation and stability of social relationships within groups has been relatively ignored. We experimentally tested how predation threat influenced fine-scale social network structure using Trinidadian guppies (Poecilia reticulata). When perceived predation risk was high, individuals developed stable and more differentiated social ties compared to when perceived risk was low. Intriguingly, social differentiation coincided with shoals being somewhat smaller under high-perceived risk, suggesting a possible conflict between forming stable social relationships and larger social groups. Individuals most at risk of predation (large and bold individuals) showed the most exaggerated responses in several social measures. Taken together, we provide the first experimental evidence that proximate risk of predation can increase the intensity of social relationships and fine-scale social structure in animal populations.DPC acknowledges funding from the National Environmental Research Council (NE/E001181/1) and Leverhulme Trust (RPG-175) and SKD and DPC acknowledge funding from The Danish Council for Independent Research (DFF – 1323-00105)

Parents' assessment of parent-child interaction interventions – a longitudinal study in 101 families

<p>Abstract</p> <p>Background</p> <p>The aim of the study was to describe families with small children who participated in parent-child interaction interventions at four centres in Sweden, and to examine long term and short term changes regarding the parents' experience of parental stress, parental attachment patterns, the parents' mental health and life satisfaction, the parents' social support and the children's problems.</p> <p>Methods</p> <p>In this longitudinal study a consecutive sample of 101 families (94 mothers and 54 fathers) with 118 children (median age 3 years) was assessed, using self-reports, at the outset of the treatment (T1), six months later (T2) and 18 months after the beginning of treatment (T3). Analysis of the observed differences was carried out using Wilcoxon's Signed-Rank test and Cohen's d.</p> <p>Results</p> <p>The results from commencement of treatment showed that the parents had considerable problems in all areas examined. At the outset of treatment (T1) the mothers showed a higher level of problem load than the fathers on almost all scales. In the families where the children's problems have also been measured (children from the age of four) it appeared that they had problems of a nature and degree otherwise found in psychiatric populations. We found a clear general trend towards a positive development from T1 to T2 and this development was also reinforced from T2 to T3. Aggression in the child was one of the most common causes for contact. There were few undesired or unplanned interruptions of the treatment, and the attrition from the study was low.</p> <p>Conclusion</p> <p>This study has shown that it is possible to reach mothers as well as fathers with parenting problems and to create an intervention program with very low dropout levels – which is of special importance for families with small children displaying aggressive behaviour. The parents taking part in this study showed clear improvement trends after six months and this development was reinforced a year later. This study suggests the necessity of clinical development and future research concerning the role of fathers in parent-child interaction interventions.</p

Melanism in Peromyscus Is Caused by Independent Mutations in Agouti

Identifying the molecular basis of phenotypes that have evolved independently can provide insight into the ways genetic and developmental constraints influence the maintenance of phenotypic diversity. Melanic (darkly pigmented) phenotypes in mammals provide a potent system in which to study the genetic basis of naturally occurring mutant phenotypes because melanism occurs in many mammals, and the mammalian pigmentation pathway is well understood. Spontaneous alleles of a few key pigmentation loci are known to cause melanism in domestic or laboratory populations of mammals, but in natural populations, mutations at one gene, the melanocortin-1 receptor (Mc1r), have been implicated in the vast majority of cases, possibly due to its minimal pleiotropic effects. To investigate whether mutations in this or other genes cause melanism in the wild, we investigated the genetic basis of melanism in the rodent genus Peromyscus, in which melanic mice have been reported in several populations. We focused on two genes known to cause melanism in other taxa, Mc1r and its antagonist, the agouti signaling protein (Agouti). While variation in the Mc1r coding region does not correlate with melanism in any population, in a New Hampshire population, we find that a 125-kb deletion, which includes the upstream regulatory region and exons 1 and 2 of Agouti, results in a loss of Agouti expression and is perfectly associated with melanic color. In a second population from Alaska, we find that a premature stop codon in exon 3 of Agouti is associated with a similar melanic phenotype. These results show that melanism has evolved independently in these populations through mutations in the same gene, and suggest that melanism produced by mutations in genes other than Mc1r may be more common than previously thought

Variance in brain volume with advancing age: implications for defining the limits of normality

Background: Statistical models of normal ageing brain tissue volumes may support earlier diagnosis of increasingly common, yet still fatal, neurodegenerative diseases. For example, the statistically defined distribution of normal ageing brain tissue volumes may be used as a reference to assess patient volumes. To date, such models were often derived from mean values which were assumed to represent the distributions and boundaries, i.e. percentile ranks, of brain tissue volume. Since it was previously unknown, the objective of the present study was to determine if this assumption was robust, i.e. whether regression models derived from mean values accurately represented the distributions and boundaries of brain tissue volume at older ages. Materials and Methods: We acquired T1-w magnetic resonance (MR) brain images of 227 normal and 219 Alzheimer’s disease (AD) subjects (aged 55-89 years) from publicly available databanks. Using nonlinear regression within both samples, we compared mean and percentile rank estimates of whole brain tissue volume by age. Results: In both the normal and AD sample, mean regression estimates of brain tissue volume often did not accurately represent percentile rank estimates (errors=-74% to 75%). In the normal sample, mean estimates generally underestimated differences in brain volume at percentile ranks below the mean. Conversely, in the AD sample, mean estimates generally underestimated differences in brain volume at percentile ranks above the mean. Differences between ages at the 5th percentile rank of normal subjects were ~39% greater than mean differences in the AD subjects. Conclusions: While more data are required to make true population inferences, our results indicate that mean regression estimates may not accurately represent the distributions of ageing brain tissue volumes. This suggests that percentile rank estimates will be required to robustly define the limits of brain tissue volume in normal ageing and neurodegenerative disease