Effects of burning on vegetation, soil physicochemistry and prokaryotic microbial communities in surface and subsurface peat.

Prescribed burning is a common management strategy in peatlands that has the potential to affect soil physicochemistry, alter biogeochemical cycles and trigger changes in vegetation structure. How burning affects prokaryotic community composition across different soil profiles is not well understood. This study explored the effects of prescribed burning on the diversity of prokaryotic communities in peat soils.

Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition.

Climate warming is known to impact ecosystem composition and functioning. However, it remains largely unclear how soil microbial communities respond to long-term, moderate warming. In this study, we used Illumina sequencing and microarrays (GeoChip 5.

Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species.

Although recombination is accepted to be common in bacteria, for many species robust phylogenies with well-resolved branches can be reconstructed from whole genome alignments of strains, and these are generally interpreted to reflect clonal relationships. Using new methods based on the statistics of single-nucleotide polymorphism (SNP) splits, we show that this interpretation is incorrect. For many species, each locus has recombined many times along its line of descent, and instead of many loci supporting a common phylogeny, the phylogeny changes many thousands of times along the genome alignment.

Long-term nitrogen deposition increases heathland carbon sequestration.

The large increases in reactive nitrogen (N) deposition in developed countries since the Industrial Revolution have had a marked impact on ecosystem functioning, including declining species richness, shifts in species composition, and increased N leaching. A potential mitigation of these harmful effects is the action of N as a fertiliser, which, through increasing primary productivity (and subsequently, organic matter production), has the potential to increase ecosystem carbon (C) storage. Here we report the response of an upland heath to 10years of experimental N addition.

Predicting the Responses of Soil Nitrite-Oxidizers to Multi-Factorial Global Change: A Trait-Based Approach.

Soil microbial diversity is huge and a few grams of soil contain more bacterial taxa than there are bird species on Earth. This high diversity often makes predicting the responses of soil bacteria to environmental change intractable and restricts our capacity to predict the responses of soil functions to global change. Here, using a long-term field experiment in a California grassland, we studied the main and interactive effects of three global change factors (increased atmospheric CO2 concentration, precipitation and nitrogen addition, and all their factorial combinations, based on global change scenarios for central California) on the potential activity, abundance and dominant taxa of soil nitrite-oxidizing bacteria (NOB).

State-space models' dirty little secrets: even simple linear Gaussian models can have estimation problems.

State-space models (SSMs) are increasingly used in ecology to model time-series such as animal movement paths and population dynamics. This type of hierarchical model is often structured to account for two levels of variability: biological stochasticity and measurement error. SSMs are flexible.

A Robust ANOVA Approach to Estimating a Phylogeny from Multiple Genes.

In this article, we address the issue of estimating the phylogenetic tree based on sequence data across a set of genes. Recognizing that the individual gene trees may not all share the same evolutionary history due to lateral gene transfer or differences in rates of evolution for instance, we develop a robust algorithm for tree estimation based on pairwise distances computed gene by gene. A robust analysis of variance (ANOVA) is used to combine the distances across all genes giving a summary distance for all genes.

Combining distance matrices on identical taxon sets for multi-gene analysis with singular value decomposition.

We present a simple and effective method for combining distance matrices from multiple genes on identical taxon sets to obtain a single representative distance matrix from which to derive a combined-gene phylogenetic tree. The method applies singular value decomposition (SVD) to extract the greatest common signal present in the distances obtained from each gene. The first right eigenvector of the SVD, which corresponds to a weighted average of the distance matrices of all genes, can thus be used to derive a representative tree from multiple genes.

Inertia in an ombrotrophic bog ecosystem in response to 9 years' realistic perturbation by wet deposition of nitrogen, separated by form.

Wet deposition of nitrogen (N) occurs in oxidized (nitrate) and reduced (ammonium) forms. Whether one form drives vegetation change more than the other is widely debated, as field evidence has been lacking. We are manipulating N form in wet deposition to an ombrotrophic bog, Whim (Scottish Borders), and here report nine years of results.

Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments.

Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures.

Monitoring field susceptibility to imidacloprid in the cat flea: a world-first initiative twelve years on.

In 2001, an international surveillance initiative was established, utilising a validated larval development inhibition assay to track the susceptibility of cat flea isolates to imidacloprid. In 2009, an Australian node was incorporated into the programme, joining laboratories in the United States and Europe. Field isolates of Ctenocephalides felis eggs were submitted to participating laboratories and, where egg quantity and quality was sufficient, were placed in the imidacloprid discriminating dose bioassay for evaluation.

Fitting nonstationary general-time-reversible models to obtain edge-lengths and frequencies for the barry-hartigan model.

Among models of nucleotide evolution, the Barry and Hartigan (BH) model (also known as the General Markov Model) is very flexible as it allows separate arbitrary substitution matrices along edges. For a given tree, the estimates of the BH model are a set of joint probability matrices, each giving the pairwise frequencies of nucleotides at the ends of the edge. We have previously shown that, due to an identifiability problem, these cannot be expected to consistently estimate the actual pairwise frequencies.

Phylogenetic analysis based on spectral methods.

Whole-genome or multiple gene phylogenetic analysis is of interest since single gene analysis often results in poorly resolved trees. Here, the use of spectral techniques for analyzing multigene data sets is explored. The protein sequences are treated as categorical time series, and a measure of similarity between a pair of sequences, the spectral covariance, is based on the common periodicity between these two sequences.

Pattern classification of phylogeny signals.

In this paper we propose the minimum entropy clustering (MEC) method for clustering genes based on their phylogenetic signals. This entropy based method will cluster two genes together when their concatenation can decrease the entropy. An integral feature of MEC is that it chooses the number of clusters automatically, which is a major advantage over the other methods.

Examining protein structure and similarities by spectral analysis technique.

The spectral envelope, a frequency based technique for analyzing categorical time series, is applied to amino acid sequences to examine their periodicity. The periodic signatures of such sequences is related to the secondary structure of the folding patterns in the gene. For a pair of sequences, we define a spectral envelope covariance which emphasizes the common periodicities in the two sequences.

Test a clade in phylogenetic trees.

We develop a new method for testing a portion of a tree (called a clade) based on multiple tests of many 4-taxon trees in this paper. This is particularly useful when the phylogenetic tree constructed by other methods have a clade that is difficult to explain from a biological point of view. The statement about the test of the clade can be made through the multiple P values from these individual tests.

The comparison of the confidence regions in phylogeny.

In this paper, several different procedures for constructing confidence regions for the true evolutionary tree are evaluated both in terms of coverage and size without considering model misspecification. The regions are constructed on the basis of tests of hypothesis using six existing tests: Shimodaira Hasegawa (SH), SOWH, star form of SOWH (SSOWH), approximately unbiased (AU), likelihood weight (LW), generalized least squares, plus two new tests proposed in this paper: single distribution nonparametric bootstrap (SDNB) and single distribution parametric bootstrap (SDPB). The procedures are evaluated on simulated trees both with small and large number of taxa.

Estimation of rates-across-sites distributions in phylogenetic substitution models.

Previous work has shown that it is often essential to account for the variation in rates at different sites in phylogenetic models in order to avoid phylogenetic artifacts such as long branch attraction. In most current models, the gamma distribution is used for the rates-across-sites distributions and is implemented as an equal-probability discrete gamma. In this article, we introduce discrete distribution estimates with large numbers of equally spaced rate categories allowing us to investigate the appropriateness of the gamma model.

Laryngoscopic intubation: learning and performance.

Background: Many healthcare professionals are trained in direct laryngoscopic tracheal intubation (LEI), which is a potentially lifesaving procedure. This study attempts to determine the number of successful LEI exposures required during training to assure competent performance, with special emphasis on defining competence itself.

Methods: Analyses were based on a longitudinal study of novices under training conditions in the operating room.

Testing for differences in rates-across-sites distributions in phylogenetic subtrees.

It has long been recognized that the rates of molecular evolution vary amongst sites in proteins. The usual model for rate heterogeneity assumes independent rate variation according to a rate distribution. In such models the rate at a site, although random, is assumed fixed throughout the evolutionary tree.