The impact of multiple protein sequence alignment on phylogenetic estimation

Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will phylogenetic reconstructions. Over the last decade or so, new multiple sequence alignment methods have been developed to improve comparative analyses of protein structure, but these new methods have not been typically used in phylogenetic analyses. In this paper, we report on a simulation study that we performed to evaluate the consequences of using these new multiple sequence alignment methods in terms of the resultant phylogenetic reconstruction. We find that while alignment accuracy is positively correlated with phylogenetic accuracy, the amount of improvement in phylogenetic estimation that results from an improved alignment can range from quite small to substantial. We observe that phylogenetic accuracy is most highly correlated with alignment accuracy when sequences are most difficult to align, and that variation in alignment accuracy can have little impact on phylogenetic accuracy when alignment error rates are generally low. We discuss these observations and implications for future work.     

SEASONAL PATTERNS IN THE BELOWGROUND BIOMASS OF SPARTINA ALTERNIFLORA (GRAMINEAE) ACROSS A TIDAL GRADIENT

Belowground biomass of two ht forms of the salt marsh cordgrass, Spartina alterniflora, in a New England salt marsh exhibited a seasonal cycle. Biomass was highest in midsummer with no secondary peak in biomass corresponding with the autumn dieback of aboveground parts. Total annual biomass production and the maximum depth that living tissue penetrated into the substrate decreased with increasing tidal ht. Substrate characteristics (soil aeration, pH, nutrient levels) known to affect aboveground biomass of S. alterniflora also decreased with increasing tidal ht and may similarly affect belowground biomass across the same tidal gradient.     

Heavy metal fractionation during the co-composting of biosolids,deinking paper fibre and green waste

Due to the introduction of the European Union Landfill Directive, composting has become a potentially viable disposal route for some organic wastes. As waste-derived compost is frequently added to soil to improve soil quality, it is important to quantify the environmental risk posed by potentially toxic elements contained within it. Here we used a sequential chemical extraction procedure to investigate the temporal dynamics of heavy metals (Cu, Zn, Pb and Ni) during the co-composting of biosolids, deinking paper fibre and green waste. Overall, composting over 26 weeks reduced the availability of Ni, had no effect on Pb and slightly increased the availability of Cu and Zn. We conclude that although the total Cu and Ni concentrations in the compost exceed legislative guidelines for land application, due to their recalcitrant nature within the compost, this compost posed very little threat to soil or plant quality if used in agriculture or land restoration.     

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees

Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of those sequences that maximize likelihood under the Jukes-Cantor model is uninformative in the worst possible sense. For all inputs, all trees optimize the likelihood score. Second, we show that a greedy heuristic that uses GTR+Gamma ML to optimize the alignment and the tree can produce very poor alignments and trees. Therefore, the excellent performance of SATé-II and SATé-I is not because ML is used as an optimization criterion for choosing the best tree/alignment pair but rather due to the particular divide-and-conquer realignment techniques employed.     

An experimental study of Quartets MaxCut and other supertree methods

Background  

Supertree methods represent one of the major ways by which the Tree of Life can be estimated, but despite many recent algorithmic innovations, matrix representation with parsimony (MRP) remains the main algorithmic supertree method.     

Modification of Fertility of Soil Materials for Restoration of Acid Grassland Habitat

Use of composts for habitat restoration offers advantages in terms of efficient use of resources. Chemical amendment of compost to reduce its pH and P availability was investigated in order to improve suitability for use in reclamation of blocky quarry waste to acidic grassy heathland. The effect of these amendments was observed on competition between two grass species: Agrostis capillaris and Festuca ovina. A factorial, pot‐scale greenhouse experiment was set up using two composts (one a mixture of green waste and catering waste, and the other a mixture of green waste and sewage sludge). In addition, two soils were collected from upland acidic grassland to provide a natural comparison. S⁰ was applied to reduce soil pH, and Fe(OH)₃ from a coal waste treatment plant was applied to counteract the expected increase in P availability due to acidification of the composts by S⁰. Addition of S⁰ significantly reduced soil solution pH and addition of Fe(OH)₃ significantly reduced soil solution P concentration. In one compost S⁰ reduced the biomass of F. ovina while increasing that of A. capillaris, whereas Fe(OH)₃ had no significant effect on the biomass of either species. Although S⁰ and Fe(OH)₃ did adjust the chemical properties of the soil solution, Fe(OH)₃ did not bind P strongly enough to make it unavailable to plants. Further work is required, however, the use of chemically amended composts provides a sustainable sink for organic wastes and we conclude from this study that they have great potential for large‐scale restoration of blocky waste tips.     

Dietary phospholipids, hepatic lipid metabolism and cardiovascular disease

PURPOSE OF REVIEW: An increasing number of studies in experimental animals suggest that dietary phospholipids might be of benefit in the treatment of fatty liver disease. This raises the possibility that synthetic or naturally occurring phospholipid isolates could be used as hepatoprotective nutraceuticals or functional foods. The aim of the present article is to review published data describing the beneficial effects of dietary phospholipids on hepatic lipid metabolism and their potential to affect atherosclerosis and cardiovascular disease. RECENT FINDINGS: Consistent results have been obtained supporting the concept that phospholipid from various sources (i.e., soybean, safflower, egg and fish roe) can reduce liver lipid levels. The primary site of action for this effect appears to be in the intestinal lumen, where dietary phospholipids are able to interfere with neutral sterol absorption. Results have also been obtained suggesting that dietary phospholipids can stimulate bile acid and cholesterol secretion. Additional work suggests that dietary phospholipids can have a beneficial effect on plasma lipid and lipoprotein levels. SUMMARY: The concept of using naturally occurring compounds such as phospholipid to treat or prevent hepatic steatosis is very attractive. Controlled human trials are, however, required to verify the efficacy of this approach. It is also important that additional research be conducted to determine the extent to which certain phospholipids have the ability to increase plasma HDL levels and potentially affect the onset or development of cardiovascular disease.     

Assay and Electrophoresis of Superoxide Dismutase from Red Spruce (Picea rubens Sarg.), Loblolly Pine (Pinus taeda L.), and Scotch Pine (Pinus sylvestris L.) : A Method for Biomonitoring

This paper reports a method for extracting the antioxidant enzyme superoxide dismutase (SOD) from the needles of red spruce (Picea rubens Sarg.), loblolly pine (Pinus taeda L.), and scotch pine (Pinus sylvestris L.) with high efficiency and free from interfering compounds. The extraction employs phosphate buffer with polyvinylpolypyrrolidone and Triton X-100 followed by dialysis overnight. The isozymes of SOD in each species were separated electrophoretically and tested for their sensitivity to KCN and H₂O₂. An isozyme resistant to these inhibitors was found in the spruce but not the pine needles. The isozymes from the spruce needles were examined for individual responses to aging and H₂O₂ inhibition. Four of the five CuZn isozymes in spruce were found to have increased significantly but equally by October of their first year and two of those four isozymes were found to be more sensitive to H₂O₂. The response of the SOD isozymes in loblolly pine seedlings to O₃ was also examined and the isozymes were found to be induced equally. Because the SOD activity in the young pine needles was too low to electrophorese, the SOD activity from the pines in the O₃ experiment had to be partially purified using CHCl₃ and ethanol, then concentrated.     

A simulation study comparing supertree and combined analysis methods using SMIDGen

Background  

Supertree methods comprise one approach to reconstructing large molecular phylogenies given multi-marker datasets: trees are estimated on each marker and then combined into a tree (the "supertree") on the entire set of taxa. Supertrees can be constructed using various algorithmic techniques, with the most common being matrix representation with parsimony (MRP). When the data allow, the competing approach is a combined analysis (also known as a "supermatrix" or "total evidence" approach) whereby the different sequence data matrices for each of the different subsets of taxa are concatenated into a single supermatrix, and a tree is estimated on that supermatrix.     

Scaling statistical multiple sequence alignment to large datasets

Background

Multiple sequence alignment is an important task in bioinformatics, and alignments of large datasets containing hundreds or thousands of sequences are increasingly of interest. While many alignment methods exist, the most accurate alignments are likely to be based on stochastic models where sequences evolve down a tree with substitutions, insertions, and deletions. While some methods have been developed to estimate alignments under these stochastic models, only the Bayesian method BAli-Phy has been able to run on even moderately large datasets, containing 100 or so sequences. A technique to extend BAli-Phy to enable alignments of thousands of sequences could potentially improve alignment and phylogenetic tree accuracy on large-scale data beyond the best-known methods today.

Results

We use simulated data with up to 10,000 sequences representing a variety of model conditions, including some that are significantly divergent from the statistical models used in BAli-Phy and elsewhere. We give a method for incorporating BAli-Phy into PASTA and UPP, two strategies for enabling alignment methods to scale to large datasets, and give alignment and tree accuracy results measured against the ground truth from simulations. Comparable results are also given for other methods capable of aligning this many sequences.

Conclusions

Extensions of BAli-Phy using PASTA and UPP produce significantly more accurate alignments and phylogenetic trees than the current leading methods.