Effect of the spatial distribution of physical aquifer properties on modelled water table depth and stream discharge in a headwater catchment

Water table depth and its dynamics on hillslopes are often poorly predicted despite they control both water transit time within the catchment and solute fluxes at the catchment outlet. This paper analyses how relaxing the assumption of lateral homogeneity of physical properties can improve simulations of water table depth and dynamics. Four different spatial models relating hydraulic conductivity to topography have been tested: a simple linear relationship, a linear relationship with two different topographic indexes, two <i>Ks</i> domains with a transitional area. The Hill-Vi model has been modified to test these hypotheses. The studied catchment (Kervidy-Naizin, Western France) is underlain by schist crystalline bedrock. A shallow and perennial groundwater highly reactive to rainfall events mainly develops in the weathered saprolite layer. The results indicate that (1) discharge and the water table in the riparian zone are similarly predicted by the four models, (2) distinguishing two <i>Ks</i> domains constitutes the best model and slightly improves prediction of the water table upslope, and (3) including spatial variations in the other parameters such as porosity or rate of hydraulic conductivity decrease with depth does not improve the results. These results underline the necessity of better investigations of upslope areas in hillslope hydrology

Rapidly Computing the Phylogenetic Transfer Index

Given trees T and T_o on the same taxon set, the transfer index phi(b,T_o) is the number of taxa that need to be ignored so that the bipartition induced by branch b in T is equal to some bipartition in T_o. Recently, Lemoine et al. [Lemoine et al., 2018] used the transfer index to design a novel bootstrap analysis technique that improves on Felsenstein\u27s bootstrap on large, noisy data sets. In this work, we propose an algorithm that computes the transfer index for all branches b in T in O(n log^3 n) time, which improves upon the current O(n^2)-time algorithm by Lin, Rajan and Moret [Lin et al., 2012]. Our implementation is able to process pairs of trees with hundreds of thousands of taxa in minutes and considerably speeds up the method of Lemoine et al. on large data sets. We believe our algorithm can be useful for comparing large phylogenies, especially when some taxa are misplaced (e.g. due to horizontal gene transfer, recombination, or reconstruction errors)

Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference

Many phylogenetic algorithms search the space of possible trees using topological rearrangements and some optimality criterion. FastME is such an approach that uses the balanced minimum evolution (BME) principle, which computer studies have demonstrated to have high accuracy. FastME includes two variants: balanced subtree prune and regraft (BSPR) and balanced nearest neighbor interchange (BNNI). These algorithms take as input a distance matrix and a putative phylogenetic tree. The tree is modified using SPR or NNI operations, respectively, to reduce the BME length relative to the distance matrix, until a tree with (locally) shortest BME length is found. Following computer simulations, it has been conjectured that BSPR and BNNI are consistent, i.e. for an input distance that is a tree-metric, they converge to the corresponding tree. We prove that the BSPR algorithm is consistent. Moreover, even if the input contains small errors relative to a tree-metric, we show that the BSPR algorithm still returns the corresponding tree. Whether BNNI is consistent remains open

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree. The Phylogeny.fr platform transparently chains programs to automatically perform these tasks. It is primarily designed for biologists with no experience in phylogeny, but can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. Phylogeny.fr offers three main modes. The ‘One Click’ mode targets non-specialists and provides a ready-to-use pipeline chaining programs with recognized accuracy and speed: MUSCLE for multiple alignment, PhyML for tree building, and TreeDyn for tree rendering. All parameters are set up to suit most studies, and users only have to provide their input sequences to obtain a ready-to-print tree. The ‘Advanced’ mode uses the same pipeline but allows the parameters of each program to be customized by users. The ‘A la Carte’ mode offers more flexibility and sophistication, as users can build their own pipeline by selecting and setting up the required steps from a large choice of tools to suit their specific needs. Prior to phylogenetic analysis, users can also collect neighbors of a query sequence by running BLAST on general or specialized databases. A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. Phylogeny.fr is available at: http://www.phylogeny.fr

A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism

<p>Abstract</p> <p>Background</p> <p>The <it>Plasmodium falciparum </it>genome (3D7 strain) published in 2002, revealed ~5,400 genes, mostly based on <it>in silico </it>predictions. Experimental data is therefore required for structural and functional assessments of <it>P. falciparum </it>genes and expression, and polymorphic data are further necessary to exploit genomic information to further qualify therapeutic target candidates. Here, we undertook a large scale analysis of a <it>P. falciparum </it>FcB1-schizont-EST library previously constructed by suppression subtractive hybridization (SSH) to study genes expressed during merozoite morphogenesis, with the aim of: 1) obtaining an exhaustive collection of schizont specific ESTs, 2) experimentally validating or correcting <it>P. falciparum </it>gene models and 3) pinpointing genes displaying protein polymorphism between the FcB1 and 3D7 strains.</p> <p>Results</p> <p>A total of 22,125 clones randomly picked from the SSH library were sequenced, yielding 21,805 usable ESTs that were then clustered on the <it>P. falciparum </it>genome. This allowed identification of 243 protein coding genes, including 121 previously annotated as hypothetical. Statistical analysis of GO terms, when available, indicated significant enrichment in genes involved in "entry into host-cells" and "actin cytoskeleton". Although most ESTs do not span full-length gene reading frames, detailed sequence comparison of FcB1-ESTs versus 3D7 genomic sequences allowed the confirmation of exon/intron boundaries in 29 genes, the detection of new boundaries in 14 genes and identification of protein polymorphism for 21 genes. In addition, a large number of non-protein coding ESTs were identified, mainly matching with the two A-type rRNA units (on chromosomes 5 and 7) and to a lower extent, two atypical rRNA loci (on chromosomes 1 and 8), TARE subtelomeric regions (several chromosomes) and the recently described telomerase RNA gene (chromosome 9).</p> <p>Conclusion</p> <p>This FcB1-schizont-EST analysis confirmed the actual expression of 243 protein coding genes, allowing the correction of structural annotations for a quarter of these sequences. In addition, this analysis demonstrated the actual transcription of several remarkable non-protein coding loci: 2 atypical rRNA, TARE region and telomerase RNA gene. Together with other collections of <it>P. falciparum </it>ESTs, usually generated from mixed parasite stages, this collection of FcB1-schizont-ESTs provides valuable data to gain further insight into the <it>P. falciparum </it>gene structure, polymorphism and expression.</p

Scaling properties of protein family phylogenies

One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of balance) of a large set of protein phylogenies with a set of species phylogenies. The comparative analysis shows that both sets of phylogenies share remarkably similar scaling behavior, suggesting the universality of branching rules and of the evolutionary processes that drive biological diversification from gene to species level. In order to explain such generality, we propose a simple model which allows us to estimate the proportion of evolvability/robustness needed to approximate the scaling behavior observed in the phylogenies, highlighting the relevance of the robustness of a biological system (species or protein) in the scaling properties of the phylogenetic trees. Thus, the rules that govern the incapability of a biological system to diversify are equally relevant both at the gene and at the species level.Comment: Replaced with final published versio

Mesoscale productivity fronts and local fishing opportunities in the European Seas

This study evaluates the relationship between both commercial and scientific spatial fisheries data and a new satellite-based estimate of potential fish production (Ocean Productivity available to Fish, OPFish) in the European Seas. To construct OPFish, we used productivity frontal features derived from chlorophyll-a horizontal gradients, which characterize 10%–20% of the global phytoplankton production that effectively fuels higher trophic levels. OPFish is relatively consistent with the spatial distribution of both pelagic and demersal fish landings and catches per unit of effort (LPUEs and CPUEs, respectively). An index of harvest relative to ocean productivity (HP index) is calculated by dividing these LPUEs or CPUEs with OPFish. The HP index reflects the intensity of fishing by gear type with regard to local fish production. Low HP levels indicate lower LPUEs or CPUEs than expected from oceanic production, suggesting over-exploitation, while high HP levels imply more sustainable fishing. HP allows comparing the production-dependent suitability of local fishing intensities. Our results from bottom trawl data highlight that over-exploitation of demersal species from the shelves is twice as high in the Mediterranean Sea than in the North-East Atlantic. The estimate of HP index by dominant pelagic and demersal gears suggests that midwater and bottom otter trawls are associated with the lowest and highest overfishing, respectively. The contrasts of fishing intensity at local scales captured by the HP index suggest that accounting for the local potential fish production can promote fisheries sustainability in the context of ecosystem-based fisheries management as required by international marine policies

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

Supplementary tables S1, sections 2.1–2.3, and figures S1–S11 are available at Molecular Biology and Evolution online (http://www.mbe.oxfordjournals.org/).Recent sequencing and computing advances have enabled phylogenetic analyses to expand to both entire genomes and large clades, thus requiring more efficient and accurate methods designed specifically for the phylogenomic context. Here, we present SPIMAP, an efficient Bayesian method for reconstructing gene trees in the presence of a known species tree. We observe many improvements in reconstruction accuracy, achieved by modeling multiple aspects of evolution, including gene duplication and loss (DL) rates, speciation times, and correlated substitution rate variation across both species and loci. We have implemented and applied this method on two clades of fully sequenced species, 12 Drosophila and 16 fungal genomes as well as simulated phylogenies and find dramatic improvements in reconstruction accuracy as compared with the most popular existing methods, including those that take the species tree into account. We find that reconstruction inaccuracies of traditional phylogenetic methods overestimate the number of DL events by as much as 2–3-fold, whereas our method achieves significantly higher accuracy. We feel that the results and methods presented here will have many important implications for future investigations of gene evolution.National Science Foundation (U.S.) (CAREER award NSF 0644282