Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria

Xenoturbella and the acoelomorph worms (Xenacoe-lomorpha) are simple marine animals with controversial affinities. They have been placed as the sister group of all other bilaterian animals (Nephrozoa hypothesis), implying their simplicity is an ancient characteristic [1, 2]; alternatively, they have been linked to the complex Ambulacraria (echinoderms and hemichordates) in a Glade called the Xenambulacraria [3,5], suggesting their simplicity evolved by reduction from a complex ancestor. The difficulty resolving this problem implies the phylogenetic signal supporting the correct solution is weak and affected by inadequate modeling, creating a misleading non-phylogenetic signal. The idea that the Nephrozoa hypothesis might be an artifact is prompted by the faster molecular evolutionary rate observed within the Acoelomorpha. Unequal rates of evolution are known to result in the systematic artifact of long branch attraction, which would be predicted to result in an attraction between long-branch acoelomorphs and the outgroup, pulling them toward the root [6]. Other biases inadequately accommodated by the models used can also have strong effects, exacerbated in the context of short internal branches and long terminal branches [7]. We have assembled a large and informative dataset to address this problem. Analyses designed to reduce or to emphasize misleading signals show the Nephrozoa hypothesis is supported under conditions expected to exacerbate errors, and the Xenambulacraria hypothesis is preferred in conditions designed to reduce errors. Our reanalyses of two other recently published datasets [1, 2] produce the same result. We conclude that the Xenacoelomorpha are simplified relatives of the Ambulacraria

Temporal and spatial variations in the parasitoid complex of the horse chestnut leafminer during its invasion of Europe

The enemy release hypothesis posits that the initial success of invasive species depends on the scarcity and poor adaptation of native natural enemies such as predators and parasitoids. As for parasitoids, invading hosts are first attacked at low rates by a species-poor complex of mainly generalist species. Over the years, however, parasitoid richness may increase either because the invading host continuously encounters new parasitoid species during its spread (geographic spread-hypothesis) or because local parasitoids need different periods of time to adapt to the novel host (adjustment-hypothesis). Both scenarios should result in a continuous increase of parasitoid richness over time. In this study, we reconstructed the development of the hymenopteran parasitoid complex of the invasive leafminer Cameraria ohridella (Lepidoptera, Gracillariidae). Our results show that the overall parasitism rate increases as a function of host residence time as well as geographic and climatic factors, altogether reflecting the historic spread of C. ohridella. The same variables also explain the individual parasitism rates of several species in the parasitoid complex, but fail to explain the abundance of others. Evidence supporting the “geographic spread-hypothesis” was found in the parasitism pattern of Cirrospilus talitzkii (Hymenoptera, Eulophidae), while that of Pediobius saulius, another eulophid, indicated an increase of parasitism rates by behavioral, phenological or biological adjustments. Compared to fully integrated host-parasitoid associations, however, parasitism rates of C. ohridella are still very low. In addition, the parasitoid complex lacks specialists, provided that the species determined are valid and not complexes of cryptic (and presumably more specialized) species. Probably, the adjustment of specialist parasitoids requires more than a few decades, particularly to invaders which establish in ecological niches free of native hosts, thus eliminating any possibility of recruitment of pre-adapted parasitoids

Cadophora margaritata sp. nov. and other fungi associated with the longhorn beetles Anoplophora glabripennis and Saperda carcharias in Finland

Symbiosis with microbes is crucial for survival and development of wood-inhabiting longhorn beetles (Coleoptera: Cerambycidae). Thus, knowledge of the endemic fungal associates of insects would facilitate risk assessment in cases where a new invasive pest occupies the same ecological niche. However, the diversity of fungi associated with insects remains poorly understood. The aim of this study was to investigate fungi associated with the native large poplar longhorn beetle (Saperda carcharias) and the recently introduced Asian longhorn beetle (Anoplophora glabripennis) infesting hardwood trees in Finland. We studied the cultivable fungal associates obtained from Populus tremula colonised by S. carcharias, and Betula pendula and Salix caprea infested by A. glabripennis, and compared these to the samples collected from intact wood material. This study detected a number of plant pathogenic and saprotrophic fungi, and species with known potential for enzymatic degradation of wood components. Phylogenetic analyses of the most commonly encountered fungi isolated from the longhorn beetles revealed an association with fungi residing in the Cadophora-Mollisia species complex. A commonly encountered fungus was Cadophora spadicis, a recently described fungus associated with wood-decay. In addition, a novel species of Cadophora, for which the name Cadophora margaritata sp. nov. is provided, was isolated from the colonised wood.Peer reviewe

OMA standalone: orthology inference among public and custom genomes and transcriptomes.

Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many analyses lies in identifying orthologs-corresponding genes across multiple species-but this is far from trivial. The Orthologous MAtrix (OMA) database is a leading resource for identifying orthologs among publicly available, complete genomes. Here, we describe the OMA pipeline available as a standalone program for Linux and Mac. When run on a cluster, it has native support for the LSF, SGE, PBS Pro, and Slurm job schedulers and can scale up to thousands of parallel processes. Another key feature of OMA standalone is that users can combine their own data with existing public data by exporting genomes and precomputed alignments from the OMA database, which currently contains over 2100 complete genomes. We compare OMA standalone to other methods in the context of phylogenetic tree inference, by inferring a phylogeny of Lophotrochozoa, a challenging clade within the protostomes. We also discuss other potential applications of OMA standalone, including identifying gene families having undergone duplications/losses in specific clades, and identifying potential drug targets in nonmodel organisms. OMA standalone is available under the permissive open source Mozilla Public License Version 2.0

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

International audienceThe Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e. the protein sequence associated for every protein-coding gene in all genomes). In this update article, we present six major new developments in OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part of the OMA pipeline; (iii) better support for plant genomes and in particular homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of orthologs; (v) statically computed hierarchical orthologous groups subsets downloadable in OrthoXML format; and (vi) possibility to export parts of the all-against-all computations and to combine them with custom data for 'client-side' orthology prediction. OMA can be accessed through the OMA Browser and various programmatic interfaces at http://omabrowser.org

Defend or raise? Optimising flood risk reduction strategies

Flood risk reduction can be provided by interventions such as raising land or constructing flood defences. This paper introduces an approach to optimise the selection of risk reduction strategies. It expands existing economic optimization approaches for flood defences, by introducing (largely) analytical formulations to include the effects of approaches to mitigate flood consequences. The method considers the size of the protected area and associated damages, the costs and dimensioning of interventions and the likelihood of flooding. It is applied in several practical cases. Within the context of this economic model, we conclude that a system of flood defences is more economical than a landfill for larger areas. Fills are preferred for small areas and/or for low costs. A combination of strategies is preferred when the value protected by the flood defence is low compared to the value protected by the fill, or when the high value development is relatively small in size. The sensitivity of outcomes to the choice of the main input parameters is presented, as well as implications of the results and selection of strategies in developing and developed countries. Overall, this approach supports decision makers in developing effective strategies to manage and reduce flood risk.Hydraulic Structures and Flood Ris