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Molluscs are the second most species-rich phylum in the animal kingdom, yet only 11 genomes of this group have been published so far. Here, we present the draft genome sequence of the pulmonate freshwater snail Radix auricularia. Six whole genome shotgun libraries with different layouts were sequenced. The resulting assembly comprises 4,823 scaffolds with a cumulative length of 910 Mb and an overall read coverage of 72×. The assembly contains 94.6% of a metazoan core gene collection, indicating an almost complete coverage of the coding fraction. The discrepancy of ∼690 Mb compared with the estimated genome size of R. auricularia (1.6 Gb) results from a high repeat content of 70% mainly comprising DNA transposons. The annotation of 17,338 protein coding genes was supported by the use of publicly available transcriptome data. This draft will serve as starting point for further genomic and population genetic research in this scientifically important phylum.
One of the major problems in evolutionary biology is to elucidate the relationships between historical events and the tempo and mode of lineage divergence. The development of relaxed molecular clock models and the increasing availability of DNA sequences resulted in more accurate estimations of taxa divergence times. However, finding the link between competing historical events and divergence is still challenging. Here we investigate assigning constrained-age priors to nodes of interest in a time-calibrated phylogeny as a means of hypothesis comparison. These priors are equivalent to historic scenarios for lineage origin. The hypothesis that best explains the data can be selected by comparing the likelihood values of the competing hypotheses, modelled with different priors. A simulation approach was taken to evaluate the performance of the prior-based method and to compare it with an unconstrained approach. We explored the effect of DNA sequence length and the temporal placement and span of competing hypotheses (i.e. historic scenarios) on selection of the correct hypothesis and the strength of the inference. Competing hypotheses were compared applying a posterior simulation analogue of the Akaike Information Criterion and Bayes factors (obtained after calculation of the marginal likelihood with three estimators: Harmonic Mean, Stepping Stone and Path Sampling). We illustrate the potential application of the prior-based method on an empirical data set to compare competing geological hypotheses explaining the biogeographic patterns in Pleurodeles newts. The correct hypothesis was selected on average 89% times. The best performance was observed with DNA sequence length of 3500-10000 bp. The prior-based method is most reliable when the hypotheses compared are not temporally too close. The strongest inferences were obtained when using the Stepping Stone and Path Sampling estimators. The prior-based approach proved effective in discriminating between competing hypotheses when used on empirical data. The unconstrained analyses performed well but it probably requires additional computational effort. Researchers applying this approach should rely only on inferences with moderate to strong support. The prior-based approach could be applied on biogeographical and phylogeographical studies where robust methods for historical inferences are still lacking.
Aim: Predicting future changes in species richness in response to climate change is one of the key challenges in biogeography and conservation ecology. Stacked species distribution models (S‐SDMs) are a commonly used tool to predict current and future species richness. Macroecological models (MEMs), regression models with species richness as response variable, are a less computationally intensive alternative to S‐SDMs. Here, we aim to compare the results of two model types (S‐SDMS and MEMs), for the first time for more than 14,000 species across multiple taxa globally, and to trace the uncertainty in future predictions back to the input data and modelling approach used.
Location: Global land, excluding Antarctica.
Taxon: Amphibians, birds and mammals.
Methods: We fitted S‐SDMs and MEMs using a consistent set of bioclimatic variables and model algorithms and conducted species richness predictions under current and future conditions. For the latter, we used four general circulation models (GCMs) under two representative concentration pathways (RCP2.6 and RCP6.0). Predicted species richness was compared between S‐SDMs and MEMs and for current conditions also to extent‐of‐occurrence (EOO) species richness patterns. For future predictions, we quantified the variance in predicted species richness patterns explained by the choice of model type, model algorithm and GCM using hierarchical cluster analysis and variance partitioning.
Results: Under current conditions, species richness predictions from MEMs and S‐SDMs were strongly correlated with EOO‐based species richness. However, both model types over‐predicted areas with low and under‐predicted areas with high species richness. Outputs from MEMs and S‐SDMs were also highly correlated among each other under current and future conditions. The variance between future predictions was mostly explained by model type.
Main conclusions: Both model types were able to reproduce EOO‐based patterns in global terrestrial vertebrate richness, but produce less collinear predictions of future species richness. Model type by far contributes to most of the variation in the different future species richness predictions, indicating that the two model types should not be used interchangeably. Nevertheless, both model types have their justification, as MEMs can also include species with a restricted range, whereas S‐SDMs are useful for looking at potential species‐specific responses.
Diatoms are thought to provide about 40% of total global photosynthesis and diatoms of the genus Coscinodiscus are an important, sometimes dominant, cosmopolitan component of the marine diatom community. The oomycete parasitoid Lagenisma coscinodisci is widespread in the northern hemisphere on its hosts in the genus Coscinodiscus. Because of its potential ecological importance, it would be a suitable pathogen model to investigate plankton/parasite interactions, but the species cannot be cultivated on media without its host, so far. Thus, it was the aim of this study to explore the potential of dual culture of host and pathogen in the laboratory and to optimise cultivation to ensure a long-term cultivation of the pathogen. Here, we report successful cultivation of a single spore strain of L. coscinodisci (Isla), on several Coscinodiscus species and strains, as well as the establishment of a cultivation routine with Coscinodiscus granii (CGS1 and CG36), which enabled us to maintain the single spore strain for more than 3 years in 6 cm Petri dishes and 10 ml tissue culture flasks. This opens up the opportunity to study the processes and mechanism in plankton/parasitoid interactions under controlled conditions.
Holocarpic oomycetes are poorly known but widespread parasites in freshwater and marine ecosystems. Most of the holocarpic species seem to belong to clades that diverge before the two crown lineages of the oomycetes, the Saprolegniomycetes and the Peronosporomycetes. Recently, the genus Miracula was described to accommodate Miracula helgolandica, a holocarpic parasitoid of Pseudo-nitzschia diatoms, which received varying support for its placement as the earliest-diverging oomycete lineage. In the same phylogenetic reconstruction, Miracula helgolandica was grouped with some somewhat divergent sequences derived from environmental sequencing, indicating that Miracula would not remain monotypic. Here, a second species of Miracula is reported, which was found as a parasitoid in the limnic centric diatom Pleurosira leavis. Its life-cycle stages are described and depicted in this study and its phylogenetic placement in the genus Miracula revealed. As a consequence, the newly discovered species is introduced as Miracula moenusica.
Olpidiopsis is a genus of obligate holocarpic endobiotic oomycetes. Most of the species classified in the genus are known only from their morphology and life cycle, and a few have been examined for their ultrastructure or molecular phylogeny. However, the taxonomic placement of all sequenced species is provisional, as no sequence data are available for the type species, O. saprolegniae, to consolidate the taxonomy of species currently placed in the genus. Thus, efforts were undertaken to isolate O. saprolegniae from its type host, Saprolegnia parasitica and to infer its phylogenetic placement based on 18S rDNA sequences. As most species of Olpidiopsis for which sequence data are available are from rhodophyte hosts, we have also isolated the type species of the rhodophyte-parasitic genus Pontisma, P. lagenidioides and obtained partial 18S rDNA sequences. Phylogenetic reconstructions in the current study revealed that O. saprolegniae from Saprolegnia parasitica forms a monophyletic group with a morphologically similar isolate from S. ferax, and a morphologically and phylogenetically more divergent species from S. terrestris. However, they were widely separated from a monophyletic, yet unsupported clade containing P. lagenidioides and red algal parasites previously classified in Olpidiopsis. Consequently, all holocarpic parasites in red algae should be considered to be members of the genus Pontisma as previously suggested by some researchers. In addition, a new species of Olpidiopsis, O. parthenogenetica is introduced to accommodate the pathogen of S. terrestris.
Microthlaspi erraticum is widely distributed in temperate Eurasia, but restricted to Ca2+-rich habitats, predominantly on white Jurassic limestone, which is made up by calcium carbonate, with little other minerals. Thus, naturally occurring Microthlaspi erraticum individuals are confronted with a high concentration of Ca2+ ions while Mg2+ ion concentration is relatively low. As there is a competitive uptake between these two ions, adaptation to the soil condition can be expected. In this study, it was the aim to explore the genomic consequences of this adaptation by sequencing and analysing the genome of Microthlaspi erraticum. Its genome size is comparable with other diploid Brassicaceae, while more genes were predicted. Two Mg2+ transporters known to be expressed in roots were duplicated and one showed a significant degree of positive selection. It is speculated that this evolved due to the pressure to take up Mg2+ ions efficiently in the presence of an overwhelming amount of Ca2+ ions. Future studies on plants specialized on similar soils and affinity tests of the transporters are needed to provide unequivocal evidence for this hypothesis. If verified, the transporters found in this study might be useful for breeding Brassicaceae crops for higher yield on Ca2+-rich and Mg2+ -poor soils.
La biodiversité comprend la plénitude de la vie dans toutes ses formes. Sa protection et son usage durable doivent ainsi être une partie intégrante d’une politique orientée vers l’avenir et ancrer de plus en plus dans la conscience politique et publique. La condition préalable pour cela est une meilleure compréhension des effets des actions humaines sur la biodiversité et une connaissance plus approfondie de sa valeur. La recherche scientifique contribue de façon indispensable à la préservation des biomes, des espèces et gènes. Elle ne se limite pas à fournir les connaissances fondamentales qui sont nécessaires pour arrêter le progrès de la disparition de la biodiversité. Bien plus, ce sont les chercheurs eux-mêmes qui, ensemble avec leurs partenaires locaux, élaborent des stratégies pour un usage durable de la biodiversité. Explorer la flore et la faune du continent africain, et mesurer les changements observés dans leur milieu naturel afin de les réduire, tels sont les objectifs de BIOTA (Biodiversity Monitoring Transect Analysis in Africa / Transect d´Analyse du suivi de la Biodiversité en Afrique de l´Ouest). Ce réseau de recherche a été créé en 1999 ensemble par les chercheurs africains et allemands. Vu la grande importance de BIOTA, cette initiative est non seulement financée par le Ministère fédérale de l’Education et de la Recherche, mais entre-temps aussi par plusieurs Etats africains et institutions partenaires. «BIOTA Ouest» a été lancé au début de 2001. Parmi les résultats de cette coopération réussie figurent le centre de biodiversité à Ouagadougou (Burkina Faso) et l’Atlas «BIOTA Ouest» actuel. Je me réjouis de l’apparition de cet atlas, qui constitue une vue d’ensemble compréhensive aussi bien que compréhensible des nombreux résultats de recherche et recommandations pratiques, car la biodiversité est une condition essentielle pour le fonctionnement de l’écosystème et, partant, le fondement de la vie humaine et de l’activité économique.
La biodiversité comprend la plénitude de la vie dans toutes ses formes. Sa protection et son usage durable doivent ainsi être une partie intégrante d’une politique orientée vers l’avenir et ancrer de plus en plus dans la conscience politique et publique. La condition préalable pour cela est une meilleure compréhension des effets des actions humaines sur la biodiversité et une connaissance plus approfondie de sa valeur. La recherche scientifique contribue de façon indispensable à la préservation des biomes, des espèces et gènes. Elle ne se limite pas à fournir les connaissances fondamentales qui sont nécessaires pour arrêter le progrès de la disparition de la biodiversité. Bien plus, ce sont les chercheurs eux-mêmes qui, ensemble avec leurs partenaires locaux, élaborent des stratégies pour un usage durable de la biodiversité. Explorer la flore et la faune du continent africain, et mesurer les changements observés dans leur milieu naturel afin de les réduire, tels sont les objectifs de BIOTA (Biodiversity Monitoring Transect Analysis in Africa / Transect d´Analyse du suivi de la Biodiversité en Afrique de l´Ouest). Ce réseau de recherche a été créé en 1999 ensemble par les chercheurs africains et allemands. Vu la grande importance de BIOTA, cette initiative est non seulement financée par le Ministère fédérale de l’Education et de la Recherche, mais entre-temps aussi par plusieurs Etats africains et institutions partenaires. «BIOTA Ouest» a été lancé au début de 2001. Parmi les résultats de cette coopération réussie figurent le centre de biodiversité à Ouagadougou (Burkina Faso) et l’Atlas «BIOTA Ouest» actuel. Je me réjouis de l’apparition de cet atlas, qui constitue une vue d’ensemble compréhensive aussi bien que compréhensible des nombreux résultats de recherche et recommandations pratiques, car la biodiversité est une condition essentielle pour le fonctionnement de l’écosystème et, partant, le fondement de la vie humaine et de l’activité économique.
La biodiversité comprend la plénitude de la vie dans toutes ses formes. Sa protection et son usage durable doivent ainsi être une partie intégrante d’une politique orientée vers l’avenir et ancrer de plus en plus dans la conscience politique et publique. La condition préalable pour cela est une meilleure compréhension des effets des actions humaines sur la biodiversité et une connaissance plus approfondie de sa valeur. La recherche scientifique contribue de façon indispensable à la préservation des biomes, des espèces et gènes. Elle ne se limite pas à fournir les connaissances fondamentales qui sont nécessaires pour arrêter le progrès de la disparition de la biodiversité. Bien plus, ce sont les chercheurs eux-mêmes qui, ensemble avec leurs partenaires locaux, élaborent des stratégies pour un usage durable de la biodiversité. Explorer la flore et la faune du continent africain, et mesurer les changements observés dans leur milieu naturel afin de les réduire, tels sont les objectifs de BIOTA (Biodiversity Monitoring Transect Analysis in Africa / Transect d´Analyse du suivi de la Biodiversité en Afrique de l´Ouest). Ce réseau de recherche a été créé en 1999 ensemble par les chercheurs africains et allemands. Vu la grande importance de BIOTA, cette initiative est non seulement financée par le Ministère fédérale de l’Education et de la Recherche, mais entre-temps aussi par plusieurs Etats africains et institutions partenaires. «BIOTA Ouest» a été lancé au début de 2001. Parmi les résultats de cette coopération réussie figurent le centre de biodiversité à Ouagadougou (Burkina Faso) et l’Atlas «BIOTA Ouest» actuel. Je me réjouis de l’apparition de cet atlas, qui constitue une vue d’ensemble compréhensive aussi bien que compréhensible des nombreux résultats de recherche et recommandations pratiques, car la biodiversité est une condition essentielle pour le fonctionnement de l’écosystème et, partant, le fondement de la vie humaine et de l’activité économique.