State tomography for two qubits using reduced densities

The optimal state determination (or tomography) is studied for a composite system of two qubits when measurements can be performed on one of the qubits and interactions of the two qubits can be implemented. The goal is to minimize the number of interactions to be used. The algebraic method applied in the paper leads to an extension of the concept of mutually unbiased measurements.Comment: 8 pages LATE

Prioritization of fish communities with a view to conservation and restoration on a large scale European basin, the Loire (France)

The hierarchical organization of important sites for the conservation or the restoration of fish communities is a great challenge for managers, especially because of financial or time constraints. In this perspective, we developed a methodology, which is easy to implement in different locations. Based on the fish assemblage characteristics of the Loire basin (France), we created a synthetic conservation value index including the rarity, the conservation status and the species origin. The relationship between this new synthetic index and the Fish-Based Index allowed us to establish a classification protocol of the sites along the Loire including fish assemblages to be restored or conserved. Sites presenting disturbed fish assemblages, a low rarity index, few threatened species, and a high proportion of non-native species were considered as important for the restoration of fish biodiversity. These sites were found mainly in areas where the assemblages are typical of the bream zone, e.g. with a higher number of eurytopic and limnophilic species. On the contrary, important sites for conservation were defined as having an important conservation potential (high RI, a lot of threatened species, and few nonnatives fish species) and an undisturbed fish assemblage similar to the expected community if habitats are undisturbed. Important sites for conservation were found in the Loire basin’s medium reaches which host assemblages typical for the grayling and the barbell zones, e.g. with a higher number of rheophilic species. The synthetic conservation value index could be adapted and completed with other criteria according to management priorities and capacities

Megaphylogeny resolves global patterns of mushroom evolution

Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.Fil: Varga, Torda. Hungarian Academy Of Sciences; HungríaFil: Krizsán, Krisztina. Hungarian Academy Of Sciences; HungríaFil: Földi, Csenge. Hungarian Academy Of Sciences; HungríaFil: Dima, Bálint. Eötvös Loránd University; HungríaFil: Sánchez-García, Marisol. Clark University; Estados UnidosFil: Lechner, Bernardo Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Micología y Botánica. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Micología y Botánica; ArgentinaFil: Sánchez-Ramírez, Santiago. University of Toronto; CanadáFil: Szöllosi, Gergely J.. Eötvös Loránd University; HungríaFil: Szarkándi, János G.. University Of Szeged; HungríaFil: Papp, Viktor. Szent István University; HungríaFil: Albert, László. Hungarian Mycological Society; HungríaFil: Andreopoulos, William. United States Department Of Energy. Joint Genome Institute; Estados UnidosFil: Angelini, Claudio. Jardin Botanico Nacional Ma. Moscoso; República DominicanaFil: Antonín, Vladimír. Moravian Museum; República ChecaFil: Barry, Kerrie W.. United States Department Of Energy. Joint Genome Institute; Estados UnidosFil: Bougher, Neale L.. Western Australian Herbarium; AustraliaFil: Buchanan, Peter. Manaaki Whenua-landcare Research; Nueva ZelandaFil: Buyck, Bart. Muséum National d'Histoire Naturelle; FranciaFil: Bense, Viktória. Hungarian Academy Of Sciences; HungríaFil: Catcheside, Pam. State Herbarium Of South Australia; AustraliaFil: Chovatia, Mansi. United States Department Of Energy. Joint Genome Institute; Estados UnidosFil: Cooper, Jerry. Manaaki Whenua-landcare Research; Nueva ZelandaFil: Dämon, Wolfgang. Oberfeldstrasse 9; AustriaFil: Desjardin, Dennis. San Francisco State University; Estados UnidosFil: Finy, Péter. Zsombolyai U. 56.; HungríaFil: Geml, József. Naturalis Biodiversity Center; Países BajosFil: Haridas, Sajeet. United States Department Of Energy. Joint Genome Institute; Estados UnidosFil: Hughes, Karen. University of Tennessee; Estados UnidosFil: Justo, Alfredo. Clark University; Estados UnidosFil: Karasinski, Dariusz. Polish Academy of Sciences; Poloni

RecPhyloXML: a format for reconciled gene trees.

A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc.-along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs. Here, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative-albeit flexible-specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities. http://phylariane.univ-lyon1.fr/recphyloxml/

Ancient horizontal gene transfer and the last common ancestors

Background The genomic history of prokaryotic organismal lineages is marked by extensive horizontal gene transfer (HGT) between groups of organisms at all taxonomic levels. These HGT events have played an essential role in the origin and distribution of biological innovations. Analyses of ancient gene families show that HGT existed in the distant past, even at the time of the organismal last universal common ancestor (LUCA). Most gene transfers originated in lineages that have since gone extinct. Therefore, one cannot assume that the last common ancestors of each gene were all present in the same cell representing the cellular ancestor of all extant life. Results Organisms existing as part of a diverse ecosystem at the time of LUCA likely shared genetic material between lineages. If these other lineages persisted for some time, HGT with the descendants of LUCA could have continued into the bacterial and archaeal lineages. Phylogenetic analyses of aminoacyl-tRNA synthetase protein families support the hypothesis that the molecular common ancestors of the most ancient gene families did not all coincide in space and time. This is most apparent in the evolutionary histories of seryl-tRNA synthetase and threonyl-tRNA synthetase protein families, each containing highly divergent “rare” forms, as well as the sparse phylogenetic distributions of pyrrolysyl-tRNA synthetase, and the bacterial heterodimeric form of glycyl-tRNA synthetase. These topologies and phyletic distributions are consistent with horizontal transfers from ancient, likely extinct branches of the tree of life. Conclusions Of all the organisms that may have existed at the time of LUCA, by definition only one lineage is survived by known progeny; however, this lineage retains a genomic record of heterogeneous genetic origins. The evolutionary histories of aminoacyl-tRNA synthetases (aaRS) are especially informative in detecting this signal, as they perform primordial biological functions, have undergone several ancient HGT events, and contain many sites with low substitution rates allowing deep phylogenetic reconstruction. We conclude that some aaRS families contain groups that diverge before LUCA. We propose that these ancient gene variants be described by the term “hypnologs”, reflecting their ancient, reticulate origin from a time in life history that has been all but erased”.National Science Foundation (U.S.) (Grant DEB 0830024)Exobiology Program (U.S.) (Grant NNX10AR85G)United States. National Aeronautics and Space Administration (Postdoctoral Program

Haemoproteus infection status of collared flycatcher males changes within a breeding season

In ecological studies of haemosporidian parasites, prevalence is typically considered as a stable attribute. However, little is known about the possible within-host dynamics of these parasites that may originate from environmental fluctuations, parasite life cycles and the ability of hosts to suppress or clear infection. We sampled the blood of male collared flycatchers Ficedula albicollis twice within a breeding season and investigated the determinants of initial infection status and change in infection status. We found that older males tended to be initially more infected at courtship. Change in infection status was unrelated to male traits, but a widespread disappearance of Haemoproteus pallidus infection from the blood was detected between courtship and nestling rearing. The probability of change in infection status increased with the time elapsed between sampling occasions. This suggests that the disappearance of infection from the blood was due to either an active parasite suppression mechanism or the beginning of the latent phase in the parasite life cycle. Initial infection status or disappearance of infection from the blood showed no correlation with breeding success. These results show that H. pallidus infection status and thus prevalence are dynamically changing attributes and this has widespread practical and ecological implications.Peer Reviewe