Improved Phylogenetic Analyses Corroborate a Plausible Position of Martialis heureka in the Ant Tree of Life

Martialinae are pale, eyeless and probably hypogaeic predatory ants. Morphological character sets suggest a close relationship to the ant subfamily Leptanillinae. Recent analyses based on molecular sequence data suggest that Martialinae are the sister group to all extant ants. However, by comparing molecular studies and different reconstruction methods, the position of Martialinae remains ambiguous. While this sister group relationship was well supported by Bayesian partitioned analyses, Maximum Likelihood approaches could not unequivocally resolve the position of Martialinae. By re-analysing a previous published molecular data set, we show that the Maximum Likelihood approach is highly appropriate to resolve deep ant relationships, especially between Leptanillinae, Martialinae and the remaining ant subfamilies. Based on improved alignments, alignment masking, and tree reconstructions with a sufficient number of bootstrap replicates, our results strongly reject a placement of Martialinae at the first split within the ant tree of life. Instead, we suggest that Leptanillinae are a sister group to all other extant ant subfamilies, whereas Martialinae branch off as a second lineage. This assumption is backed by approximately unbiased (AU) tests, additional Bayesian analyses and split networks. Our results demonstrate clear effects of improved alignment approaches, alignment masking and data partitioning. We hope that our study illustrates the importance of thorough, comprehensible phylogenetic analyses using the example of ant relationships

Feasibility study towards comparison of the g (2)(0) measurement in the visible range

This work reports on the pilot study, performed by INRIM, NPL and PTB, on the measurement of the g^(2)(0) parameter in the visible spectral range of a test single-photon source based on a colour centre in diamond. The development of single-photon sources is of great interest to the metrology community as well as the burgeoning quantum technologies industry. Measurement of the g^(2)(0) parameter plays a vital role in characterising and understanding single-photon emission. This comparison has been conducted by each partner individually using its own equipment at INRIM laboratories, which were responsible for the operation of the sourc

Towards a standard procedure for the measurement of the multi-photon component in a CW telecom heralded single-photon source

Single-photon sources are set to be a fundamental tool for metrological applications as well as for quantum information related technologies. Because of their upcoming widespread dissemination, the need for their characterization and standardization is becoming of the utmost relevance. Here, we illustrate a strategy to provide a quantitative estimate of the multi-photon component of a single-photon source, showing the results achieved in a pilot study for the measurement of the second order autocorrelation function $g^{(2)}$ of a low-noise CW heralded single-photon source prototype (operating at telecom wavelength $\lambda=1550$ nm) realized in INRiM. The results of this pilot study, involving PTB, NPL and INRiM, will help to build up a robust and unambiguous procedure for the characterization of the emission of a single-photon source

Photoproduction of Long-Lived Holes and Electronic Processes in Intrinsic Electric Fields Seen through Photoinduced Absorption and Dichroism in Ca_3Ga_{2-x}Mn_xGe_3O_{12} Garnets

Long-lived photoinduced absorption and dichroism in the Ca_3Ga_{2-x}Mn_xGe_3O_{12} garnets with x < 0.06 were examined versus temperature and pumping intensity. Unusual features of the kinetics of photoinduced phenomena are indicative of the underlying electronic processes. The comparison with the case of Ca_3Mn_2Ge_3O_{12}, explored earlier by the authors, permits one to finally establish the main common mechanisms of photoinduced absorption and dichroism caused by random electric fields of photoproduced charges (hole polarons). The rate of their diffusion and relaxation through recombination is strongly influenced by the same fields, whose large statistical straggling is responsible for a broad continuous set of relaxation components (observed in the relaxation time range from 1 to about 1000 min). For Ca_3Ga_{2-x}Mn_xGe_3O_{12}, the time and temperature dependences of photoinduced absorption and dichroism bear a strong imprint of structure imperfection increasing with x.Comment: 20 pages, 10 figure

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

The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences

<p>Abstract</p> <p>Background</p> <p>Enormous molecular sequence data have been accumulated over the past several years and are still exponentially growing with the use of faster and cheaper sequencing techniques. There is high and widespread interest in using these data for phylogenetic analyses. However, the amount of data that one can retrieve from public sequence repositories is virtually impossible to tame without dedicated software that automates processes. Here we present a novel bioinformatics pipeline for downloading, formatting, filtering and analyzing public sequence data deposited in GenBank. It combines some well-established programs with numerous newly developed software tools (available at <url>http://software.zfmk.de/</url>).</p> <p>Results</p> <p>We used the bioinformatics pipeline to investigate the phylogeny of the megadiverse insect order Hymenoptera (sawflies, bees, wasps and ants) by retrieving and processing more than 120,000 sequences and by selecting subsets under the criteria of compositional homogeneity and defined levels of density and overlap. Tree reconstruction was done with a partitioned maximum likelihood analysis from a supermatrix with more than 80,000 sites and more than 1,100 species. In the inferred tree, consistent with previous studies, "Symphyta" is paraphyletic. Within Apocrita, our analysis suggests a topology of Stephanoidea + (Ichneumonoidea + (Proctotrupomorpha + (Evanioidea + Aculeata))). Despite the huge amount of data, we identified several persistent problems in the Hymenoptera tree. Data coverage is still extremely low, and additional data have to be collected to reliably infer the phylogeny of Hymenoptera.</p> <p>Conclusions</p> <p>While we applied our bioinformatics pipeline to Hymenoptera, we designed the approach to be as general as possible. With this pipeline, it is possible to produce phylogenetic trees for any taxonomic group and to monitor new data and tree robustness in a taxon of interest. It therefore has great potential to meet the challenges of the phylogenomic era and to deepen our understanding of the tree of life.</p