Does nutrient enrichment compensate fungicide effects on litter decomposition and decomposer communities in streams?
Contributors: Diego Fernández, Mallikarjun Tummala, Verena C. Schreiner, Sofia Duarte, Cláudia Pascoal, Carola Winkelmann, Daniela Mewes, Katherine Muñoz, Ralf B. Schäfer
... Nutrient and pesticide pollution are widespread agricultural stressors. Fungicides may affect freshwater fungi, which play an important role in litter decomposition (LD), whereas moderate nutrient enrichment can stimulate LD. We examined potential interaction effects of nutrients and fungicides on decomposer communities and LD in a 14-day two-factorial (fungicide and nutrient treatments) mesocosm experiment. Fungicide exposure was limited to 4days to simulate episodic contamination. Only the microbial community responded significantly to the experimental factors, though non-significant increases >20% were found for invertebrate decomposer weight gain and LD under high-nutrient conditions. Fungal community structure responded more strongly to fungicides than sporulation. Sporulation responded strongest to nutrients. Bacterial community structure was affected by both factors, although only nutrients influenced bacterial density. Our results suggest effects from fungicides at field-relevant levels on the microbial community. Whether these changes propagate to invertebrate communities and LD remains unclear and should be analysed under longer and recurrent fungicide exposure.
Contributors: Panos Bravakos, Georgios Kotoulas, Katerina Skaraki, Adriani Pantazidou, Athena Economou-Amilli
... Strains of Cyanobacteria isolated from mats of 9 thermal springs of Greece have been studied for their taxonomic evaluation. A polyphasic taxonomic approach was employed which included: morphological observations by light microscopy and scanning electron microscopy, maximum parsimony, maximum likelihood and Bayesian analysis of 16S rDNA sequences, secondary structural comparisons of 16S–23S rRNA Internal Transcribed Spacer sequences, and finally environmental data. The 17 cyanobacterial isolates formed a diverse group that contained filamentous, coccoid and heterocytous strains. These included representatives of the polyphyletic genera of Synechococcus and Phormidium, and the orders Oscillatoriales, Spirulinales, Chroococcales and Nostocales. After analysis, at least 6 new taxa at the genus level provide new evidence in the taxonomy of Cyanobacteria and highlight the abundant diversity of thermal spring environments with many potential endemic species or ecotypes.
Ancient Neotropical origin and recent recolonisation: Phylogeny, biogeography and diversification of the Riodinidae (Lepidoptera: Papilionoidea)
Contributors: Marianne Espeland, Jason P.W. Hall, Philip J. DeVries, David C. Lees, Mark Cornwall, Yu-Feng Hsu, Li-Wei Wu, Dana L. Campbell, Gerard Talavera, Roger Vila
... We present the first dated higher-level phylogenetic and biogeographic analysis of the butterfly family Riodinidae. This family is distributed worldwide, but more than 90% of the c. 1500 species are found in the Neotropics, while the c. 120 Old World species are concentrated in the Southeast Asian tropics, with minor Afrotropical and Australasian tropical radiations, and few temperate species. Morphologically based higher classification is partly unresolved, with genera incompletely assigned to tribes. Using 3666bp from one mitochondrial and four nuclear markers for each of 23 outgroups and 178 riodinid taxa representing all subfamilies, tribes and subtribes, and 98 out of 145 described genera of riodinids, we estimate that Riodinidae split from Lycaenidae about 96Mya in the mid-Cretaceous and started to diversify about 81Mya. The Riodinidae are monophyletic and originated in the Neotropics, most likely in lowland proto-Amazonia. Neither the subfamily Euselasiinae nor the Nemeobiinae are monophyletic as currently constituted. The enigmatic, monotypic Neotropical genera Styx and Corrachia (most recently treated in Euselasiinae: Corrachiini) are highly supported as derived taxa in the Old World Nemeobiinae, with dispersal most likely occurring across the Beringia land bridge during the Oligocene. Styx and Corrachia, together with all other nemeobiines, are the only exclusively Primulaceae-feeding riodinids. The steadily increasing proliferation of the Neotropical Riodininae subfamily contrasts with the decrease in diversification in the Old World, and may provide insights into factors influencing the diversification rate of this relatively ancient clade of Neotropical insects.
Original Article - Tumor heterogeneity uncovered by dynamic expression of long noncoding RNA at single-cell resolution
Contributors: Wangxiong Hu, Tingzhang Wang, Yanmei Yang, Shu Zheng
... The expression of long noncoding RNA (lncRNA) is thought to be more cell-type specific than the expression of protein-coding genes. However, the expression profile of individual cells regarding lncRNA remains to be elucidated. Here, we comprehensively investigated the pattern of lncRNA expression across five glioblastoma tumors (414 cells) and two cell lines (GBM6 and GBM8, 127 cells). We found that there were more than 1,000 lncRNAs that varied between any two cells and that there was frequent gain and loss of lncRNA expression during tumor cell proliferation, suggesting a great heterogeneity in lncRNA expression across different single cells in glioblastoma.
Evaluating uncertainties in the calibration of isotopic reference materials and multi-element isotopic tracers (EARTHTIME Tracer Calibration Part II)
Contributors: Noah M. McLean, Daniel J. Condon, Blair Schoene, Samuel A. Bowring
... A statistical approach to evaluating uncertainties in the calibration of multi-element isotopic tracers has been developed and applied to determining the isotopic composition of mixed U–Pb (202Pb–205Pb–233U–235U) tracers used for accurate isotope dilution U–Pb geochronology. Our experiment, part of the EARTHTIME initiative, directly links the tracer calibration to first-principles measurements of mass and purity that are all traceable to SI units, thereby quantifying the accuracy and precision of U–Pb dates in absolute time. The calibration incorporates new more accurate and precise purity measurements for a number of commonly used Pb and U reference materials, and requires inter-relating their isotopic compositions and uncertainties. Similar methods can be used for other isotope systems that utilize multiple isotopic standards for calibration purposes. We also detail the inter-calibration of three publicly available U–Pb gravimetric solutions, which can be used to bring the same first-principles traceability to in-house U–Pb tracers from other laboratories. Accounting for uncertainty correlations in the tracer isotope ratios yields a tracer calibration contribution to the relative uncertainty of a 206Pb/238U date that is only half of the relative uncertainty in the 235U/205Pb ratio of the tracer, which was historically used to approximate the tracer related uncertainty contribution to 206Pb/238U dates. The tracer uncertainty contribution to 206Pb/238U dates has in this way been reduced to <300ppm when using the EARTHTIME and similarly calibrated tracers.
Short Communication - Phylogenetic position and evolutionary history of the turtle and whale barnacles (Cirripedia: Balanomorpha: Coronuloidea)
Contributors: Ryota Hayashi, Benny K.K. Chan, Noa Simon-Blecher, Hiromi Watanabe, Tamar Guy-Haim, Takahiro Yonezawa, Yaniv Levy, Takuho Shuto, Yair Achituv
... Barnacles of the superfamily Coronuloidea are obligate epibionts of various marine mammals, marine reptiles and large crustaceans. We used five molecular markers: 12S rDNA, 16S rDNA, 18S rDNA, 28S rDNA and Histone 3 to infer phylogenetic relationships among sixteen coronuloids, representing most of the recent genera of barnacles of this superfamily. Our analyses confirm the monophyly of Coronuloidea and that this superfamily and Tetraclitoidea are sister groups. The six-plated Austrobalanus clusters with these two superfamilies. Based on BEAST and ML trees, Austrobalanus is basal and sister to the Coronuloidea, but the NJ tree places Austrobalanus within the Tetraclitoidae, and in the MP tree it is sister to both Coronuloidea and Tetraclitoidae. Hence the position of Austrobalanus remains unresolved. Within the Coronuloidea we identified four clades. Chelonibia occupies a basal position within the Coronuloidea which is in agreement with previous studies. The grouping of the other clades does not conform to previous studies. Divergence time analyses show that some of the time estimates are congruent with the fossil record while some others are older, suggesting the possibility of gaps in the fossil record.
Molecular phylogenetics of Oestroidea (Diptera: Calyptratae) with emphasis on Calliphoridae: Insights into the inter-familial relationships and additional evidence for paraphyly among blowflies
Contributors: M.A.T. Marinho, A.C.M. Junqueira, D.F. Paulo, M.C. Esposito, M.H. Villet, A.M.L. Azeredo-Espin
... The superfamily Oestroidea, comprising ∼15,000 species, is a large and ecologically diverse clade within the order Diptera. Among its six commonly recognized families, Calliphoridae seems to be crucial for understanding evolutionary relationships in the group, as it is recognized as a controversial paraphyletic grouping. To further investigate this matter, the ITS2, 28S, COI and 16S regions were used to infer phylogenetic relationships in Oestroidea with maximum-parsimony (MP), maximum-likelihood (ML) and Bayesian inference (BI) methods. For the BI analyses, a deep evaluation of different data partitioning strategies was conducted, including consideration of structural conformation (ITS2 and 16S) and codon position (COI) information. Results suggest the existence of two main clades in Oestroidea: (Tachinidae+Mesembrinellinae) and (Rhiniinae, (Sarcophagidae+Calliphoridae sensu stricto)). Oestridae was recovered as sister group of the remaining Oestroidea in the MP trees while it was placed closer to the (Rhiniinae+Sarcophagidae+Calliphoridae sensu stricto) group in the ML and BI trees. A paraphyletic Calliphoridae was recovered, confirming the exclusion of Rhiniinae, a clade recently promoted to family status and therefore already excluded. Mesembrinellinae could also be considered a distinct group apart from Calliphoridae, although further studies are required. Consideration of structural and codon position information led to a significant increase in the log-likelihoods of the analyses, which were accompanied by small changes in the inferred topologies, branch lengths and posterior probability support values. However, as model complexity increases, so does uncertainty across the estimated parameters, including tree topologies, and phylogenies inferred under very parameter-rich models may be less reliable even when possessing higher log-likelihoods.