Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles

<p>Abstract</p> <p>Background</p> <p>Phylogenies often contain both well-supported and poorly supported nodes. Determining how much additional data might be required to eventually recover most or all nodes with high support is an important pragmatic goal, and simulations have been used to examine this question. Most simulations have been based on few empirical loci, and suggest that well supported phylogenies can be determined with a very modest amount of data. Here we report the results of an empirical phylogenetic analysis of all 10 genera and 25 of 48 species of the new world pond turtles (family Emydidae) based on one mitochondrial (1070 base pairs) and seven nuclear loci (5961 base pairs), and a more biologically realistic simulation analysis incorporating variation among gene trees, aimed at determining how much more data might be necessary to recover weakly-supported nodes with strong support.</p> <p>Results</p> <p>Our mitochondrial-based phylogeny was well resolved, and congruent with some previous mitochondrial results. For example, all genera, and all species except <it>Pseudemys concinna</it>, <it>P. peninsularis</it>, and <it>Terrapene carolina </it>were monophyletic with strong support from at least one analytical method. The Emydinae was recovered as monophyletic, but the Deirochelyinae was not. Based on nuclear data, all genera were monophyletic with strong support except <it>Trachemys</it>, and all species except <it>Graptemys pseudogeographica</it>, <it>P. concinna</it>, <it>T. carolina</it>, and <it>T. coahuila </it>were monophyletic, generally with strong support. However, the branches subtending most genera were relatively short, and intergeneric relationships within subfamilies were mostly unsupported.</p> <p>Our simulations showed that relatively high bootstrap support values (i.e. ≥ 70) for all nodes were reached in all datasets, but an increase in data did not necessarily equate to an increase in support values. However, simulations based on a single empirical locus reached higher overall levels of support with less data than did the simulations that were based on all seven empirical nuclear loci, and symmetric tree distances were much lower for single versus multiple gene simulation analyses.</p> <p>Conclusion</p> <p>Our empirical results provide new insights into the phylogenetics of the Emydidae, but the short branches recovered deep in the tree also indicate the need for additional work on this clade to recover all intergeneric relationships with confidence and to delimit species for some problematic groups. Our simulation results suggest that moderate (in the few-to-tens of kb range) amounts of data are necessary to recover most emydid relationships with high support values. They also suggest that previous simulations that do not incorporate among-gene tree topological variance probably underestimate the amount of data needed to recover well supported phylogenies.</p

Use of the polymerase chain reaction for screening and evaluation of recombinant baculovirus clones

We report the application of the PCR for screening and high-resolution characterization of recombinant baculovirus clones. Starting with less than 10 nanograms of viral DNA, it is possible to 1) demonstrate that the DNA sequence to be expressed has not been deleted or rearranged during the co-transfection or homologous recombination events, 2) test for the presence of wild-type virus in the isolate and 3) generate amplified DNA that can be used for nucleotide sequence analysis or high-resolution restriction analysis. The method is based upon PCR of genomic viral DNA prepared from primary amplified stocks of extracellular virus using a small-scale procedure. The approach has special relevance for definitive characterization of recombinant virus used to express point mutant proteins and for characterization of recombinant virus generated through use of mixed oligonucleotides or random mutagenesis

Magnetometry via a double-pass continuous quantum measurement of atomic spin

We argue that it is possible in principle to reduce the uncertainty of an atomic magnetometer by double-passing a far-detuned laser field through the atomic sample as it undergoes Larmor precession. Numerical simulations of the quantum Fisher information suggest that, despite the lack of explicit multi-body coupling terms in the system's magnetic Hamiltonian, the parameter estimation uncertainty in such a physical setup scales better than the conventional Heisenberg uncertainty limit over a specified but arbitrary range of particle number N. Using the methods of quantum stochastic calculus and filtering theory, we demonstrate numerically an explicit parameter estimator (called a quantum particle filter) whose observed scaling follows that of our calculated quantum Fisher information. Moreover, the quantum particle filter quantitatively surpasses the uncertainty limit calculated from the quantum Cramer-Rao inequality based on a magnetic coupling Hamiltonian with only single-body operators. We also show that a quantum Kalman filter is insufficient to obtain super-Heisenberg scaling, and present evidence that such scaling necessitates going beyond the manifold of Gaussian atomic states.Comment: 17 pages, updated to match print versio

A nonextensive approach to Bose-Einstein condensation of trapped interacting boson gas

In the Bose-Einstein condensation of interacting atoms or molecules such as 87Rb, 23Na and 7Li, the theoretical understanding of the transition temperature is not always obvious due to the interactions or zero point energy which cannot be exactly taken into account. The S-wave collision model fails sometimes to account for the condensation temperatures. In this work, we look at the problem within the nonextensive statistics which is considered as a possible theory describing interacting systems. The generalized energy Uq and the particle number Nq of boson gas are given in terms of the nonextensive parameter q. q>1 (q<1) implies repulsive (attractive) interaction with respect to the perfect gas. The generalized condensation temperature Tcq is derived versus Tc given by the perfect gas theory. Thanks to the observed condensation temperatures, we find q ~ 0.1 for 87Rb atomic gas, q ~ 0.95 for 7Li and q ~ 0.62 for 23Na. It is concluded that the effective interactions are essentially attractive for the three considered atoms, which is consistent with the observed temperatures higher than those predicted by the conventional theory

Multi-scale modeling study of the source contributions to near-surface ozone and sulfur oxides levels over California during the ARCTAS-CARB period

Chronic high surface ozone (O_3) levels and the increasing sulfur oxides (SO_x = SO_2 + SO_4) ambient concentrations over South Coast (SC) and other areas of California (CA) are affected by both local emissions and long-range transport. In this paper, multi-scale tracer, full-chemistry and adjoint simulations using the STEM atmospheric chemistry model are conducted to assess the contribution of local emission sourcesto SC O_3 and to evaluate the impacts of transported sulfur and local emissions on the SC sulfur budgetduring the ARCTAS-CARB experiment period in 2008. Sensitivity simulations quantify contributions of biogenic and fire emissions to SC O_3 levels. California biogenic and fire emissions contribute 3–4 ppb to near-surface O_3 over SC, with larger contributions to other regions in CA. During a long-range transport event from Asia starting from 22 June, high SO_x levels (up to ~0.7 ppb of SO_2 and ~1.3 ppb of SO_4) is observed above ~6 km, but they did not affect CA surface air quality. The elevated SO_x observed at 1–4 km is estimated to enhance surface SO_x over SC by ~0.25 ppb (upper limit) on ~24 June. The near-surface SO_x levels over SC during the flight week are attributed mostly to local emissions. Two anthropogenic SO_x emission inventories (EIs) from the California Air Resources Board (CARB) and the US Environmental Protection Agency (EPA) are compared and applied in 60 km and 12 km chemical transport simulations, and the results are compared withobservations. The CARB EI shows improvements over the National Emission Inventory (NEI) by EPA, but generally underestimates surface SC SO_x by about a factor of two. Adjoint sensitivity analysis indicated that SO_2 levels at 00:00 UTC (17:00 local time) at six SC surface sites were influenced by previous day maritime emissions over the ocean, the terrestrial emissions over nearby urban areas, and by transported SO_2 from the north through both terrestrial and maritime areas. Overall maritime emissions contribute 10–70% of SO2 and 20–60% fine SO_4 on-shore and over the most terrestrial areas, with contributions decreasing with in-land distance from the coast. Maritime emissions also modify the photochemical environment, shifting O_3 production over coastal SC to more VOC-limited conditions. These suggest an important role for shipping emission controls in reducing fine particle and O_3 concentrations in SC

Global distribution and bioclimatic characterization of alpine biomes

Although there is a general consensus on the distribution and ecological features of terrestrial biomes, the allocation of alpine ecosystems in the global biogeographic system is still unclear. Here, we delineate a global map of alpine areas above the treeline by modelling regional treeline elevation at 30 m resolution, using global forest cover data and quantile regression. We then used global datasets to 1) assess the climatic characteristics of alpine ecosystems using principal component analysis, 2) define bioclimatic groups by an optimized cluster analysis and 3) evaluate patterns of primary productivity based on the normalized difference vegetation index. As defined here, alpine biomes cover 3.56 Mkm(2) or 2.64% of land outside Antarctica. Despite temperature differences across latitude, these ecosystems converge below a sharp threshold of 5.9 degrees C and towards the colder end of the global climatic space. Below that temperature threshold, alpine ecosystems are influenced by a latitudinal gradient of mean annual temperature and they are climatically differentiated by seasonality and continentality. This gradient delineates a climatic envelope of global alpine biomes around temperate, boreal and tundra biomes as defined in Whittaker's scheme. Although alpine biomes are similarly dominated by poorly vegetated areas, world ecoregions show strong differences in the productivity of their alpine belt irrespectively of major climate zones. These results suggest that vegetation structure and function of alpine ecosystems are driven by regional and local contingencies in addition to macroclimatic factors

Multi-scale modeling study of the source contributions to near-surface ozone and sulfur oxides levels over California during the ARCTAS-CARB period

Chronic high surface ozone (O3) levels and the increasing sulfur oxides (SOx = SO2+SO4) ambient concentrations over South Coast (SC) and other areas of California (CA) are affected by both local emissions and long-range transport. In this paper, multi-scale tracer, full-chemistry and adjoint simulations using the STEM atmospheric chemistry model are conducted to assess the contribution of local emission sourcesto SC O3 and to evaluate the impacts of transported sulfur and local emissions on the SC sulfur budgetduring the ARCTAS-CARB experiment period in 2008. Sensitivity simulations quantify contributions of biogenic and fire emissions to SC O3 levels. California biogenic and fire emissions contribute 3–4 ppb to near-surface O3 over SC, with larger contributions to other regions in CA. During a long-range transport event from Asia starting from 22 June, high SOx levels (up to ~0.7 ppb of SO2 and ~1.3 ppb of SO4) is observed above ~6 km, but they did not affect CA surface air quality. The elevated SOx observed at 1–4 km is estimated to enhance surface SOx over SC by ~0.25 ppb (upper limit) on ~24 June. The near-surface SOx levels over SC during the flight week are attributed mostly to local emissions. Two anthropogenic SOx emission inventories (EIs) from the California Air Resources Board (CARB) and the US Environmental Protection Agency (EPA) are compared and applied in 60 km and 12 km chemical transport simulations, and the results are compared withobservations. The CARB EI shows improvements over the National Emission Inventory (NEI) by EPA, but generally underestimates surface SC SOx by about a factor of two. Adjoint sensitivity analysis indicated that SO2 levels at 00:00 UTC (17:00 local time) at six SC surface sites were influenced by previous day maritime emissions over the ocean, the terrestrial emissions over nearby urban areas, and by transported SO2 from the north through both terrestrial and maritime areas. Overall maritime emissions contribute 10–70% of SO2 and 20–60% fine SO4 on-shore and over the most terrestrial areas, with contributions decreasing with in-land distance from the coast. Maritime emissions also modify the photochemical environment, shifting O3 production over coastal SC to more VOC-limited conditions. These suggest an important role for shipping emission controls in reducing fine particle and O3concentrations in SC

The reason why doping causes superconductivity in LaFeAsO

The experimental observation of superconductivity in LaFeAsO appearing on doping is analyzed with the group-theoretical approach that evidently led in a foregoing paper (J. Supercond 24:2103, 2011) to an understanding of the cause of both the antiferromagnetic state and the accompanying structural distortion in this material. Doping, like the structural distortions, means also a reduction of the symmetry of the pure perfect crystal. In the present paper we show that this reduction modifies the correlated motion of the electrons in a special narrow half-filled band of LaFeAsO in such a way that these electrons produce a stable superconducting state