Analyzing and reconstructing reticulation networks under timing constraints

Reticulation networks are now frequently used to model the history of life for various groups of organisms whose evolutionary past is likely to include reticulation events like horizontal gene transfer or hybridization. However, the reconstructed networks are rarely guaranteed to be temporal. If a reticulation network is temporal, then it satisfies the two biologically motivated timing constraints of instantaneously occurring reticulation events and successively occurring speciation events. On the other hand, if a reticulation network is not temporal, it is always possible to resolve this issue by adding a number of additional unsampled or extinct taxa. In the first half of the paper, we show that deciding whether a given number of additional taxa is sufficient to transform a non-temporal reticulation network into a temporal one is an NP-complete problem. As one is often given a set of gene trees instead of a network in the context of hybridization, this motivates the second half of the paper which provides an algorithm for reconstructing a temporal hybridization network that simultaneously explains the ancestral history of two trees or indicates that no such network exists. We highlight two practical applications of this algorithm and illustrate the second application on a grass data set

Characterization of Infrared Dark Clouds -- NH3_3 Observations of an Absorption-contrast Selected IRDC Sample

Despite increasing research in massive star formation, little is known about its earliest stages. Infrared Dark Clouds (IRDCs) are cold, dense and massive enough to harbour the sites of future high-mass star formation. But up to now, mainly small samples have been observed and analysed. To understand the physical conditions during the early stages of high-mass star formation, it is necessary to learn more about the physical conditions and stability in relatively unevolved IRDCs. Thus, for characterising IRDCs studies of large samples are needed. We investigate a complete sample of 218 northern hemisphere high-contrast IRDCs using the ammonia (1,1)- and (2,2)-inversion transitions. We detected ammonia (1,1)-inversion transition lines in 109 of our IRDC candidates. Using the data we were able to study the physical conditions within the star-forming regions statistically. We compared them with the conditions in more evolved regions which have been observed in the same fashion as our sample sources. Our results show that IRDCs have, on average, rotation temperatures of 15 K, are turbulent (with line width FWHMs around 2 km s$^{-1}$), have ammonia column densities on the order of $10^{14}$ cm$^{-2}$ and molecular hydrogen column densities on the order of $10^{22}$ cm$^{-2}$. Their virial masses are between 100 and a few 1000 M$_\odot$. The comparison of bulk kinetic and potential energies indicate that the sources are close to virial equilibrium. IRDCs are on average cooler and less turbulent than a comparison sample of high-mass protostellar objects, and have lower ammonia column densities. Virial parameters indicate that the majority of IRDCs are currently stable, but are expected to collapse in the future.Comment: 21 pages, 11 figures, 7 tables. Paper accepted for publication in Astronomy & Astrophysic

Influence of the Dufour effect on convection in binary gas mixtures

Linear and nonlinear properties of convection in binary fluid layers heated from below are investigated, in particular for gas parameters. A Galerkin approximation for realistic boundary conditions that describes stationary and oscillatory convection in the form of straight parallel rolls is used to determine the influence of the Dufour effect on the bifurcation behaviour of convective flow intensity, vertical heat current, and concentration mixing. The Dufour--induced changes in the bifurcation topology and the existence regimes of stationary and traveling wave convection are elucidated. To check the validity of the Galerkin results we compare with finite--difference numerical simulations of the full hydrodynamical field equations. Furthermore, we report on the scaling behaviour of linear properties of the stationary instability.Comment: 14 pages and 10 figures as uuencoded Postscript file (using uufiles

Laboratory Efficacy of Chemical Repellents for Reducing Blackbird Damage in Rice and Sunflower Crops

Nonlethal alternatives are needed to manage blackbird (Icterids) damage to rice and sunflower production in the United States. We evaluated 4 registered fungicides on rice seeds (i.e., Allegiance® FL, Thiram 42-S, Trilex®, and Vitavax® 200 preplant seed treatments) and 2 foliar pesticides on sunflower seeds (CobaltTM insecticide and Flock Buster bird repellent) as candidate blackbird repellents. Red-winged blackbirds (Agelaius phoeniceus) preferred untreated rice relative to rice treated with Thiram (P \u3c 0.001) and Vitavax (P \u3c 0.001), and untreated sunflower relative to sunflower treated with Cobalt (P \u3c 0.001). Blackbirds preferred untreated sunflower relative to sunflower treated with Flock Buster repellent on day 1 of a 4-day preference test (P \u3c 0.001). We observed no difference in consumption of treated versus untreated rice during the Allegiance preference test (P = 0.928), and blackbirds preferred rice treated with Trilex relative to untreated rice (P = 0.003). Although repellency was positively related to tested concentrations of Thiram (P = 0.010), Trilex (P = 0.026), and Vitavax (P \u3c 0.001), maximum repellency was \u3c50% during our concentration-response tests of these seed treatments. Repellency was also positively related to tested concentrations of Cobalt (P \u3c 0.001), and we observed \u3e80% repellency of sunflower treated with Cobalt at ≥50% of the label rate. We observed no concentration-response relationship for the Allegiance seed treatment (P = 0.341) and Flock Buster repellent (P = 0.952). We recommend implementation of supplemental field studies to compare laboratory efficacy, repellency, and chemical residues of effective avian repellents throughout periods of needed crop protection

A New Galactic 6cm Formaldehyde Maser

We report the detection of a new H2CO maser in the massive star forming region G23.71-0.20 (IRAS 18324-0820), i.e., the fifth region in the Galaxy where H2CO maser emission has been found. The new H2CO maser is located toward a compact HII region, and is coincident in velocity and position with 6.7 GHz methanol masers and with an IR source as revealed by Spitzer/IRAC GLIMPSE data. The coincidence with an IR source and 6.7 GHz methanol masers suggests that the maser is in close proximity to an embedded massive protostar. Thus, the detection of H2CO maser emission toward G23.71-0.20 supports the trend that H2CO 6cm masers trace molecular material very near young massive stellar objects.Comment: Accepted for publication in The Astrophysical Journal Letter

Influence of the Soret effect on convection of binary fluids

Convection in horizontal layers of binary fluids heated from below and in particular the influence of the Soret effect on the bifurcation properties of extended stationary and traveling patterns that occur for negative Soret coupling is investigated theoretically. The fixed points corresponding to these two convection structures are determined for realistic boundary conditions with a many mode Galerkin scheme for temperature and concentration and an accurate one mode truncation of the velocity field. This solution procedure yields the stable and unstable solutions for all stationary and traveling patterns so that complete phase diagrams for the different convection types in typical binary liquid mixtures can easily be computed. Also the transition from weakly to strongly nonlinear states can be analyzed in detail. An investigation of the concentration current and of the relevance of its constituents shows the way for a simplification of the mode representation of temperature and concentration field as well as for an analytically manageable few mode description.Comment: 30 pages, 12 figure

PLoS Genet.

The Helicobacter pylori cag pathogenicity island (cagPAI) encodes a type IV secretion system. Humans infected with cagPAI-carrying H. pylori are at increased risk for sequelae such as gastric cancer. Housekeeping genes in H. pylori show considerable genetic diversity; but the diversity of virulence factors such as the cagPAI, which transports the bacterial oncogene CagA into host cells, has not been systematically investigated. Here we compared the complete cagPAI sequences for 38 representative isolates from all known H. pylori biogeographic populations. Their gene content and gene order were highly conserved. The phylogeny of most cagPAI genes was similar to that of housekeeping genes, indicating that the cagPAI was probably acquired only once by H. pylori, and its genetic diversity reflects the isolation by distance that has shaped this bacterial species since modern humans migrated out of Africa. Most isolates induced IL-8 release in gastric epithelial cells, indicating that the function of the Cag secretion system has been conserved despite some genetic rearrangements. More than one third of cagPAI genes, in particular those encoding cell-surface exposed proteins, showed signatures of diversifying (Darwinian) selection at more than 5% of codons. Several unknown gene products predicted to be under Darwinian selection are also likely to be secreted proteins (e.g. HP0522, HP0535). One of these, HP0535, is predicted to code for either a new secreted candidate effector protein or a protein which interacts with CagA because it contains two genetic lineages, similar to cagA. Our study provides a resource that can guide future research on the biological roles and host interactions of cagPAI proteins, including several whose function is still unknown

The Effect of European Starlings and Ambient Air Temperature on \u3cem\u3eSalmonella enterica\u3c/em\u3e Contamination within Cattle Feed Bunks

European starlings (Sturnus vulgaris) are a known risk factor for the occurrence of microorganisms that are pathogenic to cattle and humans in concentrated animal feeding operations (CAFOs). Starling use of CAFOs is known to vary in response to weather; starling control operations on CAFOs often are timed to coincide with favorable environmental conditions to maximize take. The totality of this information suggests that disease risks in CAFOs associated with starlings may be influenced by environmental factors, such as temperature. In this study, we assessed the risk of Salmonella enterica contamination of cattle feed by modeling the interaction between starling numbers and ambient air temperatures using data previously reported from Texas CAFOs. We compared these interaction models to the previously published additive models for S. enterica contamination of cattle feed using an information-theoretic approach to model selection that ranked and weighted models in terms of their support by the data, using bias-adjusted Akaike’s Information Criterion (AICc) and Akaike weights (Wi). Our results indicate that the interaction between European starlings and ambient air temperature better explained the occurrence of S. enterica in cattle feed than any of the previously reported models. Specifically, the risk of S. enterica contamination of cattle feed by starlings was greatest when winter temperatures were highest (10°C). Thus, we conclude that the risk of S. enterica contamination of cattle feed by starlings will be worst on the few winter days when daytime high temperatures are above freezing and large numbers of birds are present. Because these conditions will be most common in the late winter and early spring, we recommend that starling control operations on feedlots and dairies be conducted as early in the winter as possible to mitigate the risks of disease created by large foraging flocks of starlings

The effect of European starlings and ambient air temperature on \u3ci\u3eSalmonella enterica\u3c/i\u3e contamination within cattle feed bunks

European starlings (Sturnus vulgaris) are a known risk factor for the occurrence of microorganisms that are pathogenic to cattle and humans in concentrated animal feeding operations (CAFOs). Starling use of CAFOs is known to vary in response to weather; starling control operations on CAFOs often are timed to coincide with favorable environmental conditions to maximize take. The totality of this information suggests that disease risks in CAFOs associated with starlings may be influenced by environmental factors, such as temperature. In this study, we assessed the risk of Salmonella enterica contamination of cattle feed by modeling the interaction between starling numbers and ambient air temperatures using data previously reported from Texas CAFOs. We compared these interaction models to the previously published additive models for S. enterica contamination of cattle feed using an information-theoretic approach to model selection that ranked and weighted models in terms of their support by the data, using bias-adjusted Akaike’s Information Criterion (AICc) and Akaike weights (Wi). Our results indicate that the interaction between European starlings and ambient air temperature better explained the occurrence of S. enterica in cattle feed than any of the previously reported models. Specifically, the risk of S. enterica contamination of cattle feed by starlings was greatest when winter temperatures were highest (10°C). Thus, we conclude that the risk of S. enterica contamination of cattle feed by starlings will be worst on the few winter days when daytime high temperatures are above freezing and large numbers of birds are present. Because these conditions will be most common in the late winter and early spring, we recommend that starling control operations on feedlots and dairies be conducted as early in the winter as possible to mitigate the risks of disease created by large foraging flocks of starlings