Abstract
The reconstruction of ancestral scenarios is widely used to study the evolution of characters along phylogenetic trees. One commonly uses the marginal posterior probabilities of the ...character states, or the joint reconstruction of the most likely scenario. However, marginal reconstructions provide users with state probabilities, which are difficult to interpret and visualize, whereas joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences.
We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts (namely, the Brier score) to associate each node in the tree to a set of likely states. A unique state is predicted in tree regions with low uncertainty, whereas several states are predicted in uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated with the same states and use graph visualization tools. The method is implemented in the PastML program and web server.
The results on simulated data demonstrate the accuracy and robustness of the approach. PastML was applied to the phylogeography of Dengue serotype 2 (DENV2), and the evolution of drug resistances in a large HIV data set. These analyses took a few minutes and provided convincing results. PastML retrieved the main transmission routes of human DENV2 and showed the uncertainty of the human-sylvatic DENV2 geographic origin. With HIV, the results show that resistance mutations mostly emerge independently under treatment pressure, but resistance clusters are found, corresponding to transmissions among untreated patients.
Highly efficient ammonia synthesis at a low temperature is desirable for future energy and material sources. We accomplished efficient electrocatalytic low-temperature ammonia synthesis with the ...highest yield ever reported. The maximum ammonia synthesis rate was 30 099 μmol g
h
over a 9.9 wt% Cs/5.0 wt% Ru/SrZrO
catalyst, which is a very high rate. Proton hopping on the surface of the heterogeneous catalyst played an important role in the reaction, revealed by
IR measurements. Hopping protons activate N
even at low temperatures, and they moderate the harsh reaction condition requirements. Application of an electric field to the catalyst resulted in a drastic decrease in the apparent activation energy from 121 kJ mol
to 37 kJ mol
. N
dissociative adsorption is markedly promoted by the application of the electric field, as evidenced by DFT calculations. The process described herein opens the door for small-scale, on-demand ammonia synthesis.
The formation of the Ontong Java Nui super oceanic plateau (OJN), which is based on the model that the submarine Ontong Java Plateau (OJP), Manihiki Plateau (MP), and Hikurangi Plateau (HP) were once ...its contiguous fragments, could have been the largest globally consequential volcanic event in Earth's history. This OJN hypothesis has been debated given the paucity of evidence, for example, the differences in crustal thickness, the compositional gap between MP and OJP basalts and the apparent older age of both plateaus relative to HP remain unresolved. Here we investigate the geochemical and
Ar-
Ar ages of dredged rocks recovered from the OJP's eastern margin. Volcanic rocks having compositions that match the low-Ti MP basalts are reported for the first time on the OJP and new ~ 96-116 Ma and 67-68 Ma
Ar-
Ar age data bridge the temporal gap between OJP and HP. These results provide new evidence for the Ontong Java Nui hypothesis and a framework for an integrated tectonomagmatic evolution of the OJP, MP, and HP. The isotopic data imply four mantle components in the source of OJN that are also expressed in present-day Pacific hotspots sources, indicating origin from (and longevity of) the Pacific Large Low Shear-wave Velocity Province.
Summary
An F2 population of 239 chickens was obtained by an intercross between Nagoya (NAG), a native Japanese breed with low growth, and White Plymouth Rock (WPR), a Western breed with high growth. ...Using SNP markers obtained by restriction site‐associated DNA sequencing, genome‐wide QTL analysis was performed and it revealed three QTL for early postnatal growth in the F2 population at genome‐wide 5% significance levels. The most highly significant QTL affecting body weights at 2–4 weeks of age and weight gains at 2–3 and 0–4 weeks was located on GGA4 between 34.0 and 65.6 Mb with LOD scores of 3.9–5.9 and it explained 4.9–9.9% of the total variance of the traits. The analysis provided evidence for significant QTL on GGA2 between 105.6 and 125.2 Mb (LOD = 4.6) and on GGA1 between 51.1 and 61.6 Mb (LOD = 4.0) which had effects on body weight at 3 weeks and body weight gain at 0–1 week respectively. These two genomic regions explained 6.6 and 6.9% of the phenotypic F2 variance of the corresponding traits respectively. The allele derived from WPR at all QTL increased the corresponding traits. Neither sex‐specific nor epistatic QTL was detected. The results showed that the GGA4 QTL affecting multiple traits is a key locus responsible for early growth in our chicken cross, suggesting that this QTL may make a great contribution to genetic improvement of growth performance of the NAG breed with a low growth rate.
Silent aspiration of oropharyngeal pathogenic organisms is a significant risk factor causing pneumonia in the elderly. We hypothesized that regular oral hygiene care will affect the presence of ...oropharyngeal bacteria. Professional cleaning of the oral cavity and/or the gargling of a disinfectant liquid solution was performed over a five-month period in three facilities for the dependent elderly. Total oropharyngeal bacteria, streptococci, staphylococci, Candida, Pseudomonas, and black-pigmented Bacteroides species were monitored. The levels of these oropharyngeal bacteria decreased or disappeared after weekly professional oral health care, i.e., cleaning of teeth, dentures, tongue, and oral mucous membrane by dental hygienists. After lunch, gargling with povidone iodine was shown to be less effective than professional oral care. These findings indicate that weekly professional mechanical cleaning of the oral cavity, rather than a daily chemical disinfection of the mouth, can be an important strategy to prevent aspiration pneumonia in the dependent elderly.
1. Comprehensive knowledge of innate fear in chickens has important implications for understanding the adaptation of native Japanese chickens in modern production and behavioural changes caused by ...modern breeding goals. Innate fear behaviour seen in chicks from six native Japanese chicken breeds;, Ingie (IG), Nagoya (NAG), Oh-Shamo (OSM), Tosa-Jidori (TJI), Tosa-Kukin (TKU) and Ukokkei (UK), were compared with those in two lines of White Leghorn (WL-G and WL-T) in tonic immobility (TI) and open field (OF) tests.
2. TI and OF tests were conducted for 267 chicks at 0-1 days of age in the eight breeds. Raw data for four TI traits and 13 OF traits were corrected for environmental factors. Breed differences were analysed by the Kruskal-Wallis test followed by the Steel Dwass post hoc test. Principal component (PC) analyses were conducted.
3. The results showed that OSM was the least sensitive to fear in both the TI and OF tests. The WL-G birds showed higher sensitivity to TI fear but lower sensitivity to OF fear. The PC analysis of OF traits classified the tested breeds into three groups: least (OSM and WL-G), moderate (IG, WL-T, NAG, TJI and TKU) and most sensitive (UK).
Olivine-free metasomatic mantle-derived xenoliths, frequently recovered from kimberlite and lamprophyre intrusions on the continents, are seldom described from oceanic settings. We report the ...mineralogy, geochemistry and Sr-Nd-Hf-Pb-Os isotopic compositions of a unique K-rich, hydrous mantle nodule sourced from a 34 Ma ultramafic lamprophyre (alnöite) pipe on the island of Malaita, Ontong Java Plateau, SW Pacific. The Ontong Java Plateau, the most voluminous oceanic large igeous province, has a >100 km thick lithospheric root reminiscent of thick lithospheres that characterize cratonic settings. The phlogopite, amphibole, clinopyroxene and ilmenite-rich nature of the Malaita metasomatic nodule bears striking similarity to cratonic mica-amphibole-rutile-ilmenite-diopside (MARID) suite xenoliths, and it provides a tangible example of heavily overprinted oceanic mantle lithosphere.
The nodule phlogopite 40Ar/39Ar age of 44.7 ± 1.8 Ma (95% confidence level) predates the 34 Ma alnöites, but is contemporaneous with 44 Ma alkali basalts on Malaita. Geodynamic reconstructions of the Ontong Java Plateau position within the Pacific realm demonstrate that alnöite magma and K-rich metasomatic nodule formation occurred within a strictly oceanic environment during the Eocene, away from subduction zones. The elevated incompatible trace element concentrations coupled with low highly siderophile element contents suggest that the K-rich metasomatic nodule formed by olivine-absent crystallisation from low-volume mantle-derived melt comparable to alnöite, but not the Malaita alkali basalts. A genetic link between the Malaita metasomatic nodule and alnöite is further suggested by overlapping Sr-Nd-Hf-Pb isotopic compositions (87Sr/86Sr45Ma = 0.70419–0.70423; εNd45Ma = +3.5; εHf45Ma = +5.3; 206Pb/204Pb45Ma = 18.66–18.71; 207Pb/204Pb45Ma = 15.61). These isotopic compositions are generally more enriched than those of mantle-derived peridotites and 122 Ma plateau-building basalts at Ontong Java, but share similarities with pyroxenite xenoliths from Malaita previously interpreted to represent ancient recycled crustal material. Mixing models between melts derived from fertile mantle and the more enriched pyroxenite, as well as recycled sedimentary material, can account for the composition of the K-rich metasomatic nodule. Extremely low contents of highly siderophile elements and high 187Os/188Os45Ma (0.1824–0.1997) can also be reconciled with the involvement of recycled crustal components in the complex origin of the K-rich hydrous nodule.
K-rich hydrous metasomatized mantle lithosphere could represent an enriched source component that is required for the formation of many oceanic intraplate basaltic provinces. As such, strongly metasomatized oceanic lithosphere provides an alternative to recycled crust components within the convecting mantle to explain enriched mantle signatures observed in oceanic basalts worldwide. However, constraining the volumetric abundance of strongly metasomatized oceanic lithosphere, possibly revealed by seismic mid-lithospheric discontinuities, is required before its importance can be established.
The existence of K-rich metasomatic components within oceanic plateau lithosphere may also have implications for Archean continental crust formation models. The K-rich mantle component required to explain sanukitoid magma formation associated with continental crust building TTG magmatism may not be restricted to a subduction channel environment, but it can equally reside within overthickened oceanic lithosphere. Thus, oceanic plateaus away from subduction zones could have served as nucleation points for growth of continental crust during the Archean.
Highlights ► Social isolation after early weaning (EI) impairs monoaminergic axonal development (MAD). ► EI has no influence on the number of monoaminergic cells. ► Voluntary running coincidence with ...EI prevents the impairment of MAD induced by EI.
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