Likelihood analysis of the flavour anomalies and g – 2 in the general two Higgs doublet model

We present a likelihood analysis of the general two Higgs doublet model, using the most important currently measured flavour observables, in view of the anomalies in charged current tree-level and neutral current one-loop rare decays of B mesons in b → cl$$ \overline{\nu} $$ ν ¯ and b → sμ+μ− transitions, respectively. We corroborate that the model explains the latter and it is able to simultaneously fit the experimental values of the R(D) charged current ratio at 1σ, but it can not accommodate the D* charmed meson observables R(D*) and FL(D*). We find that the fitted values for the angular observables in b → sμ+μ− transitions exhibit better agreement with the general two Higgs double model in comparison to the SM. We also make predictions for future collider observables BR(t → ch), BR(h → bs), BR(h → τμ), BR(Bs → τ+τ−), BR(B+ → K+τ+τ−) and the flavour violating decays of the τ lepton, BR(τ → 3μ) and BR(τ → μγ). The model predicts values of BR(t → ch), BR(Bs → τ+τ−) and BR(B+ → K+τ+τ−) that are out of reach of future experiments, but its predictions for BR(h → bs) and BR(h → τμ) are within the future sensitivity of the HL-LHC or the ILC. We also find that the predictions for the τ → 3μ and τ → μγ decays are well within the projected limits of the Belle II experiment. Finally, using the latest measurement of the Fermilab Muon g − 2 Collaboration, we performed a simultaneous fit to ∆aμ constrained by the charged anomalies, finding solutions at the 1σ level. Once the neutral anomalies are included, however, a simultaneous explanation is unfeasible.

The Complete Mitochondrial Genomes of Four Species in the Subfamily Limenitidinae (Lepidoptera, Nymphalidae) and a Phylogenetic Analysis

The complete mitogenomes of four species, Neptis thisbe, Neptis obscurior, Athyma zeroca, and Aldania raddei, were sequenced with sizes ranging from 15,172 bp (N. obscurior) to 16,348 bp (Al. raddei). All four mitogenomes display similar nucleotide content and codon usage of protein-coding genes (PCGs). Typical cloverleaf secondary structures are identified in 21 tRNA genes, while trnS1 (AGN) lacks the dihydrouridine (DHC) arm. The gene orientation and arrangement of the four mitogenomes are similar to that of other typical mitogenomes of Lepidoptera. The Ka/Ks ratio of 13 PCGs among 58 Limenitidinae species reveals that cox1 had the slowest evolutionary rate, while atp8 and nad6 exhibited a higher evolutionary rate. The phylogenetic analysis reveals that tribe-levels are well-supported monophyletic groups. Additionally, Maximum Likelihood analysis recovered the relationship (Parthenini + ((Chalingini + (Cymothoini + Neptini)) + (Adoliadini + Limenitidini))). However, a Bayesian analysis based on the same dataset recovered the relationship (Parthenini + (Adoliadini + ((Cymothoini + Neptini) + (Chalingini + Limenitidini)))). These results will offer valuable data for the future study of the phylogenetic relationships for Limenitidinae.

A Global Phylogenomic Study of the Thelypteridaceae

Abstract— The generic classification of the Thelypteridaceae has been the subject of much controversy. Proposed taxonomic systems have varied from recognizing the approximately 1200 species in the family within the single genus Thelypteris, to systems favoring upwards of 30 genera. Insights on intrafamilial relationships, especially for neotropical taxa, have been gained from recent phylogenetic studies; however, in the most recent classification, 10 of 30 recognized genera are either non-monophyletic or untested. We sequenced 407 nuclear loci for 621 samples, representing all recognized genera and approximately half the known species diversity. These were analyzed using both maximum likelihood analysis of a concatenated matrix and multi-species coalescent methods. Our phylogenomic results, informed by recently published morphological evidence, provide the foundation for a generic classification which recircumscribed 14 genera and recognized seven new genera. The 37 monophyletic genera sampled demonstrate greater geographic coherence than previous taxonomic concepts suggested. Additionally, our results demonstrate that certain morphological characters, such as frond division, are evolutionarily labile and are thus inadequate for defining genera.

Cosmological parameters from the likelihood analysis of the galaxy power spectrum and bispectrum in real space

We present a joint likelihood analysis of the halo power spectrum and bispectrum in real space. We take advantage of a large set of numerical simulations and of an even larger set of halo mock catalogs to provide a robust estimate of the covariance properties. We derive constraints on bias and cosmological parameters assuming a theoretical model from perturbation theory at one-loop for the power spectrum and tree-level for the bispectrum. By means of the Deviance Information Criterion, we select a reference bias model dependent on seven parameters that can describe the data up to k max,P = 0.3 h Mpc-1 for the power spectrum and k max,B = 0.09 h Mpc-1 for the bispectrum at redshift z = 1. This model is able to accurately recover three selected cosmological parameters even for the rather extreme total simulation volume of 1000h -3 Gpc3. With the same tools, we study how relations among bias parameters can improve the fit while reducing the parameter space. In addition, we compare common approximations to the covariance matrix against the full covariance estimated from the mocks, and quantify the (non-negligible) effect of ignoring the cross-covariance between the two statistics. Finally, we explore different selection criteria for the triangular configurations to include in the analysis, showing that excluding nearly equilateral triangles rather than simply imposing a fixed maximum k max,B on all triangle sides can lead to a better exploitation of the information contained in the bispectrum.

Phylogenomics of Salvia L. subgenus Calosphace (Lamiaceae)

The evolutionary relationships of Salvia have been difficult to estimate. In this study, we used the Next Generation Sequencing method Hyb-Seq to evaluate relationships among 90 Lamiaceae samples, including representatives of Mentheae, Ocimeae, Salvia subgenera Audibertia, Leonia, Salvia, and 69 species of subgenus Calosphace, representing 32 of Epling's sections. A bait set was designed in MarkerMiner using available transcriptome data to enrich 119 variable nuclear loci. Nuclear and chloroplast loci were assembled with hybphylomaker (HPM), followed by coalescent approach analyses for nuclear data (ASTRAL, BEAST) and a concatenated Maximum Likelihood analysis of chloroplast loci. The HPM assembly had an average of 1,314,368 mapped reads for the sample and 527 putative exons. Phylogenetic inferences resolved strongly supported relationships for the deep-level nodes, agreeing with previous hypotheses which assumed that subgenus Audibertia is sister to subgenus Calosphace. Within subgenus Calosphace, we recovered eight monophyletic sections sensu Epling, Cardinalis, Hastatae, Incarnatae, and Uricae in all the analyses (nDNA and cpDNA), Biflorae, Lavanduloideae, and Sigmoideae in nuclear analyses (ASTRAL, BEAST) and Curtiflorae in ASTRAL trees. Network analysis supports deep node relationships, some of the main clades, and recovers reticulation within the core Calosphace. The chloroplast phylogeny resolved deep nodes and four monophyletic Calosphace sections. Placement of S. axillaris is distinct in nuclear evidence and chloroplast, as sister to the rest of the S. subg. Calosphace in chloroplast and a clade with “Hastatae clade” sister to the rest of the subgenus in nuclear evidence. We also tested the monophyly of S. hispanica, S. polystachia, S. purpurea, and S. tiliifolia, including two samples of each, and found that S. hispanica and S. purpurea are monophyletic. Our baits can be used in future studies of Lamiaceae phylogeny to estimate relationships between genera and among species. In this study, we presented a Hyb-Seq phylogeny for complex, recently diverged Salvia, which could be implemented in other Lamiaceae.

Identification of Fungal Community Associated with Deterioration of Optical Observation Instruments of Museums in Northern Vietnam

Fungi are the most harmful microorganisms responsible for the deterioration of nonmetallic materials such as glass, polymers, and composites. To date, biological aspects of glass deterioration have been poorly investigated. The present study aimed to evaluate the diversity of the fungal community colonizing eyepieces of binoculars collected from museums of the northern provinces of Vietnam and the biodeterioration effects on accurate glass reproductions. A total of 40 isolates belonging to 14 genera were identified based on internal transcribed spacer (ITS) sequencing, morphological features, and maximum likelihood analysis. The most abundant fungal genera included Aspergillus (43.8%) and Penicillium (31.3%). Among those detected, Byssochlamys, Curvularia, Phomopsis, Coprinellus, Perenniporia, Talaromyces, Pithomyces, Neopestalotiopsis, Trichoderma, Pleospora, and Humicola were found for the first time. Of the 40 strains tested, 8 strains showed great organic acid production, and the extent of mycelium covered from 33.6 to 46.24%. Specifically, the highest extracellular polymeric substance production was observed in Byssochlamys spectabilis BXMA1-2 (14.96 g/L), Aspergillus niger BXMA5-2 (12.17 g/L), and Aspergillus ochraceopetaliformis BMLC1-2 (9.89 g/L). Glass biodeterioration experiments revealed that the light transmission through the fungal-treated glasses was decreased by 30–42.2% as compared to the nontreated glass. In addition, the main alterations resulted from hyphal fingerprints and spots, leading to apparent damage and biocorrosion.

Profile likelihood analysis for a stochastic model of diffusion in heterogeneous media

We compute profile likelihoods for a stochastic model of diffusive transport motivated by experimental observations of heat conduction in layered skin tissues. This process is modelled as a random walk in a layered one-dimensional material, where each layer has a distinct particle hopping rate. Particles are released at some location, and the duration of time taken for each particle to reach an absorbing boundary is recorded. To explore whether these data can be used to identify the hopping rates in each layer, we compute various profile likelihoods using two methods: first, an exact likelihood is evaluated using a relatively expensive Markov chain approach; and, second, we form an approximate likelihood by assuming the distribution of exit times is given by a Gamma distribution whose first two moments match the moments from the continuum limit description of the stochastic model. Using the exact and approximate likelihoods, we construct various profile likelihoods for a range of problems. In cases where parameter values are not identifiable, we make progress by re-interpreting those data with a reduced model with a smaller number of layers.