Predictive powers of chiral perturbation theory in Compton scattering off protons

We study low-energy nucleon Compton scattering in the framework of baryon chiral perturbation theory (B$\chi$PT) with pion, nucleon, and $\Delta$(1232) degrees of freedom, up to and including the next-to-next-to-leading order (NNLO). We include the effects of order $p^2$, $p^3$ and $p^4/\varDelta$, with $\varDelta\approx 300$ MeV the $\Delta$-resonance excitation energy. These are all "predictive" powers in the sense that no unknown low-energy constants enter until at least one order higher (i.e, $p^4$). Estimating the theoretical uncertainty on the basis of natural size for $p^4$ effects, we find that uncertainty of such a NNLO result is comparable to the uncertainty of the present experimental data for low-energy Compton scattering. We find an excellent agreement with the experimental cross section data up to at least the pion-production threshold. Nevertheless, for the proton's magnetic polarizability we obtain a value of $(4.0\pm 0.7)\times 10^{-4}$ fm$^3$, in significant disagreement with the current PDG value. Unlike the previous $\chi$PT studies of Compton scattering, we perform the calculations in a manifestly Lorentz-covariant fashion, refraining from the heavy-baryon (HB) expansion. The difference between the lowest order HB$\chi$PT and B$\chi$PT results for polarizabilities is found to be appreciable. We discuss the chiral behavior of proton polarizabilities in both HB$\chi$PT and B$\chi$PT with the hope to confront it with lattice QCD calculations in a near future. In studying some of the polarized observables, we identify the regime where their naive low-energy expansion begins to break down, thus addressing the forthcoming precision measurements at the HIGS facility.Comment: 24 pages, 9 figures, RevTeX4, revised version published in EPJ

Utility of low-copy nuclear markers in phylogenetic reconstruction of Hypericum L. (Hypericaceae)

Primers and sequence variation for two low-copy nuclear genes (LCG) not previously used for phylogenetic inference in the genus Hypericum, PHYC and EMB2765, are presented here in comparison with the fast-evolving nuclear intergenic spacer ITS. Substitution rates in the LCG markers were half those reported in ITS for Hypericum, which might help avoid the problems caused by substitution saturation and difficulties to establish homologies that afflict the latter marker. We included representatives of all major clades within Hypericum and found that levels of phylogenetic resolution, clade support values and internal character consistency were similar to, or even higher than, those of ITS-based phylogenies. The presence of at least two copies in EMB2765 in Hypericum imposed a methodological challenge that was circumvented by the design of an effective clade-specific primer. Both EMB2765 and, especially, PHYC appear to be good alternatives to the ITS marker, confirming the main phylogenetic relationships found in previous studies, but with improved resolution and support values for some basal relationships. © 2014 Springer-Verlag Wien.This work was funded by the Spanish Ministry of Education and Science (projects CGL2009-13322-C03-01/BOS and CGL2012-40129-C02-01) to I.S. and a PhD research grant AP- 2007-01698 to A.S.M. B.E.P. is supported by grants from the Swedish Research Council, the Royal Swedish Academy of Sciences, Lars Hiertas Minne fund, The Royal Physiographic Society in Lund, Helge Ax:son Johnsons fund and the Lundgrenska fundPeer Reviewe

Evolutionary networks from RADseq loci point to hybrid origins of Medicago carstiensis and Medicago cretacea

PREMISE: Although hybridization has played an important role in the evolution of many plant species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. Restriction-site-associated DNA sequencing (RADseq) has been a popular sequencing technique for the reconstruction of hybridization in the next-generation sequencing era. However, the utility of RADseq for the reconstruction of complex evolutionary networks has not been thoroughly investigated. Conflicting phylogenetic relationships in the genus Medicago have been mainly attributed to hybridization, but the specific hybrid origins of taxa have not been yet clarified. METHODS: We obtained new molecular data from diploid species of Medicago section Medicago using single-digest RADseq to reconstruct evolutionary networks from gene trees, an approach that is computationally tractable with data sets that include several species and complex hybridization patterns. RESULTS: Our analyses revealed that assembly filters to exclusively select a small set of loci with high phylogenetic information led to the most-divergent network topologies. Conversely, alternative clustering thresholds or filters on the number of samples per locus had a lower impact on networks. A strong hybridization signal was detected for M. carstiensis and M. cretacea, while signals were less clear for M. rugosa, M. rhodopea, M. suffruticosa, M. marina, M. scutellata, and M. sativa. CONCLUSIONS: Complex network reconstructions from RADseq gene trees were not robust under variations of the assembly parameters and filters. But when the most-divergent networks were discarded, all remaining analyses consistently supported a hybrid origin for M. carstiensis and M. cretacea

Data from: Annual and perennial Medicago show signatures of parallel adaptation to climate and soil in highly conserved genes

Human induced environmental change may require rapid adaptation of plant populations and crops, but the genomic basis of environmental adaptation remain poorly understood. We analyzed polymorphic loci from the perennial crop Medicago sativa (alfalfa or lucerne) and the annual legume model species M. truncatula to search for a common set of candidate genes that might contribute to adaptation to abiotic stress in both annual and perennial Medicago species. We identified a set of candidate genes of environmental adaptation associated with environmental gradients along the distribution of the two Medicago species. Candidate genes for each species were detected in homologous genomic linkage blocks using genome-environment (GEA) and genome-phenotype association analyses. Hundreds of GEA candidate genes were species-specific, of these, 13.4% (M. sativa) and 24% (M. truncatula) were also significantly associated with phenotypic traits. A set of 168 GEA candidates were shared by both species, which was 25.4% more than expected by chance. When combined, they explained a high proportion of variance for certain phenotypic traits associated with adaptation. Genes with highly conserved functions dominated among the shared candidates and were enriched in Gene Ontology terms that have shown to play a central role in drought avoidance and tolerance mechanisms by means of cellular shape modifications and other functions associated with cell homeostasis. Our results point to the existence of a molecular basis of adaptation to abiotic stress in Medicago determined by highly conserved genes and gene functions. We discuss these results in light of the recently proposed omnigenic model of complex traits.European Commission, Award: 625308 Marie Curie Intra‐European Fellowship.Peer reviewe

Phylogeny of the Centaurea group (Centaurea, Compositae) - Geography is a better predictor than morphology

The Centaurea group is part of the Circum-Mediterranean Clade (CMC) of genus Centaurea subgenus Centaurea, a mainly Mediterranean plant group with more than 200 described species. The group is traditionally split on morphological basis into three sections: Centaurea, Phalolepis and Willkommia. This division, however, is doubtful, especially in light of molecular approaches. In this study we try to resolve this phylogenetic problem and to consolidate the circumscription and delimitation of the entire group against other closely related groups. We analyzed nuclear (internal transcribed spacer of the ribosomal genes) and chloroplast (rpl32-trnL intergenic spacer) DNA regions for most of the described species of the Centaurea group using phylogenetic and network approaches, and we checked the data for recombination. Phylogeny was used to reconstruct the evolution of the lacerate-membranaceous bract appendages using parsimony. The magnitude of incomplete lineage sorting was tested estimating the effective population sizes. Molecular dating was performed using a Bayesian approach, and the ancestral area reconstruction was conducted using the Dispersal-Extinction-Cladogenesis method. Monophyly of the Centaurea group is confirmed if a few species are removed. Our results do not support the traditional sectional division. There is a high incongruence between the two markers and between genetic data and morphology. However, there is a clear relation between geography and the structure of the molecular data. Diversification in the Centaurea group mainly took place during the Pliocene and Pleistocene. The ancestral area infered for the Circum-Mediterranean Clade of Centaurea is the Eastern Mediterranean, whereas for the Centaurea group it is most likely NW-Africa. The large incongruencies, which hamper phylogenetic reconstruction, are probably the result of introgression, even though the presence of incomplete lineage sorting as an additional factor cannot be ruled out. Convergent evolution of morphological traits may have led to incongruence between morphology-based, traditional systematics and molecular results. Our results also cast major doubts about current species delimitation. © 2014 Elsevier Inc