On the von Karman-Howarth equations for Hall MHD flows

The von Karman-Howarth equations are derived for three-dimensional (3D) Hall magnetohydrodynamics (MHD) in the case of an homogeneous and isotropic turbulence. From these equations, we derive exact scaling laws for the third-order correlation tensors. We show how these relations are compatible with previous heuristic and numerical results. These multi-scale laws provide a relevant tool to investigate the non-linear nature of the high frequency magnetic field fluctuations in the solar wind or, more generally, in any plasma where the Hall effect is important.Comment: 11 page

Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates.

Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins

Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates.

Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins

The intriguing evolutionary dynamics of plant mitochondrial DNA

The mitochondrial genome of plants is-in every respect and for yet unclear reasons-very different from the well-studied one of animals. Thanks to next-generation sequencing technologies, Davila et al. precisely characterized the role played by recombination and DNA repair in controlling mitochondrial variations in Arabidopsis thaliana, thus opening new perspectives on the long-term evolution of this intriguing genome

Influence of the definition of dissipative events on their statistics

A convenient and widely used way to study the turbulent plasma in the solar corona is to do statistics of properties of events (or structures), associated with flares, that can be found in observations or in numerical simulations. Numerous papers have followed such a methodology, using different definitions of an event, but the reasons behind the choice of a particular definition (and not another one) is very rarely discussed. We give here a comprehensive set of possible event definitions starting from a one-dimensional data set such as a time-series of energy dissipation. Each definition is then applied to a time-series of energy dissipation issued from simulations of a shell-model of magnetohydrodynamic turbulence as defined in Giuliani and Carbone (1998), or from a new model of coupled shell-models designed to represent a magnetic loop in the solar corona. We obtain distributions of the peak dissipation power, total energy, duration and waiting-time associated to each definition. These distributions are then investigated and compared, and the influence of the definition of an event on statistics is discussed. In particular, power-law distributions are more likely to appear when using a threshold. The sensitivity of the distributions to the definition of an event seems also to be weaker for events found in a highly intermittent time series. Some implications on statistical results obtained from observations are discussed.Comment: 8 pages, 13 figures. Submitted to Astronomy&Astrophysic

The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

GC-biased gene conversion (gBGC) is a recombination-associated evolutionary process that accelerates the fixation of guanine or cytosine alleles, regardless of their effects on fitness. gBGC can increase the overall rate of substitutions, a hallmark of positive selection. Many fast-evolving genes and noncoding sequences in the human genome have GC-biased substitution patterns, suggesting that gBGC—in contrast to adaptive processes—may have driven the human changes in these sequences. To investigate this hypothesis, we developed a substitution model for DNA sequence evolution that quantifies the nonlinear interacting effects of selection and gBGC on substitution rates and patterns. Based on this model, we used a series of lineage-specific likelihood ratio tests to evaluate sequence alignments for evidence of changes in mode of selection, action of gBGC, or both. With a false positive rate of less than 5% for individual tests, we found that the majority (76%) of previously identified human accelerated regions are best explained without gBGC, whereas a substantial minority (19%) are best explained by the action of gBGC alone. Further, more than half (55%) have substitution rates that significantly exceed local estimates of the neutral rate, suggesting that these regions may have been shaped by positive selection rather than by relaxation of constraint. By distinguishing the effects of gBGC, relaxation of constraint, and positive selection we provide an integrated analysis of the evolutionary forces that shaped the fastest evolving regions of the human genome, which facilitates the design of targeted functional studies of adaptation in humans

A simplified numerical model of coronal energy dissipation based on reduced MHD

A 3D model intermediate between cellular automata (CA) models and the reduced magnetohydrodynamic (RMHD) equations is presented to simulate solar impulsive events generated along a coronal magnetic loop. The model consists of a set of planes distributed along a magnetic loop between which the information propagates through Alfven waves. Statistical properties in terms of power-laws for energies and durations of dissipative events are obtained, and their agreement with X-ray and UV flares observations is discussed. The existence of observational biases is also discussed.Comment: 11 pages, 9 figures Accepted for publication in Astronomy & Astrophysic

Decay laws for three-dimensional magnetohydrodynamic turbulence

Decay laws for three-dimensional magnetohydrodynamic turbulence are obtained from high-resolution numerical simulations using up to 512^3 modes...