The Iso-regularization Descent Algorithm for the LASSO

International audienceFollowing the introduction by Tibshirani of the LASSO technique for feature selection in regression, two algorithms were proposed by Osborne et al. for solving the associated problem. One is an homotopy method that gained popularity as the LASSO modification of the LARS algorithm. The other is a finite-step descent method that follows a path on the constraint polytope, and seems to have been largely ignored. One of the reason may be that it solves the constrained formulation of the LASSO, as opposed to the more practical regularized formulation. We give here an adaptation of this algorithm that solves the regularized problem, has a simpler formulation, and outperforms state-of-the-art algorithms in terms of speed

Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait

Physiological novelties are often studied at macro-evolutionary scales such that their micro-evolutionary origins remain poorly understood. Here, we test the hypothesis that key components of a complex trait can evolve in isolation and later be combined by gene flow. We use C4 photosynthesis as a study system, a derived physiology that increases plant productivity in warm, dry conditions. The grass Alloteropsis semialata includes C4 and non-C4 genotypes, with some populations using laterally-acquired C4 -adaptive loci, providing an outstanding system to track the spread of novel adaptive mutations. Using genome data from C4 and non-C4 A. semialata individuals spanning the species' range, we infer and date past migrations of different parts of the genome. Our results show that photosynthetic types initially diverged in isolated populations, where key C4 components were acquired. However, rare but recurrent subsequent gene flow allowed the spread of adaptive loci across genetic pools. Indeed, laterally-acquired genes for key C4 functions were rapidly passed between populations with otherwise distinct gene pools. Thus, our intraspecific study of C4 -related genomic variation indicates that components of adaptive traits can evolve separately and later be combined through secondary gene flow, leading to the assembly and optimization of evolutionary innovations. This article is protected by copyright. All rights reserved

Entanglement study of the 1D Ising model with Added Dzyaloshinsky-Moriya interaction

We have studied occurrence of quantum phase transition in the one-dimensional spin-1/2 Ising model with added Dzyaloshinsky-Moriya (DM) interaction from bi- partite and multi-partite entanglement point of view. Using exact numerical solutions, we are able to study such systems up to 24 qubits. The minimum of the entanglement ratio R $\equiv$ \tau 2/\tau 1 < 1, as a novel estimator of QPT, has been used to detect QPT and our calculations have shown that its minimum took place at the critical point. We have also shown both the global-entanglement (GE) and multipartite entanglement (ME) are maximal at the critical point for the Ising chain with added DM interaction. Using matrix product state approach, we have calculated the tangle and concurrence of the model and it is able to capture and confirm our numerical experiment result. Lack of inversion symmetry in the presence of DM interaction stimulated us to study entanglement of three qubits in symmetric and antisymmetric way which brings some surprising results.Comment: 18 pages, 9 figures, submitte

Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

C4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C4 and non-C4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C4 physiology away from its region of origin

Continued adaptation of C4 photosynthesis after an initial burst of changes in the andropogoneae grasses

C4 photosynthesis is a complex trait that sustains fast growth and high productivity in tropical and subtropical conditions and evolved repeatedly in flowering plants. One of the major C4 lineages is Andropogoneae, a group of ∼ 1,200 grass species that includes some of the world's most important crops and species dominating tropical and some temperate grasslands. Previous efforts to understand C4 evolution in the group have compared a few model C4 plants to distantly related C3 species, so that changes directly responsible for the transition to C4 could not be distinguished from those that preceded or followed it. In this study, we analyse the genomes of 66 grass species, capturing the earliest diversification within Andropogoneae as well as their C3 relatives. Phylogenomics combined with molecular dating and analyses of protein evolution show that many changes linked to the evolution of C4 photosynthesis in Andropogoneae happened in the Early Miocene, between 21 and 18 Ma, after the split from its C3 sister lineage, and before the diversification of the group. This initial burst of changes was followed by an extended period of modifications to leaf anatomy and biochemistry during the diversification of Andropogoneae, so that a single C4 origin gave birth to a diversity of C4 phenotypes during 18 million years of speciation events and migration across geographic and ecological spaces. Our comprehensive approach and broad sampling of the diversity in the group reveals that one key transition can lead to a plethora of phenotypes following sustained adaptation of the ancestral state

Energy Loss versus Shadowing in the Drell-Yan Reaction on Nuclei

We present a new analysis of the E772 and E866 experiments on the nuclear dependence of Drell-Yan (DY) lepton pair production resulting from the bombardment of $^2H$, Be, C, Ca, Fe, and W targets by 800 GeV/c protons at Fermilab. We employ a light-cone formulation of the DY reaction in the rest frame of the nucleus, where the dimuons detected at small values of Bjorken x_2 << 1 may be considered to originate from the decay of a heavy photon radiated from an incident quark in a bremsstrahlung process. We infer the energy loss of the quark by examining the suppression of the nuclear-dependent DY ratios seen as a function of projectile momentum fraction x_1 and dimuon mass M. Shadowing, which also leads to nuclear suppression of dimuons, is calculated within the same approach employing the results of phenomenological fits to deep inelastic scattering data from HERA. The analysis yields -dE/dz =2.73 +/- 0.37 +/- 0.5 GeV/fm for the rate of quark energy loss per unit path length, a value consistent with theoretical expectations including the effects of the inelastic interaction of the incident proton at the surface of the nucleus. This is the first observation of a nonzero energy loss effect in such experiments.Comment: 43 pages including 17 figure

Shadowing in Inelastic Scattering of Muons on Carbon, Calcium and Lead at Low XBj

Nuclear shadowing is observed in the per-nucleon cross-sections of positive muons on carbon, calcium and lead as compared to deuterium. The data were taken by Fermilab experiment E665 using inelastically scattered muons of mean incident momentum 470 GeV/c. Cross-section ratios are presented in the kinematic region 0.0001 < XBj <0.56 and 0.1 < Q**2 < 80 GeVc. The data are consistent with no significant nu or Q**2 dependence at fixed XBj. As XBj decreases, the size of the shadowing effect, as well as its A dependence, are found to approach the corresponding measurements in photoproduction.Comment: 22 pages, incl. 6 figures, to be published in Z. Phys.

Leaf anatomy explains the strength of C4 activity within the grass species Alloteropsis semialata

C4 photosynthesis results from anatomical and biochemical characteristics that together concentrate CO2 around ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), increasing productivity in warm conditions. This complex trait evolved through the gradual accumulation of components, and particular species possess only some of these, resulting in weak C4 activity. The consequences of adding C4 components have been modelled and investigated through comparative approaches, but the intraspecific dynamics responsible for strengthening the C4 pathway remain largely unexplored. Here, we evaluate the link between anatomical variation and C4 activity, focusing on populations of the photosynthetically diverse grass Alloteropsis semialata that fix various proportions of carbon via the C4 cycle. The carbon isotope ratios in these populations range from values typical of C3 to those typical of C4 plants. This variation is statistically explained by a combination of leaf anatomical traits linked to the preponderance of bundle sheath tissue. We hypothesize that increased investment in bundle sheath boosts the strength of the intercellular C4 pump and shifts the balance of carbon acquisition towards the C4 cycle. Carbon isotope ratios indicating a stronger C4 pathway are associated with warmer, drier environments, suggesting that incremental anatomical alterations can lead to the emergence of C4 physiology during local adaptation within metapopulations

Biological and geophysical feedbacks with fire in the Earth system

Roughly 3% of the Earth's land surface burns annually, representing a critical exchange of energy and matter between the land and atmosphere via combustion. Fires range from slow smouldering peat fires, to low-intensity surface fires, to intense crown fires, depending on vegetation structure, fuel moisture, prevailing climate, and weather conditions. While the links between biogeochemistry, climate and fire are widely studied within Earth system science, these relationships are also mediated by fuels—namely plants and their litter—that are the product of evolutionary and ecological processes. Fire is a powerful selective force and, over their evolutionary history, plants have evolved traits that both tolerate and promote fire numerous times and across diverse clades. Here we outline a conceptual framework of how plant traits determine the flammability of ecosystems and interact with climate and weather to influence fire regimes. We explore how these evolutionary and ecological processes scale to impact biogeochemical and Earth system processes. Finally, we outline several research challenges that, when resolved, will improve our understanding of the role of plant evolution in mediating the fire feedbacks driving Earth system processes. Understanding current patterns of fire and vegetation, as well as patterns of fire over geological time, requires research that incorporates evolutionary biology, ecology, biogeography, and the biogeosciences