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

Ghosts of glaciers and the disjunct distribution of a threatened California moth (Euproserpinus euterpe)

The Kern Primrose Sphinx moth (Euproserpinus euterpe) is a threatened moth twice thought to have gone extinct. It was historically known only from a small basin in the southern Sierra Nevada of California, but a new putative population was recently discovered 115 km to the west. Analysis of both nuclear and mitochondrial DNA suggest discontinuous genetic breaks between the Kern Primrose Sphinx, its closest relative the Phaeton Sphinx (Euproserpinus phaeton), and at least one additional species discovered during the course of this study. Geographic distance is well correlated with genetic distance within species, but not between species. Genetic discontinuities show the influence of past glacial events and suggest recent range expansions, though not always congruent with other phylogeographic studies from the region. Our phylogeographic results demonstrate that past glacial events, the altitudinal suppression of suitable habitat, and isolation may have been more important than population-level ecological factors such as differences in habitat (e.g. sand dunes, oak forest, montane grasslands) in promoting speciation. Effective conservation of the genetic diversity of the widespread Phaeton Sphinx and its two geographically restricted relatives requires genetic data at the population level because relatively few localized populations harbor most of the genetic variation

Long-range quantum discord in critical spin systems

We show that quantum correlations as quantified by quantum discord can characterize quantum phase transitions by exhibiting nontrivial long-range decay as a function of distance in spin systems. This is rather different from the behavior of pairwise entanglement, which is typically short-ranged even in critical systems. In particular, we find a clear change in the decay rate of quantum discord as the system crosses a quantum critical point. We illustrate this phenomenon for first-order, second-order, and infinite-order quantum phase transitions, indicating that pairwise quantum discord is an appealing quantum correlation function for condensed matter systems

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

Transverse Ising Model: Markovian evolution of classical and quantum correlations under decoherence

The transverse Ising Model (TIM) in one dimension is the simplest model which exhibits a quantum phase transition (QPT). Quantities related to quantum information theoretic measures like entanglement, quantum discord (QD) and fidelity are known to provide signatures of QPTs. The issue is less well explored when the quantum system is subjected to decoherence due to its interaction, represented by a quantum channel, with an environment. In this paper we study the dynamics of the mutual information $I(\rho_{AB})$, the classical correlations $C(\rho_{AB})$ and the quantum correlations $Q(\rho_{AB})$, as measured by the QD, in a two-qubit state the density matrix of which is the reduced density matrix obtained from the ground state of the TIM in 1d. The time evolution brought about by system-environment interactions is assumed to be Markovian in nature and the quantum channels considered are amplitude damping, bit-flip, phase-flip and bit-phase-flip. Each quantum channel is shown to be distinguished by a specific type of dynamics. In the case of the phase-flip channel, there is a finite time interval in which the quantum correlations are larger in magnitude than the classical correlations. For this channel as well as the bit-phase-flip channel, appropriate quantities associated with the dynamics of the correlations can be derived which signal the occurrence of a QPT.Comment: 8 pages, 7 figures, revtex4-1, version accepted for publication in Eur. Phys. J.

Study of Loschmidt Echo for a qubit coupled to an XY-spin chain environment

We study the temporal evolution of a central spin-1/2 (qubit) coupled to the environment which is chosen to be a spin-1/2 transverse XY spin chain. We explore the entire phase diagram of the spin-Hamiltonian and investigate the behavior of Loschmidt echo(LE) close to critical and multicritical point(MCP). To achieve this, the qubit is coupled to the spin chain through the anisotropy term as well as one of the interaction terms. Our study reveals that the echo has a faster decay with the system size (in the short time limit) close to a MCP and also the scaling obeyed by the quasiperiod of the collapse and revival of the LE is different in comparison to that close to a QCP. We also show that even when approached along the gapless critical line, the scaling of the LE is determined by the MCP where the energy gap shows a faster decay with the system size. This claim is verified by studying the short-time and also the collapse and revival behavior of the LE at a quasicritical point on the ferromagnetic side of the MCP. We also connect our observation to the decoherence of the central spin.Comment: Accepted for publication in EPJ

A global database of C4 photosynthesis in grasses

C3,C4 or Crassulacean acid metabolism (CAM) photosynthetic pathways represent a fundamental axis of trait variation in plants,with importance at scales from genome to biome. Knowing the distribution of these pathways among wild species is a crucial first step in understanding the patterns and processes of photosynthetic evolution and its role in ecological processes at large scales (e.g. changes in the composition of biomes under global change). C4 photosynthesis is most prevalent in the Poaceae (grasses), which account for about half of all C4 species (Sage et al.,1999a).Research on the evolution and ecology of these plants has undergone a renaissance during the last 7 yr, catalyzed by phylogenetic analyses showing multiple parallel C4 origins (e.g. Christin et al. , 2007; Vicentini et al., 2008; GPWG II, 2012), insights into the distribution of C4 species and assembly of the C4 grassland biome (Edwards & Still, 2008; Edwards & Smith, 2010; Edwards et al., 2010), and efforts to introduce the C4 pathway into rice (Hibberd et al., 2008; von Caemmerer et al., 2012). C4 photosynthesis is an excellent model for investigating complex trait evolution, because of the broad knowledge base describing its biochemical basis, evolutionary history, and ecological interactions (Christin et al., 2010)

ELM triggering conditions for the integrated modeling of H-mode plasmas

Recent advances in the integrated modeling of ELMy H-mode plasmas are presented. A model for the H-mode pedestal and for the triggering of ELMs predicts the height, width, and shape of the H-mode pedestal and the frequency and width of ELMs. Formation of the pedestal and the L-H transition is the direct result of ExB flow shear suppression of anomalous transport. The periodic ELM crashes are triggered by either the ballooning or peeling MHD instabilities. The BALOO, DCON, and ELITE ideal MHD stability codes are used to derive a new parametric expression for the peeling-ballooning threshold. The new dependence for the peeling-ballooning threshold is implemented in the ASTRA transport code. Results of integrated modeling of DIII-D like discharges are presented and compared with experimental observations. The results from the ideal MHD stability codes are compared with results from the resistive MHD stability code NIMROD.Comment: 12th International Congress on Plasma Physics, 25-29 October 2004, Nice (France

Automorphic Equivalence within Gapped Phases of Quantum Lattice Systems

Gapped ground states of quantum spin systems have been referred to in the physics literature as being `in the same phase' if there exists a family of Hamiltonians H(s), with finite range interactions depending continuously on $s \in [0,1]$, such that for each $s$, H(s) has a non-vanishing gap above its ground state and with the two initial states being the ground states of H(0) and H(1), respectively. In this work, we give precise conditions under which any two gapped ground states of a given quantum spin system that 'belong to the same phase' are automorphically equivalent and show that this equivalence can be implemented as a flow generated by an $s$-dependent interaction which decays faster than any power law (in fact, almost exponentially). The flow is constructed using Hastings' 'quasi-adiabatic evolution' technique, of which we give a proof extended to infinite-dimensional Hilbert spaces. In addition, we derive a general result about the locality properties of the effect of perturbations of the dynamics for quantum systems with a quasi-local structure and prove that the flow, which we call the {\em spectral flow}, connecting the gapped ground states in the same phase, satisfies a Lieb-Robinson bound. As a result, we obtain that, in the thermodynamic limit, the spectral flow converges to a co-cycle of automorphisms of the algebra of quasi-local observables of the infinite spin system. This proves that the ground state phase structure is preserved along the curve of models $H(s), 0\leq s\leq 1$.Comment: Updated acknowledgments and new email address of S

Fertility, Living Arrangements, Care and Mobility

There are four main interconnecting themes around which the contributions in this book are based. This introductory chapter aims to establish the broad context for the chapters that follow by discussing each of the themes. It does so by setting these themes within the overarching demographic challenge of the twenty-first century – demographic ageing. Each chapter is introduced in the context of the specific theme to which it primarily relates and there is a summary of the data sets used by the contributors to illustrate the wide range of cross-sectional and longitudinal data analysed