Adaptive evolution of molecular phenotypes

Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak.Comment: Figures are not optimally displayed in Firefo

Improving green manure quality with phosphate rocks in Ontario Canada

Phosphate rock (PR) was applied to one conventional and two organic dairy fields and planted with buckwheat (Fagopyrum esculentum) as a green manure crop. In total, five types of PR were applied at three application rates in order to determine the yield, concentration of P in the aboveground tissue and the P uptake of buckwheat. It was found that PR of relatively high carbonate substitution and small particle diameter could increase buckwheat tissue concentrations to a quality such that mineralization of the buckwheat mulch could occur. Buckwheat mulch and residual PR increased soil P flux as determined by anion exchange membranes in situ in the following spring. This provides evidence that buckwheat of high P quality has the potential to supply P to a subsequent crop

Effects of geometric constraints on the nuclear multifragmentation process

We include in statistical model calculations the facts that in the nuclear multifragmentation process the fragments are produced within a given volume and have a finite size. The corrections associated with these constraints affect the partition modes and, as a consequence, other observables in the process. In particular, we find that the favored fragmenting modes strongly suppress the collective flow energy, leading to much lower values compared to what is obtained from unconstrained calculations. This leads, for a given total excitation energy, to a nontrivial correlation between the breakup temperature and the collective expansion velocity. In particular we find that, under some conditions, the temperature of the fragmenting system may increase as a function of this expansion velocity, contrary to what it might be expected.Comment: 16 pages, 5 figure

Statistical multifragmentation model with discretized energy and the generalized Fermi breakup. I. Formulation of the model

The Generalized Fermi Breakup recently demonstrated to be formally equivalent to the Statistical Multifragmentation Model, if the contribution of excited states are included in the state densities of the former, is implemented. Since this treatment requires the application of the Statistical Multifragmentation Model repeatedly on the hot fragments until they have decayed to their ground states, it becomes extremely computational demanding, making its application to the systems of interest extremely difficult. Based on exact recursion formulae previously developed by Chase and Mekjian to calculate the statistical weights very efficiently, we present an implementation which is efficient enough to allow it to be applied to large systems at high excitation energies. Comparison with the GEMINI++ sequential decay code shows that the predictions obtained with our treatment are fairly similar to those obtained with this more traditional model.Comment: 8 pages, 6 figure

Dynamics and structure of an aging binary colloidal glass

We study aging in a colloidal suspension consisting of micron-sized particles in a liquid. This system is made glassy by increasing the particle concentration. We observe samples composed of particles of two sizes, with a size ratio of 1:2.1 and a volume fraction ratio 1:6, using fast laser scanning confocal microscopy. This technique yields real-time, three-dimensional movies deep inside the colloidal glass. Specifically, we look at how the size, motion and structural organization of the particles relate to the overall aging of the glass. Particles move in spatially heterogeneous cooperative groups. These mobile regions tend to be richer in small particles, and these small particles facilitate the motion of nearby particles of both sizes.Comment: 7 pages; submitted to Phys. Rev. E. Revised with 1 new figure, improved tex

Coupling and higher-order effects in the 12C(d,p)13C and 13C(p,d)12C reactions

Coupled channels calculations are performed for the 12C(d,p)13C and 13C(p,d)12C reactions between 7 and 60 MeV to study the effect of inelastic couplings in transfer reactions. The effect of treating transfer beyond Born approximation is also addressed. The coupling to the 12C 2+ state is found to change the peak cross-section by up to 15 %. Effects beyond Born approximation lead to a significant renormalization of the cross-sections, between 5 and 10 % for deuteron energies above 10 MeV, and larger than 10 % for lower energies. We also performed calculations including the remnant term in the transfer operator, which has a small impact on the 12C(d,p)13C(g.s.) and 13C(p,d)12C(g.s.) reactions. Above 30 MeV deuteron energy, the effect of the remnant term is larger than 10 % for the 12C(d,p)13C(3.09 MeV) reaction and is found to increase with decreasing neutron separation energy for the 3.09 MeV state of 13C. This is of importance for transfer reactions with weakly bound nuclei.Comment: 7 pages, 7 figures, submitted to Phys. Rev.