Stability and response of polygenic traits to stabilizing selection and mutation

When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are equivalent. Furthermore, the genetic variance that is maintained by mutation-selection balance is $2 \mu/S$ per locus, where $\mu$ is the mutation rate and $S$ the strength of stabilizing selection. In reality, alleles vary in their effects, making the fitness landscape asymmetric, and complicating analysis of the equilibria. We show that that the resulting genetic variance depends on the fraction of alleles near fixation, which contribute by $2 \mu/S$, and on the total mutational effects of alleles that are at intermediate frequency. The interplay between stabilizing selection and mutation leads to a sharp transition: alleles with effects smaller than a threshold value of $2\sqrt{\mu / S}$ remain polymorphic, whereas those with larger effects are fixed. The genetic load in equilibrium is less than for traits of equal effects, and the fitness equilibria are more similar. We find that if the optimum is displaced, alleles with effects close to the threshold value sweep first, and their rate of increase is bounded by $\sqrt{\mu S}$. Long term response leads in general to well-adapted traits, unlike the case of equal effects that often end up at a sub-optimal fitness peak. However, the particular peaks to which the populations converge are extremely sensitive to the initial states, and to the speed of the shift of the optimum trait value.Comment: Accepted in Genetic

The Larson-Tinsley Effect in the UV: Interacting vs. `Normal' Spiral Galaxies

We compare the UV-optical colors of a well-defined set of optically-selected pre-merger interacting galaxy pairs with those of normal spirals. The shorter wavelength colors show a larger dispersion for the interacting galaxies than for the spirals. This result can best be explained by higher star formation rates on average in the interacting galaxies, combined with higher extinctions on average. This is consistent with earlier studies, that found that the star formation in interacting galaxies tends to be more centrally concentrated than in normal spirals, perhaps due to gas being driven into the center by the interaction. As noted in earlier studies, there is a large variation from galaxy to galaxy in the implied star formation rates of the interacting galaxies, with some galaxies having enhanced rates but others being fairly quiescent.Comment: To appear in the Astronomical Journal. 22 pages, 22 figure

Large Pseudo-Counts and L2L_2-Norm Penalties Are Necessary for the Mean-Field Inference of Ising and Potts Models

Mean field (MF) approximation offers a simple, fast way to infer direct interactions between elements in a network of correlated variables, a common, computationally challenging problem with practical applications in fields ranging from physics and biology to the social sciences. However, MF methods achieve their best performance with strong regularization, well beyond Bayesian expectations, an empirical fact that is poorly understood. In this work, we study the influence of pseudo-count and $L_2$-norm regularization schemes on the quality of inferred Ising or Potts interaction networks from correlation data within the MF approximation. We argue, based on the analysis of small systems, that the optimal value of the regularization strength remains finite even if the sampling noise tends to zero, in order to correct for systematic biases introduced by the MF approximation. Our claim is corroborated by extensive numerical studies of diverse model systems and by the analytical study of the $m$-component spin model, for large but finite $m$. Additionally we find that pseudo-count regularization is robust against sampling noise, and often outperforms $L_2$-norm regularization, particularly when the underlying network of interactions is strongly heterogeneous. Much better performances are generally obtained for the Ising model than for the Potts model, for which only couplings incoming onto medium-frequency symbols are reliably inferred.Comment: 25 pages, 17 figure

Using neutral cline decay to estimate contemporary dispersal: a generic tool and its application to a major crop pathogen

Dispersal is a key parameter of adaptation, invasion and persistence. Yet standard population genetics inference methods hardly distinguish it from drift and many species cannot be studied by direct mark-recapture methods. Here, we introduce a method using rates of change in cline shapes for neutral markers to estimate contemporary dispersal. We apply it to the devastating banana pest Mycosphaerella fijiensis, a wind-dispersed fungus for which a secondary contact zone had previously been detected using landscape genetics tools. By tracking the spatio-temporal frequency change of 15 microsatellite markers, we find that σ, the standard deviation of parent–offspring dispersal distances, is 1.2 km/generation1/2. The analysis is further shown robust to a large range of dispersal kernels. We conclude that combining landscape genetics approaches to detect breaks in allelic frequencies with analyses of changes in neutral genetic clines offers a powerful way to obtain ecologically relevant estimates of dispersal in many species

Quantum Fluctuations of Mass for a Mirror in Vacuum

A mirror in vacuum is coupled to fluctuating quantum fields. As a result, its energy-momentum and mass fluctuate. We compute the correlation spectra of force and mass fluctuations for a mirror at rest in vacuum (of a scalar field in a two-dimensional space-time). The obtained expressions agree with a mass correction equal to a vacuum energy stored by the mirror. We introduce a Lagrangian model which consistently describes a scalar field coupled to a scatterer, with inertial mass being a quantum variable.Comment: 6 page

Environments of Redshift Survey Compact Groups of Galaxies

Redshift Survey Compact Groups (RSCGs) are tight knots of N >= 3 galaxies selected from the CfA2+SSRS2 redshift survey. The selection is based on physical extent and association in redshift space alone. We measured 300 new redshifts of fainter galaxies within 1 h^{-1} Mpc of 14 RSCGs to explore the relationship between RSCGs and their environments. 13 of 14 RSCGs are embedded in overdense regions of redshift space. The systems range from a loose group of 5 members to an Abell cluster. The remaining group, RSCG 64, appears isolated. RSCGs are isolated and distinct from their surroundings to varying degrees, as are the Hickson Compact Groups. Among the 13 embedded RSCGs, 3 are distinct from their general environments (RSCG 9, RSCG 11 and RSCG 85).Comment: 35 pages, including 10 figures and 5 tables, accepted for publication in the Astronomical Journa

On the Scalar Manifold of Exceptional Supergravity

We construct two parametrizations of the non compact exceptional Lie group G=E7(-25), based on a fibration which has the maximal compact subgroup K=(E6 x U(1))/Z_3 as a fiber. It is well known that G plays an important role in the N=2 d=4 magic exceptional supergravity, where it describes the U-duality of the theory and where the symmetric space M=G/K gives the vector multiplets' scalar manifold. First, by making use of the exponential map, we compute a realization of G/K, that is based on the E6 invariant d-tensor, and hence exhibits the maximal possible manifest [(E6 x U(1))/Z_3]-covariance. This provides a basis for the corresponding supergravity theory, which is the analogue of the Calabi-Vesentini coordinates. Then we study the Iwasawa decomposition. Its main feature is that it is SO(8)-covariant and therefore it highlights the role of triality. Along the way we analyze the relevant chain of maximal embeddings which leads to SO(8). It is worth noticing that being based on the properties of a "mixed" Freudenthal-Tits magic square, the whole procedure can be generalized to a broader class of groups of type E7.Comment: Talk given at the XVII European Workshop on String Theory, held at the University of Padua, September 5-9, 201

Is the New Zealand EEZ regulatory framework international best practice?

New Zealand is fortunate to have a very large and diverse marine area. It supports a wide array of marine life with high biodiversity in seabirds, marine mammals and invertebrates. It contains significant petroleum and mineral resources. It also supports a substantial fishing industry. Our seas include the territorial sea (virtually the same as the coastal marine area) out to the 12 nautical mile limit, the exclusive economic zone or EEZ, and the extended continental shelf that extends some distance beyond the 200 nautical mile limit of the EEZ in some places. How the EEZ and the other seas under New Zealand’s control are managed is of critical national and international importance. At the 2011 EDS Conference Raewyn Peart presented on “Oceans governance framework: An appraisal”. She concluded that New Zealand’s EEZ management was lagging behind international best practice because New Zealand had no mechanism for integration; no provision for marine spatial planning in the EEZ; no agency responsible for oceans management; no EEZ environmental assessment legislation; no EEZ marine protected areas legislation; and old and poorly performing marine mammal and wildlife (seabird) legislation. One of the authors of this paper also spoke at the 2011 EDS Conference, and identified a number of shortcomings in the law to regulate offshore petroleum activity, especially in regard to well integrity which is the ‘fence at the top of the cliff’. A lot has happened since 2011. This paper appraises the present state of our offshore environmental legislation, focussing on three issues that are at the fore: the lack of strategic or spatial planning, especially for marine protection purposes; the shortcomings in regulation of petroleum well integrity; and the challenges we face in achieving integrated management. The paper concludes that New Zealand has a lot of work to do by international standards, although it must also be acknowledged that other jurisdictions also struggle to address these issues. Although this paper focuses on the EEZ it also comments on the management of land and the territorial sea

The contribution of statistical physics to evolutionary biology

Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. We discuss aspects of population genetics that have embraced methods from physics: amongst others, non-equilibrium statistical mechanics, travelling waves, and Monte-Carlo methods have been used to study polygenic evolution, rates of adaptation, and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics, for example, by following the distribution of paths taken by a population through time.Comment: 18 pages, 3 figures, glossary. Accepted in Trend in Ecology and Evolution (to appear in print in August 2011

Study of pyridine-mediated electrochemical reduction of CO2 to methanol at high CO2 pressure

© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim The recently proposed highly efficient route of pyridine-catalyzed CO 2 reduction to methanol was explored on platinum electrodes at high CO 2 pressure. At 55 bar (5.5 MPa) of CO 2 , the bulk electrolysis in both potentiostatic and galvanostatic regimes resulted in methanol production with Faradaic yields of up to 10 % for the first 5–10 C cm −2 of charge passed. For longer electrolysis, the methanol concentration failed to increase proportionally and was limited to sub-ppm levels irrespective of biasing conditions and pyridine concentration. This limitation cannot be removed by electrode reactivation and/or pre-electrolysis and appears to be an inherent feature of the reduction process. In agreement with bulk electrolysis findings, the CV analysis supported by simulation indicated that hydrogen evolution is still the dominant electrode reaction in pyridine-containing electrolyte solution, even with an excess CO 2 concentration in the solution. No prominent contribution from either a direct or coupled CO 2 reduction was found. The results obtained suggest that the reduction of CO 2 to methanol is a transient process that is largely decoupled from the electrode charge transfer