The evolutionary consequences of niche construction: a theoretical investigation using two-locus theory

This paper addresses the joint evolution of environment-altering (niche constructing) traits, and traits whose fitness depends on alterable sources of natural selection in environments. We explore the evolutionary consequences of this niche construction using a two-locus population genetic model. The novel conclusions are that niche construction can (1) cause evolutionary inertia and momentum, (2) lead to the fixation of otherwise deleterious alleles, (3) support stable polymorphisms where none are expected, (4) eliminate what would otherwise be stable polymorphisms, and (5) influence disequilibrium. The results suggest that the changes that organisms bring about in their niche can themselves be an important source of natural selection pressures, and imply that evolution may proceed in cycles of selection and niche construction.     

Use of Plant Strategy Ordination,DCA and ANOVA to elucidate relationships among habitats of Salix planifolia and Salix monticola

Abstract. Detrended Correspondence Analysis (DCA) was used on a data set of 112 species from 14 stands dominated by Salix planifolia and/or S. monticola. Environmental variables were determined which might be important to explain differences in stand vegetation composition, and willow stature (height), in willow carrs in the Rocky Mountain National Park. Correlation of environmental variables with DCA stand scores indicate that peat depth and soil redox potential are highly related to the primary DCA axis. Soils in stands of S. planifolia are more reduced in the early summer and have greater peat depths, than soils in stands of S. monticola. The second DCA axis is related to a water chemistry gradient of hydrogen ion, sulphate, and ammonium concentration. Four environmental variables selected by correlation analysis were regressed on stand scores from the first two DCA axes. Regression coefficients of August soil redox potential and soil water pH were significantly non-zero on the primary DCA axis. In addition to overall vegetation relationships elucidated by DCA, the relationships between willow stature and environmental variables were tested by simultaneous ANOVAs. ANOVA results and DCA ordinations indicate that S. planifolia and S. monticola plants achieve the greatest stature in the least reduced soils, and in shallow peat. Competitive, stress tolerant, and ruderal plant strategy theory applied to the vegetation data produced an arrangement of stands highly correlated to the DCA Axis 1 stand arrangement. These correlations indicate that the primary axis of vegetation structure can be extracted either by species composition, or species morphology/physiology relationships. Concurrent use of DCA and plant strategy theory is suggested as a tool for the prediction of community composition.     

Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory

The nearly neutral theory of molecular evolution predicts larger generation-time effects for synonymous than for nonsynonymous substitutions. This prediction is tested using the sequences of 49 single-copy genes by calculating the average and variance of synonymous and nonsynonymous substitutions in mammalian star phylogenies (rodentia, artiodactyla, and primates). The average pattern of the 49 genes supports the prediction of the nearly neutral theory, with some notable exceptions.The nearly neutral theory also predicts that the variance of the evolutionary rate is larger than the value predicted by the completely neutral theory. This prediction is tested by examining the dispersion index (ratio of the variance to the mean), which is positively correlated with the average substitution number. After weighting by the lineage effects, this correlation almost disappears for nonsynonymous substitutions, but not quite so for synonymous substitutions. After weighting, the dispersion indices of both synonymous and nonsynonymous substitutions still exceed values expected under the simple Poisson process. The results indicate that both the systematic bias in evolutionary rate among the lineages and the episodic type of rate variation are contributing to the large variance. The former is more significant to synonymous substitutions than to nonsynonymous substitutions. Isochore evolution may be similar to synonymous substitutions. The rate and pattern found here are consistent with the nearly neutral theory, such that the relative contributions of drift and selection differ between the two types of substitutions. The results are also consistent with Gillespie's episodic selection theory.     

Optimized Effective Potential for Atoms and Molecules

We describe the optimized effective potential method of density functional theory and the semi-analytical approximation due to Krieger, Li and Iafrate. Results for atomic and molecular systems including correlation contributions are presented and compared with conventional Kohn–Sham methods. The combination of the exact exchange energy functional with the correlation energy functional of Colle and Salvetti works extremely well for atomic systems, while further improvement is required for molecular systems.     

An Analysis of the Metabolic Theory of the Origin of the Genetic Code

A computer program was used to test Wong's coevolution theory of the genetic code. The codon correlations between the codons of biosynthetically related amino acids in the universal genetic code and in randomly generated genetic codes were compared. It was determined that many codon correlations are also present within random genetic codes and that among the random codes there are always several which have many more correlations than that found in the universal code. Although the number of correlations depends on the choice of biosynthetically related amino acids, the probability of choosing a random genetic code with the same or greater number of codon correlations as the universal genetic code was found to vary from 0.1% to 34% (with respect to a fairly complete listing of related amino acids). Thus, Wong's theory that the genetic code arose by coevolution with the biosynthetic pathways of amino acids, based on codon correlations between biosynthetically related amino acids, is statistical in nature. Received: 8 August 1996 / Accepted: 26 December 1996     

Perturbation analysis of a two-locus model with directional selection and recombination

A population genetic two-locus model with additive, directional selection and recombination is considered. It is assumed that recombination is weaker than selection; i.e., the recombination parameter r is smaller than the selection coefficients. This assumption is appropriate for describing the effects of two-locus selection at the molecular level. The model is formulated in terms of ordinary differential equations (ODES) for the gamete frequencies x = (x ₁, x ₂, x ₃, x ₄), defined on the simplex S ₄. The ODEs are analyzed using first a regular pertubation technique. However, this approach yields satisfactory results only if r is very small relative to the selection coefficients and if the initial values x(0) are in the interior part of S ₄. To cope with this problem, a novel two-scale perturbation method is proposed which rests on the theory of averaging of vectorfields. It is demonstrated that the zeroth-order solution of this two-scale approach approximates the numerical solution of the model well, even if recombination rate is on the order of the selection coefficients.     

Optimal local propensities for model proteins

Lattice models of proteins were used to examine the role of local propensities in stabilizing the native state of a protein, using techniques drawn from spin-glass theory to characterize the free-energy landscapes. In the strong evolutionary limit, optimal conditions for folding are achieved when the contributions from local interactions to the stability of the native state is small. Further increasing the local interactions rapidly decreases the foldability. © 1995 Wiley-Liss, Inc.     

Theoretical and experimental determination of SAR patterns for spherical tissue models in a rectangular resonant cavity

Specific absorption rates (SARs) were determined theoretically and experimentally for several spherical models of tissue exposed to electrical fields of TE101 mode in a rectangular cavity of 57.3 MHz resonant frequency. The approximate theoretical SAR can be calculated according to the Mie theory by superposition of four plane waves representing the fields excited in the cavity. The theoretical and thermographically determined SAR patterns in spheres with radii of 5, 7.5, and 10 cm and with conductivities of 0.1, 1, and 10 S/m were compared. For a sphere with radius less than 7.5 cm and conductivity less than 1 S/m, the SAR was quite uniform. When conductivity was increased to 10 S/m, the SAR patterns showed higher absorption in the periphery of the largest sphere (10-cm radius). These characteristics are important in evaluating the scaling technique of exposing a model of a human to very-high-frequency fields to obtain power absorption data in humans exposed to high-frequency or very-low-frequency fields.     

Effective cryoprotection of thylakoid membranes by ATP

Freezing of isolated spinach thylakoids in the presence of NaCl uncoupled photophosphorylation from electron flow and increased the permeability of the membranes to protons. Addition of ATP prior to freezing diminished membrane inactivation. On a molar basis, ATP was at least 100 times more effective in protecting thylakoids from freezing damage than low-molecularweight carbohydrates such as sucrose and glucose. The cryoprotective effectiveness of ATP was increased by Mg²⁺. In the absence of carbohydrates, preservation of thylakoids during freezing in 100 mM NaCl was saturated at about 1–2 mM ATP, but under these conditions membranes were not fully protected. However, in the presence of small amounts of sugars which did not significantly prevent thylakoid inactivation during freezing, ATP concentrations considerably lower than 0.5 mM caused nearly complete membrane protection. Neither ADP nor AMP could substitute for ATP. These findings indicate that cryoprotection by ATP cannot be explained by a colligative mechanism. It is suggested that ATP acts on the chloroplast coupling factor, either by modifying its conformation or by preventing its release from the membranes. The results are discussed in regard to freezing injury and resistance in vivo.Abbreviations CF₁ chloroplast coupling factor - Hepes 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid - PMS phenazine methosulfate - Tris 2-amino-2-(hydroxymethyl)-1,3-propandiol     

On the eigenvalue distribution of genetic and phenotypic dispersion matrices: Evidence for a nonrandom organization of quantitative character variation

A quantitative genetic model of random pleiotropy is introduced as reference model for detecting the kind and degree of organization in quantitative genetic variation. In this model the genetic dispersion matrix takes the form of G = BB ^T, where B is a general, real, Gaussian random matrix. The eigenvalue density of the corresponding ensemble of random matrices (_G) is considered. The first two moments are derived for variance-covariance matrices G as well as for correlation matrices R, and an approximate expression of the density function is given. The eigenvalue distribution of all empirical correlation matrices deviates from that of a random pleiotropy model by a very large leading eigenvalue associated with a size factor. However the frequency-distribution of the remaining eigenvalues shows only minor deviations in mammalian skeletal data. A prevalence of intermediate eigenvalues in insect data may be caused by the inclusion of many functionally unrelated characters. Hence two kinds of deviations from random organization have been found: a mammal like and an insect like organization. It is concluded that functionally related characters are on the average more tightly correlated than by chance (= mammal like organization), while functionally unrelated characters appear to be less correlated than by random pleiotropy (insect like organization).