The neutral theory is dead. The current significance and standing of neutral and nearly neutral theories

Comparative studies of DNA sequences provide opportunities for testing the neutral and the selection theories of molecular evolution. In particular, the separate estimation of the numbers of synonymous and nonsynonymous substitutions is a powerful tool for detecting selection of the latter. The difference in the patterns of these two types of substitutions of mammalian genes turned out to be in accord with the slightly deleterious or nearly neutral mutation theory for nonsynonymous changes. Interaction systems at the amino acid level were suggested to be responsible for such nearly neutral, or very weak, selection. Synonymous substitutions are not strictly neutral, but because of their minute effect, random drift predominates such that the rate of substitution is only slightly less than the completely neutral prediction. It was concluded that the strictly neutral theory has not held up as well as the nearly neutral theory, yet remains invaluable as a null hypothesis for detecting selection. On the other hand, the main difference between the nearly neutral and the traditional selection theories is that the former predicts rapid evolution in small populations, whereas the latter predicts rapid evolution in large populations.     

The neutral theory is dead. Long live the neutral theory

The neutral theory of molecular evolution has been instrumental in organizing our thinking about the nature of evolutionary forces shaping variation at the DNA level. More importantly, it has provided empiricists with a strong set of testable predictions and hence, a useful null hypothesis against which to test for the presence of selection. Evidence indicates that the neutral theory cannot explain key features of protein evolution nor patterns of biased codon usage in certain species. Whereas we now have a reasonable model of selection acting on synonymous changes in Drosophila, protein evolution remains poorly understood. Despite limitations in the applicability of the neutral theory, it is likely to remain an integral part of the quest to understand molecular evolution.     

Dynamics of neutral biodiversity

Hubbell's neutral model has become a major paradigm in ecology. Whereas the steady-state structure is well understood, results about the dynamical aspects of the model are scarce. Here we derive dynamical equations for the Simpson diversity index. Both mean and variance of the diversity are proven to satisfy stable linear system dynamics. We show that in the stationary limit we indeed recover previous results, and we supplement this with numerical simulations to validate the dynamical part of our analytical computations. These findings are especially relevant for experiments in microbial ecology, where the Simpson diversity index can be accurately measured as a function of time.     

Microvillar membrane neutral endopeptidases

Recent developments on neutral endopeptidase (NEP, EC 3.4.24.11) are described. These include (1) the development of a novel colorimetric assay with a chromogenic substrate (Glutaryl-Gly-Gly-Phe-2-naphthylamide) coupled with aminopeptidase M (EC 3.4.11.2). (2) A detergent form of the pig kidney enzyme has been purified by immuno-adsorbent chromatography and its molecular properties compared with other forms of the enzyme from rabbit kidney and pig intestine. (3) Rat kidney microvilli contain two endopeptidases of about equal activity when assayed with [125I]iodo-insulin B chain as substrate. One is similar to the rabbit and pig endopeptidases in being sensitive to inhibition by phosphoamidon. The other is insensitive to the inhibitor, though susceptible to chelating agents. The two enzymes are resolvable and have been partially characterized. (4) Endopeptidases of the phosphoramidon-sensitive type are present in various tissues in addition to the principal locations in brush borders of kidney and intestine.     

Invasibility of neutral communities

Comparative data in invasion ecology show that (i) disturbance enhances community invasibility, (ii) there is a positive relationship between residence time of an invader and its success, (iii) there are broadly constant proportions of newly arrived species to those that become established and dominant (“tens rule”), and (iv) invasive species have higher growth rates in comparison with non-invasive species. I use a simple neutral model to test whether these patterns occur in communities with all species identical and no species-specific interactions. In the model, local communities are grouped into continents with immigration rates smaller between than within the continents. Species coming from the other continent are considered to be alien and their fates are recorded. In the model, disturbance predictably increases species numbers and numbers of individuals of aliens. However, the model makes different predictions on effects of disturbance on three processes involved in alien species spreading: establishment (positive effect of disturbance), naturalization (negative effect) and dominance (positive effect). The predictions do not change if variation of growth rates is incorporated into the model. The model also predicts positive relationship between residence time and abundance. Total community size had little effect on success of alien species. The broad agreement of the predictions of the neutral model with the patterns from the field suggests that some of these general patterns of community invasibility are to some degree fully independent of any specific biological assumptions and by themselves may not provide many insights on underlying biological processes. Aggregate data should therefore be used with great caution and statistical patterns must be removed by means of generating null model predictions.     

Microbial transformation of neutral fraction and upgraded neutral fraction of Polish tall oil

Summary Microbial transformations of neutral fraction (NF) and upgraded neutral fraction (UNF) of Polish tall oil byMycobacterium sp. MB 3683 were performed. Final metabolites and yields were compared to bioconversion of pure -sitosterol. Additionally, origin of a new metabolite —5-androsta-3,6,17-trione was proved by transformation of UNF in the presence of labeled -sitosterol.     

Aminopropyl solid phase extraction and 2 D TLC of neutral glycosphingolipids and neutral lysoglycosphingolipids

Methods for isolation of neutral lysoglycosphingolipids (n-lyso-GSLs) such as glucosylsphingosine and galactosylsphingosine normally involve mild alkaline or acid hydrolysis followed by multiple chromatography steps, yielding relatively low recoveries of n-lyso-GSLs and neutral glycosphingolipids (n-GSLs). We now describe a new technique for isolating these compounds using one chromatography step, resulting in quantitative recovery of n-GSLs and n-lyso-GSLs. Lipids are extracted using a modified Folch procedure in which recovery is optimized by reextracting the Folch upper phase with water-saturated butanol. The extract is applied to an aminopropyl solid phase column from which both n-GSLs and n-lyso-GSLs elute in the same fraction. Separation is achieved using a new two-dimensional thin-layer chromatography procedure. The usefulness of this technique for biological samples was tested by examining Glc[4,5-(3)H]ceramide and Glc[4,5-(3)H]sphingosine accumulation in metabolically-labeled neurons treated with an inhibitor of lysosomal glucocerebrosidase. Accurate quantification of both lipids was obtained with Glc[4,5-(3)H]ceramide and Glc[4,5-(3)H]sphingosine accumulating at levels of 20 nmol/mg DNA and 40 pmol/mg DNA, respectively. This simple and rapid technique can therefore be used for the analysis of lyso-GSLs and GSLs in the same tissue, which may permit the determination of their metabolic pathways in normal and in pathological tissues, such as those taken from Gaucher and Krabbe's disease patients.     

Heterogeneous periodicity of drosophila mtDNA: new refutations of neutral and nearly neutral evolution

We found a consistent 3-site periodicity of the X29 values for the heterogeneity of the distribution of the second base in relation to the first base of dinucleotides separated by 0 (contiguous), 1, 2, 3 ... 17 (K) nucleotide sites in Drosophila mtDNA. Triplets of X29 values were found where the first was over 300 and the second and third ranged between 37 and 114 (previous studies). In this study, the periodicity was significant until separation of 2011K, and a structure of deviations from randomness among dinucleotides was found. The most deviant dinucleotides were G-G, G-C and C-G for the first, second and third element of the triplet, respectively. In these three cases there were more dinucleotides observed than expected. This inter-bases correlation and periodicity may be related to the tertiary structure of circular DNA, like that of prokaryotes and mitochondria, to protect and preserve it. The mtDNA with 19.517 bp was divided into four equal segments of 4.879 bp. The fourth sub-segment presented a very low proportion of G and C, the internucleotide interaction was weaker in this sub-segment and no periodicity was found. The maintenance of this mtDNA structure and organization for millions of generations, in spite of a high recurrent mutation rate, does not support the notion of neutralism or near neutralism. The high level of internucleotide interaction and periodicity indicate that every nucleotide is co-adapted with the residual genome.     

Effects of neutral salts and alcohols on the activity of Streptomyces caespitosus neutral protease

Streptomyces caespitosus neutral protease (ScNP) is one of the smallest metalloproteinase with a molecular mass of 14 kDa. Effects of solvent composition on ScNP activity were examined using a peptide substrate. The k(cat)/K(m) values of ScNP exhibited bell-shaped pH-dependence with the optimal pH of 6.4-7.0 and the pK(a) values of 5.0 +/- 0.1 and 8.3 +/- 0.1. ScNP activity increased in an exponential fashion with increasing [NaCl]. The relative k(cat)/K(m) value at 3.6 M NaCl to that at 0 M NaCl was 3.7, and the degree of the activation at x M NaCl was expressed as 1.2 (x) (x < 2.0) and 1.4(x) (x > 2.0). On the other hand, ScNP activity decreased with increasing concentrations of LiCl, KCl, NaBr, LiBr, KBr and NaClO(4). Alcohols inhibited ScNP activity with the IC(50) values, the concentration required for decreasing the activity at 50% of the maximum, of 0.77-6.54 M. The order of the inhibitory potency was 1-butanol, 2-methyl-1-propanol, 2-methyl-2-butanol > 2-methyl-2-propanol, 2-butanol, 1-propanol > 2-propanol > ethanol > methanol. The activities recovered completely by the dilution of alcohols, suggesting that the ScNP inhibition by alcohols is reversible. These characteristics of ScNP are compared with those of human matrix metalloproteinase 7 and thermolysin.     

Activation of myocardial neutral triglyceride lipase and neutral cholesterol esterase by cAMP-dependent protein kinase

Lipolysis of intracellular triglycerides in the heart has been shown to be regulated by hormones. However, activation of myocardial triglyceride lipase in a cell-free system has not been directly demonstrated. In the present studies, initial attempts to demonstrate cAMP-dependent activation of triglyceride lipase using the 1,000 X g supernatant fraction (S1) of mouse heart homogenate were unsuccessful, presumably due to the masking effects of high levels of lipoprotein lipase activity even when assayed at pH 7.4 and in the absence of apolipoprotein C-II. Myocardial lipoprotein lipase in the 40,000 X g supernatant fraction was then removed by heparin-Sepharose affinity chromatography. The lipoprotein lipase-free fractions were shown to contain neutral triglyceride lipase and neutral cholesterol esterase of about equal activities. The triglyceride lipase and cholesterol esterase activities fell progressively during preincubation in the presence of 5 mM Mg2+. Additions of cAMP and ATP resulted in 40-70% activation of both triglyceride lipase and cholesterol esterase. The activation was blocked by protein kinase inhibitor and was restored by the addition of exogenous cAMP-dependent protein kinase. Since lipoprotein lipase has no activity toward cholesteryl oleate, activation of cholesterol esterase in untreated S1 was readily demonstrable. Both triglyceride lipase and cholesterol esterase activities were present in homogenates prepared from isolated rat heart myocytes. We conclude that the myocardium contains a hormone-sensitive lipase that is regulated in a fashion similar to that of the adipose tissue enzyme.     

Thermodynamics of neutral protein evolution

Naturally evolving proteins gradually accumulate mutations while continuing to fold to stable structures. This process of neutral evolution is an important mode of genetic change and forms the basis for the molecular clock. We present a mathematical theory that predicts the number of accumulated mutations, the index of dispersion, and the distribution of stabilities in an evolving protein population from knowledge of the stability effects (delta deltaG values) for single mutations. Our theory quantitatively describes how neutral evolution leads to marginally stable proteins and provides formulas for calculating how fluctuations in stability can overdisperse the molecular clock. It also shows that the structural influences on the rate of sequence evolution observed in earlier simulations can be calculated using just the single-mutation delta deltaG values. We consider both the case when the product of the population size and mutation rate is small and the case when this product is large, and show that in the latter case the proteins evolve excess mutational robustness that is manifested by extra stability and an increase in the rate of sequence evolution. All our theoretical predictions are confirmed by simulations with lattice proteins. Our work provides a mathematical foundation for understanding how protein biophysics shapes the process of evolution.     

A neutral theory of biogenesis

The selective Darwinian theory of chemical evolution is critically reviewed and the tentative conclusion is reached that neither the theoretical analyses nor the experiments with phages can really prove it. An alternative proposal is put forth which considers the possibility that the biogenetic process has been driven by stochastic forces, e.g. it took place in the absence of Darwinian selection which, in turn, started only when the first protocells came into existence. The dynamics of the early self-organization of living structures should be understood in terms of self-assembly. The complexification of living matter is thus not represented as a gradual phenomenon but as a series of abrupt and relatively fast transitions consisting in the aggregation of pre-systems which had evolved by their own. The shift towards new and variegated states proposed by the bifurcation theory are not considered particularly relevant for reasons reported in the text, nor is it believed that dissipation can entirely account for the order observed in living cells.     

Polarizability of neutral copper clusters

A theoretical study of the electric-field effect on the electronic structures and related properties of the cation compound containing 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) and imidazole unit has been carried out, using the density functional theory (DFT) at the (U) B3LYP/6-31+G(d,p) level. The changes and regularities of geometric and electronic properties of the researched compound under electric field were revealed in detail. The results show the following: (1) Electric field has a very important effect on the orbital energy, dipole moment, natural population, and structure of the cation compound. Most of these properties are changed orderly with the increase of the electric-field intensity. (2) It is very interesting to find that in the present different electric-field intensities, the structure of cation compound after getting an electron becomes bis-radical form, that is, no mater in or out of electric-field, the cation compound will exist in a triplet state after getting an electron. (3) When getting an electron, the change of the cation structure mainly appears on the imizadole head, and when losing an electron, the change mainly appears on the TEMPO head. These theoretical results considering the electric-field effect for the cation compound help to explain the related experimental phenomena and further to direct the functional molecular design of this kind of compound.     

DNA and the neutral theory

The neutral theory claims that the great majority of evolutionary changes at the molecular (DNA) level are caused not by Darwinian selection but by random fixation of selectively neutral or nearly neutral mutants. The theory also asserts that the majority of protein and DNA polymorphisms are selectively neutral and that they are maintained in the species by mutational input balanced by random extinction. In conjunction with diffusion models (the stochastic theory) of gene frequencies in finite populations, it treats these phenomena in quantitative terms based on actual observations. Although the theory has been strongly criticized by the 'selectionists', supporting evidence has accumulated over the years. Particularly, the recent outburst of DNA sequence data lends strong support to the theory both with respect to evolutionary base substitutions and DNA polymorphism, including rapid evolutionary base substitutions in pseudogenes. In addition, the observed pattern of synonymous codon choice can now be readily explained in the framework of this theory. I review these recent findings in the light of the neutral theory.