The genetic balance between varying population size and selective neutrality

This note extends to an arbitrary offspring distribution the generalized model for random fluctuation of allele frequency, where population size is permitted to fluctuate randomly from generation to generation. Martingale methods analogous to those of Seneta (1974) and Heyde and Seneta (1975) are applied to discuss conditions for Pr(Y(1–Y)>0)>0, where Y is the (almost sure) limiting frequency of one allele. An overlapping generation study of the same phenomenon has recently been made by Heyde (1981).     

Emergent neutrality

Community ecology is in a current state of creative ferment, stimulated by the development of neutral models of community organization. Here, I reflect on recent papers by Scheffer and van Nes, and by Gravel et al., which illuminate how neutrality can emerge from ecological and evolutionary processes, thus suggesting ways to unify neutral and niche perspectives.     

Niches, rather than neutrality, structure a grassland pioneer guild

Pioneer species are fast-growing, short-lived gap exploiters. They are prime candidates for neutral dynamics because they contain ecologically similar species whose low adult density is likely to cause widespread recruitment limitation, which slows competitive dynamics. However, many pioneer guilds appear to be differentiated according to seed size. In this paper, we compare predictions from a neutral model of community structure with three niche-based models in which trade-offs involving seed size form the basis of niche differentiation. We test these predictions using sowing experiments with a guild of seven pioneer species from chalk grassland. We find strong evidence for niche structure based on seed size: specifically large-seeded species produce fewer seeds but have a greater chance of establishing on a per-seed basis. Their advantage in establishment arises because there are more microsites suitable for their germination and early establishment and not directly through competition with other seedlings. In fact, seedling densities of all species were equally suppressed by the addition of competitors' seeds. By the adult stage, despite using very high sowing densities, there were no detectable effects of interspecific competition on any species. The lack of interspecific effects indicates that niche differentiation, rather than neutrality, prevails.     

A trade-off between neutrality and adaptability limits the optimization of viral quasispecies

Theoretical studies of quasispecies usually focus on two properties of those populations at the mutation-selection equilibrium, namely asymptotic growth rate and population diversity. It has been postulated that, as a consequence of the high error rate of quasispecies replication, an increase of neutrality facilitates population optimization by reducing the amount of mutations with a deleterious effect on fitness. In this study we analyse how the optimization of equilibrium properties is affected when a quasispecies evolves in an environment perturbed through frequent bottleneck events. By means of a simple model we demonstrate that high neutrality may be detrimental when the population has to overcome repeated reductions in the population size, and that the property to be optimized in this situation is the time required to regenerate the quasispecies, i.e. its adaptability. In the scenario described, neutrality and adaptability cannot be simultaneously optimized. When fitness is equated with long-term survivability, high neutrality is the appropriate strategy in constant environments, while populations evolving in fluctuating environments are fitter when their neutrality is low, such that they can respond faster to perturbations. Our results might be relevant to better comprehend how a minority virus could displace the circulating quasispecies, a fact observed in natural infections and essential in viral evolution.     

Selective neutrality and enzyme kinetics

This article appeals to a recent theory of enzyme evolution to show that the properties, neutral or adaptive, which characterize the observed allelic variation in natural populations can be inferred from the functional parameters, substrate specificity, and reaction rate. This study delineates the following relations between activity variables, and the forces—adaptive or neutral—determining allelic variation: (1) Enzymes with broad substrate specificity: The observed polymorphism is adaptive; mutations in this class of enzymes can result in increased fitness of the organism and hence be relevant for positive selection. (2) Enzymes with absolute substrate specificity and diffusion-controlled rates: Observed allelic variation will be absolutely neutral; mutations in this class of enzymes will be either deleterious or have no effect on fitness. (3) Enzymes with absolute or group specificity and nondiffusion-controlled rates: Observed variation will be partially neutral; mutants which are selectively neutral may become advantageous under an appropriate environmental condition or different genetic background. We illustrate each of the relations between kinetic properties and evolutionary states with examples drawn from enzymes whose evolutionary dynamics have been intensively studied. Received: 12 December 1996 / Accepted: 22 April 1997     

Large-Scale Diversity of Slope Fishes: Pattern Inconsistency between Multiple Diversity Indices

Large-scale studies focused on the diversity of continental slope ecosystems are still rare, usually restricted to a limited number of diversity indices and mainly based on the empirical comparison of heterogeneous local data sets. In contrast, we investigate large-scale fish diversity on the basis of multiple diversity indices and using 1454 standardized trawl hauls collected throughout the upper and middle slope of the whole northern Mediterranean Sea (36°3′- 45°7′ N; 5°3′W - 28°E). We have analyzed (1) the empirical relationships between a set of 11 diversity indices in order to assess their degree of complementarity/redundancy and (2) the consistency of spatial patterns exhibited by each of the complementary groups of indices. Regarding species richness, our results contrasted both the traditional view based on the hump-shaped theory for bathymetric pattern and the commonly-admitted hypothesis of a large-scale decreasing trend correlated with a similar gradient of primary production in the Mediterranean Sea. More generally, we found that the components of slope fish diversity we analyzed did not always show a consistent pattern of distribution according either to depth or to spatial areas, suggesting that they are not driven by the same factors. These results, which stress the need to extend the number of indices traditionally considered in diversity monitoring networks, could provide a basis for rethinking not only the methodological approach used in monitoring systems, but also the definition of priority zones for protection. Finally, our results call into question the feasibility of properly investigating large-scale diversity patterns using a widespread approach in ecology, which is based on the compilation of pre-existing heterogeneous and disparate data sets, in particular when focusing on indices that are very sensitive to sampling design standardization, such as species richness.     

Quantifying Phylogenetic Beta Diversity: Distinguishing between 'True' Turnover of Lineages and Phylogenetic Diversity Gradients

The evolutionary dissimilarity between communities (phylogenetic beta diversity PBD) has been increasingly explored by ecologists and biogeographers to assess the relative roles of ecological and evolutionary processes in structuring natural communities. Among PBD measures, the PhyloSor and UniFrac indices have been widely used to assess the level of turnover of lineages over geographical and environmental gradients. However, these indices can be considered as 'broad-sense' measures of phylogenetic turnover as they incorporate different aspects of differences in evolutionary history between communities that may be attributable to phylogenetic diversity gradients. In the present study, we extend an additive partitioning framework proposed for compositional beta diversity to PBD. Specifically, we decomposed the PhyloSor and UniFrac indices into two separate components accounting for 'true' phylogenetic turnover and phylogenetic diversity gradients, respectively. We illustrated the relevance of this framework using simple theoretical and archetypal examples, as well as an empirical study based on coral reef fish communities. Overall, our results suggest that using PhyloSor and UniFrac may greatly over-estimate the level of spatial turnover of lineages if the two compared communities show contrasting levels of phylogenetic diversity. We therefore recommend that future studies use the 'true' phylogenetic turnover component of these indices when the studied communities encompass a large phylogenetic diversity gradient.     

Robustness, evolvability, and neutrality

Biological systems, from macromolecules to whole organisms, are robust if they continue to function, survive, or reproduce when faced with mutations, environmental change, and internal noise. I focus here on biological systems that are robust to mutations and ask whether such systems are more or less evolvable, in the sense that they can acquire novel properties. The more robust a system is, the more mutations in it are neutral, that is, without phenotypic effect. I argue here that such neutral change--and thus robustness--can be a key to future evolutionary innovation, if one accepts that neutrality is not an essential feature of a mutation. That is, a once neutral mutation may cause phenotypic effects in a changed environment or genetic background. I argue that most, if not all, neutral mutations are of this sort, and that the essentialist notion of neutrality should be abandoned. This perspective reconciles two opposing views on the forces dominating organismal evolution, natural selection and random drift: neutral mutations occur and are especially abundant in robust systems, but they do not remain neutral indefinitely, and eventually become visible to natural selection, where some of them lead to evolutionary innovations.     

Phylogenetic analysis of genes of the influenza virus. Relationship between adaptability and neutrality

Detailed phylogenetic analysis of the gene family of hemagglutinin H3 of influenza A-type virus was fulfilled, taking into account the domain structure of protein and positions of antigen determinants. The densities of distribution of fixed synonimic replacements between domains HA1 and HA2 were shown to be actually equal (rho (HA1) = rho (HA2], and those of nonsynonimic ones to be unequal: their ratios were rho (HA1): rho (HA2) = 2.8 for nonepidemic branches, and rho (HA1): rho (HA2) = 7.7 for epidemic ones. For the positions of antigen determinants (agd) these densities differ still stronger from HA2: rho (agd): rho (HA2) = 10 for nonepidemic branches, and rho (agd): rho (HA2) = 36 for epidemic ones. In total, the rate of fixation of nonsynonimic replacements per position of antigen determinants for epidemic branches is 32 times higher than for nonepidemic ones. The absolute value of this estimation is K(ns)d = (9.1 +/- 0.7).10(-3) of nonsynonimic replacements per nonsynonimic position per year and seems to be twice as much as the maximum rate of neutral fixations Ks = (4.28 +/- 0.68).10(-3). Therefore, the epidemic reproduction of influenza virus is highly adaptive, exactly being focused on positions of antigen determinants. The evolution of influenza virus is stochastic process, both with the neutral and adaptive fixations.     

Diversity of fatty acid-binding protein structure and function: studies with fluorescent ligands

The mammalian fatty acid-binding proteins (FABP) are localized in many distinct cell types. They bind long chain fatty acidsin vitro, however, their functions and mechanisms of actionin vivo remain unknown. The present studies have sought to understand the relationships among these proteins, and to address the possible role of FABP in cellular fatty acid traffic. A series of anthroyloxy-labeled fluorescent fatty acids have been used to examine the physicochemical properties of the fatty acid-binding sites of different members of the FABP family. The fatty acid probes have also been used to study the rate and mechanism of fatty acid transfer from different FABP types to phospholipid membranes. The results of these studies show a number of interesting and potentially important differences between FABP family members. An examination of adipocyte and heart FABP (A- and H-FABP) shows that their fatty acid-binding sites are less hydrophobic than the liver FABP (L-FABP) site, and that the bound ligand experiences less motional constraint within the A- and H-FABP binding sites than within the L-FABP binding site. In keeping with these differences in structural properties, it was found that anthroyloxy-fatty acid transfer from A- and H-FABP to membranes is markedly faster than from L-FABP. Moreover, the mechanism of fatty acid transfer was found to be similar for the highly homologous logous A- and H-FABP, whereby transfer to phospholipid membranes appears to occur via transient collisional interactions between the FABP and membranes. Transfer of fatty acids from L-FABP, in contrast, occurs via an aqueous phase diffusion mechanism. Other studies utilized fluorescent fatty acid and monoacylglycerol derivatives to compare how the two FABP which are present in high abundance in the proximal small intestine interact with the two major products of dietary triacylglycerol hydrolysis. The results showed that whereas L-FABP binds both fatty acid and monoacylglycerol derivatives, intestinal FABP (I-FABP) appears to bind fatty acid but not monoacylglycerol. In summary, studies with fluorescent ligands have demonstrated unique properties for different FABP family members. A number of these differences appear to correlate with the degree of primary sequence homology between the proteins, and suggest functional diversity within the FABP family.Abbreviations FABP Fatty Acid-Binding Protein - L-FABP Liver FABP - H-FABP Heart FABP - A-FABP Adipocyte FABP - I-FABP Intestinal FABP - AOffa n-(9-anthroyloxy)fatty acid - MG Monoacylglycerol - NBD-PE N-(7-nitro-2,1,3-benzoxadiazol-4-yl)phosphatidylethanolamine     

The homozygosity test of neutrality

An earlier paper showed that the homozygosity (of a population or sample) was a good statistic for testing departures from selective neutrality in the direction of heterozygote advantage or disadvantage. It is here shown that homozygosity is also influenced by the presence of deleterious alleles and by other departures from neutrality, but at a lower order of magnitude of effect if the selection coefficients are of the same small order of magnitude. Tables are provided for the significance points and moments of the homozygosity, under the null hypothesis of neutrality.     

Trophic Niche in a Raptor Species: The Relationship between Diet Diversity,Habitat Diversity and Territory Quality

Recent research reports that many populations of species showing a wide trophic niche (generalists) are made up of both generalist individuals and individuals with a narrow trophic niche (specialists), suggesting trophic specializations at an individual level. If true, foraging strategies should be associated with individual quality and fitness. Optimal foraging theory predicts that individuals will select the most favourable habitats for feeding. In addition, the “landscape heterogeneity hypothesis” predicts a higher number of species in more diverse landscapes. Thus, it can be predicted that individuals with a wider realized trophic niche should have foraging territories with greater habitat diversity, suggesting that foraging strategies, territory quality and habitat diversity are inter-correlated. This was tested for a population of common kestrels Falco tinnunculus. Diet diversity, territory occupancy (as a measure of territory quality) and habitat diversity of territories were measured over an 8-year period. Our results show that: 1) territory quality was quadratically correlated with habitat diversity, with the best territories being the least and most diverse; 2) diet diversity was not correlated with territory quality; and 3) diet diversity was negatively correlated with landscape heterogeneity. Our study suggests that niche generalist foraging strategies are based on an active search for different prey species within or between habitats rather than on the selection of territories with high habitat diversity.     

Phagosome neutrality in host defense

Activation of proteases in the phagosomes of neutrophils occurs by neutralization of the phagosomal pH by NADPH oxidase. In this issue, Savina et al. (2006) show that dendritic cell phagosomes also recruit NADPH oxidase but with different results. Here, the neutralization of phagosomal pH reduces protease activity, which preserves antigens for crosspresentation on class I MHC molecules.     

Testing the generalized neutrality hypothesis

Various tests of the hypothesis of selective neutrality based on gene frequency are now available. These tests take as null hypothesis the concept of “strict neutrality”: all new mutants are required to be selectively identical to each other. For evolutionary questions, however, (as opposed to those of genetic polymorphism), a wider null hypothesis might be of interest. Since deleterious alleles have essentially no evolutionary importance, one might wish to test the null hypothesis that only neutral or deleterious mutations occur. The principal alternative to this hypothesis is that there exists heterotic selection of some form for some alleles tending to maintain a level of genetic polymorphism higher than that under neutrality. In this paper an assessment is made of the usefulness of a test of strict neutrality first proposed by this author (Ewens, 1972) as a test of null hypothesis of “generalized neutrality,” i.e. that only neutral or deleterious alleles occur. At the same time some remarks will be made about estimation of the fundamental parameter θ defining these processes.     

Microsatellites or the eukaryotic genome: life cycle concept and neutrality issues

Microsatellite markers have a great discriminating power. Widely exploited in many disciplines such as forensic science, medical genetics, conservation biology and molecular ecology, they are also used in human population genetics to illuminate our origins. However, strikingly, their fundamental evolutionary mechanisms remain obscure, because of the difficulty of disentangling the complex and numerous factors involved. After a brief summary of their basic characteristics, the concept of life cycle size-dependant is explored. The major mechanisms known to explain the four different phases of their life (conception, birth, growing and senescence/renaissance) are discussed. Emerging questions about their neutrality are also investigated, pointing out a real need to improve our understanding of their mutational dynamics.