Age- and sex-distribution of the mutation load

We investigate the age and sex distribution of genetic fitness under mutation–selection balance by means of simple one-locus two-allele models. We find that the extent of age and sex variation in the mutation load is very dependent on the average effect of new mutations. If the average heterozygote selective effect of new mutations is large, then age and sex differences may constitute a significant fraction of the total load, and be significant as compared to standing genetic variation. Whether the mutation load will increase or decrease with age depends on the age- and sex-specific effects of the new mutations, and on the rate of accumulation of mutations in the germ line as individuals age. We argue that the load will most likely increase with age in animals with continuous germ-cell division throughout life, and that this will occur even when mutations have unconditionally deleterious effects. We show that a male-biased mutation rate is likely to result in both a male-biased mutation load and a load that increases with male age. This revised version was published online in July 2006 with corrections to the Cover Date.     

Differences in the processing of DNA ends in Arabidopsis thaliana and tobacco: possible implications for genome evolution

Surprising species-specific differences in non-homologous end-joining (NHEJ) of genomic double-strand breaks (DSBs) have been reported for the two dicotyledonous plants Arabidopsis thaliana and Nicotiana tabacum. In Arabidopsis deletions were, on average, larger than in tobacco and not associated with insertions. To establish the molecular basis of the phenomenon we analysed the fate of free DNA ends in both plant species by biolistic transformation of leaf tissue with linearized plasmid molecules. Southern blotting indicated that, irrespective of the nature of the ends (blunt, 5 or 3 overhangs), linearized full-length DNA molecules were, on average, more stable in tobacco than in Arabidopsis. The relative expression of a -glucuronidase gene encoded by the plasmid was similar in both plant species when the break was distant from the marker gene. However, if a DSB was introduced between the promoter and the open reading frame of the marker, transient expression was halved in Arabidopsisas compared to tobacco. These results indicate that free DNA ends are more stable in tobacco than in Arabidopsis, either due to lower DNA exonuclease activity or due to a better protection of DNA break ends or both. Exonucleolytic degradation of DNA ends might be a driving force in the evolution of genome size as the Arabidopsis genome is more than twenty times smaller than the tobacco genome.     

Expansion of genome coding regions by acquisition of new genes

As it is the case for non-coding regions, the coding regions of organisms can be expanded or shrunk during evolutionary processes. However, the dynamics of coding regions are expected to be more correlated with functional complexity and diversity than are the dynamics of non-coding regions. Hence, it is interesting to investigate the increase of diversity in coding regions – the origin and evolution of new genes – because this provides a new component to the genetic variation underlying the diversity of living organisms. Here, we examine what is known about the mechanisms responsible for the increase in gene number. Every mechanism affects genomes in a distinct way and to a different extent and it appears that certain organisms favor particular mechanisms. The detail of some interesting gene acquisitions reveals the extreme dynamism of genomes. Finally, we discuss what is known about the fate of new genes and conclude that many of the acquisitions are likely to have been driven by natural selection; they increase functional complexity, diversity, and/or adaptation of species. Despite this, the correlation between complexity of life and gene number is low and closely related species (with very similar life histories) can have very different number of genes. We call this phenomenon the G-value paradox.     

Probabilistic sampling of protein conformations: New hope for brute force?

Protein structure prediction from sequence alone by "brute force" random methods is a computationally expensive problem. Estimates have suggested that it could take all the computers in the world longer than the age of the universe to compute the structure of a single 200-residue protein. Here we investigate the use of a faster version of our FOLDTRAJ probabilistic all-atom protein-structure-sampling algorithm. We have improved the method so that it is now over twenty times faster than originally reported, and capable of rapidly sampling conformational space without lattices. It uses geometrical constraints and a Leonard-Jones type potential for self-avoidance. We have also implemented a novel method to add secondary structure-prediction information to make protein-like amounts of secondary structure in sampled structures. In a set of 100,000 probabilistic conformers of 1VII, 1ENH, and 1PMC generated, the structures with smallest Calpha RMSD from native are 3.95, 5.12, and 5.95A, respectively. Expanding this test to a set of 17 distinct protein folds, we find that all-helical structures are "hit" by brute force more frequently than beta or mixed structures. For small helical proteins or very small non-helical ones, this approach should have a "hit" close enough to detect with a good scoring function in a pool of several million conformers. By fitting the distribution of RMSDs from the native state of each of the 17 sets of conformers to the extreme value distribution, we are able to estimate the size of conformational space for each. With a 0.5A RMSD cutoff, the number of conformers is roughly 2N where N is the number of residues in the protein. This is smaller than previous estimates, indicating an average of only two possible conformations per residue when sterics are accounted for. Our method reduces the effective number of conformations available at each residue by probabilistic bias, without requiring any particular discretization of residue conformational space, and is the fastest method of its kind. With computer speeds doubling every 18 months and parallel and distributed computing becoming more practical, the brute force approach to protein structure prediction may yet have some hope in the near future.     

Diminishing returns in social evolution: the not-so-tragic commons

A challenge for evolutionary theory is to understand how cooperation can occur in the presence of competition and cheating, a problem known as the tragedy of commons. Here I examine how varying the fitness returns from reproductive competition or cooperation affects the negative impact of competition on a social group. Varying linear returns does not affect the impact of competition. However, diminishing returns, where additional investments in either competition or cooperation give smaller and smaller rewards, reduce the effects of competition on the group. I show that diminishing returns are common in many systems, including social vertebrates, microbes, social insects and mutualisms among species. This suggests that the tragedy of the commons is not so tragic and that the disruptive effects of competition upon social life will often be minor.     

Social learning and the replication process: an experimental investigation

Human cultural traits typically result from a gradual process that has been described as analogous to biological evolution. This observation has led pioneering scholars to draw inspiration from population genetics to develop a rigorous and successful theoretical framework of cultural evolution. Social learning, the mechanism allowing information to be transmitted between individuals, has thus been described as a simple replication mechanism. Although useful, the extent to which this idealization appropriately describes the actual social learning events has not been carefully assessed. Here, we used a specifically developed computer task to evaluate (i) the extent to which social learning leads to the replication of an observed behaviour and (ii) the consequences it has for fitness landscape exploration. Our results show that social learning does not lead to a dichotomous choice between disregarding and replicating social information. Rather, it appeared that individuals combine and transform information coming from multiple sources to produce new solutions. As a consequence, landscape exploration was promoted by the use of social information. These results invite us to rethink the way social learning is commonly modelled and could question the validity of predictions coming from models considering this process as replicative.     

Snowpack,fire, and forest disturbance: interactions affect montane invasions by non‐native shrubs

Montane regions worldwide have experienced relatively low plant invasion rates, a trend attributed to increased climatic severity, low rates of disturbance, and reduced propagule pressure relative to lowlands. Manipulative experiments at elevations above the invasive range of non‐native species can clarify the relative contributions of these mechanisms to montane invasion resistance, yet such experiments are rare. Furthermore, global climate change and land use changes are expected to cause decreases in snowpack and increases in disturbance by fire and forest thinning in montane forests. We examined the importance of these factors in limiting montane invasions using a field transplant experiment above the invasive range of two non‐native lowland shrubs, Scotch broom (Cytisus scoparius) and Spanish broom (Spartium junceum), in the rain–snow transition zone of the Sierra Nevada of California. We tested the effects of canopy closure, prescribed fire, and winter snow depth on demographic transitions of each species. Establishment of both species was most likely at intermediate levels of canopy disturbance, but at this intermediate canopy level, snow depth had negative effects on winter survival of seedlings. We used matrix population models to show that an 86% reduction in winter snowfall would cause a 2.8‐fold increase in population growth rates in Scotch broom and a 3.5‐fold increase in Spanish broom. Fall prescribed fire increased germination rates, but decreased overall population growth rates by reducing plant survival. However, at longer fire return intervals, population recovery between fires is likely to keep growth rates high, especially under low snowpack conditions. Many treatment combinations had positive growth rates despite being above the current invasive range, indicating that propagule pressure, disturbance, and climate can all strongly affect plant invasions in montane regions. We conclude that projected reductions in winter snowpack and increases in forest disturbance are likely to increase the risk of invasion from lower elevations.     

Microbeam PIXE analysis of Na,K, Mg,and Ca in severely damaged cardiac tissue

The aim of the study was to measure with microbeam PIXE elements such as Na, K, Mg, and Ca in cardiac tissue after various treatments in vivo, which affect the cardiomyocyte integrity. It was assumed that local deviations from normal electrolyte levels indicate the degree of cardiac damage. The first step in this feasibility study was comparison of severely damaged cardiac tissues with controls. Severe cardiac damage was introduced by the so-called Ca paradox. Experiments were performed with isolated rat hearts, perfused retrogradely with an oxygenated crystalloid buffer. Results indicated that severe cardiac damage was accompanied with almost complete disappearance of the normal intracellular electrolyte composition as a result of the loss of membrane integrity. Identifications of smaller and more locally present ischemic damages on basis of altered electrolyte levels appeared to be feasible. However, the prerequisite was that the mobility of electrolytes be kept under control during tissue sampling and sample preparation, when physiological mechanisms stop to maintain gradients.     

Intron–Genome Size Relationship on a Large Evolutionary Scale

The intron–genome size relationship was studied across a wide evolutionary range (from slime mold and yeast to human and maize), as well as the relationship between genome size and the ratio of intervening/coding sequence size. The average intron size is scaled to genome size with a slope of about one-fourth for the log-transformed values; i.e., on the global scale its increase in evolution is lower than the increase in genome size by four orders of magnitude. There are exceptions to the general trend. In baker's yeast introns are extraordinarily long for its genome size. Tetrapods also have longer introns than expected for their genome sizes. In teleost fish the mean intron size does not differ significantly, notwithstanding the differences in genome size. In contrast to previous reports, avian introns were not found to be significantly shorter than introns of mammals, although avian genomes are smaller than genomes of mammals on average by about a factor of 2.5. The extra-/intragenic ratio of noncoding DNA can be higher in fungi than in animals, notwithstanding the smaller fungal genomes. In vertebrates and invertebrates taken separately, this ratio is increasing as the increase in genome size. Two hypotheses are proposed to explain the variation in the extra-/intragenic ratio of noncoding DNA in organisms with similar numbers of genes: transition (dynamic) and equilibrium (static). According to the transition model, this variation arises with the rapid shift of genome size because the bulk of extragenic DNA can be changed more rapidly than the finely interspersed intron sequences. The equilibrium model assumes that this variation is a result of selective adjustment of genome size with constraints imposed on the intron size due to its putative link to chromatin structure (and constraints of the splicing machinery). Received: 23 October 1997 / Accepted: 14 April 1999