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Register a new userTowards an improved understanding of molecular evolution: the relative roles of selection, drift, and everything in between
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A major goal of molecular evolutionary biology is to identify loci or regions of the genome under selection versus those evolving in a neutral manner. Correct identification allows accurate inference of the evolutionary process and thus comprehension of historical and contemporary processes driving phenotypic change and adaptation. A fundamental difficulty lies in distinguishing sites targeted by selection from both sites linked to these targets and sites fully independent of selection. These three categories of sites necessitate attention in light of the debate over the relative importance of selection versus neutrality and the neutral theory. Modern genomic insights have proved that complex processes such as linkage, demography, and biased gene conversion complicate our understanding of the role of neutral versus selective processes in evolution. In this perspective, we first highlight the importance of the genomic and (a)biotic context of new mutations to identify the targets of natural selection. We then present mechanisms that may constrain the evolution of genomes and bias the inference of selection. We discuss these mechanisms within the two critical levels that they occur: the population level and the molecular level. We highlight that they should be taken into account to correctly distinguish sites across the genome subject to selective or non-selective forces and stress that a major current field-wide goal is to quantify the absolute importance of these mechanisms.
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How cooperation emerges in human societies is still a puzzle. Evolutionary game theory has been the standard framework to address this issue. In most models, every individual plays with all others, and then reproduce and die according to what they earn. This amounts to assuming that selection takes place at a slow pace with respect to the interaction time scale. We show that, quite generally, if selection speeds up, the evolution outcome changes dramatically. Thus, in games such as Harmony, where cooperation is the only equilibrium and the only rational outcome, rapid selection leads to dominance of defectors. Similar non trivial phenomena arise in other binary games and even in more complicated settings such as the Ultimatum game. We conclude that the rate of selection is a key element to understand and model the emergence of cooperation, and one that has so far been overlooked.
We discuss two different ways of chromosomes and genomes evolution. Purifying selection dominates in large panmictic populations, where Mendelian law of independent gene assortment is valid. If the populations are small, recombination processes are not effective enough to ensure an independent assortment of linked genes and larger clusters of genes could be inherited as the genetic units. There are whole clusters of genes which tend to complement in such conditions instead of single pairs of alleles like in the case of purifying selection. Computer simulations have shown that switching in-between complementation and purification strategies has a character of a phase transition. This is also responsible for specific distribution of recombination events observed along eukaryotic chromosomes - higher recombination rate is observed in subtelomeric regions than in central parts of chromosomes - for sympatric speciation and probably for non-monotonous relation between reproduction potential and genetic distance between parents.
If two species exhibit different nonlinear responses to a single shared resource, and if each species modifies the resource dynamics such that this favors its competitor, they may stably coexist. This coexistence mechanism, known as relative nonlinearity of competition, is well understood theoretically, but less is known about its evolutionary properties and its prevalence in real communities. We address this challenge by using adaptive dynamics theory and individual-based simulations to compare community stabilization and evolutionary stability of species that coexist by relative nonlinearity. In our analysis, evolution operates on the species density-compensation strategies, and we consider a trade-off between population growth rates at high and low resource availability. We confirm previous findings that, irrespective of the particular model of density dependence, there are many combinations of overcompensating and undercompensating density-compensation strategies that allow stable coexistence by relative nonlinearity. However, our analysis also shows that most of these strategy combinations are not evolutionarily stable and will be outcompeted by an intermediate density-compensation strategy. Only very specific trade-offs lead to evolutionarily stable coexistence by relative nonlinearity. As we find no reason why these particular trade-offs should be common in nature, we conclude that the sympatric evolution and evolutionary stability of relative nonlinearity, while possible in principle, seems rather unlikely. We speculate that this may, at least in part, explain why empirical demonstrations of this coexistence mechanism are rare, noting, however, that the difficulty to detect relative nonlinearity in the field [...]
The role of positive selection in human evolution remains controversial. On the one hand, scans for positive selection have identified hundreds of candidate loci and the genome-wide patterns of polymorphism show signatures consistent with frequent positive selection. On the other hand, recent studies have argued that many of the candidate loci are false positives and that most apparent genome-wide signatures of adaptation are in fact due to reduction of neutral diversity by linked recurrent deleterious mutations, known as background selection. Here we analyze human polymorphism data from the 1,000 Genomes project (Abecasis et al. 2012) and detect signatures of pervasive positive selection once we correct for the effects of background selection. We show that levels of neutral polymorphism are lower near amino acid substitutions, with the strongest reduction observed specifically near functionally consequential amino acid substitutions. Furthermore, amino acid substitutions are associated with signatures of recent adaptation that should not be generated by background selection, such as the presence of unusually long and frequent haplotypes and specific distortions in the site frequency spectrum. We use forward simulations to show that the observed signatures require a high rate of strongly adaptive substitutions in the vicinity of the amino acid changes. We further demonstrate that the observed signatures of positive selection correlate more strongly with the presence of regulatory sequences, as predicted by ENCODE (Gerstein et al. 2012), than the positions of amino acid substitutions. Our results establish that adaptation was frequent in human evolution and provide support for the hypothesis of King and Wilson (King and Wilson 1975) that adaptive divergence is primarily driven by regulatory changes.
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to date unproven, hypothesis is that this disadvantage is equal to the fractional cost relative to the total resting metabolic expenditure. This hypothesis has found a recent resurgence as a powerful tool for quantitatively understanding the strength of selection among different classes of organisms. Our work explores the validity of the hypothesis from first principles through a generalized metabolic growth mode
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