Fertility selection,genetic selection and evolution

The relationship between fertility selection as measured by the correlation in progeny number between parents and offspring, and selection at individual loci is investigated in humans. Estimates for the magnitude of fertility selection (0.1) and the rate of gene substitution (0.5 gene substitutions per generation per genome) are used in various mathematical models for selection. It is found that the observed magnitude of fertility selection cannot be explained by non‐epistatic directional selection at individual loci. A symmetric quantitative directional selection model is consistent with the observed data. But it is possible that fertility selection does not have a genetic basis.     

Directed evolution of barnase stability using proteolytic selection

We report the construction of a phage-displayed repertoire of mutants of the ribonuclease barnase from Bacillus amyloliquefaciens. The construction was guided by the natural variability between two closely related ribonucleases, barnase and binase from Bacillus intermedius. This repertoire was selected using a proteolytic selection method, allowing sorting of the library according to the resistance of the mutants toward proteolysis. Susceptibility toward proteolysis has been correlated with flexibility and unfolding, and is thus expected to yield mutants with increased thermal stability.Enrichment of barnase mutants with specific combinations of amino acid residues at four of the randomised positions was observed. Three of these enriched amino acid residues are present in neither barnase nor binase. For some of the mutations, the improvement in proteolytic stability does not lead to a pronounced improvement in thermodynamic stability, indicating that the factors governing the proteolytic stability in some cases may be different from those governing the thermodynamic stability, e.g. propensity to local unfolding.The results obtained add important knowledge to a novel use of phage display technology for selection of thermodynamically stable proteins. Only by carefully establishing the parameters that can be adjusted, and recognising the influence this will have on the outcome of selection, will it be possible to realise the powerful technique of proteolytic selection.     

核糖体展示及体外分子选择与进化

核糖体展示是20世纪90年代中期发展起来的一种简便而有效的体外分子选择与进化技术。它也是第一种完全在体外进行蛋白质或多肽分子选择与进化的方法。本主要概述了体外核糖体展示技术的建立基础、基本原理和技术特点等,并跟踪了目前该领域的最新研究进展和发展前景。     

社区水平森林景观格局动态特征与驱动因素

基于高分辨率SPOT-5影像、TM影像和农户调查数据,以及相关辅助数据,选取三峡库区典型森林大县石柱县三星乡石星村为样区,利用景观格局指数与Logistic回归分析法,对1994—2014年间的森林景观格局的动态特征及其影响因素进行分析,旨在丰富人们对社区水平森林景观格局动态的理解和认识,为森林景观恢复和可持续经营策略的制定提供科学依据。结果表明:(1)样区森林景观一直占据20年间景观基质的主导地位,空间分布上退化原始林主要集中分布在中东部低山、深丘区,次生林、退化林地和人工林呈镶嵌格局,分散于主要基质性景观中;(2)20年间样区森林景观整体呈先减少后增加的"U"型格局,表现为1994—2004年间的退化与2004—2014年间的恢复两个截然相反的过程,且这一过程主要发生在森林景观与水田、旱地、居民点、道路等接壤区;(3)2004—2014年间森林景观的演化趋势与1994—2004年间整体上呈反向趋势,空间格局上,这一阶段森林景观的恢复主要出现在1994—2004年间森林景观所发生退化的区域;(4)20年间样区森林景观在斑块水平上呈明显异质性分布,3个截面年份不同森林景观破碎化程度的总排序均为退化林地人工林次生林退化原始林,且退化原始林、次生林和退化林地的破碎度变化趋势相同,均为先增后减;(5)20年间样区森林景观在景观水平上的破碎度呈现先增强后减弱趋势,且2014年的破碎化程度恢复至低于1994年的水平,进一步说明在退化后的森林景观恢复过程中,生态完整性的恢复速度远低于破碎速度;(6)社会经济因素对20年间样区森林景观变化的影响最突出,其中,最主要的影响因素是人口密度变化,先增后减的变化使生态压力随之增减,进而导致森林景观的退化与恢复。其次是农民人均纯收入变化,特别是2004—2014年农民人均纯收入的增加,促进能源结构的转型,减少了对森林景观的依赖和干扰。空间距离对森林景观的影响具有稳定的持续作用,居民对森林景观的干扰多经由距离因素而实现。自然因素控制大地貌格局,中短时期内对森林景观变化影响不大,次生林和退化林地因处于适宜开发的边缘地带,受自然环境影响较大。     

Genetic robustness and selection at the protein level for synonymous codons

Synonymous codons are neutral at the protein level, therefore natural selection at the protein level should have no effect on their frequencies. Synonymous codons, however, differ in their capacity to reduce the effects of errors: after mutation, certain codons keep on coding for the same amino acid or for amino acids with similar properties, while other synonymous codons produce very different amino acids. Therefore, the impact of errors on a coding sequence (genetic robustness) can be measured by analysing its codon usage. I analyse the codon usage of sequenced nuclear and cytoplasmic genomes and I show that there is an extensive variation in genetic robustness at the DNA sequence level, both among genomes and among genes of the same genome. I also show theoretically that robustness can be adaptive, that is natural selection may lead to a preference for codons that reduce the impact of errors. If selection occurs only among the mutants of a codon (e.g. among the progeny before the adult phase), however, the codons that are more sensitive to the effects of mutations may increase in frequency because they manage to get rid more easily of deleterious mutations. I also suggest other possible explanations for the evolution of genetic robustness at the codon level.     

Variability selection in hominid evolution

Variability selection (abbreviated as VS) is a process considered to link adaptive change to large degrees of environment variability. Its application to hominid evolution is based, in part, on the pronounced rise in environmental remodeling that took place over the past several million years. The VS hypothesis differs from prior views of hominid evolution, which stress the consistent selective effects associated with specific habitats or directional trends (e.g., woodland, savanna expansion, cooling). According to the VS hypothesis, wide fluctuations over time created a growing disparity in adaptive conditions. Inconsistency in selection eventually caused habitat-specific adaptations to be replaced by structures and behaviors responsive to complex environmental change. Key hominid adaptations, in fact, emerged during times of heightened variability. Early bipedality, encephalized brains, and complex human sociality appear to signify a sequence of VS adaptations—i.e., a ratcheting up of versatility and responsiveness to novel environments experienced over the past 6 million years. The adaptive results of VS cannot be extrapolated from selection within a single environmental shift or relatively stable habitat. If some complex traits indeed require disparities in adaptive setting (and relative fitness) in order to evolve, the VS idea counters the prevailing view that adaptive change necessitates long-term, directional consistency in selection. © 1998 Wiley-Liss, Inc.     

Stabilizing selection on sperm number revealed by artificial selection and experimental evolution

Sperm competition is taxonomically widespread in animals and is usually associated with large sperm production, being the number of sperm in the competing pool the prime predictor of fertilization success. Despite the strong postcopulatory selection acting directionally on sperm production, its genetic variance is often very high. This can be explained by trade‐offs between sperm production and traits associated with mate acquisition or survival, that may contribute to generate an overall stabilizing selection. To investigate this hypothesis, we first artificially selected male guppies (Poecilia reticulata) for high and low sperm production for three generations, while simultaneously removing sexual selection. Then, we interrupted artificial selection and restored sexual selection. Sperm production responded to divergent selection in one generation, and when we restored sexual selection, both high and low lines converged back to the mean sperm production of the original population within two generations, indicating that sperm number is subject to strong stabilizing total sexual selection (i.e., selection acting simultaneously on all traits associated with reproductive success). We discuss the possible mechanisms responsible for the maintenance of high genetic variability in sperm production despite strong selection acting on it.     

The robustness of the weak selection approximation for the evolution of altruism against strong selection

The weak selection approximation of population genetics has made possible the analysis of social evolution under a considerable variety of biological scenarios. Despite its extensive usage, the accuracy of weak selection in predicting the emergence of altruism under limited dispersal when selection intensity increases remains unclear. Here, we derive the condition for the spread of an altruistic mutant in the infinite island model of dispersal under a Moran reproductive process and arbitrary strength of selection. The simplicity of the model allows us to compare weak and strong selection regimes analytically. Our results demonstrate that the weak selection approximation is robust to moderate increases in selection intensity and therefore provides a good approximation to understand the invasion of altruism in spatially structured population. In particular, we find that the weak selection approximation is excellent even if selection is very strong, when either migration is much stronger than selection or when patches are large. Importantly, we emphasize that the weak selection approximation provides the ideal condition for the invasion of altruism, and increasing selection intensity will impede the emergence of altruism. We discuss that this should also hold for more complicated life cycles and for culturally transmitted altruism. Using the weak selection approximation is therefore unlikely to miss out on any demographic scenario that lead to the evolution of altruism under limited dispersal.     

Sexual selection and the adaptive evolution of mammalian ejaculate proteins

An elevated rate of substitution characterizes the molecular evolution of reproductive proteins from a wide range of taxa. Although the selective pressures explaining this rapid evolution are yet to be resolved, recent evidence implicates sexual selection as a potentially important explanatory factor. To investigate this hypothesis, we sought evidence of a high rate of adaptive gene evolution linked to postcopulatory sexual selection in muroid rodents, a model vertebrate group displaying a broad range of mating systems. Specifically, we sequenced 7 genes from diverse rodents that are expressed in the testes, prostate, or seminal vesicles, products of which have the potential to act in sperm competition. We inferred positive Darwinian selection in these genes by estimation of the ratio of nonsynonymous (d(N), amino acid changing) to synonymous (d(S), amino acid retaining) substitution rates (omega = d(N)/d(S)). Next, we tested whether variation in this ratio among lineages could be attributed to interspecific variation in mating systems, as inferred from the variation in these rodents' relative testis sizes (RTS). Four of the 7 genes examined (Prm1, Sva, Acrv1, and Svs2, but not Svp2, Msmb, or Spink3) exhibit unambiguous evidence of positive selection. One of these, the seminal vesicle-derived protein Svs2, also shows some evidence for a concentration of positive selection in those lineages in which sperm competition is common. However, this was not a general trend among all the rodent genes we examined. Using the same methods, we then reanalyzed previously published data on 2 primate genes, SEMG1 and SEMG2. Although SEMG2 also shows evidence of positive selection concentrated in lineages subject to high levels of sperm competition, no such trend was found for SEMG1. Overall, despite a high rate of positive selection being a feature of many ejaculate proteins, these results indicate that the action of sexual selection potentially responsible for elevated evolutionary rates may be difficult to detect on a gene-by-gene basis. Although the extreme diversity of reproductive phenotypes exhibited in nature attests to the power of sexual selection, the extent to which this force predominates in driving the rapid molecular evolution of reproductive genes therefore remains to be determined.     

Teaching evolution using a card game: negative frequency-dependent selection

Teaching biological evolution can be difficult on a number of levels, be it student confusion arising from prior conceptions and the controversy surrounding evolution, or simply because the material is complex. Games and simulations can help to convey complex topics and also to increase variety in teaching methods. Here I describe a card game that can be used to teach the advanced topic of protected polymorphism in higher education settings. Protected polymorphism is allelic variation resulting from negative frequency-dependent selection; when the fitness of an allele increases when it becomes rare, the allele will be ‘protected’ from extinction. Negative frequency-dependent selection is proposed to maintain genetic variation in nature, which is required for evolution by natural selection. Protected polymorphisms primarily play a role in biological interactions, such as immune systems, plant-pathogen interactions, sexual selection and predator-prey interactions. The card game described here uses plant pollination alleles as an example. The game is played using eleven stocks of traditional playing cards per group of about six students. Specific topics addressed include negative frequency-dependent selection, polyploidy, dominance, selfing and inbreeding depression.     

Cultural selection drives the evolution of human communication systems

Human communication systems evolve culturally, but the evolutionary mechanisms that drive this evolution are not well understood. Against a baseline that communication variants spread in a population following neutral evolutionary dynamics (also known as drift models), we tested the role of two cultural selection models: coordination- and content-biased. We constructed a parametrized mixed probabilistic model of the spread of communicative variants in four 8-person laboratory micro-societies engaged in a simple communication game. We found that selectionist models, working in combination, explain the majority of the empirical data. The best-fitting parameter setting includes an egocentric bias and a content bias, suggesting that participants retained their own previously used communicative variants unless they encountered a superior (content-biased) variant, in which case it was adopted. This novel pattern of results suggests that (i) a theory of the cultural evolution of human communication systems must integrate selectionist models and (ii) human communication systems are functionally adaptive complex systems.     

Phenotypic selection on morphology at independence in the Chinstrap penguin Pygoscelis antarctica

Every year, shortly after the emancipation of chicks at our study colony (Deception Island, South Shetlands), hundreds of carcasses of presumably starved Chinstrap penguin Pygoscelis antarctica chicks are washed on the shore. In 1997 we measured the flippers of fresh carcasses and compared their lengths with those of live chicks about to become independent. There was a highly significant difference of 6.5 mm between both distributions, which suggests strong directional phenotypic selection on skeletal size operating through its association with body reserves at independence. Given that heritabilities of flipper length and body weight measured on 36 families are 0.73(± 0.32) and 0.075(± 0.081), and that both characters show a genetic correlation of 0.44(± 0.14), we can expect an evolutionary response to this selection episode. Assuming that the target of selection is weight at emancipation (heavier chicks carry proportionally larger reserves), and that flipper length changes as a consequence of its genetic correlation with weight, we can predict a response of 1.32–2.87 mm or 0.23–0.51 standard deviation units for flipper length. This substantial evolutionary response may be countered by other selective pressures affecting other life stages of these birds. Selection on reserve storage capacity at independence may affect morphological traits also in other species.     

Positive selection in the evolution of cancer

We hypothesize that forms of antagonistic coevolution have forged strong links between positive selection at the molecular level and increased cancer risk. By this hypothesis, evolutionary conflict between males and females, mothers and foetuses, hosts and parasites, and other parties with divergent fitness interests has led to rapid evolution of genetic systems involved in control over fertilization and cellular resources. The genes involved in such systems promote cancer risk as a secondary effect of their roles in antagonistic coevolution, which generates evolutionary disequilibrium and maladaptation. Evidence from two sources: (1) studies on specific genes, including SPANX cancer/testis antigen genes, several Y-linked genes, the pem homebox gene, centromeric histone genes, the breast cancer gene BRCA1, the angiogenesis gene ANG, cadherin genes, cytochrome P450 genes, and viral oncogenes; and (2) large-scale database studies of selection on different functional categories of genes, supports our hypothesis. These results have important implications for understanding the evolutionary underpinnings of cancer and the dynamics of antagonistically-coevolving molecular systems.     

Population structure, levels of selection, and the evolution of intracellular symbionts

Many obligately intracellular symbionts exhibit a characteristic set of genetic changes that include an increase in substitution rates, loss of many genes, and apparent destabilization of many proteins and structural RNAs. Authors have suggested that these changes are due to increased mutation rates, or, more commonly, decreased effective population size due to population bottlenecks at the symbiont or, perhaps, host level. I propose that the increase in substitution rates and accumulation of deleterious mutations is a consequence of the population structure imposed on the endosymbionts by strict host association, loss of horizontal transmission and potentially conflicting levels of selection. I analyze a population genetic model of endosymbiont evolution, and demonstrate that substitution rates will increase, and the effect of those substitutions on endosymbiont fitness will become more deleterious as horizontal transmission among hosts decreases. Additionally, I find that there is a critical level of horizontal transmission below which natural selection cannot effectively purge deleterious mutations, leading to an expected loss of fitness over time. This critical level varies across loci with the degree of correlation between host and endosymbiont fitness, and may help explain differential retention and loss of certain genes.     

Sexual selection expedites the evolution of pesticide resistance

The evolution of insecticide resistance by crop pests and disease vectors causes serious problems for agriculture and health. Sexual selection can accelerate or hinder adaptation to abiotic challenges in a variety of ways, but the effect of sexual selection on resistance evolution is little studied. Here, we examine this question using experimental evolution in the pest insect Tribolium castaneum. The experimental removal of sexual selection slowed the evolution of resistance in populations treated with pyrethroid pesticide, and also reduced the rate at which resistance was lost from pesticide‐free populations. These results suggest that selection arising from variance in mating and fertilization success can augment natural selection on pesticide resistance, meaning that sexual selection should be considered when designing strategies to limit the evolution of pesticide resistance.     

The effects of stochastic and episodic movement of the optimum on the evolution of the G‐matrix and the response of the trait mean to selection

Theoretical and empirical results demonstrate that the G ‐matrix, which summarizes additive genetic variances and covariances of quantitative traits, changes over time. Such evolution and fluctuation of the G ‐matrix could potentially have wide‐ranging effects on phenotypic evolution. Nevertheless, no studies have yet addressed G ‐matrix stability and evolution when movement of an intermediate optimum includes large, episodic jumps or stochasticity. Here, we investigate such scenarios by using simulation‐based models of G ‐matrix evolution. These analyses yield four important insights regarding the evolution and stability of the G ‐matrix. (i) Regardless of the model of peak movement, a moving optimum causes the G ‐matrix to orient towards the direction of net peak movement, so that genetic variance is enhanced in that direction (the variance enhancement effect). (ii) Peak movement skews the distribution of breeding values in the direction of movement, which impedes the response to selection. (iii) The stability of the G ‐matrix is affected by the overall magnitude and direction of peak movement, but modes and rates of peak movement have surprisingly small effects (the invariance principle). (iv) Both episodic and stochastic peak movement increase the probability that a population will fall below its carrying capacity and go extinct. We also present novel equations for the response of the trait mean to multivariate selection, which take into account the higher moments of the distribution of breeding values.     

Levels and limits in artificial selection of communities

Artificial selection of individuals has been determinant in the elaboration of the Darwinian theory of natural selection. Nowadays, artificial selection of ecosystems has proven its efficiency and could contribute to a theory of natural selection at several organisation levels. Here, we were not interested in identifying mechanisms of adaptation to selection, but in establishing the proof of principle that a specific structure of interaction network emerges under ecosystem artificial selection. We also investigated the limits in ecosystem artificial selection to evaluate its potential in terms of managing ecosystem function. By artificially selecting microbial communities for low CO₂ emissions over 21 generations (n = 7560), we found a very high heritability of community phenotype (52%). Artificial selection was responsible for simpler interaction networks with lower interaction richness. Phenotype variance and heritability both decreased across generations, suggesting that selection was more likely limited by sampling effects than by stochastic ecosystem dynamics.     

Natural selection in chemical evolution

We propose that chemical evolution can take place by natural selection if a geophysical process is capable of heterotrophic formation of liposomes that grow at some base rate, divide by external agitation, and are subject to stochastic chemical avalanches, in the absence of nucleotides or any monomers capable of modular heredity. We model this process using a simple hill-climbing algorithm, and an artificial chemistry that is unique in exhibiting conservation of mass and energy in an open thermodynamic system. Selection at the liposome level results in the stabilization of rarely occurring molecular autocatalysts that either catalyse or are consumed in reactions that confer liposome level fitness; typically they contribute in parallel to an increasingly conserved intermediary metabolism. Loss of competing autocatalysts can sometimes be adaptive. Steady-state energy flux by the individual increases due to the energetic demands of growth, but also of memory, i.e. maintaining variations in the chemical network. Self-organizing principles such as those proposed by Kauffman, Fontana, and Morowitz have been hypothesized as an ordering principle in chemical evolution, rather than chemical evolution by natural selection. We reject those notions as either logically flawed or at best insufficient in the absence of natural selection. Finally, a finite population model without elitism shows the practical evolutionary constraints for achieving chemical evolution by natural selection in the lab.