Adaptive cis-regulatory changes may involve few mutations

A long-standing debate in evo-devo research concerns the relative role of protein-coding and cis-regulatory regions in adaptation. Recent studies of genetic adaptation have revealed that the number of substitutions contributing to phenotypic variation is lower in cis-regulatory than in structural regions, which has led to the idea that cis-regulatory regions are less important in phenotypic adaptation. However, the number of substitutions is not the only important factor, the "size" of the adaptive contribution of these substitutions is important too. A geometrical reasoning predicts that, given their lesser pleiotropic effects, cis-regulatory substitutions should have a larger average adaptive contribution than protein-coding substitutions. Thus it is possible that even with a lower number of adaptive mutations, cis-regulatory regions may contribute at the same level or even more than protein-coding regions.     

Addressing Undergraduate Student Misconceptions about Natural Selection with an Interactive Simulated Laboratory

Although evolutionary theory is considered to be a unifying foundation for biological education, misconceptions about basic evolutionary processes such as natural selection inhibit student understanding. Even after instruction, students harbor misconceptions about natural selection, suggesting that traditional teaching methods are insufficient for correcting these confusions. This has spurred an effort to develop new teaching methods and tools that effectively confront student misconceptions. In this study, we designed an interactive computer-based simulated laboratory to teach the principles of evolution through natural selection and to correct common student misconceptions about this process. We quantified undergraduate student misconceptions and understanding of natural selection before and after instruction with multiple-choice and open-response test questions and compared student performance across gender and academic levels. While our lab appeared to be effective at dispelling some common misconceptions about natural selection, we did not find evidence that it was as successful at increasing student mastery of the major principles of natural selection. Student performance varied across student academic level and question type, but students performed equally across gender. Beginner students were more likely to use misconceptions before instruction. Advanced students showed greater improvement than beginners on multiple-choice questions, while beginner students reduced their use of misconceptions in the open-response questions to a greater extent. These results suggest that misconceptions can be effectively addressed through computer-based simulated laboratories. Given the level of misconception use by beginner and advanced undergraduates and the gains in performance recorded after instruction at both academic levels, natural selection should continue to be reviewed through upper-level biology courses.     

Before Darwin: Transformist Concepts in European Natural History

Lack of consideration of the complex European scientific scene from the late 18th century to the mid-decades of the 19th century has produced partial and often biased reconstructions of priorities, worries, implicit and explicit philosophical and at times political agendas characterizing the early debates on species. It is the purpose of this paper firstly to critically assess some significant attempts at broadening the historiographic horizon concerning the immediate context to Darwins intellectual enterprise, and to devote the second part to arguing that a multi-faceted European debate on the transformation of life forms had already occurred in Europe around 1800. Of this debate, contrary to long cherished views, Lamarcks was only one voice, amongst many. Naturalists active in different national contexts elaborated solutions and proposed doctrines that shared several viewpoints, yet clearly stemmed from a variety of disciplinary traditions and problematic contexts.     

Mutation rate and pattern of microsatellites in common carp (<Emphasis Type="Italic">Cyprinus carpio</Emphasis> L.)

Microsatellites are popular molecular markers in genetic and evolutionary studies. Their mutational dynamics have been extensively studied in humans and fruit flies, but few data were available in fish. By genotyping 55 individuals of a F1 pedigree, we investigated the mutation rates and patterns of 49 microsatellites in one of the most important fresh water fish species, the common carp (Cyprinus carpio L.). The overall mutation rate of the 49 loci was 5.56×10⁻⁴/locus/generation (95% confidence interval 1.52×10⁻⁴ and 1.63×10⁻³). The change of allele size was between +2 to −5 repeat units, assuming that the mutation allele arose from the parental allele most similar in size to the mutant.     

Darwin's sexual selection: Understanding his ideas in context

Darwin's writings need to be seen in their fullness, as opposed to quote-mining individual sentences without the context of his passages. Sometimes Darwin wrote at length, apparently favorably, about ideas that he subsequently undermined, replacing them with a more integrative view that reflected his own broad compass. Darwin understood that nature is not simple, that not all members of a group may have evolved under the same selective regime, and that variation of all kinds is fundamental to selection in its several forms. Sexual selection requires sexual dimorphism; it is not centred on variation within sexes but on selection for the ability to acquire mates. “Mutual sexual selection” was rejected by Darwin for every species except humans. Mating success is not a matter of mere numbers but of the transmission of the most attractive features to the opposite sex. The term “sexual selection” should only be used when one sex uses a feature not present in the other sex to attract mates or repel rivals for mates.     

一个具选择、突变、迁移的群体的遗传差分模型

假设一个群体是由“单位点—双基因”的个体所组成的,在该群体内存在选择、突变、迁移、生死等效应的作用。本文给出了在上述假设下并满足:(1)世代重叠,选择、突变、迁移、生死等效应的作用均在世代遗传之间完成;(2)群体适当大,个体间交配随机,符合孟德尔式遗传;(3)没有任何意外的灾祸等约定的群体遗传的数学模型。通过模型分析,我们能够进一步用数学语言来解释一些生命现象。模型分析指出:虽然某些群体不满足Hardy-Weinberg定律所叙述的条件,但可能具有和Hardy-Weinberg定律的结论相似的结果。该文中还就几个主要参数的变化讨论了群体遗传和进化的某些性质,如平衡等。最后,我们给出了该模型的一个数值例子。     

Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites

The impact of synonymous nucleotide substitutions on fitness in mammals remains controversial. Despite some indications of selective constraint, synonymous sites are often assumed to be neutral, and the rate of their evolution is used as a proxy for mutation rate. We subdivide all sites into four classes in terms of the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold synonymous sites and intron sites residing outside transposable elements. The distribution of the rate of evolution across all synonymous sites is trimodal. Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed by G, is approximately 10% below that at such intron sites. In contrast, rate of evolution at postCpreG synonymous sites is approximately 30% above that at such intron sites. Finally, synonymous and intron postC and preG sites evolve at similar rates. The relationship between the levels of polymorphism at the corresponding synonymous and intron sites is very similar to that between their rates of evolution. Within every class, synonymous sites are occupied by G or C much more often than intron sites, whose nucleotide composition is consistent with neutral mutation-drift equilibrium. These patterns suggest that synonymous sites are under weak selection in favor of G and C, with the average coefficient s approximately 0.25/Ne approximately 10(-5), where Ne is the effective population size. Such selection decelerates evolution and reduces variability at sites with symmetric mutation, but has the opposite effects at sites where the favored nucleotides are more mutable. The amino-acid composition of proteins dictates that many synonymous sites are CpGprone, which causes them, on average, to evolve faster and to be more polymorphic than intron sites. An average genotype carries approximately 10(7) suboptimal nucleotides at synonymous sites, implying synergistic epistasis in selection against them.     

不忘初心，砥砺前行

2022年是中国科学院西北高原生物研究所 (以下简称西高所) 建所60周年 (1962―2022)。西高所的兽类学研究也走过了60年的历程,经历了从无到有,从小到大不断发展壮大的过程。60年来,西高所的兽类学研究始终立足青藏高原,立足基础和应用基础研究,面向国家需求,围绕为区域经济和生态保护服务,在不同阶段开展了大量相应的工作,培养了大批科技人才,出版了多个学术刊物,为我国的兽类学及兽类生态学发展做出了重大贡献。     

Selection, mutation and sexual reproduction in an infinite haploid population with a genome of finite length

We present a model which describes mutation, selection and sexual reproduction in an infinite haploid population with a finite genome. Each generation is described using an approximation which assures a certain persistent form of the distribution of the number of deleterious elements. The steady state exists and is determined. In addition, we conclude that the introduction of sexual reproduction increases the mean fitness in the equilibrium.     

Selection in yeast II: The fitness distribution of new mutations inSaccharomyces cerevisiae and its use in a computer simulation

Summary The fitness distribution of new mutations inSaccharomyces cerevisiae strain Montrachet was determined for cells on agar irradiated for four periods of time with ultraviolet light. The fitness distributions were obtained by converting a large number of colony diameters into relative fitnesses. The distributions were then used to perform a computer simulation with the purpose of predicting the potential of a stock culture to increase in general fitness through selection, given a frequency and magnitude of mutations.     

An Analytical Model of Gene Evolution with 9 Mutation Parameters: An Application to the Amino Acids Coded by the Common Circular Code

We develop here an analytical evolutionary model based on a trinucleotide mutation matrix 64× 64 with nine substitution parameters associated with the three types of substitutions in the three trinucleotide sites. It generalizes the previous models based on the nucleotide mutation matrices 4× 4 and the trinucleotide mutation matrix 64× 64 with three and six parameters. It determines at some time t the exact occurrence probabilities of trinucleotides mutating randomly according to these nine substitution parameters. An application of this model allows an evolutionary study of the common circular code of eukaryotes and prokaryotes and its 12 coded amino acids. The main property of this code is the retrieval of the reading frames in genes, both locally, i.e. anywhere in genes and in particular without a start codon, and automatically with a window of a few nucleotides. However, since its identification in 1996, amino acid information coded by has never been studied. Very unexpectedly, this evolutionary model demonstrates that random substitutions in this code and with particular values for the nine substitutions parameters retrieve after a certain time of evolution a frequency distribution of these 12 amino acids very close to the one coded by the actual genes.     

Degeneracy: A design principle for achieving robustness and evolvability

Robustness, the insensitivity of some of a biological system's functionalities to a set of distinct conditions, is intimately linked to fitness. Recent studies suggest that it may also play a vital role in enabling the evolution of species. Increasing robustness, so is proposed, can lead to the emergence of evolvability if evolution proceeds over a neutral network that extends far throughout the fitness landscape. Here, we show that the design principles used to achieve robustness dramatically influence whether robustness leads to evolvability. In simulation experiments, we find that purely redundant systems have remarkably low evolvability while degenerate, i.e. partially redundant, systems tend to be orders of magnitude more evolvable. Surprisingly, the magnitude of observed variation in evolvability can neither be explained by differences in the size nor the topology of the neutral networks. This suggests that degeneracy, a ubiquitous characteristic in biological systems, may be an important enabler of natural evolution. More generally, our study provides valuable new clues about the origin of innovations in complex adaptive systems.     

Male-female interactions in Drosophila melanogaster: model with one-locus and three-alleles

We develop a fertility model of fitness that is general in that it does not assume that the fitnesses of the mating combinations are symmetrical or that they are additive or multilicative (i. e., that they can be inferred from fitnesses of the two genotypes involved in a mating). %he model considers one locus with three alleles. An experimental test with Drosophila rnelanogaster confirms that the fitnesses of the mating types depart from both additivity (or multiplicativity) and symmetry although this last property is of no consequence for the development of analytical models). urnerical simulations yield the same, or very nearly the same, equilibrium freuencies as the analytical model, independently of whether or not Hardy-Weinberg equilibrium Trequencies are assumed at the beginning of each selection cycle.     

神农架川金丝猴投食群TRIM5 alpha基因的变异及其进化分析

目的:本研究探索神农架大龙潭川金丝猴TRIM5alpha蛋白序列的特征、变异、该基因进化特点以及该基因的遗传多样性,对金丝猴的保护和研究具有重要的意义。方法:从神农架川金丝猴投食群随机选择41个个体,采集毛发并提取基因组DNA,设计引物,对其TRIM5 alpha基因编码序列进行PCR扩增和测序,最后对序列进行比对和分析。结果:在神农架川金丝猴投食群41个个体中,TRIM5alpha基因不存在与Cyp A假基因序列融合的现象。与恒河猴序列不同而与人类相似的是,川金丝猴中没有发现TFP339-341型,而只发现△△Q339-341型。41个个体TRIM5alpha蛋白序列没发现任何非同义突变位点,显示该基因在该种群中具有很低的遗传多样性。编码序列的进化分析表明,Coiled-coil结构域和SPRY结构域在进化中经历了明显的正向选择,Ring结构域和B-box结构域则经历了纯化选择。结论:川金丝猴TRIM5 alpha基因存在很多独特变异位点,且经历了明显的正向选择。对投食群的研究表明该基因编码序列在该种群中多样性很低,这从侧面反映了该总群较低的遗传多样性。针对这种情况,建议在种群复壮的工作中,适当引入一批有效的建群者。     

Captive breeding reveals larval performance and adult body size differences between two geographical populations of the stag beetle Aegus chelifer chelifer (Coleoptera: Lucanidae)

Stag beetles usually have great intraspecific variation in their body sizes, which can be affected by both environmental and genetic factors. However, direct studies on wild-caught specimens may be insufficient to clarify such variation due to the confounding effects of ecological variance in natural habitats. To evaluate this, the stag beetle Aegus chelifer chelifer MacLeay, 1819 was collected from within two localities (Bangkok metropolitan area and Chanthaburi province) in Thailand and then reared under the same condition to investigate the differences in morphological characteristics between the wild-caught and captive-bred beetles and between the two geographical populations. Narrow-sense heritabilities (h²) of the observed traits in adults were not significant. Variation in the body size of captive-bred specimens was less than in the wild-caught specimens and the overlap of the body size variation between the two populations was lower in the captive-bred beetles. The Chanthaburi population had a significantly larger body size than the Bangkok population. Allometric slopes and intercepts were also significantly different between the two geographic populations. Captive-bred larvae showed similar relative growth rates, but male larvae from the Chanthaburi population had a longer feeding period, and so a larger adult body size, than those from the Bangkok population. The differences between the two populations could be explained by adaptation through larval performances and body size in order to respond to their habitats.     

Gene Network Polymorphism Is the Raw Material of Natural Selection: The Selfish Gene Network Hypothesis

Population genetics, the mathematical theory of modern evolutionary biology, defines evolution as the alteration of the frequency of distinct gene variants (alleles) differing in fitness over the time. The major problem with this view is that in gene and protein sequences we can find little evidence concerning the molecular basis of phenotypic variance, especially those that would confer adaptive benefit to the bearers. Some novel data, however, suggest that a large amount of genetic variation exists in the regulatory region of genes within populations. In addition, comparison of homologous DNA sequences of various species shows that evolution appears to depend more strongly on gene expression than on the genes themselves. Furthermore, it has been demonstrated in several systems that genes form functional networks, whose products exhibit interrelated expression profiles. Finally, it has been found that regulatory circuits of development behave as evolutionary units. These data demonstrate that our view of evolution calls for a new synthesis. In this article I propose a novel concept, termed the selfish gene network hypothesis, which is based on an overall consideration of the above findings. The major statements of this hypothesis are as follows. (1) Instead of individual genes, gene networks (GNs) are responsible for the determination of traits and behaviors. (2) The primary source of microevolution is the intraspecific polymorphism in GNs and not the allelic variation in either the coding or the regulatory sequences of individual genes. (3) GN polymorphism is generated by the variation in the regulatory regions of the component genes and not by the variance in their coding sequences. (4) Evolution proceeds through continuous restructuring of the composition of GNs rather than fixing of specific alleles or GN variants.     

In silico modelling of directed evolution: Implications for experimental design and stepwise evolution

We model the process of directed evolution (DE) in silico using genetic algorithms. Making use of the NK fitness landscape model, we analyse the effects of mutation rate, crossover and selection pressure on the performance of DE. A range of values of K, the epistatic interaction of the landscape, are considered, and high- and low-throughput modes of evolution are compared. Our findings suggest that for runs of or around ten generations’ duration—as is typical in DE—there is little difference between the way in which DE needs to be configured in the high- and low-throughput regimes, nor across different degrees of landscape epistasis. In all cases, a high selection pressure (but not an extreme one) combined with a moderately high mutation rate works best, while crossover provides some benefit but only on the less rugged landscapes. These genetic algorithms were also compared with a “model-based approach” from the literature, which uses sequential fixing of the problem parameters based on fitting a linear model. Overall, we find that purely evolutionary techniques fare better than do model-based approaches across all but the smoothest landscapes.