发育重演律与生物进化

发育重演律是生物个体发育的一般规律,该规律认为生物个体的发育是类囊胚不断形成和演化的过程,并认为生物进化亦是类囊胚不断形成和演化的过程.因类囊胚层级不断增加而导致的生物体结构复杂程度提高的演化为纵向进化,而不能提高生物体复杂程度的演化为横向演化,生物的纵向进化具有周期性.生物种系进化与个体发育之间具有严格的对应关系,一个物种经历的纵向进化的周期数与该物种所属个体完成发育所经历的细胞分化的周期数相等.     

Strong links between genomic and anatomical diversity in both mammalian olfactory chemosensory systems

Mammalian olfaction comprises two chemosensory systems: the odorant-detecting main olfactory system (MOS) and the pheromone-detecting vomeronasal system (VNS). Mammals are diverse in their anatomical and genomic emphases on olfactory chemosensation, including the loss or reduction of these systems in some orders. Despite qualitative evidence linking the genomic evolution of the olfactory systems to specific functions and phenotypes, little work has quantitatively tested whether the genomic aspects of the mammalian olfactory chemosensory systems are correlated to anatomical diversity. We show that the genomic and anatomical variation in these systems is tightly linked in both the VNS and the MOS, though the signature of selection is different in each system. Specifically, the MOS appears to vary based on absolute organ and gene family size while the VNS appears to vary according to the relative proportion of functional genes and relative anatomical size and complexity. Furthermore, there is little evidence that these two systems are evolving in a linked fashion. The relationships between genomic and anatomical diversity strongly support a role for natural selection in shaping both the anatomical and genomic evolution of the olfactory chemosensory systems in mammals.     

Systems for in vivo hypermutation: a quest for scale and depth in directed evolution

Traditional approaches to the directed evolution of genes of interest (GOIs) place constraints on the scale of experimentation and depth of evolutionary search reasonably achieved. Engineered genetic systems that dramatically elevate the mutation of target GOIs in vivo relieve these constraints by enabling continuous evolution, affording new strategies in the exploration of sequence space and fitness landscapes for GOIs. We describe various in vivo hypermutation systems for continuous evolution, discuss how different architectures for in vivo hypermutation facilitate evolutionary search scale and depth in their application to problems in protein evolution and engineering, and outline future opportunities for the field.     

Feedback selection and the evolution of modifiers

The problem of modifier evolution was examined with regard to the idea that modifier evolution can be considered as a result of selection for adaptation speed in populations far from equilibrium. This kind of selection was called feedback selection in order to emphasize the difference to theories which consider modifier evolution near the equilibrium. The basic principles of this kind of selection are derived for asexual populations and the problem of dominance is discussed in the light of this concept. In general the results support the view, that the genetic properties of a character are selected along with the character itself.This work was supported by the Austrian Fonds zur Förderung der Wissenschaftlichen Forschung (Proj. Nr. 3502).     

Interactions of genetic and cultural evolution: Models and examples

This paper proposes models and examples of five principal modes of interaction between genes and culture in human evolution. Because genes and culture ultimately interact in the minds of individuals, the models are focused on individual level processes of constrained microevolution. The central hypotheses are (1) that cultural evolution as well as genetic evolution commonly proceeds by the differential transmission of alternative instructions among individuals, (2) that genetic and cultural processes directly interact through mutual influence on each other's differentials of transmission in a population, (3) that the cultural process is often self-selecting by its own criteria, and (4) that these criteria generally operate to enhance rather than oppose human adaptation. Evolutionary change at higher levels, which is particularly important in sociocultural evolution, is interpreted as restructuring the nature and extent of the variability available at the individual level. To clarify the conceptual differences of the models and hopefully to stimulate related analyses in other areas, I discuss selected examples of each of these interactions. I conclude with some remarks on the relative importance of the models to human ecology and evolution.     

REVIEW: Optimality models in the age of experimental evolution and genomics

Optimality models have been used to predict evolution of many properties of organisms. They typically neglect genetic details, whether by necessity or design. This omission is a common source of criticism, and although this limitation of optimality is widely acknowledged, it has mostly been defended rather than evaluated for its impact. Experimental adaptation of model organisms provides a new arena for testing optimality models and for simultaneously integrating genetics. First, an experimental context with a well‐researched organism allows dissection of the evolutionary process to identify causes of model failure – whether the model is wrong about genetics or selection. Second, optimality models provide a meaningful context for the process and mechanics of evolution, and thus may be used to elicit realistic genetic bases of adaptation – an especially useful augmentation to well‐researched genetic systems. A few studies of microbes have begun to pioneer this new direction. Incompatibility between the assumed and actual genetics has been demonstrated to be the cause of model failure in some cases. More interestingly, evolution at the phenotypic level has sometimes matched prediction even though the adaptive mutations defy mechanisms established by decades of classic genetic studies. Integration of experimental evolutionary tests with genetics heralds a new wave for optimality models and their extensions that does not merely emphasize the forces driving evolution.     

The evolution and evolutionary consequences of marginal thermostability in proteins

When we seek to explain the characteristics of living systems in their evolutionary context, we are often interested in understanding how and why certain properties arose through evolution, and how these properties then affected the continuing evolutionary process. This endeavor has been assisted by the use of simple computational models that have properties characteristic of natural living systems but allow simulations over evolutionary timescales with full transparency. We examine a model of the evolution of a gene under selective pressure to code for a protein that exists in a prespecified folded state at a given growth temperature. We observe the emergence of proteins with modest stabilities far below those possible with the model, with a denaturation temperature tracking the simulation temperature, despite the absence of selective pressure for such marginal stability. This demonstrates that neither observations of marginally stable proteins, nor even instances where increased stability interferes with function, provide evidence that marginal stability is an adaptation. Instead the marginal stability is the result of a balance between predominantly destabilizing mutations and selection that shifts depending on effective population size. Even if marginal stability is not an adaptation, the natural tendency of proteins toward marginal stability, and the range of stabilities that occur during evolution, may have significant effect on the evolutionary process.     

The old REH theory remains unsatisfactory and the new REH theory is problematical - a reply to holmquist and jukes

Summary In response to criticism of REH theory (Fitch 1980), Holmquist and Jukes (1981) have mostly avoided the criticism or misunderstood it. Since they themselves state in their response that Amino acid sequence data alone cannot be used to estimate total nucleotide substitutions, they agree with the criticism. Most of their paper treats the newer theory (here designated as the REHN theory) which attempts to use the nucleotide sequences encoding proteins to better estimate total nucleotide substitutions (Holmquist and Pearl 1980). Since I made no criticism of REHN theory, their comments are frequently beside the point of my original criticism of REH theory. Nevertheless, it is shown here that REHN theory is also unsatisfactory in that: One, the varions are now more clearly defined but in such a way as to preclude the same codon from suffering a nucleotide substitution in more than one evolutionary interval. Two, the set of codons that accepts silent substitutions is identical to the set that accepts amino acid changing nucleotide substitutions. Three, the uncertainty in the REH estimate is considerable in that alternative excellent fits to the same observatuonal data may give alternative REH values that differ significantly even before stochastic variation and selective bias are considered. Four, the fit of their model to data is an irrelevancy where there are zero degrees of freedom.     

Domains within the mammalian ornithine decarboxylase messenger RNA have evolved independently and episodically

Summary Ornithine decarboxylase (ODC) is the first enzyme in the polyamine biosynthetic pathway. We have studied the evolutionary history of the mammalian ODC mRNA, focusing on the rate of accumulation of sequence divergence within specific subregions of the molecule. The phylogenetic relationships among the mRNAs from several mammalian species, including two mouse species, rat, hamster, and human, were determined based upon the numbers of synonymous substitutions in pair-wise comparisons of mRNA coding regions. The separation times for the mRNAs were very similar to those for the corresponding species, suggesting that ODC is encoded by orthologous genes in the different species. Analysis of divergence patterns in four subregions, or domains, of the mRNA (the 5untranslated region, the coding region, and two domains of the 3-untranslated region) showed that the domains have evolved in a noncoordinate fashion. Furthermore, evolution of each subregion has been episodic, with periods of both rapid and slow sequence divergence. We suggest that the episodic pattern of ODC mRNA evolution may indicate the existence of selection pressures that were exerted in a time- and domain-specific manner during mammalian speciation.     

Historical Contingency Drives Compensatory Evolution and Rare Reversal of Phage Resistance

Bacteria and lytic viruses (phages) engage in highly dynamic coevolutionary interactions over time, yet we have little idea of how transient selection by phages might shape the future evolutionary trajectories of their host populations. To explore this question, we generated genetically diverse phage-resistant mutants of the bacterium Pseudomonas syringae. We subjected the panel of mutants to prolonged experimental evolution in the absence of phages. Some populations re-evolved phage sensitivity, whereas others acquired compensatory mutations that reduced the costs of resistance without altering resistance levels. To ask whether these outcomes were driven by the initial genetic mechanisms of resistance, we next evolved independent replicates of each individual mutant in the absence of phages. We found a strong signature of historical contingency: some mutations were highly reversible across replicate populations, whereas others were highly entrenched. Through whole-genome sequencing of bacteria over time, we also found that populations with the same resistance gene acquired more parallel sets of mutations than populations with different resistance genes, suggesting that compensatory adaptation is also contingent on how resistance initially evolved. Our study identifies an evolutionary ratchet in bacteria–phage coevolution and may explain previous observations that resistance persists over time in some bacterial populations but is lost in others. We add to a growing body of work describing the key role of phages in the ecological and evolutionary dynamics of their host communities. Beyond this specific trait, our study provides a new insight into the genetic architecture of historical contingency, a crucial component of interpreting and predicting evolution.     

Molecular adaptation and the origin of land plants

The origin and diversification of land plants was one of the most important biological radiations. Land plants are crucial components of all modern terrestrial ecosystems. The first land plants had to adapt to a wide array of new environmental challenges including desiccation, varying temperatures, and increased UV radiation. There have been numerous studies of the morphological adaptations to life on land. However the molecular adaptations to life on land have only recently gained attention. These studies have greatly benefited from the recent advances in our understanding of the phylogenetic relationships between and among the charophycean algae and the basal land plant groups. In this review I summarize the current knowledge of a variety of physiological and biochemical adaptations to land including plant growth hormones, isoprene, phenolics, and heat shock proteins.     

Hominid cultural transmission and the evolution of language

This paper presents the hypothesis that linguistic capacity evolved through the action of natural selection as an instrument which increased the efficiency of the cultural transmission system of early hominids. We suggest that during the early stages of hominization, hominid social learning, based on indirect social learning mechanisms and true imitation, came to constitute cumulative cultural transmission based on true imitation and the approval or disapproval of the learned behaviour of offspring. A key factor for this transformation was the development of a conceptual capacity for categorizing learned behaviour in value terms - positive or negative, good or bad. We believe that some hominids developed this capacity for categorizing behaviour, and such an ability allowed them to approve or disapprove of their offsprings- learned behaviour. With such an ability, hominids were favoured, as they could transmit to their offspring all their behavioural experience about what can and cannot be done. This capacity triggered a cultural transmission system similar to the human one, though pre-linguistic. We suggest that the adaptive advantage provided by this new system of social learning generated a selection pressure in favour of the development of a linguistic capacity allowing children to better understand the new kind of evaluative information received from parents.     

Phylogeny and biogeography of Zelkova (Ulmaceae sensu stricto) as inferred from leaf morphology, ITS sequence data and the fossil record

To address the evolution and geographical diversification of the genus Zelkova (Ulmaceae) a phylogenetic analysis of morphological data and the sequences of the internal transcribed spacers (ITS1 and ITS2) of nuclear ribosomal DNA were used. Cladistic analyses suggested that the Chinese species Z. schneideriana and Z. sinica are basal within Zelkova. The western Asian Z. carpinifolia either appears nested between the East Asian Z. schneideriana and Z. sinica and a clade formed by the Japanese Z. serrata and two Mediterranean species, Z. abelicea and Z. sicula (ITS), or forms a clade with Z. serrata that is sister to a clade Z. abelicea plus Z. sicula (morphology). Nucleotide data suggested that gene flow occurred between Z. schneideriana and Z. serrata, and Z. carpinifolia and a lineage ancestral to Z. abelicea/sicula. Character evolution in Zelkova appears to have gone from long leaves with numerous secondary veins, coarse to shallow teeth with blunt or slightly pointed apex and small stomata, to leaves that are either long or short with numerous or few secondary veins, coarse teeth with cuspidate or obtuse apex or conspicuously shallow teeth, and dimorphic stomata displaying ‘giant stomata’ surrounded by a ring of small stomata or uniform large stomata. These results are in agreement with fossil data. Early Cainozoic fossils attributed to Zelkova from North America and Central Asia closely resemble the modern Z. schneideriana and Z. carpinifolia. The genus could have originated in the northern Pacific area and migrated to Europe after the Turgai Strait was closed during the Late Oligocene. Geographical differentiation may have started with the isolation of Chinese populations (leading to modern Z. schneideriana and Z. sinica) from high‐latitude Eurasian (North American) populations. This widespread Early Cainozoic type may have diversified into the western Asian Z. carpinifolia and the more derived Japanese and Mediterranean species during the latest Cainozoic. The modern Japanese and European/western Asian species would have differentiated relatively late, while two locally endemic Mediterranean species are the result of the cooling and development of a Mediterranean climate belt in Europe during the Pleistocene. Fossils from the Miocene and Pliocene of Europe resemble modern Z. carpinifolia and Z. serrata. Differentiation of the two Mediterranean species Z. abelicea and Z. sicula in the Late Cainozoic cannot be traced by leaf morphology. © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society, 2005, 147 , 129–157.     

Oxygen-quenched chlorophyll a fluorescence and electron transport in barley during greening

Seedlings of barley ( Hordeum vulgare L. cv. Conquest) were dark-grown for 7 days and then transferred to light. The time courses of chlorophyll a fluorescence induction underwent changes during greening periods of from 3 to 48 h. Yields of variable fluorescence during greening correlated with electron transport capacity via photosystem II (PS II) except at the early stage from 3 to 6 h. The discrepancy may result from there being only a small amount of light harvesting complex associated with PSII for 3 to 6 h greening. Oxygen quenching effects were interpreted as indicating the development of the electron transport system and the organization of light harvesting complex associated with PSII. The most intensive O₂ quenching of relative fluorescence is found during the early stage of greening when the ratio of the primary quinone electron acceptor (Q) to chlorophyll is high.     

Landscape and oceanic barriers shape dispersal and population structure in the island nematode Pristionchus pacificus

In this study evolutionary host plant patterns at ranks from order to species were analysed using spatial evolutionary and ecological vicariance analysis (SEEVA), based on a multigene phylogeny of 45 ascomycete fungal species. The objective was to understand speciation events and host associations in Ophiognomonia (Gnomoniaceae). Species of this genus are perithecial fungi that occur as endophytes, pathogens, and latent saprobes on plants in the families of Betulaceae, Fagaceae, Juglandaceae, Lauraceae, Malvaceae, Platanaceae, Rosaceae, Salicaceae, and Sapindaceae. A second objective was to determine whether speciation events are influenced by host conservatism, host specialization, or host switching at different taxonomic host ranks. Host differences between sister clades were interpreted using the divergence index (D) from the SEEVA analysis, ranging from 0 for no divergence to 1 for maximum possible divergence. Several fungal subclades showed clear patterns of host order/family conservatism (D = 1.00) for hosts in Betulaceae, Fagaceae, Juglandaceae, and Rosaceae. Clear trends of host specialization at host genus and species ranks (D = 1.00) were suggested within these host families. Independent host jumps were observed for two species at the family rank and three at the order rank. As a result of this study, host specificity and specialization is hypothesized as a mechanism that can strongly contribute to speciation patterns in fungal pathogens. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 1–16.     

The tortoise and the hare: ecology of angiosperm dominance and gymnosperm persistence

Gymnosperms, and conifers in particular, are sometimes very productive trees yet angiosperms dominate most temperate and tropical vegetation. Current explanations for angiosperm success emphasize the advantages of insect pollination and seed dispersal by animals for the colonization of isolated habitats. Differences between gymnosperm and angiosperm reproductive and vegetative growth rates have been largely ignored. Gymnosperms are all woody, perennial and usually have long reproductive cycles. Their leaves are not as fully vascularized as those of angiosperms and are more stereotyped in shape and size. Gymnosperm tracheids are generally more resistant to solute flow than angiosperm vessels. A consequence of the less efficient transport system is that maximum growth rates of gymnosperms are lower than maximum growth rates of angiosperms in well lit, well watered habitats. Gymnosperm seedlings may be particularly uncompetitive since their growth depends on a single cohort of relatively inefficient leaves. Later, some gymnosperms attain a higher productivity than co-occurring angiosperm trees by accumulating several cohorts of leaves with a higher total leaf area. These functional constraints on gymnosperm growth rates suggest that gymnosperms will be restricted to areas where growth of angiosperm competitors is reduced, for example, by cold or nutrient shortages. Biogeographic evidence supports this prediction since conifers are largely confined to high latitudes and elevations or nutrient-poor soils. Experimental studies show that competition in the regeneration niche (between conifer seedlings and angiosperm herbs and shrubs) is common and significantly affects conifer growth and survival, Fast-growing angiosperms, especially herbs and shrubs, may also change the frequency of disturbance regimes thereby excluding slower-growing gymnosperms. Shade-tolerant and early successional conifers share similar characteristics of slow initial growth and low plasticity to a change in resources. Shade-tolerant gymnosperms would be expected to occur only where forest openings are small or otherwise unsuitable for rapid filling by fast-growing angiosperm trees, lianas or shrubs. The limited evidence available suggests that shade-tolerant conifers are confined to forests with small gap sizes where large disturbances are very rare. The regeneration hypothesis for gymnosperm exclusion by angiosperms is consistent with several aspects of the fossil record such as the early disappearance of gymnosperms from early successional environments where competition with angiosperms would have been most severe. However there are unresolved difficulties in interpreting process from paleoecological pattern which prevent the testing of alternative hypotheses.     

Experimental evolution in Drosophila melanogaster: interaction of temperature and food quality selection regimes

Abstract. In Drosophila , both the phenotypic and evolutionary effect of temperature on adult size involves alterations to larval resource processing and affects other life-history traits, that is, development time but most notably, larval survival. Therefore, thermal evolution of adult body size might not be independent of simultaneous adaptation of larval traits to resource availability. Using experimental evolution lines adapted to high and low temperatures at different levels of food, we show that selection pressures interact in shaping larval resource processing. Evolution on poor food invariably leads to lower resource acquisition suggesting a cost to feeding behavior. However, following low temperature selection, lower resource acquisition led to a higher adult body size, probably by more efficient allocation to growth. In contrast, following high temperature selection, low resource acquisition benefited larval survival, possibly by reducing feeding-associated costs. We show that evolved differences to larval resource processing provide a possible proximate mechanism to variation in a suite of correlated life-history traits during adaptation to different climates. The implication for natural populations is that in nature, thermal evolution drives populations to opposite ends of an adult size versus larval survival trade-off by altering resource processing, if resource availability is limited.     

蛋白质定向进化的研究进展

在工业生物催化过程和生物细胞工厂构建方面,蛋白质定向进化被广泛地应用于酶的分子改造.蛋白质定向进化不仅可以针对某一目的蛋白进行改造,还可以改善代谢途径、优化代谢网络、获得期望表型细胞.为了获得更高效的突变效率,快捷、高通量的筛选方法,提高蛋白质定向进化的效果,研究者不断开发蛋白质体内、体外进化方法,取得了新的进展和应用.本文介绍了最近发展的蛋白质定向进化技术的原理、方法及特点,总结了突变文库的筛选方法和蛋白质定向进化的最新应用,最后讨论了蛋白质定向进化存在的挑战和未来发展方向.     

Evolution of the bovine lysozyme gene family: Changes in gene expression and reversion of function

Recruitment of lysozyme to a digestive function in ruminant artiodactyls is associated with amplification of the gene. At least four of the approximately ten genes are expressed in the stomach, and several are expressed in nonstomach tissues. Characterization of additional lysozymelike sequences in the bovine genome has identified most, if not all, of the members of this gene family. There are at least six stomachlike lysozyme genes, two of which are pseudogenes. The stomach lysozyme pseudogenes show a pattern of concerted evolution similar to that of the functional stomach genes. At least four nonstomach lysozyme genes exist. The nonstomach lysozyme genes are not monophyletic. A gene encoding a tracheal lysozyme was isolated, and the stomach lysozyme of advanced ruminants was found to be more closely related to the tracheal lysozyme than to the stomach lysozyme of the camel or other nonstomach lysozyme genes of ruminants. The tracheal lysozyme shares with stomach lysozymes of advanced ruminants the deletion of amino acid 103, and several other adaptive sequence characteristics of stomach lysozymes. I suggest here that tracheal lysozyme has reverted from a functional stomach lysozyme. Tracheal lysozyme then represents a second instance of a change in lysozyme gene expression and function within ruminants. Correspondence to: D.M. Irwin