地下鼠视觉系统对昼夜节律调节研究进展

地下鼠由于其特殊的生活环境,视觉系统表现出明显的退化和进化镶嵌的特征:视觉器官退化,由视觉诱导产生行为反应的脑区及视觉投射严重退化,但是有关感受光周期的"非成像"视觉通路结构高度发达.即与成像和运动知觉有关的结构退化,有助于感受光周期的结构却选择性地保留.很多研究表明地下鼠的视觉系统依然保留有感知光周期节律并产生与外界昼夜循环同步的生理功能.与光周期有关的季节性繁殖、内分泌、行为活动以及体温变化等也表现出相应节律性.本文对地下鼠昼夜节律研究现状进行了综述,旨在对地下鼠的适应性进化特征加以补充,有助于开展地下啮齿类视觉系统功能的研究,更进一步阐明生物进化与环境的关系.     

进化基因组学

进化基因组学是一门刚刚起步的新兴学科,在诞生以来的10余年里取得了巨大的进展。通过基因组数据的比较诠释基因功能、研究生物进化,和通过分析新基因起源研究基因组本身的进化是进化基因组学研究的两大主要内容。它的诞生在生物学各分支学科都产生了巨大的影响,今后必将在人类理解生命起源和发展的过程中发挥越来越重要的作用。     

横向基因传递:生物进化的重要机制——获得性可能遗传

一向以来,人们倾向于认为基因从父母代向子代的纵向传递是表型遗传的唯一方式,后天获得的性状和特性是不能遗传的;而且基因突变是进化的主要途径。但是自然界的许多现象并不能用这些观点解释。近年来,在多种生物中已发现了基因从一个个体向另一个个体传递的现象,即横向的基因传递,并且发现横向基因传递是生物进化的一个重要机制,甚至比基因突变更重要。本文综述了生物体之间的各种横向基因传递现象,并提出了获得性可能在符合孟德尔定律的条件下遗传的假说。     

生物进化理论的新进展

介绍了近年来有关生物进化理论研究的新成果,分别对进化的方式、速率和原因等核心问题进行了例证说明,初步引入了非线性科学中的自组织理论,并比较了经典进化论与新兴学说的立论依据与差别。对于正确理解生物进化的过程具有一定的参考价值。     

调控进化与形态多样性

揭示导致生物体形态和结构多样性产生的原因和机制, 是进化生物学研究的重要内容。进化发育生物学的研究表明, 许多复杂的形态结构及其多样性, 都是通过对古老调控网络的修饰或改造来完成的。也就是说, 生物体形态和结构的多样化并不是像以前认为的是由基因编码区的变化造成的, 而更多的是取决于基因的调控进化。作为控制基因表达的关键组分, 基因调控区的顺式调控元件通过与特定反式作用因子结合, 精细调控基因表达的时、空和量。因此, 调控元件的获得、丢失、修饰或者改变都能引起基因表达模式的变化, 是形态和结构多样性产生的主要原因。本文结合近年来国际上在基因的调控进化方面所取得的进展, 总结了真核生物中基因调控的方式和特点, 阐述了调控进化的基本式样, 揭示了调控进化在生物进化(特别是形态和结构多样化)中的作用。     

细胞壁与细胞进化

介绍各种细胞壁的组成特点,分析了细胞壁在生物进化过程中可能发生的变化,从理论和现实角度对细胞壁演化引起的细胞进化进行了深入的讨论。     

重复基因的进化一回顾与进展

基因重复是普遍存在的生物学现象, 是基因组和遗传系统多样化的重要推动力量, 在生物进化过程中发挥着极其重要的作用。基因重复有何利弊, 基因发生重复后, 2个重复子拷贝的保留在基因功能方面是否存在偏好性, 子拷贝在表达和进化速率上如何分化, 以及重复基因为什么会被保留下来一直是进化生物学领域研究的热点问题之一。该文对以上重复基因研究的热点问题进行了介绍, 并对重复基因的进化机制和理论模型及其近年来的一些主要研究进展进行了综述。     

重复基因的进化－－回顾与进展

基因重复是普遍存在的生物学现象, 是基因组和遗传系统多样化的重要推动力量, 在生物进化过程中发挥着极其重要的作用。基因重复有何利弊, 基因发生重复后, 2个重复子拷贝的保留在基因功能方面是否存在偏好性, 子拷贝在表达和进化速率上如何分化, 以及重复基因为什么会被保留下来一直是进化生物学领域研究的热点问题之一。该文对以上重复基因研究的热点问题进行了介绍, 并对重复基因的进化机制和理论模型及其近年来的一些主要研究进展进行了综述。     

非一致性水文频率计算的基因途径Ⅰ:水文基因遗传、变异和进化原理

随机水文过程受到随机性和确定性因素的综合影响,其时间序列不仅具有反映遗传特性的纯随机成分,还含有反映变异特性的确定性跳跃、趋势、周期成分和随机性相依成分,使得随机水文过程表现出复杂的变化形态和演变规律.为了对上述复杂的变化形态和演变规律进行统一认识,本文从随机过程模拟和时间序列分析两个角度描述了非一致性水文序列的遗传和变异特性或规律,同时对非一致性水文频率计算途径进行比较,说明非一致性研究面临的主要问题.在此基础上,本文借鉴生物基因概念来定义水文基因,并分别利用常规矩、权函数矩、概率权重矩、线性矩等描述水文基因的构建和表达过程;同时定义跳跃、趋势、周期、相依和纯随机成分为构成水文基因的5种水文碱基,综合考虑非一致性水文序列的遗传成分和变异成分,并阐述其遗传、变异和进化原理,以揭示水文要素概率分布遗传、变异和进化的演变规律.     

微分方程在描述两群体进化过程中的应用

为了解释生物进化各种过程,在一定的条件下,通过定向选择推导出的微分方程可以研究两个共享同一资源但同时又互不杂交的同类群体的进化过程。虽然人们的直觉是大群体往往能占有生存的良机,但是这种认识是片面的。通过微分方程的各种模拟结果可以得出结论：一方面在简单的适应面上,即当一个群体发生有利突变而产生具有优势的后代,那么无论初始条件如何这个群体将最后侵蚀掉另一群体。大群体因有利突变等概率产生而有更大的几率获得生存的优势。另一方面在略微复杂的适应面上,如果两个群体都发生有利突变只是发生的时间不同。在相同的境遇下,小群体相比大群体反而有更大的可能存活下来而不被灭绝。     

Simulation of the evolution of genomic complexity.

A general evolutionary trend is the generation of organisms of increasing complexity, notwithstanding that reduction and simplification phenomena do occur in the evolutionary process. This paper proposes an evolutionary model incorporating the mechanisms of gene amplification and deletion. The evolutionary process leading to genomic complexity and the coexistence of simpler organisms with complicated ones were both simulated using the proposed model. The model was also used to investigate the influence of various factors on the evolution of complexity. The simulations indicated that the evolution of complexity is largely influenced by adaptation to complicated environments. Nevertheless, complex organisms require relatively more resources for survival and replication, which limits the on going tendency towards complexity. Moreover, the analysis showed that if the environment varies rapidly and the profit obtained from complexity is greater than the resources consumed, selection will tend to favor complexity. However, high living cost will tend to limit the trend of complexity and if the environment is relatively stable, reduction and simplification will become the dominant trends.     

Ontophylogenetic studies of Paleozoic ammonoides

In this work the main directions of study of ontogeny and phylogeny of Paleozoic ammonoids are discussed, and the results of studies of the Permian families of this subclass are presented. It is shown that the morphogenetic evolution of taxa of different rank is caused by manifestation of major phylogenetic moduses and their various combinations. Thus, development can proceed in the direction of morphological complexity and in the direction of simplification. The conclusion about the role of family in the evolutionary history of ammonoids, which depends on the complexity of its structure, was made: the more complex it is, the greater the perspective taxon can be for formation of new groups of the supraspecific rank.     

Genetic-evolutionary basis of symbiosis doctrine

The author presents the current notion of symbiosis as one of the main adaptation of an organism to changeable environment. Symbiosis is considered as a super organism genetic system within which there are different interactions (including mutualism and antagonism). Genetic integration of symbiotic partners can be realized as cross regulation of their genes, exchange of gene products (proteins, RNA), gene amplification and sometimes gene transfer between organisms. On the phenotypic level these processes result in signal interactions, integration of partner metabolic systems and development of symbiotic organs. Co-evolution is considered as an assemblage of micro- and macroevolution processes basing on pre-adaptations and proceeding under influence of different forms of natural selection (individual, frequency-depended and kin selection). Symbiosis can be compared with sexual process since both are the forms of organism integration characterized by different genetic mechanisms and evolutionary consequences. The genome evolution in symbiotic microorganisms can proceed by: 1) simplification of genome in obligate symbiosis (loss of genes that are necessary for independent existence, transfer of some genes to the host organism); 2) complication of genome in facultative symbiosis (increase in genome plasticity, structural and functional differentiation of genome into systems controlling free-living and symbiotic parts of life cycle). Most of symbiotic interactions are correlated to an increase in genetic plasticity of an organism that can lead to evolutionary saltations and origin of new forms of life.     

Evolutionary trends in the prokaryotic community and prokaryotic community-phage systems

The Evolutionary Constructor software has been used for computer simulation of the life and evolution of communities of unicellular haploid organisms (prokaryotic cells). Opposite trends of the community evolution (simplification and complication of the genome) have been studied. It has been demonstrated that species with reduced genomes tend to replace genetically and metabolically rich species under highly favorable environmental conditions. Under unfavorable conditions, the opposite tendency is observed. It has also been shown that introduction of phages capable of killing the cells into the system may radically change the current evolutionary trend.     

Genome reduction as the dominant mode of evolution

A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron‐rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases of reductive evolution are consistent with a general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification.     

A general multivariate extension of Fisher's geometrical model and the distribution of mutation fitness effects across species

The evolution of complex organisms is a puzzle for evolutionary theory because beneficial mutations should be less frequent in complex organisms, an effect termed "cost of complexity." However, little is known about how the distribution of mutation fitness effects (f(s)) varies across genomes. The main theoretical framework to address this issue is Fisher's geometric model and related phenotypic landscape models. However, it suffers from several restrictive assumptions. In this paper, we intend to show how several of these limitations may be overcome. We then propose a model of f(s) that extends Fisher's model to account for arbitrary mutational and selective interactions among n traits. We show that these interactions result in f(s) that would be predicted by a much smaller number of independent traits. We test our predictions by comparing empirical f(s) across species of various gene numbers as a surrogate to complexity. This survey reveals, as predicted, that mutations tend to be more deleterious, less variable, and less skewed in higher organisms. However, only limited difference in the shape of f(s) is observed from Escherichia coli to nematodes or fruit flies, a pattern consistent with a model of random phenotypic interactions across many traits. Overall, these results suggest that there may be a cost to phenotypic complexity although much weaker than previously suggested by earlier theoretical works. More generally, the model seems to qualitatively capture and possibly explain the variation of f(s) from lower to higher organisms, which opens a large array of potential applications in evolutionary genetics.     

Multihost experimental evolution of a plant RNA virus reveals local adaptation and host-specific mutations

For multihost pathogens, adaptation to multiple hosts has important implications for both applied and basic research. At the applied level, it is one of the main factors determining the probability and the severity of emerging disease outbreaks. At the basic level, it is thought to be a key mechanism for the maintenance of genetic diversity both in host and pathogen species. Using Tobacco etch potyvirus (TEV) and four natural hosts, we have designed an evolution experiment whose strength and novelty are the use of complex multicellular host organism as hosts and a high level of replication of different evolutionary histories and lineages. A pattern of local adaptation, characterized by a higher infectivity and virulence on host(s) encountered during the experimental evolution was found. Local adaptation only had a cost in terms of performance on other hosts in some cases. We could not verify the existence of a cost for generalists, as expected to arise from antagonistic pleiotropy and other genetic mechanisms generating a fitness trade-off between hosts. This observation confirms that this classical theoretical prediction lacks empirical support. We discuss the reasons for this discrepancy between theory and experiment in the light of our results. The analysis of full genome consensus sequences of the evolved lineages established that all mutations shared between lineages were host specific. A low degree of parallel evolution was observed, possibly reflecting the various adaptive pathways available for TEV in each host. Altogether, these results reveal a strong adaptive potential of TEV to new hosts without severe evolutionary constraints.     

Increases in environmental entropy demand evolution

An application of the entropic theory of perception to evolutionary systems indicates that environmental entropy increases will exert pressures on an organism to adapt. We speculate that the instability caused by such environmental changes will also cause an increase in the mutation rate of organisms leading to an eventual increase in their complexity. Such complexity generation allows organisms to adapt to the more entropic environment. Although we conclude that increases in environmental entropy cause an organism to evolve into a more complex organism, increases in entropy may not be necessary for complexity generationper se.     

Structural Constraints in the Evolution of the Tetrapod Skull Complexity: Williston’s Law Revisited Using Network Models

Ever since the appearance of the first land vertebrates, the skull has undergone a simplification by loss and fusion of bones in all major groups. This well-documented evolutionary trend is known as “Williston’s Law”. Both loss and fusion of bones are developmental events that generate, at large evolutionary scales, a net reduction in the number of skull bones. We reassess this evolutionary trend by analyzing the patterns of skull organization captured in network models in which nodes represent bones and links represent suture joints. We also evaluate the compensatory process of anisomerism (bone specialization) suggested to occur as a result of this reduction by quantifying the heterogeneity and the ratio of unpaired bones in real skulls. Finally, we perform simulations to test the differential effect of bone losses in skull evolution. We show that the reduction in bone number during evolution is accompanied by a trend toward a more complex organization, rather than toward simplification. Our results indicate that the processes by which bones are lost or fused during development are central to explain the evolution of the morphology of the skull. Our simulations suggest that the evolutionary trend of increasing morphological complexity can be caused as a result of a structural constraint, the systematic loss of less connected bones during development.