分子生物学与进化的新理论

论述了由于分子生物学取得的成就,而形成的生物进化的新理论,并阐述了若干新理论指导生产实践取得的巨大应用成果。     

The theory of everything and molecular evolution

The theory of everything is discussed in relationship to early bacterial molecular evolution. The emphasis is on time, space (or location at the molecular level), the universal construction kit (elements contained in periodic table) and change per units of time that were necessary for early bacterial molecular evolution to occur.     

Recognition and molecular evolution in bacteria

One principal function of biological molecules in bacteria is to recognize other molecules. This allows cells to assemble for regulated enzymatic catalysis and the integration of biochemical pathways. Recognition is also an essential and a specific property in base pairing of DNA in the double helix. Therefore, recognition events must have been central to early self-assembly of primitive genetic material, genomes, cells, genetic recombination and especially in enzyme-substrate-product recognition events. Molecular recognition events are examined with an emphasis on their central role in early prokaryotic evolution.     

DNA重排及体外分子进化

ＤＮＡ重排是目前为止最简便、最有效的体外定向进化技术,可以对单一基因、质粒、代谢途径、部分甚至整个基因组进行改造。本综述了ＤＮＡ重排的基本原理、特点、与其它体外进化技术的不同,着重介绍了其在体外分子进化上的广泛应用,并对应用前景进行了展望。     

Molecular evolution and optimization

Microbial populations (and life) not only evolve, they optimize. The transition from a random, unorganized, lifeless Earth to the present situation, where the Earth is virtually covered with nucleic acids and diverse and complex species, required numerous molecular changes and the integration of metabolic pathways over billions of years. Primitive prokaryotic life was dependent on and constrained by the physical-chemical conditions on the Earth, while slowly reshaping conditions present. In this review, molecular evolution and molecular optimization are examined with an emphasis on the order in which evolutionary events occurred.     

RNA editing by the host ADAR system affects the molecular evolution of the Zika virus

Zika virus (ZIKV) is a mosquito‐transmitted flavivirus, linked to microcephaly and fetal death in humans. Here, we investigate whether host‐mediated RNA editing of adenosines (ADAR) plays a role in the molecular evolution of ZIKV. Using complete coding sequences for the ZIKV polyprotein, we show that potential ADAR substitutions are underrepresented at the ADAR‐resistant GA dinucleotides of both the positive and negative strands, that these changes are spatially and temporally clustered (as expected of ADAR editing) for three branches of the viral phylogeny, and that ADAR mutagenesis can be linked to its codon usage. Furthermore, resistant GA dinucleotides are enriched on the positive (but not negative) strand, indicating that the former is under stronger purifying selection than the latter. ADAR editing also affects the evolution of the rhabdovirus sigma. Our study now documents that host ADAR editing is a mutation and evolutionary force of positive‐ as well as negative‐strand RNA viruses.     

Genetic variation: molecular mechanisms and impact on microbial evolution

On the basis of established knowledge of microbial genetics one can distinguish three major natural strategies in the spontaneous generation of genetic variations in bacteria. These strategies are: (1) small local changes in the nucleotide sequence of the genome, (2) intragenomic reshuffling of segments of genomic sequences and (3) the acquisition of DNA sequences from another organism. The three general strategies differ in the quality of their contribution to microbial evolution. Besides a number of non-genetic factors, various specific gene products are involved in the generation of genetic variation and in the modulation of the frequency of genetic variation. The underlying genes are called evolution genes. They act for the benefit of the biological evolution of populations as opposed to the action of housekeeping genes and accessory genes which are for the benefit of individuals. Examples of evolution genes acting as variation generators are found in the transposition of mobile genetic elements and in so-called site-specific recombination systems. DNA repair systems and restriction-modification systems are examples of modulators of the frequency of genetic variation. The involvement of bacterial viruses and of plasmids in DNA reshuffling and in horizontal gene transfer is a hint for their evolutionary functions. Evolution genes are thought to undergo biological evolution themselves, but natural selection for their functions is indirect, at the level of populations, and is called second-order selection. In spite of an involvement of gene products in the generation of genetic variations, evolution genes do not programmatically direct evolution towards a specific goal. Rather, a steady interplay between natural selection and mixed populations of genetic variants gives microbial evolution its direction.     

Phylogenomics and molecular evolution of foot-and-mouth disease virus

This report describes the use of Bayesian methods to analyze polyprotein coding region sequences (n = 217) obtained from GenBank to define the genome-wide phylogeny of foot and mouth disease virus (FMDV). The results strongly supported the monophyly of five FMDV serotypes, O, A, Asia 1, C, and SAT 3, while sequences for the two remaining FMDV serotypes, SAT 1 and SAT 2 did not separate into entirely distinct clades. The phylogenomic tree revealed three sister-group relationships, serotype O + Asia 1, A + C, and SAT 1 + 3 + 2, with a new branching pattern: {[(O, Asia 1), (A, C)], (SAT 1, 2, 3)}. Within each serotype, there was no apparent periodic, geographic, or host species influence on the evolution of global FMDVs. Analysis of the polyprotein coding region of these sequences provided evidence for the influence of purifying selection on the evolution of FMDV. Using a Bayesian coalescent approach, the evolutionary rate of FMDV isolates that circulated during the years 1932-2007 was estimated to be 1.46 × 10(-3) substitutions/site/year, and the most recent common ancestor of the virus existed approximately 481 years ago. Bayesian skyline plot revealed a population expansion in the early 20(th) century that was followed by a rapid decline in population size from the late 20(th) century to the present day. These findings provide new insights into the mechanisms that impact on the evolution of this important livestock pathogen.     

A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock

Current understanding of the diversification of birds is hindered by their incomplete fossil record and uncertainty in phylogenetic relationships and phylogenetic rates of molecular evolution. Here we performed the first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution. Our approach used multiple fossil time constraints scattered throughout the phylogenetic tree and accounts for uncertainties in time constraints, branch lengths, and heterogeneity of rates of DNA evolution. We estimated that the major vertebrate lineages originated in the Permian; the 95% credible intervals of our estimated ages of the origin of archosaurs (258 MYA), the amniote-amphibian split (356 MYA), and the archosaur-lizard divergence (278 MYA) bracket estimates from the fossil record. The origin of modern orders of birds was estimated to have occurred throughout the Cretaceous beginning about 139 MYA, arguing against a cataclysmic extinction of lineages at the Cretaceous/Tertiary boundary. We identified fossils that are useful as time constraints within vertebrates. Our timescale reveals that rates of molecular evolution vary across genes and among taxa through time, thereby refuting the widely used mitogenomic or cytochrome b molecular clock in birds. Moreover, the 5-Myr divergence time assumed between 2 genera of geese (Branta and Anser) to originally calibrate the standard mitochondrial clock rate of 0.01 substitutions per site per lineage per Myr (s/s/l/Myr) in birds was shown to be underestimated by about 9.5 Myr. Phylogenetic rates in birds vary between 0.0009 and 0.012 s/s/l/Myr, indicating that many phylogenetic splits among avian taxa also have been underestimated and need to be revised. We found no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather than per unit of time, as recently suggested. Our analysis advances knowledge of rates of DNA evolution across birds and other vertebrates and will, therefore, aid comparative biology studies that seek to infer the origin and timing of major adaptive shifts in vertebrates.     

Evolution of the plastid ribosomal RNA operon in a nongreen parasitic plant: Accelerated sequence evolution,altered promoter structure,and tRNA pseudogenes

The nucleotide sequence of a 7.4 kb region containing the entire plastid ribosomal RNA operon of the nongreen parasitic plant Epifagus virginiana has been determined. Analysis of the sequence indicates that all four rRNA genes are intact and almost certainly functional. In contrast, the split genes for tRNA^Ile and tRNA^Ala present in the 16S-23S rRNA spacer region have become pseudogenes, and deletion upstream of the 16S rRNA gene has removed a tRNA^Val gene and most of the promoter region for the rRNA operon. The rate of nucleotide substitution in 16S and 23S rRNAs is several times higher in Epifagus than in tobacco, a related photosynthetic plant. Possible reasons for this, including relaxed translational constraints, are discussed.     

HIV-1 evolution: frustrating therapies,but disclosing molecular mechanisms

Replication of HIV-1 under selective pressure frequently results in the evolution of virus variants that replicate more efficiently under the applied conditions. For example, in patients on antiretroviral therapy, such evolution can result in variants that are resistant to the HIV-1 inhibitors, thus frustrating the therapy. On the other hand, virus evolution can help us to understand the molecular mechanisms that underlie HIV-1 replication. For example, evolution of a defective virus mutant can result in variants that overcome the introduced defect by restoration of the original sequence or by the introduction of additional mutations in the viral genome. Analysis of the evolution pathway can reveal the requirements of the element under study and help to understand its function. Analysis of the escape routes may generate new insight in the viral life cycle and result in the identification of unexpected biological mechanisms. We have developed in vitro HIV-1 evolution into a systematic research tool that allows the study of different aspects of the viral replication cycle. We will briefly review this method of forced virus evolution and provide several examples that illustrate the power of this approach.     

Planktic foraminiferal molecular evolution and their polyphyletic origins from benthic taxa

Phylogenetic analyses based on partial sequences of the small subunit (SSU) ribosomal (r) RNA gene have shown that the planktic and benthic foraminifera form a distinct monophyletic group within the eukaryotes. In order to determine the evolutionary relationships between benthic and planktic foraminifers, representatives of spinose and non-spinose planktic genera have been placed within a molecular SSU rDNA phylogeny containing sequences of the benthic suborders available to date. Our phylogenetic analysis shows that the planktic foraminifers are polyphyletic in origin, not evolving solely from a single ‘globigerinid-like’ lineage in the Mid-Jurassic, but derived from at least two ancestral benthic lines. The benthic ancestor of Neogloboquadrina dutertrei may have entered the plankton later than the Mid-Jurassic, and further investigation of related extant species should provide an indication of the timing of this event. The evolutionary origin of the non-spinose species Globorotalia menardii remains unclear. The divergences of the planktic spinose species generally support recent phylogenies based on the fossil record, which infer a radiation from a globigerinid common ancestor in the Mid- to Late Oligocene. The branching pattern indicates that there are possibly four distinct groups within the main spinose clade, with large evolutionary distances being observed between them. Globigerinoides conglobatus clusters strongly with Globigerinoides ruber and are divergent from Globigerinella siphonifera, Orbulina universa and Globigerinoides sacculifer.Conserved regions of the SSU rRNA gene show sufficient variation to discriminate foraminifers at the species level. Large genetic differences have been observed between the pink and white forms of Gs. ruber and between Ge. siphonifera Type I and II. The two types of Ge. siphonifera cannot be discriminated by traditional palaeontological methods, which has considerable implications for tracing fossil lineages and for the estimation of molecular evolutionary rates based upon the fossil record. The conserved regions show a high degree of sequence identity within a species, providing signature sequences for species identification. The variable regions of the gene may prove informative for population level studies in some species although complete sequence identity was observed in G. sacculifer and O. universa between specimens collected from the Caribbean and Western Pacific.     

Time scale of Poxvirus evolution

Unlike in vertebrates and RNA viruses, the molecular clock has not been estimated so far for DNA viruses. The extended conserved central region (102 kb) of the orthopoxvirus genome and the DNA polymerase gene (3 kb) were analyzed in viruses representing several genera of the family Poxviridae. Analysis was based on the known dating of the variola virus (VARV) transfer from Western Africa to South America and previous data on the phylogenetic relatedness of modern West African and South American isolates of VARV. The mutation accumulation rate was for the first time estimated for these DNA viruses at (0.9–1.2) × 10^?6 substitutions per site per year. It was assumed that poxviruses diverged from an ancestor approximately 500,000 years ago to form the recent species and that the ancestor of the genus Orthopoxvirus emerged approximately 300,000 years ago and gave origin to the modern species approximately 14,000 years ago.     

The molecular evolution of ZFY-related genes in birds and mammals

Summary We report the isolation and nucleotide sequence determination of clones derived from five ZFY-related zinc-finger genes from birds and mammals. These sequences are analyzed with reference to the previously published human genes, ZFX and ZFY, and mouse genes, Zfx, Zfa, Zfy-1, and Zfy-2. The analysis indicates that ZFY-related genes are highly conserved in birds and mammals, and that the rate of nucleotide substitution in the Y-linked genes is not as high as predicted. However, the mouse Zfy-1 and Zfy-2 genes are markedly divergent members of the ZFY gene family; we suggest this relates to X-inactivation of the mouse gene Zfx.     

African Haplogroup L mtDNA sequences show violations of clock-like evolution

A set of 96 complete mtDNA sequences that belong to the three major African haplogroups (L1, L2, and L3) was analyzed to determine if mtDNA has evolved as a molecular clock. Likelihood ratio tests (LRTs) were carried out with each of the haplogroups and with combined haplogroup sequence sets. Evolution has not been clock-like, neither for the coding region nor for the control region, in combined sets of African haplogroup L mtDNA sequences. In tests of individual haplogroups, L2 mtDNAs showed violations of a molecular clock under all conditions and in both the control and coding regions. In contrast, haplogroup L1 and L3 sequences, both for the coding and control regions, show clock-like evolution. In clock tests of individual L2 subclades, the L2a sequences showed a marked violation of clock-like evolution within the coding region. In addition, the L2a and L2c branch lengths of both the coding and control regions were shorter relative to those of the L2b and L2d sequences, a result that indicates lower levels of sequence divergence. Reduced median network analyses of the L2a sequences indicated the occurrence of marked homoplasy at multiple sites in the control region. After exclusion of the L2a and L2c sequences, African mtDNA coding region evolution has not significantly departed from a molecular clock, despite the results of neutrality tests that indicate the mitochondrial coding region has evolved under nonneutral conditions. In contrast, control region evolution is clock-like only at the haplogroup level, and it thus appears to have evolved essentially independently from the coding region. The results of the clock tests, the network analyses, and the branch length comparisons all caution against the use of simple mtDNA clocks.     

植物种群分子进化中对生境的适应——对荒漠植物遗传多样性研究结果的初步分析

长期以来,自然选择理论与中性理论对生物分子进化中的环境适应机理存在着激烈争论。目前,在植物种群分子进化中对生境适应的研究中正面临着一些难题：中性突变是分子水平进化的唯一原因,自然选择发挥主要作用的适应性进化是否存在于分子水平,选择与中性两种学说两种机制完全不同,如何才能将两者联系和统一起来,部分学者利用建立各种模型来描述自然选择对分子标记位点以及连锁序列的直接作用,如生态位宽度变异假设等。本研究小组以新疆阜康荒漠植物为研究对象,通过对两种重要荒漠植物遗传多样性的研究,分析两种植物各亚种群不同生境的生态因子与其遗传变异的关系,讨论生态位宽度变异假设,揭示遗传变异的产生与维持。中性论者与选择论者都试图解释生物环境适应与分子变异之间的关系。中性论和选择论是反映进化的两个侧面,它们不是绝对的,可以相互转化。     

The effects of kin selection on rates of molecular evolution in social insects

The evolution of sociality represented a major transition point in biological history. The most advanced societies, such as those displayed by social insects, consist of reproductive and nonreproductive castes. The caste system fundamentally affects the way natural selection operates. Specifically, selection acts directly on reproductive castes, such as queens, but only indirectly through the process of kin selection on nonreproductive castes, such as workers. In this study, we present theoretical analyses to determine the rate of substitution at loci expressed exclusively in the queen or worker castes. We show that the rate of substitution is the same for queen- and worker-selected loci when the queen is singly mated. In contrast, when a queen is multiply mated, queen-selected loci show higher rates of substitution for adaptive alleles and lower rates of substitution for deleterious alleles than worker-selected loci. We compare our theoretical expectations to previously obtained genomic data from the honeybee, Apis mellifera, where queens mate multiply and the fire ant, Solenopsis invicta, where queens mate singly and find that rates of evolution of queen- and worker-selected loci are consistent with our predictions. Overall, our research tests theoretical expectations using empirically obtained genomic data to better understand the evolution of advanced societies.     

The molecular evolution of pancreatic ribonuclease

Summary The primary structures of pancreatic ribonucleases from 26 species (18 artiodactyls, horse, whale, 5 rodents and turtle) are known. Several species contain identical ribonucleases (cow/bison; sheep/goat), other species show polymorphism (arabian camel) or the presence of two structural gene loci (guinea pig pancreas contains two ribonucleases that differ at 31 positions). 26 different sequences (including the ribonuclease from bovine seminal plasma which is paralogous to the pancreatic ribonucleases) were used to construct a most parsimonious tree. A second tree that most closely approximates current biological opinion requires 402 whereas the most parsimonious tree requires 389 nucleotide substitutions. The artiodactyl part of the most parsimonious tree conforms quite well with the biological one of this order, except for the position of the giraffe which is placed with the pronghorn. Other parts of the most parsimonious tree agree less with the biological tree, probably as a result of the occurrence of many parallel and back substitutions. Bovine seminal ribonuclease was found to be the result of a gene duplication which occurred before the divergence of the true ruminants, but after the divergence of this group from the cameloids.The evolutionary rate of ribonuclease was found to be 390, 3.0 and 11 nucleotide substitutions per 10⁹ yrs per ribonuclease gene, codon and covarion respectively. However, there is much variation in evolutionary rate in different taxa. Values ranging from about 100 (in the bovidae) to about 700 (in the rodents) nucleotide substitutions per 10⁹ yrs per gene were found.A method for counting parallel and back mutations is presented. The 389 nucleotide substitutions in the most parsimonious tree occur at 88 codon positions; 154 of them are the result of parallel and back mutations. Parallel evolution to a similar structure, including the presence of 2 sites with carbohydrate, was demonstrated in an extensive region at the surface of pig and guinea pig ribonuclease B. The presence of carbohydrate probably is important in a number of species. A correlation between the presence of heavily glycosidated ribonucleases and coecal digestion was observed. Hypothetical sequences of ancestral ungulate ribonucleases contain many recognition sites for carbohydrate attachment; this suggests that herbivores with coecal digestion might have preceded the true ruminants in mammalian evolution.