Adaptive protein evolution in Drosophila

For over 30 years a central question in molecular evolution has been whether natural selection plays a substantial role in evolution at the DNA sequence level. Evidence has accumulated over the last decade that adaptive evolution does occur at the protein level, but it has remained unclear how prevalent adaptive evolution is. Here we present a simple method by which the number of adaptive substitutions can be estimated and apply it to data from Drosophila simulans and D. yakuba. We estimate that 45% of all amino-acid substitutions have been fixed by natural selection, and that on average one adaptive substitution occurs every 45 years in these species.     

Adaptive protein evolution at the Adh locus in Drosophila

Proteins often differ in amino-acid sequence across species. This difference has evolved by the accumulation of neutral mutations by random drift, the fixation of adaptive mutations by selection, or a mixture of the two. Here we propose a simple statistical test of the neutral protein evolution hypothesis based on a comparison of the number of amino-acid replacement substitutions to synonymous substitutions in the coding region of a locus. If the observed substitutions are neutral, the ratio of replacement to synonymous fixed differences between species should be the same as the ratio of replacement to synonymous polymorphisms within species. DNA sequence data on the Adh locus (encoding alcohol dehydrogenase, EC 1.1.1.1) in three species in the Drosophila melanogaster species subgroup do not fit this expectation; instead, there are more fixed replacement differences between species than expected. We suggest that these excess replacement substitutions result from adaptive fixation of selectively advantageous mutations.     

Adaptive evolution drives divergence of a hybrid inviability gene between two species of Drosophila

Speciation--the splitting of one species into two--occurs by the evolution of any of several forms of reproductive isolation between taxa, including the intrinsic sterility and inviability of hybrids. Abundant evidence shows that these hybrid fitness problems are caused by incompatible interactions between loci: new alleles that become established in one species are sometimes functionally incompatible with alleles at interacting loci from another species. However, almost nothing is known about the genes involved in such hybrid incompatibilities or the evolutionary forces that drive their divergence. Here we identify a gene that causes epistatic inviability in hybrids between two fruitfly species, Drosophila melanogaster and D. simulans. Our population genetic analysis reveals that this gene--which encodes a nuclear pore protein--evolved by positive natural selection in both species' lineages. These results show that a lethal hybrid incompatibility has evolved as a by-product of adaptive protein evolution.     

Complete replacement of mitochondrial DNA in Drosophila

The introduction of foreign mitochondria or mitochondrial DNA into a cell is a useful technique for clarifying the molecular mechanisms responsible for the maintenance of mitochondria. Novel combinations of mitochondrial and nuclear genomes have been studied in mammalian cells in culture and in yeast. In Drosophila, we have recently constructed heteroplasmic flies possessing both endogenous mitochondrial DNA and foreign mitochondrial DNA by intra- and interspecific transplantation of germ plasm. During the maintenance of these heteroplasmic lines, flies of D. melanogaster are produced that no longer possess their own mitochondrial DNA but retain the foreign mitochondrial DNA from D. mauritiana. .These flies are fertile and the foreign mitochondrial DNA is stably maintained in their offspring. Here we report the complete replacement of endogenous mitochondrial DNA with that from another multicellular species. Molecular and genetic analysis of this replacement in Drosophila should provide new insight into the functional interaction between nuclear and organelle genomes.     

Dynamics of DNA in vitro evolution

In vitro evolution has become a very important research area in recent years. From a practical point of view, it provides a powerful and reliable tool for engineering functional molecules (DNA, RNA or proteins) in reasonably short periods of time. From a theoretical point of view, since in vitro evolution is analogous to natural evolution in many respects, the study of the dynamic details of in vitro evolution may provide some instructive insights into the process of evolution. In this review, we summarize current theoretical and exper-imental studies, including several efforts made by our group, on the dynamics of DNA in vitro evolution.     

Adaptive evolution in the stomach lysozymes of foregut fermenters

The convergent evolution of a fermentative foregut in two groups of mammals offers an opportunity to study adaptive evolution at the protein level. The appearance of this mode of digestion has been accompanied by the recruitment of lysozyme as a bacteriolytic enzyme in the stomach both in the ruminants (for example the cow) and later in the colobine monkeys (for example the langur). The stomach lysozymes of these two groups share some physicochemical and catalytic properties that appear to adapt them for functioning in the stomach fluid. To examine the basis for these shared properties, we sequenced langur stomach lysozyme and compared it to other lysozymes of known sequence. Tree analysis suggest that, after foregut fermentation arose in monkeys, the langur lysozyme gained sequence similarity to cow stomach lysozyme and evolved two times faster than the other primate lysozymes. This rapid evolution, coupled with functional and sequence convergence upon cow stomach lysozyme, could imply that positive darwinian selection has driven about 50% of the evolution of langur stomach lysozyme.     

Genetic control and evolution of sexually dimorphic characters in Drosophila

Sexually dimorphic abdominal pigmentation and segment morphology evolved recently in the melanogaster species group of the fruitfly Drosophila. Here we show that these traits are controlled by the bric à brac [corrected] (bab) gene, which integrates regulatory inputs from the homeotic and sex-determination pathways. bab expression is modulated segment- and sex-specifically in sexually dimorphic species, but is uniform in sexually monomorphic species. We suggest that bab has an ancestral homeotic function, and that regulatory changes at the bab locus played a key role in the evolution of sexual dimorphism. Pigmentation patterns specified by bab affect mating preferences, suggesting that sexual selection has contributed to the evolution of bab regulation.     

Adaptive evolution and structure modeling of rbcL gene in Ephedra

The adaptive evolution of the rbcL gene in 14 species of Ephedra and 9 other gymnosperms was tested by the PAML program. Three large-scale selections were found in the catalytic region of the RbcL protein by branch model. Species in Ephedra with positive selection at the 365th codon site in rbcL gene were detected by branch-site model. 3D structure modeling showed that the 365th codon could change the spatial structure of the β-sheet (βG, βH, or βE) of the RbcL protein. These changes may be associated with ...     

黑腹果蝇种组组蛋白基因间内含子区的分子进化

通过分析黑腹果蝇种组(Drosophila melanogasterspecies group)9个种亚组代表种和D.pseudoobscura的组蛋白基因H2A和H2B的内含子的碱基组成、替换速率、转换/颠换比、二级结构和系统发育关系等发现:整个序列长度变异范围在201 bp(ficusphila)到232 bp(takahashii)之间,替换速率为0.82,转换明显高于颠换,内含子和外显子结合区不遵循“GT-AG”和“AT-AC”模式,而是“TT-AG”模式,二级结构与系统分化关系具有相关性.我们认为组蛋白基因H2A和H2B的内含子是先起源的,在进化过程中由于承受的选择压力不同而发生了变异.     

Mitochondrial DNA and human evolution

Mitochondrial DNAs from 147 people, drawn from five geographic populations have been analysed by restriction mapping. All these mitochondrial DNAs stem from one woman who is postulated to have lived about 200,000 years ago, probably in Africa. All the populations examined except the African population have multiple origins, implying that each area was colonised repeatedly.     

自适应DNA免疫算法在化工软测量中的应用

将T-S模糊模型与RBF神经网络相结合,构成T-S模糊RBF神经网络,提出了一种自适应DNA免疫算法优化设计T-S模糊RBF神经网络的规则后件参数的方法。该方法采用基于抗体浓度和克隆选择的更新策略调节机制,能有效地保持抗体的多样性,避免早熟收敛。将该方法应用于延迟焦化汽油干点的软测量建模,仿真结果表明了DNA免疫遗传算法在T-S模糊神经网络系统优化设计中的有效性,并可获得较高精度的模型。