中国胭脂鱼种群的遗传分析

采用RAPD和PCR—RFLP技术,分析了长江中游两个中国胭脂鱼群体的遗传结构。50个随机引物进行RAPD分析,有3个引物显示了多态,宜昌、金口群体内个体之间的遗传相似度分别为0．9274、0．9313,群体之间遗传相似度为0．9000。12个限制性内切酶分析了两群体线粒体DNAND-5／6基因的限制性片段长度多态性,仅内切酶Ncil的酶切图谱显示了多态,基因型间的核苷酸序列歧化距离为0．235%,核苷酸多样性为0．004。分析表明,长江中游两个中国胭脂鱼群体遗传结构较为单一,群体之间表现了较为明显的遗传分化。     

中国胭脂鱼的核型研究

胭脂鱼科(Catostomidae)的绝大多数现存种类分布在北美,约有14属、80种。中国胭脂鱼是该科鱼类分布在我国的唯一现生种。 北美胭脂鱼核型曾有报道,其染色体数目是100左右,可是,被某些学者认为是胭脂鱼科发生地的亚洲的一种中国胭脂鱼的核型却未有报道。故此,我们作了它的核型研究 本研究所用的材料是活体鱼的肾脏,实验鱼是四川省水产研究所(宜宾)提供的,(2♀♀,(?)(?)),染色体玻片标本的制作按我们实验室常规方法—空气干燥法进行。     

中国胭脂鱼的骨骼形态和胭脂鱼科的分类位置

中国胭脂鱼Myxocyprinus asiaticus(Bleeker)是迄今知道胭脂鱼科(Catostomidae)分布于我国的一个种,而该科的大多数种属分布于北美洲,总计有14个现存属,大约80个种(Miller,1958)。 方炳文(Fang,1934)对中国胭脂鱼除了发表一个头骨及下咽齿的照片外,主要是阐明这种鱼的体形随不同体长(实际是不同龄期)而改变的事实。Nelson(1948)作了胭脂鱼韦氏器的比较解剖,他提到中国胭脂鱼第二和第三脊椎具有分离的椎体和第一脊椎存在一对横突之外,只简单地提到它应隶属于Ictiobinae亚科。此外有人说它和Carpiodes     

池养大口胭脂鱼鱼种的食性

池养大口胭脂鱼鱼种的食性研究表明 ,大口胭脂鱼鱼种为浮游动物尺寸选择性鱼类 ,其选食行为主要受鱼体及水体中浮游动物的个体大小影响 ,与浮游动物的种类、逃跑能力、运动方式等关系不明显。并初步探讨了 3种浮游生物食性鱼类 (大口胭脂鱼、鲢、鳙 )的食物关系。     

胭脂鱼外周血细胞的显微、超微结构与细胞化学观察

胭脂鱼Myxocyprinus asiaticus(Bleeker)属鲤形目(Cypriniformes)胭脂鱼科或称亚口鱼科(Catostomidae)。该科鱼类全世界现知约有13属70种,绝大多数种类分布于北美洲,仅胭脂鱼为我国也是亚洲的特有种,分布于我国的长江和闽江。胭脂鱼在鱼类系统演化和动物地理学研究上有着极为重要的科学价值,现为国家二类水生野       

葛洲坝下游胭脂鱼的繁殖生物学和人工繁殖初报

胭脂鱼(Myxocyprinus asiaticus)属鲤形目,胭脂鱼科,是我国的一种珍稀鱼类。胭脂鱼科约有65种,几乎都分布于北美洲。在亚洲只有两种,而见于西伯利亚东部的亚口鱼(Catostomus catostomus)是与北美共有的一个种。唯有胭脂鱼是亚洲特有的物种,因此,它在鱼类学和动物地理学上占有特殊的地位,具有重要的科学价值。胭脂鱼主要分布在长江,其体型大,摄食水生无脊椎动物。胭脂鱼产卵场主要在长江上游,繁殖的仔鱼大量漂流到中下游,生长数年成熟后,溯游到上游参加繁殖。       

中国胭脂鱼线粒体控制区遗传多样性分析

利用PCR技术扩增了采自长江宜昌江段和清江的8尾中国胭脂鱼线粒体DNA控制区全序列,研究发现该种具有脊椎动物线粒体控制区的一般结构,在获得的958bp的碱基序列中,共检测出32个多态性核苷酸变异位点,多态位点比例为0.033。核苷酸的变异位点除一个为缺失外,其余全部为碱基转换。变异位点主要集中在55-365bp高变异区,而其他区域突变稀少,个体的变异在0-1.36%之间,表现出较大的个体多态性差异。中国胭脂鱼的线粒体控制区的变异远大于美国胭脂鱼（Moxostoma robustum)的0.016。     

倒刺鲃两极虫的宿主新记录及其分子系统学研究

为弄清倒刺鲃两极虫(Myxidium spinibarba)的宿主多样性和胭脂鱼(Myxocyprinus asiaticus)寄生黏孢子虫的种类组成,研究基于形态和分子数据,比较分析了寄生于不同宿主的倒刺鲃两极虫的形态学和形态计量学特征及分子系统发育关系。结果显示:寄生于胭脂鱼和中华倒刺鲃的倒刺鲃两极虫株系在形态学和形态计量学上未出现显著性差异, 18S rDNA序列相似度为99.9%—100.0%,遗传距离为0.000—0.001,符合种内变异;寄生于不同宿主倒刺鲃两极虫的株系在系统发育树中嵌合聚支,且寄生于胭脂鱼的倒刺鲃两极虫株系先分化。以上结果表明:研究中两株系与倒刺鲃两极虫为同一物种,但在分子水平已经出现分化;这是首次在胭脂鱼中检获到黏孢子虫,胭脂鱼是倒刺鲃两极虫的新宿主。     

藏北3种裸鲤同工酶的电泳分析及物种分化的探讨

对藏北高原３种裸鲤的乳酸脱氢酶（ＬＤＨ）、苹果酸脱氢酶（ＭＤＨ）和脂酶（ＥＳＴ）进行电泳分析的结果表明,３种裸鲤酶谱均表现出种间的差别,而且在同一种群个体之间也存在着明显的分化,但无性别差异。３种裸鲤被检测的３种同工酶均有沉默基因表达的现象,重复基因ＬＤＨ－Ａ^2、ＬＤＨ－Ｂ^2、s-MDH-A^2和m-MDH-B^2也在部分个体中表达。遗传距离分析表明,色林错裸鲤（Ｇ.selincuoensis)与错鄂裸鲤（Ｇ．cuoensis)之间较之于与纳木错裸鲤（Ｇ．namensis)有更近的亲缘关系。与其他四倍体鱼类相比,裸鲤鱼类同工酶在重复基因和沉默基因上都有较高的表达频率,这种情况说明裸鲤鱼类目前可能还外于多倍化后进化的早期过程并早于胭脂鱼类所处的相应时期,这与裂腹鱼类起源较晚以及青藏高原业已存在的恶劣环境条件直接相关。     

胭脂鱼的早期发育

文中较详细地描述胭脂鱼早期发育各阶段的形态特征。胭脂鱼成熟卵粒呈圆球状,为沉性卵,吸水膨胀后卵间隙较大;水温１８．７℃时,大约经１６３小时孵化出仔鱼;再经９～１０天的发育,仔鱼鳔开始充气,并开始摄食。还对胭脂鱼胚胎发育速率与水温的关系,以及胭脂鱼人工繁殖死亡率高、资源下降的原因等进行了分析和讨论。     

Evolution of the differential regulation of duplicate genes after polyploidization

Summary In the 50 million years since the polyploidization event that gave rise to the catostomid family of fishes the duplicate genes encoding isozymes have undergone different fates. Ample opportunity has been available for regulatory evolution of these duplicate genes. Approximately half the duplicate genes have lost their expressions during this time. Of the duplicate genes remaining, the majority have diverged to different extents in their expression within and among adult tissues. The pattern of divergence of duplicate gene expression is consistent with the accumulation of mutations at regulatory genes. The absence of a correlation of extent of divergence of gene expression with the level of genetic variability for isozymes at these loci is consistent with the view that the rates of regulatory gene and structural gene evolution are uncoupled. The magnitude of divergence of duplicate gene expressions varies among tissues, enzymes, and species. Little correlation was found with the extent of divergence of duplicate gene expression within a species and its degree of morphological conservatism, although species pairs which are increasingly taxonomically distant are less likely to share specific patterns of differential gene expression. Probable phylogenetic times of origin of several patterns of differential gene expression have been proposed. Some patterns of differential gene expression have evolved in recent evolutionary times and are specific to one or a few species, whereas at least one pattern of differential gene expression is present in nearly all species and probably arose soon after the polyploidization event. Multilocus isozymes, formed by polyploidization, provide a useful model system for studying the forces responsible for the maintenance of duplicate genes and the evolution of these once identical genes to new spatially and temporally specific patterns of regulation.     

Evidence for duplication and divergence of the structural gene for phosphoglucoisomerase in diploid species of clarkia

Formal genetic analysis of the mode of inheritance of the electrophoretic phenotypes for phosphoglucoisomerase (PGI) in the annual plants Clarkia rubicunda and C. xantiana showed that these diploid species have two and three genes, respectively, that specify PGI subunits. Electrophoretic examination of seven other diploid species of Clarkia revealed that species assigned to ancestral sections in the current taxonomy have two PGI genes, whereas more specialized species have three PGI genes. Together with evidence that diploid species in two closely related genera have two PGI genes, this suggests the third PGI gene arose within Clarkia. Intergenic heterodimers are formed between polypeptides specified by the third gene and one of the other PGI genes, indicating they have a high degree of structural similarity. The combined genetic, biochemical, and phylogenetic evidence suggests that the third PGI gene resulted from a process of gene duplication. The apparent Michaelis constants (F6P to G6P) of the most common electrophoretic variants of the ancestral gene in C. xantiana and in C. rubicunda are closely similar, but that of the duplicate enzyme is much higher. The intergenic heteromer has an intermediate value. Four alleles have been identified for the duplicate PGI gene in C. xantiana, including a null allele which eliminates the activity of its product. This allele is one of the few examples of a "silenced" duplicate gene. The ancestral and duplicate genes assort independently in C. xantiana. In conjunction with the substantial chromosomal rearrangements that characterize species of Clarkia, this may mean that the duplicate PGI marks a duplicated chromosomal segment that originated from a cross between partially overlapping reciprocal translocations rather than from unequal crossing over.     

Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication

Insertions and deletions (indels) in protein-coding genes are important sources of genetic variation. Their role in creating new proteins may be especially important after gene duplication. However, little is known about how indels affect the divergence of duplicate genes. We here study thousands of duplicate genes in five fish (teleost) species with completely sequenced genomes. The ancestor of these species has been subject to a fish-specific genome duplication (FSGD) event that occurred approximately 350 Ma. We find that duplicate genes contain at least 25% more indels than single-copy genes. These indels accumulated preferentially in the first 40 my after the FSGD. A lack of widespread asymmetric indel accumulation indicates that both members of a duplicate gene pair typically experience relaxed selection. Strikingly, we observe a 30-80% excess of deletions over insertions that is consistent for indels of various lengths and across the five genomes. We also find that indels preferentially accumulate inside loop regions of protein secondary structure and in regions where amino acids are exposed to solvent. We show that duplicate genes with high indel density also show high DNA sequence divergence. Indel density, but not amino acid divergence, can explain a large proportion of the tertiary structure divergence between proteins encoded by duplicate genes. Our observations are consistent across all five fish species. Taken together, they suggest a general pattern of duplicate gene evolution in which indels are important driving forces of evolutionary change.     

Higher duplicability of less important genes in yeast genomes

Gene duplication plays an important role in evolution because it is the primary source of new genes. Many recent studies showed that gene duplicability varies considerably among genes. Several considerations led us to hypothesize that less important genes have higher rates of successful duplications, where gene importance is measured by the fitness reduction caused by the deletion of the gene. Here, we test this hypothesis by comparing the importance of two groups of singleton genes in the yeast Saccharomyces cerevisiae (Sce). Group S genes did not duplicate in four other yeast species examined, whereas group D experienced duplication in these species. Consistent with our hypothesis, we found group D genes to be less important than group S genes. Specifically, 17% of group D genes are essential in Sce, compared to 28% for group S. Furthermore, deleting a group D gene in Sce reduces the fitness by 24% on average, compared to 38% for group S. Our subsequent analysis showed that less important genes have more cis-regulatory motifs, which could lead to a higher chance of subfunctionalization of duplicate genes and result in an enhanced rate of gene retention. Less important genes may also have weaker dosage imbalance effects and cause fewer genetic perturbations when duplicated. Regardless of the cause, our observation indicates that the previous finding of a less severe fitness consequence of deleting a duplicate gene than deleting a singleton gene is at least in part due to the fact that duplicate genes are intrinsically less important than singleton genes and suggests that the contribution of duplicate genes to genetic robustness has been overestimated.     

Divergence pattern of duplicate genes in protein-protein interactions follows the power law

The impact of the biological network structures on the divergence between the two copies of one duplicate gene pair involved in the networks has not been documented on a genome scale. Having analyzed the most recently updated Database of Interacting Proteins (DIP) by incorporating the information for duplicate genes of the same age in yeast, we find that there was a highly significantly positive correlation between the level of connectivity of ancient genes and the number of shared partners of their duplicates in the protein-protein interaction networks. This suggests that duplicate genes with a low ancestral connectivity tend to provide raw materials for functional novelty, whereas those duplicate genes with a high ancestral connectivity tend to create functional redundancy for a genome during the same evolutionary period. Moreover, the difference in the number of partners between two copies of a duplicate pair was found to follow a power-law distribution. This suggests that loss and gain of interacting partners for most duplicate genes with a lower level of ancestral connectivity is largely symmetrical, whereas the "hub duplicate genes" with a higher level of ancient connectivity display an asymmetrical divergence pattern in protein-protein interactions. Thus, it is clear that the protein-protein interaction network structures affect the divergence pattern of duplicate genes. Our findings also provide insights into the origin and development of biological networks.     

Rate of protein evolution versus fitness effect of gene deletion

Whether nonessential genes evolve faster than essential genes has been a controversial issue. To resolve this issue, we use the data from a nearly complete set of single-gene deletions in the yeast Saccharomyces cerevisiae to assess protein dispensability. Also, instead of the nematode, which was used previously but is only distantly related to S. cerevisiae, we use another yeast, Candida albicans, as a second species to estimate the evolutionary distances between orthologous genes in two species. Our analysis reveals only a weak correlation between protein dispensability and evolutionary rate. More important, the correlation disappears when duplicate genes are removed from the analysis. And surprisingly, the average rate of nonsynonymous substitution is considerably lower than that for single-copy genes in the yeast genome. This observation suggests that structural constraints are more important in determining the rate of evolution of a protein than dispensability because duplicate genes are on average more dispensable than single-copy genes. For duplicate genes, those with only a weak effect or no effect of deletion on fitness evolve on average faster than those with a moderate or strong effect of deletion on fitness, which in turn evolve on average faster than those with a lethal effect of deletion.     

Faster evolution of Z-linked duplicate genes in chicken

It has been shown that duplicate genes on the X chromosome evolve much faster than duplicate genes on autosomes in Drosophila melanogaster.However,whether this phenomenon is general and can be applied to other species is not known.Here we examined this issue in chicken that have heterogametic females(females have ZW sex chromosome).We compared sequence divergence of duplicate genes on the Z chromosome with those on autosomes.We found that duplications on the Z chromosome indeed evolved faster than those on autosomes and show distinct patterns of molecular evolution from autosomal duplications.Examination of the expression of duplicate genes revealed an enrichment of duplications on the Z chromosome having male-biased expression and an enrichment of duplications on the autosomes having female-biased expression.These results suggest an evolutionary trend of the recruitment of duplicate genes towards reproduction-specific function.The faster evolution of duplications on Z than on the autosomes is most likely contributed by the selective forces driving the fixation of adaptive mutations on Z.Therefore,the common phenomena observed in both flies and chicken suggest that duplicate genes on sex chromosomes have distinct dynamics and are more influenced by natural selection than antosomal duplications,regardless of the kind of sex determination systems.     

Genome Changes After Gene Duplication: Haploidy vs. Diploidy

Since genome size and the number of duplicate genes observed in genomes increase from haploid to diploid organisms, diploidy might provide more evolutionary probabilities through gene duplication. It is still unclear how diploidy promotes genomic evolution in detail. In this study, we explored the evolution of segmental gene duplication in haploid and diploid populations by analytical and simulation approaches. Results show that (1) under the double null recessive (DNR) selective model, given the same recombination rate, the evolutionary trajectories and consequences are very similar between the same-size gene-pool haploid vs. diploid populations; (2) recombination enlarges the probability of preservation of duplicate genes in either haploid or diploid large populations, and haplo-insufficiency reinforces this effect; and (3) the loss of duplicate genes at the ancestor locus is limited under recombination while under complete linkage the loss of duplicate genes is always random at the ancestor and newly duplicated loci. Therefore, we propose a model to explain the advantage of diploidy: diploidy might facilitate the increase of recombination rate, especially under sexual reproduction; more duplicate genes are preserved under more recombination by originalization (by which duplicate genes are preserved intact at a special quasi-mutation-selection balance under the DNR or haplo-insufficient selective model), so genome sizes and the number of duplicate genes in diploid organisms become larger. Additionally, it is suggested that small genomic rearrangements due to the random loss of duplicate genes might be limited under recombination.USUALLY genome size becomes larger from haploid to diploid organisms (Lynch and Conery 2003), and so does the number of duplicate genes observed in genomes (Zhang 2003). It is extensively hypothesized that diploidy might facilitate the preservation and accumulation of duplicate genes, but it is still unclear how diploidy supports the evolution of duplicate genes in detail. The superiority of diploidy is classically attributed to preventing expression of deleterious mutations (Crow and Kimura 1965), but it is also argued that the sheltering of deleterious mutations cannot adequately explain the advantages of diploidy (Perrot et al. 1991).Recombination is a common phenomenon in all three kingdoms of life, Bacteria, Eukarya, and Archaea. It has been reported that recombination influences the loss of duplicate genes (Zhang and Kishino 2004; Xue et al. 2010). In diploid organisms, if recombination between the ancestor locus and the newly duplicated locus is free, the rate of recombination is maximally 0.5, which is commonly observed especially when the two loci are located on different chromosomes. Although recombination should not be regarded as an exception in haploid organisms (Fraser et al. 2007), recombination events usually occur more frequently in diploid populations than they do in haploid populations. In other words, diploidy might facilitate the occurrence of recombination. The difference of recombination behaviors between haploid and diploid organisms is an obvious and important feature during genomic evolution.In our recent studies of genomic duplication, we proposed a new possible way of preserving and accumulating duplicate genes in genomes—originalization (Xue and Fu 2009a). As is well known, for a locus in an infinite diploid population, the frequencies of wild-type and degenerative alleles will move to an equilibrium under purifying selection and mutation, which is known as the mutation–selection balance. After genomic duplication, under two simple selective models, double null recessive (DNR, under which valid individuals require at least one active wild-type allele on the ancestor and newly duplicated loci) and haplo-insufficient (HI or partial dominant, under which valid individuals require at least two active wild-type alleles on both loci) models, a special equilibrium of allele frequencies at the ancestor and newly duplicated loci will be reached under recombination, in which the frequency of wild-type allele is kept high at both loci. Under the HI selective model this balance becomes so stable and flexible that the fixation of a degenerative allele at one of these two loci (or the balance being broken) becomes very difficult even in a modest population (Xue and Fu 2009a,b). However, if the two loci are tightly linked (recombination rate r = 0), this balance of allele frequencies does not appear. As r increases, the balance becomes more stable and the frequency of the wild-type allele at two loci becomes higher. High frequency of the wild-type allele at both loci means that duplicate genes are preserved intact in genomes, so this phenomenon was named originalization.Although many duplicate genes originated from genomic duplications in some species, such as yeast, maize, and fish (Li et al. 2005), those from segmental duplications are also very popular (Zhang et al. 2000; Leister 2004). In haploid populations, most duplication events are small segmental duplications. Therefore, to understand genomic evolution comprehensively, it is necessary to explore the evolution of segmental genomic duplication.Lynch et al. (2001) and Tanaka et al. (2009) have studied the evolution of segmental gene duplication in diploid populations theoretically. However, in this study, we further compared the evolution of segmental gene duplication in haploid vs. diploid populations by numerical and simulation approaches under the DNR and HI selective models. We observed that haploid and diploid populations with the same-size gene pool are very similar under the DNR model and the same recombination rate. Recombination enlarges the probability of preservation of duplicate genes in either haploid or diploid populations via originalization, and haplo-insufficiency reinforces this effect. The loss of duplicate genes at the ancestor locus might be limited under recombination, while under complete linkage, the loss of duplicate genes is random at the ancestor and newly duplicated loci. According to these results, we propose a model with which to explain the revolutionary genomic transition from haploidy to diploidy.     

Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast

Identification of orthologous genes across species becomes challenging in the presence of a whole-genome duplication (WGD). We present a probabilistic method for identifying orthologs that considers all possible orthology/paralogy assignments for a set of genomes with a shared WGD (here five yeast species). This approach allows us to estimate how confident we can be in the orthology assignments in each genomic region. Two inferences produced by this model are indicative of purifying selection acting to prevent duplicate gene loss. First, our model suggests that there are significant differences (up to a factor of seven) in duplicate gene half-life. Second, we observe differences between the genes that the model infers to have been lost soon after WGD and those lost more recently. Gene losses soon after WGD appear uncorrelated with gene expression level and knockout fitness defect. However, later losses are biased toward genes whose paralogs have high expression and large knockout fitness defects, as well as showing biases toward certain functional groups such as ribosomal proteins. We suggest that while duplicate copies of some genes may be lost neutrally after WGD, another set of genes may be initially preserved in duplicate by natural selection for reasons including dosage.     

Asynchronous expression of duplicate genes in angiosperms may cause apomixis, bispory, tetraspory, and polyembryony

Apomicts that produce unreduced parthenogenetic eggs are generally polyploid and occur in at least 33 of 460 families of angiosperms. Embryo sacs of these apomicts form precociously from ameiotic megaspore mother cells (diplospory) or adjacent somatic cells (apospory). Polysporic species (bisporic and tetrasporic) are sexual and occur in at least 88 families. Their embryo sacs also form precociously, but only non-critical portions of meiosis are affected. It is hypothesized that (i) the partial to complete replacement of meiosis by embryo sac formation in apomictic and polysporic species results from asynchronously-expressed duplicate genes that control female development, (ii) duplicate genes result from polyploidy or paleopolyploidy (diploidized polyploidy with chromatin from multiple genomes), (iii) apomixis results from competition between nearly complete sets of asynchronously-expressed duplicate genes, and (iv) polyspory and polyembryony result from competition between incomplete sets of asynchronously-expressed duplicate genes. Phylogenetic and genomic studies were conducted to evaluate this hypothesis. Apomictic, polysporic, and polyembryonic species tended to occur together in cosmopolitan families in which temporal variation in female development is expected, apomicts were generally polyploid with few chromosomes per genome (X = 9.6pL0.4 SE), and polysporic and polyembryonic species were paleopolyploid with many chromosomes per genome (x= 15.7pL0.6 and 13.2pL0.4, respectively). These findings support the proposed duplicate-gene asynchrony hypothesis and further suggest asexual reproduction in apomicts preserves primary genomes, sexual reproduction in polysporic and polyembryonic polyploids accelerates paleopolyploidization, and pa-leopolyploidization may sometimes eliminate gene duplications required for apomixis while retaining duplications required for polyspory or polyembryony. Hence, apomixis, with its long-term reproductive stability, may occasionally serve as an evolutionary springboard in the evolution of normal and developmentally-novel paleopolyploid sexual species and genera.