Polymorphism of the cytochrome oxidase b gene (cyt b) in Russian populations of common carp and wild common carp (Cyprinus carpio L.)

Polymorphism of the mitochondrial cyt b gene was examined in 35 individuals of common carp and wild common carp (Cyprinus carpio L.). The fish examined represented two natural populations from Khabarovsk krai (Ac and Am), Volga wild common carp, Don wild common carp, and two common carp breeds, Ropsha (strains BB and MM) common carp and Hungarian common carp. The highest level of nucleotide (pi) and haplotype (h) diversity was detected in two strains of Ropsha common carp (MM, pi = 0.67%, h = 0.7; and BB, pi = 0.21%, h = 0.9) and in one population (Am) of Amur wild common carp (pi = 0.26%; h = 0.6). The second population of Amur wild common carp (Ac) and Hungarian common carp were characterized by lower variation estimates (pi = 0.035%, h = 0.4; and pi = 0.09%, h = 0.7, respectively). Genetic homogeneity was demonstrated for the populations of Volga and Don wild common carp (pi = 0, h = 0). In the sample of the cyt b sequences examined, three lineages were identified. Lineages I and II united all haplotypes of the Am Amur wild common carp along with two haplotypes of Ropsha common carp, strain MM. The third lineage (III) was formed by the haplotypes of three individuals of Ropsha common carp strain MM, all representatives of Ropsha common carp strain BB, Hungarian common carp, Ac Amur wild common carp, and Don and Volga wild common carps. Statistically significant amino acid differences were observed only for the sequences, corresponding to haplotypes of lineage III, and the sum of sequences of lineages I and II. Effectiveness of different types of markers to differentiate the two subspecies of European and Amur wild common carp (C. c. carpio and C. c. haematopterus) is discussed, as well as the issues of the origin and dispersal of Russian common carp and wild common carp breeds.     

线粒体DNA 序列分析在中国水域真海豚物种鉴定中的初步应用

真海豚包括长喙真海豚( Delphinus capensis) 和短喙真海豚( D. delphis) 2 种, 而中国水域的真海豚到底是哪一个种或是否同时有两个种的存在, 并不清楚。本研究测定了12 头中国水域真海豚mtDNA 控制区(control region) 366 bp 和细胞色素b (cytochrome b , cyt b) 基因336 bp 的序列, 并与已发表的其它真海豚的序列合并分析,初步鉴定中国水域真海豚的分类地位。结果表明, 中国水域的真海豚与东太平洋的长喙真海豚有相同的鉴别位点, 且两者之间的核苷酸歧异度(控制区: 1.93 ±0.22 % , cyt b 基因: 0.68 ±0.19 %) 显著低于与短喙真海豚之间的差异(控制区: 2.92 ±0.41 % , cyt b 基因: 0.95 ±0.27 %) 。通过MEGA (molecular evolutionary genetic analysis) 软件中的邻接法(neighbor joining) 进行的系统发生分析中, 中国水域的真海豚与长喙真海豚聚成一支, 有明显较近的亲缘关系。因此, 中国水域的真海豚在分类上应归属于长喙真海豚。     

草鱼和鲤群体遗传变异的RAPD指纹分析

利用随机扩增多态ＤＮＡ技术对革鱼,兴国红鲤,野鲤的种群内,种群间以及种间的遗传变异亏待进行了定量分析。结果表明;草鱼与鲤的ＲＡＰＤ指纹图谱带型差异显著,草鱼与红鲤和鲤种间的平均带纹相似系数分别为０．２５８３和０．２３９４,遗传距离分别达到０．９３６２和１．２２７７。     

Genetic diversity and differentiation of Russian common carp (Cyprinus carpio L.) breeds inferred from RAPD markers

Polymorphic components of the common carp Cyprinus carpio L. genome were examined by means of polymerase chain reaction with random primers (RAPD-PCR). Using four primers, genetic diversity estimates were obtained for 12 populations and seven strains of Russian common carp breeds, as well as for European Hungarian common carp and Amur wild common carp (N = 87). The highest number of polymorphic loci was revealed in Angelinskii common carp, as well as in the samples of Altai common carp and Amur wild common carp (P = 23.8-18.7%), while the lowest number of polymorphic loci was in the BB strain of Ropsha common carp. The index of genetic diversity, H, was high (11%) in Amur wild common carp, as well as in Altai and Angelinskii common carps. In the remaining breeds, the value of this index varied from 4 to 8%. Based on summarized RAPD profile (132 bands), a dendrogram of genetic differences was constructed. In this dendrogram, all breeds examined grouped into two clusters. One of the clusters was formed by Hungarian and Angelinskii common carps, and the three samples of Altai common carp. The second cluster was formed by the group consisting of the representatives of Cherepetskskii, Stavropol, and Ropsha common carps, along with the differing from them Amur wild common carp. The observed differentiation was confirmed by the analysis of the polymorphic markers variance by the method of principle components. Evolutionary history and the reasons for genetic differentiation of Russian common carp breeds are discussed.     

Polymorphism of the cytochrome oxidase b gene (<Emphasis Type="Italic">cyt b</Emphasis>) in Russian populations of common carp and wild common carp (<Emphasis Type="Italic">Cyprinus carpio</Emphasis> L.)

Polymorphism of the mitochondrial cyt b gene was examined in 35 individuals of common carp and wild common carp (Cyprinus carpio L.). The fish examined represented two natural populations from Khabarovsk krai (Ac and Am), Volga wild common carp, Don wild common carp, and two common carp breeds, Ropsha (strains BB and MM) common carp and Hungarian common carp. The highest level of nucleotide (π) and haplotype (h) diversity was detected in two strains of Ropsha common carp (MM, π = 0.67%, h = 0.7; and BB, π = 0.21%, h = 0.9) and in one population (Am) of Amur wild common carp (π = 0.26%; h = 0.6). The second population of Amur wild common carp (Ac) and Hungarian common carp were characterized by lower variation estimates (π = 0.035%, h = 0.4; and π = 0.09%, h = 0.7, respectively). Genetic homogeneity was demonstrated for the populations of Volga and Don wild common carp (π = 0, h = 0). In the sample of the cyt b sequences examined, three lineages were identified. Lineages I and II united all haplotypes of the Am Amur wild common carp along with two haplotypes of Ropsha common carp, strain MM. The third lineage (III) was formed by the haplotypes of three individuals of Ropsha common carp strain MM, all representatives of Ropsha common carp strain BB, Hungarian common carp, Ac Amur wild common carp, and Don and Volga wild common carps. Statistically significant amino acid differences were observed only for the sequences, corresponding to haplotypes of lineage III, and the sum of sequences of lineages I and II. Effectiveness of different types of markers to differentiate the two subspecies of European and Amur wild common carp (C. c. carpio and C. c. haematopterus) is discussed, as well as the issues of the origin and dispersal of Russian common carp and wild common carp breeds.     

Genetic diversity and differentiation of Russian common carp (Cyprinus carpio L.) breeds inferred from RAPD markers

Polymorphic components of the common carp Cyprinus carpio L. genome were examined by means of polymerase chain reaction with random primers (RAPD-PCR). Using four primers, genetic diversity estimates were obtained for 12 populations and seven strains of Russian common carp breeds, as well as for European Hungarian common carp and Amur wild common carp (N = 87). The highest number of polymorphic loci was revealed in Angelinskii common carp, as well as in the samples of Altai common carp and Amur wild common carp (P = 23.8?18.7%), while the lowest number (12.8%) of polymorphic loci was in the BB strain of Ropsha common carp. The index of genetic diversity, H, was high (11%) in Amur wild common carp, as well as in Altai and Angelinskii common carps. In the remaining breeds, the value of this index varied from 4 to 8%. Based on summarized RAPD profile (132 bands), a dendrogram of genetic differences was constructed. In this dendrogram, all breeds examined grouped into two clusters. One of the clusters was formed by Hungarian and Angelinskii common carps, and the three samples of Altai common carp. The second cluster was formed by the group consisting of the representatives of Cherepetskskii, Stavropol, and Ropsha common carps, along with the differing from them Amur wild common carp. The observed differentiation was confirmed by the analysis of the polymorphic markers variance by the method of principle components. Evolutionary history and the reasons for genetic differentiation of Russian common carp breeds are discussed.     

RNA-binding proteins: If it looks like a sn(o)RNA…

Small nuclear RNAs are involved in splicing pre-mRNA, while small nucleolar RNAs facilitate ribosome biogenesis. But these distinct particles may have more in common than was first apparent: some of their RNA components share a common RNA binding protein, a common RNA structure and perhaps a common origin.     

RNA-binding proteins: if it looks like a sn(o)RNA..

Small nuclear RNAs are involved in splicing pre-mRNA, while small nucleolar RNAs facilitate ribosome biogenesis. But these distinct particles may have more in common than was first apparent: some of their RNA components share a common RNA binding protein, a common RNA structure and perhaps a common origin.     

Common and rare plant species respond differently to fertilisation and competition, whether they are alien or native

Plant traits associated with alien invasiveness may also distinguish rare from common native species. To test this, we grew 23 native (9 common, 14 rare) and 18 alien (8 common, 10 rare) herbaceous species in Switzerland from six plant families under nutrient-addition and competition treatments. Alien and common species achieved greater biomass than native and rare species did overall respectively. Across alien and native origins, common species increased total biomass more strongly in response to nutrient addition than rare species did and this difference was not confounded by habitat dissimilarities. There was a weak tendency for common species to survive competition better than rare species, which was also independent of origin. Overall, our study suggests that common alien and native plant species are not fundamentally different in their responses to nutrient addition and competition.     

Comparing G matrices: are common principal components informative?

Common principal components (CPC) analysis is a technique for assessing whether variance-covariance matrices from different populations have similar structure. One potential application is to compare additive genetic variance-covariance matrices, G. In this article, the conditions under which G matrices are expected to have common PCs are derived for a two-locus, two-allele model and the model of constrained pleiotropy. The theory demonstrates that whether G matrices are expected to have common PCs is largely determined by whether pleiotropic effects have a modular organization. If two (or more) populations have modules and these modules have the same direction, the G matrices have a common PC, regardless of allele frequencies. In the absence of modules, common PCs exist only for very restricted combinations of allele frequencies. Together, these two results imply that, when populations are evolving, common PCs are expected only when the populations have modules in common. These results have two implications: (1) In general, G matrices will not have common PCs, and (2) when they do, these PCs indicate common modular organization. The interpretation of common PCs identified for estimates of G matrices is discussed in light of these results.     

Freshman Undergraduate Biology Students�� Difficulties with the Concept of Common Ancestry

All life on earth descended from a single common ancestor that existed several billion years ago; thus, any pair of organisms will have had a common ancestor at some point in their history. This concept is fundamental to an understanding of evolution and phylogeny. Developing an understanding of this concept is an important goal of evolution education and a part of most high school and college biology curricula. This study examines freshman undergraduate biology majors’ understanding and application of the concept of common ancestry. We used a survey that asked students to provide a brief definition of common ancestry and to rate their confidence that different pairs of organisms shared a common ancestor. Our results show that, although many students in our sample could give a satisfactory definition of common ancestry, the overwhelming majority failed to apply their definitions correctly when assessing the likelihood that the pairs of organisms shared common ancestors. Instead, we found that these students do not treat common ancestry as a binary (yes/no) trait, but instead see it as a continuum from less probable to more probable. These students are more likely to think that closely related organisms have a common ancestor than those that are more distantly related and that humans are less likely to be connected to common ancestors than nonhuman organisms. This pattern is highly consistent from student to student and has important implications for teaching evolution.     

The structure of common genetic variation in United States populations

The common-variant/common-disease model predicts that most risk alleles underlying complex health-related traits are common and, therefore, old and found in multiple populations, rather than being rare or population specific. Accordingly, there is widespread interest in assessing the population structure of common alleles. However, such assessments have been confounded by analysis of data sets with bias toward ascertainment of common alleles (e.g., HapMap and Perlegen) or in which a relatively small number of genes and/or populations were sampled. The aim of this study was to examine the structure of common variation ascertained in major U.S. populations, by resequencing the exons and flanking regions of 3,873 genes in 154 chromosomes from European, Latino/Hispanic, Asian, and African Americans generated by the Genaissance Resequencing Project. The frequency distributions of private and common single-nucleotide polymorphisms (SNPs) were measured, and the extent to which common SNPs were shared across populations was analyzed using several different estimators of population structure. Most SNPs that were common in one population were present in multiple populations, but SNPs common in one population were frequently not common in other populations. Moreover, SNPs that were common in two or more populations often differed significantly in frequency from one population to another, particularly in comparisons of African Americans versus other U.S. populations. These findings indicate that, even if the bulk of alleles underlying complex health-related traits are common SNPs, geographic ancestry might well be an important predictor of whether a person carries a risk allele.     

RS-SNP: a random-set method for genome-wide association studies

Background

Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES) are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding.

Result

To develop such valuable resources in common carp (Cyprinus carpio), a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp.

Conclusion

BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3,100 microsyntenies, covering over 50% of the zebrafish genome. BES of common carp are tremendous tools for comparative mapping between the two closely related species, zebrafish and common carp, which should facilitate both structural and functional genome analysis in common carp.     

稀有种和常见种对植物群落物种丰富度格局的相对贡献

物种丰富度格局的形成不仅依赖于群落的构建过程, 同样也依赖于群落中的物种组成(如稀有种和常见种)。本文以黄土高原子午岭林区的辽东栎(Quercus wutaishanica)林为研究对象, 根据频度大小对物种进行排序, 形成稀有-常见种和常见-稀有种两条物种序列, 通过逐一添加(去除)物种, 分析引起的总体物种丰富度及其成分(α多样性和β多样性)的变化, 确定稀有种和常见种对物种丰富度格局的相对贡献。结果表明: (1)常见-稀有种序列与群落总体物种丰富度的相关性呈先剧增后平稳的对数增长曲线, 而稀有-常见种序列与群落总体的相关性与前者刚好相反, 呈先平稳后剧增的指数增长曲线; (2) α多样性在常见-稀有种序列中呈明显的对数变化曲线, 而在稀有-常见种序列中呈指数增长曲线; (3)与α多样性变化相反, β多样性在常见-稀有种序列中随物种的进入先迅速降低后逐渐平稳, 而在稀有-常见种序列中先平稳后急剧降低。可以看出, 常见种不仅主导群落的总体物种丰富度格局, 同时也是α多样性和β多样性格局的重要贡献者。因此, 常见种是群落物种丰富度格局的指示者, 也应该是优先保护的物种。     

Universal common ancestry,LUCA, and the Tree of Life: three distinct hypotheses about the evolution of life

Common ancestry is a central feature of the theory of evolution, yet it is not clear what “common ancestry” actually means; nor is it clear how it is related to other terms such as “the Tree of Life” and “the last universal common ancestor”. I argue these terms describe three distinct hypotheses ordered in a logical way: that there is a Tree of Life is a claim about the pattern of evolutionary history, that there is a last universal common ancestor is an ontological claim about the existence of an entity of a specific kind, and that there is universal common ancestry is a claim about a causal pattern in the history of life. With these generalizations in mind, I argue that the existence of a Tree of Life entails a last universal common ancestor, which would entail universal common ancestry, but neither of the converse entailments hold. This allows us to make sense of the debates surrounding the Tree, as well as our lack of knowledge about the last universal common ancestor, while still maintaining the uncontroversial truth of universal common ancestry.     

Are farm-reared quails for game restocking really common quails (Coturnix coturnix)?: a genetic approach

The common quail (Coturnix coturnix) is a popular game species for which restocking with farm-reared individuals is a common practice. In some areas, the number of released quails greatly surpasses the number of wild breeding common quail. However, common quail are difficult to raise in captivity and this casts suspicion about a possible hybrid origin of the farmed individuals from crosses with domestic Japanese quail (C. japonica). In this study we used a panel of autosomal microsatellite markers to characterize the genetic origin of quails reared for hunting purposes in game farms in Spain and of quails from an experimental game farm which was founded with hybrids that have been systematically backcrossed with wild common quails. The genotypes of these quail were compared to those of wild common quail and domestic strains of Japanese quail. Our results show that more than 85% of the game farm birds were not common quail but had domestic Japanese quail ancestry. In the experimental farm a larger proportion of individuals could not be clearly separated from pure common quails. We conclude that the majority of quail sold for restocking purposes were not common quail. Genetic monitoring of individuals raised for restocking is indispensable as the massive release of farm-reared hybrids could represent a severe threat for the long term survival of the native species.     

Microvascular surgery

LEARNING OBJECTIVES: After reading this article, the participant should be able to: 1. Describe the common room set-up, medical considerations, and technical equipment necessary to perform microvascular surgery. 2. Describe the common arterial and venous techniques in performing microvascular surgery. 3. Recognize the common flap types along with their vascular supply and innervation used for microvascular surgery. 4. Describe common techniques for flap monitoring. 5. Describe techniques and medications for thrombolytic therapy. 6. Describe common medical conditions that may preclude an optimal result in microvascular surgery. SUMMARY: This article will explore common approaches to microsurgery. It is anticipated that the readers can utilize this article for maintenance of certification educational components and take the principles outlined and apply them to their daily practice.     

Genetic divergence between Cyprinus carpio carpio and Cyprinus carpio haematopterus as assessed by mitochondrial DNA analysis,with emphasis on origin of European domestic carp

Although common carp is the major fish species in Asian and European aquaculture and many domestic varieties have occurred, there is a controversy about the origination of European domestic common carp. Some scientists affirmed that the ancestor of European domestic common carp was Danube River wild common carp, but others considered it might be Asian common carp. For elucidating origination of European domestic common carp, we chose two representative European domestic common carp strains (German mirror carp and Russian scattered scaled mirror carp) and one wild common carp strain of Cyprinus carpio carpio subspecies (Volga River wild common carp) and two Asian common carp strains, the Yangtze River wild common carp (Cyprinus carpio haematopterus) and traditionally domestic Xingguo red common carp, as experimental materials. ND5–ND6 and D-loop segments of mitochondrial DNA were amplified by polymerase chain reaction and analyzed through restriction fragment length polymorphism (RFLP) and sequencing respectively. The results revealed that HaeIII and DdeI digestion patterns of ND5–ND6 segment and sequences of control region were different between European subspecies C. carpio carpio and Asian subspecies C. carpio haematopterus. Phylogenetic analysis showed that German mirror carp and Russian scattered scaled mirror carp belonged to two subspecies, C. carpio carpio and C. carpio haematopterus, respectively. Therefore, there were different ancestors for domestic carp in Europe: German mirror carp was domesticated from European subspecies C. carpio carpio and Russian scattered scaled mirror carp originated from Asian subspecies C. carpio haematopterus.     

鲤鱼鳞被和体色在人工诱导雌核发育中的遗传变异

于1986—1988年,先后人工诱导2尾红镜鲤和4尾荷包红鲤抗寒品系雌核发育,获得雌核发育2倍体当年鱼种2133尾,其中红镜鲤685尾,荷包红鲤1448尾。通过对这些后代鳞被和体色两个质量性状的分析,发现荷包红鲤抗寒品系雌核发育2倍体(1987)中有约三分之一个体表现散鳞型鳞被和桔红色(出现由深到浅一系列变化)及少量桔黄色、肉红色个体。红镜鲤散鳞型鳞被出现体表全部覆盖不规则大型鳞片、2/3、1/2覆盖不规则的大型鳞片和散鳞型个体。体色出现桔红色、桔黄色,上述二色都出现由深到浅一系列变化和肉红色。这两个质量性状在雌核发育代中表现出数量性状的特征。