Silver carp, Hypophthalmichthys molitrix, in the Poyang Lake belong to the Ganjiang River population rather than the Changjiang River population

The Poyang Lake is the largest lake and the main nursery area in the middle basin of the Changjiang (Yangtze) River. We compared molecular genetic markers of silver carp among populations of the Changjiang River, the Ganjiang River and the Poyang Lake using the ND5/6 region of mtDNA. Analysis of restriction fragment length polymorphisms (RFLPs) of this region revealed distinct variation between the Ganjiang River and the Changjiang River populations. The Poyang Lake is linked with the Ganjiang River and the Changjiang River. Shared RFLP fragments between the Ganjiang River population and the Poyang Lake population are as high as 61.4%. The value is 47.74% between the populations of the Changjiang River and that of the Poyang Lake. Frequencies of bands peculiar to the Ganjiang River population are the same as in the Poyang Lake population. We conclude that the Poyang Lake silver carp population consists mainly of the Ganjiang River population. The water level of the Poyang Lake outlet, which is higher than that of the Changjiang River in the silver carp spawning season, supports this conclusion.

Sequence variations of the S7 ribosomal protein gene in primitive cyprinid fishes: Implication on phylogenetic analysis

Cyprinidae is the largest fish family in the world and contains about 210 genera and 2010 species. Appropriate DNA markers must be selected for the phylogenetic analyses of Cyprinidae. In present study, the 1st intron of the S7 ribosomal protein (r-protein) gene is first used to examine the relationships among cyprinid fishes. The length of the 1st intron obtained by PCR amplification ranges from 655 to 859 by in the 16 cyprinid species investigated, and is 602 by in Myxocyprinus asiaticus. Out of the alignment of 925 nucleotide sites obtained, the parsimony informative sites are 499 and occupy 54% of the total sites. The results indicate that the 1st intron sequences of the S7 r-protein gene in cyprinids are rich in informative sites and vary remarkably in sequence divergence from 2.3% between close species to 66.6% between distant species. The bootstrap values of the interior nodes in the NJ (neighbor-joining) and MP (most-parsimony) trees based on the present S7 r-protein gene data are higher than those based on cytochrome b and the d-loop region respectively. Therefore, the 1st intron sequences of the S7 r-protein gene in cyprinids are sensitive enough for phylogenetic analyses, and the 1st intron is an appropriate genetic marker for the phylogenetic reconstruction of the taxa in different cyprinid subfamilies. However, attempts to discuss whether the present S7 r-protein gene data can be applied to the phylogeny of the taxa at the level of the family or the higher categories in Cypriniformes need further studies.

An efficient method for DNA isolation from red algae

A simple, inexpensive and efficient method was developed for rapid isolation of total genomic DNA from 15 red algal species. It resulted in 0.1 mug high quality DNA from 1 mg fresh algal material, with an A(260)/A(280) ratio of 1.68 - 1.90. Using this rapidly isolated DNA, the 18S ribosomal RNA genes ( rDNA) and the nuclear ribosomal DNA of the internal transcribed spacer (ITS) regions were amplified. The tested DNA was suitable for restriction endonuclease digestion, genetic marker analysis and polymerase chain reaction (PCR) amplification, and may be valid for other genetic manipulation.

中国海域斑海豹种群资源和分子遗传特征研究

斑海豹，西北太平洋广泛分布的冷水性海洋哺乳动物，为我国的二类保护野生动物，属于濒危物种，也是唯一能在我国海域自然繁殖的鳍脚类动物。辽东湾结冰区是斑海豹在世界上8个繁殖区中最南端的一个。为了能够更好地保护斑海豹资源，对渤海海域斑海豹的栖息地、种群动态及分布时间、重金属体内积累、以及斑海豹的分子遗传特性进行了研究。结果如下： 斑海豹在渤海海域的栖息地有辽宁双台子河口水域、大连虎平岛和山东庙岛群岛海域三处，其中的上岸点分别为河口泥沙滩、海里的浅石滩和海岛周围的小岛礁三种类型。斑海豹出现在三个栖息地的时间为每年的3~5月，2002~2008年间各栖息地的斑海豹的数量变化不明显。 对斑海豹肌肉、肝和肾脏组织重金属元素含量的分析结果显示，汞（Hg）、镉（Cd）、铅（Pb）和砷（As）等有毒元素在斑海豹体内的积累远未达到致死浓度。 对斑海豹的部分mtDNA 序列分析发现，辽东湾斑海豹群体的遗传距离、控制区DNA的单元型多样度和核苷酸多样度均远小于日本群体，辽东湾群体的遗传多样性水平较低。 微卫星引物标记对辽东湾斑海豹群体的遗传多样性研究显示，平均有效等位基因数（2~4个）和期望杂合度（0.24~0.72）等指标均较低，表明辽东湾斑海豹群体遗传多样性水平下降，可能曾出现过一定程度的瓶颈效应。 对斑海豹的41个MHC-I基因的序列分析，得到40个等位基因。斑海豹MHC-I基因多态性水平高，说明辽东湾斑海豹种群MHC-I基因的丰富性。 以上研究结果对于我国辽东湾斑海豹种群的保护和管理具有一定意义。

牙鲆Paralichthys olivaceus（♀）×夏鲆Paralichthys dentaus（♂）分子遗传学及数量遗传学研究

本论文采用扩增片段长度多态性（AFLP）技术对牙鲆Paralichthys olivaceus群体和夏鲆Paralichthys dentaus 群体进行了种群鉴定和遗传结构分析。共用8 对引物对两个群体（每个群体30 个个体）进行了分析。总共产生了379 个条带，条带大小在60－1000bp。牙鲆与夏鲆的遗传多态性分别为53.83%和22.22%。牙鲆群体的多态位点数显著低于夏鲆群体。牙鲆群体和夏鲆群体种的特异条带分别为27.3% 和 29.61%。两群体平均杂和度分别为0.0701 和 0.1556，香农氏多态指数分别为0.1044 和0.2387。群体内平均遗传距离分别为0.0705 （0.0214 到0.1377）和0.1656 （0.0629 到 0.2338），两群体间的平均遗传距离为0.6328。 AFLP 技术是进行种间群体结构分析的一个很好的分子标记方法，对牙鲆和夏鲆亲本群体进行遗传背景析为今后的杂交育种阐明种间杂交的遗传机理奠定基础。 在本论文中我们采用5×8 因子交配设计建立了牙鲆P. olivaceus（♀）× 夏鲆P. dentaus（♂）杂交家系，对生长相关性状的遗传力进行分析。所有家系都混合养殖在同一养殖池中，40 日龄，在养殖池中随机采集600 个个体，测量体长，体宽，体重等数量性状；然后提取杂交子代DNA 进行家系的鉴定。首先从牙鲆的微卫星中筛选了在牙鲆、夏鲆以及杂交子代扩增多态性较好的10 对微卫星引物（Po1, Po13, Po20, Po35, Po42, Po48, Po56, Po58, Po91, Poli 23TUF）。我们采用了三对引物对600 个个体进行了家系鉴定，共有400 多个体鉴定出自己的亲本，成功率达到80％以上。基于以上结果我们认为微卫星标记可以做为一个有效的标记来代替现实的物理标记，并且可以在子代的早期进行亲本的鉴定。 在养殖过程中，我们对自交和杂交家系生长状况进行了跟踪分析，在181刘清华 牙鲆（♀）×夏鲆（♂）分子遗传学及数量遗传学研究 博士学位论文II日龄之前杂交鲆体长和体重均为未表现出杂种优势，杂种优势率值始终为负值，但是绝对值在逐渐减小。从196 日龄之后杂交鲆杂种优势开始表现出来，并且在196 日龄之后杂种优势率显著的增加。256 日龄体长杂种优势率为14.29%，体重杂种优势率为59.78%, 271 日龄体长杂种优势率达到27.36%，体重杂种优势率为 102.32%。 本研究对杂交鲆在40 日龄的体长，体高、尾柄长、尾柄高，以及全长和体重的遗传力进行了估计，5 个性状的体长半同胞遗传力h2 S 为0.00146－0.719，5个性状的全同胞遗传力h2D 为0.00121－0.632，5 个性状的半同胞和全同胞的平均遗传力h2SD 为0.001335－0.6755。其中全长的遗传力最大。实验结果说明对早期幼鱼进行体长、体重等性状实施选育策略可能会显著影响后期杂交鲆的生长。

哈氏弧菌种特异性分子标记的发现及其在哈氏弧菌快速诊断和免疫防治中的应用

哈氏弧菌是危害水产养殖业发展的重要病原菌之一，因而其免疫防治研究具有重要意义。论文发现了一个新的、编码未知功能蛋白的基因vhhP2，该基因只存在于哈氏弧菌中，具有很高的种特异性。根据此特点，建立了一种vhhP2 -PCR检测方法，并证明该方法可以快速准确地从动物血液、组织以及环境样品中检测哈氏弧菌。同时，对VhhP2进行了免疫原性检测，发现VhhP2作为亚单位疫苗具有良好的免疫保护效应。为了克服常规亚单位疫苗的缺点以及进一步提高VhhP2的免疫效应，利用表面展示技术将VhhP2蛋白定位到鱼类共生菌细胞表面，制成活体疫苗。免疫结果表明，这种表面展示型VhhP2能够大幅提高牙鲆对哈氏弧菌的抵抗能力。论文还利用VhhP2蛋白的分泌功能，将VhhP2与一株迟缓爱德华氏菌的免疫保护性抗原蛋白重组融合，制成交叉保护疫苗，并证明其对哈氏弧菌和迟缓爱德华氏菌均有一定的免疫作用。

Its length polymorphism in oysters and its use in species identification

In an effort to develop genetic markers for oyster identification, we studied length polymorphism in internal transcribed spacers (ITS) between major ribosomal RNA genes in 12 common species of Ostreidae: Crassostrea virginica, C. rhizophorae, C. gigas, C. angulata, C. sikamea, C. ariakensis, C. hongkongensis, Saccostrea echinata, S. glomerata, Ostrea angasi, O. edulis, and O. conchaphila. We designed two pairs of primers and optimized PCR conditions for simultaneous amplification of ITS 1 and ITS2 in a single PCR. Amplification was successful in all 12 species, and PCR products were visualized on high-resolution agarose gels. ITS2 was longer than ITS 1 in all Crassostrea and Saccostrea species, whereas they were about the same size in the three Ostrea species. No intraspecific variation in ITS length was detected. Among species, the length of ITS I and ITS2 was polymorphic and provided unique identification of 8 species or species pairs: C. ariakensis, C. hongkongensis, C. sikamea, O. conchaphila, C. virginica/C. rhizophorae, C. gigas/C. angulata, S. echinata/S. glonzerata, and O. angasi/O. edulis. The ITS assay provides simple, rapid and effective identification of C. ariakensis and several other oyster species. Because the primer sequences are conserved, the ITS assay may be useful in the identification of other bivalve species.

Phylogenetic relationships of five pika species (genus Ochotona) based on mitochondrial DNA restriction maps

Restriction site mapping of mitochondrial DNA (mtDNA) with 16 restriction endonucleases was used to examine the phylogenetic relationships of Ochotona cansus, O. huangensis, O. thibetana, O. curzoniae and O. erythrotis. A 1-kb length variation between O. erythrotis of subgenus Pika and other four species of subgenus Ochotona was observed, which may be a useful genetic marker for identifying the two subgenera. The phylogenetic tree constructed using PAUP based on 61 phylogenetically informative sites suggests that O. erythrotis diverged first, followed by O. cansus, while O. curzoniae and O. huangensis are sister taxa related to O. thibetana, The results indicate that both O. cansus and O. huangensis should be treated as independent species. If the base substitution rate of pikas mtDNA was 2% per million years, then the divergence time of the two subgenera, Pika and Ochotana, is about 8.8 Ma ago of late Miocence, middle Bao-dian of Chinese mammalian age, and the divergence of the four species in subgenus Ochotona would have occurred about 2.5 - 4.2 Ma ago, Yushean of Chinese mammalian age. This calculation appears to be substantiated by the fossil record.

Delimiting species without nuclear monophyly in Madagascar's mouse lemurs.

BACKGROUND: Speciation begins when populations become genetically separated through a substantial reduction in gene flow, and it is at this point that a genetically cohesive set of populations attain the sole property of species: the independent evolution of a population-level lineage. The comprehensive delimitation of species within biodiversity hotspots, regardless of their level of divergence, is important for understanding the factors that drive the diversification of biota and for identifying them as targets for conservation. However, delimiting recently diverged species is challenging due to insufficient time for the differential evolution of characters--including morphological differences, reproductive isolation, and gene tree monophyly--that are typically used as evidence for separately evolving lineages. METHODOLOGY: In this study, we assembled multiple lines of evidence from the analysis of mtDNA and nDNA sequence data for the delimitation of a high diversity of cryptically diverged population-level mouse lemur lineages across the island of Madagascar. Our study uses a multi-faceted approach that applies phylogenetic, population genetic, and genealogical analysis for recognizing lineage diversity and presents the most thoroughly sampled species delimitation of mouse lemur ever performed. CONCLUSIONS: The resolution of a large number of geographically defined clades in the mtDNA gene tree provides strong initial evidence for recognizing a high diversity of population-level lineages in mouse lemurs. We find additional support for lineage recognition in the striking concordance between mtDNA clades and patterns of nuclear population structure. Lineages identified using these two sources of evidence also exhibit patterns of population divergence according to genealogical exclusivity estimates. Mouse lemur lineage diversity is reflected in both a geographically fine-scaled pattern of population divergence within established and geographically widespread taxa, as well as newly resolved patterns of micro-endemism revealed through expanded field sampling into previously poorly and well-sampled regions.

Rare hereditary COL4A3/COL4A4 variants may be mistaken for familial focal segmental glomerulosclerosis.

Focal segmental glomerulosclerosis (FSGS) is a histological lesion with many causes, including inherited genetic defects, with significant proteinuria being the predominant clinical finding at presentation. Mutations in COL4A3 and COL4A4 are known to cause Alport syndrome (AS), thin basement membrane nephropathy, and to result in pathognomonic glomerular basement membrane (GBM) findings. Secondary FSGS is known to develop in classic AS at later stages of the disease. Here, we present seven families with rare or novel variants in COL4A3 or COL4A4 (six with single and one with two heterozygous variants) from a cohort of 70 families with a diagnosis of hereditary FSGS. The predominant clinical finding at diagnosis was proteinuria associated with hematuria. In all seven families, there were individuals with nephrotic-range proteinuria with histologic features of FSGS by light microscopy. In one family, electron microscopy showed thin GBM, but four other families had variable findings inconsistent with classical Alport nephritis. There was no recurrence of disease after kidney transplantation. Families with COL4A3 and COL4A4 variants that segregated with disease represent 10% of our cohort. Thus, COL4A3 and COL4A4 variants should be considered in the interpretation of next-generation sequencing data from such patients. Furthermore, this study illustrates the power of molecular genetic diagnostics in the clarification of renal phenotypes.

Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida.

Olfactory receptors (ORs) govern a prime sensory function. Extant birds have distinct olfactory abilities, but the molecular mechanisms underlining diversification and specialization remain mostly unknown. We explored OR diversity in 48 phylogenetic and ecologically diverse birds and 2 reptiles (alligator and green sea turtle). OR subgenomes showed species- and lineage-specific variation related with ecological requirements. Overall 1,953 OR genes were identified in reptiles and 16,503 in birds. The two reptiles had larger OR gene repertoires (989 and 964 genes, respectively) than birds (182-688 genes). Overall, birds had more pseudogenes (7,855) than intact genes (1,944). The alligator had significantly more functional genes than sea turtle, likely because of distinct foraging habits. We found rapid species-specific expansion and positive selection in OR14 (detects hydrophobic compounds) in birds and in OR51 and OR52 (detect hydrophilic compounds) in sea turtle, suggestive of terrestrial and aquatic adaptations, respectively. Ecological partitioning among birds of prey, water birds, land birds, and vocal learners showed that diverse ecological factors determined olfactory ability and influenced corresponding olfactory-receptor subgenome. OR5/8/9 was expanded in predatory birds and alligator, suggesting adaptive specialization for carnivory. OR families 2/13, 51, and 52 were correlated with aquatic adaptations (water birds), OR families 6 and 10 were more pronounced in vocal-learning birds, whereas most specialized land birds had an expanded OR family 14. Olfactory bulb ratio (OBR) and OR gene repertoire were correlated. Birds that forage for prey (carnivores/piscivores) had relatively complex OBR and OR gene repertoires compared with modern birds, including passerines, perhaps due to highly developed cognitive capacities facilitating foraging innovations.

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

Genotyping an Emiliania huxleyi (Prymnesiophyceae) bloom event in the North Sea reveals evidence of asexual reproduction

Due to the unprecedented rate at which our climate is changing, the ultimate consequence for many species is likely to be either extinction or migration to an alternate habitat. Certain species might, however, evolve at a rate that could make them resilient to the effects of a rapidly changing environment. This scenario is most likely to apply to species that have large population sizes and rapid generation times, such that the genetic variation required for adaptive evolution can be readily supplied. Emiliania huxleyi (Lohm.) Hay and Mohler (Prymnesiophyceae) is likely to be such a species as it is the most conspicuous extant calcareous phytoplankton species in our oceans with generation times of 1 day−1. Here we report on a validated set of microsatellites, in conjunction with the coccolithophore morphology motif genetic marker, to genotype 93 clonal isolates collected from across the world. Of these, 52 came from a single bloom event in the North Sea collected on the D366 UK Ocean Acidification cruise in June-July 2011. There were 26 multilocus genotypes (MLGs) encountered only once in the North Sea bloom and 8 MLGs encountered twice or up to six times. Each of these repeated MLGs exhibited Psex values of less than 0.05 indicating each repeated MLG was the product of asexual reproduction and not separate meiotic events. In addition, we show that the two most polymorphic microsatellite loci, EHMS37 and P01E05, are reporting on regions likely undergoing rapid genetic drift during asexual reproduction. Despite the small sample size, there were many more repeated genotypes than previously reported for other bloom-forming phytoplankton species, including a previously genotyped E. huxleyi bloom event. This study challenges our current assumption that sex is the predominant mode of reproduction during bloom events. Whilst genetic diversity is high amongst extant populations of E. huxleyi, the root cause for this diversity and ultimate fate of these populations still requires further examination. Nonetheless, we show that certain CMM genotypes are found everywhere; while others appear to have a regional bias.

Myeloperoxidase G-463A polymorphism and Alzheimer's disease in the ApoEurope study

Alzheimer's disease (AD) is the most common cause of dementia in the elderly. Epidemiological and molecular genetic studies have shown the existence of several genes associated with increased risk of AD, the major genetic susceptibility locus coding for apolipoprotein E (apoE). A polymorphism in the myeloperoxidase gene (MPO) has previously been associated with AD susceptibility. However, results in the literature are controversial and seem to be dependent on several factors such as gender, apoE polymorphism or the genetic structure of the population. We investigated MPO G-463A and apoE polymorphism in 265 cases and 246 controls from the ApoEurope Study. In females, we found a significant association between MPO genotype and AD (P=0.034), GG genotype frequency being lower in cases (52.4%) as compared to controls (64.2%). In men, there was no significant effect of MPO polymorphism. No interaction was found between MPO polymorphism and apoE epsilon 4 allele. In conclusion, the G-463A polymorphism of MPO was statistically associated with AD in a gender-specific manner. However, given the low significance of P value we suggest no causal effect of the MPO gene in AD, as also evidenced in a recent meta-analysis. Our results support the hypothesis of a possible linkage disequilibrium between the MPO G-463A gene polymorphism and another functional variant involved in AD.

Unmasking venom gland transcriptomes in reptile venoms

While structural studies of reptile venom toxins can be achieved using lyophilized venom samples, until now the cloning of precursor cDNAs required sacrifice of the specimen for dissection of the venom glands. Here we describe a simple and rapid technique that unmasks venom protein mRNAs present in lyophilized venom samples. To illustrate the technique we have RT-PCR-amplified a range of venom protein transcripts from cDNA libraries derived from the venoms of a hemotoxic snake, the Chinese copperhead (Deinagkistrodon acutus), a neurotoxic snake, the black mamba (Dendroaspis polylepis), and a venomous lizard, the Gila monster (Heloderma suspectum). These include a metalloproteinase and phospholipase A2 from D. acutus, a potassium channel blocker, dendrotoxin K, from D. polylepis, and exendin-4 from H. suspectum. These findings imply that the apparent absence and/or lability of mRNA in complex biological matrices is not always real and paves the way for accelerated acquisition of molecular genetic data on venom toxins for scientific and potential therapeutic purposes without sacrifice of endangered herpetofauna.