Isolation and characterization of polymorphic microsatellites in a Yangtze River fish,brass gudgeon (Coreius heterodon Bleeker)

The brass gudgeon (Coreius heterodon) is a fish of economic importance in the Yangtze River. From a (GATA)_n‐enriched genomic library, 25 microsatellites were developed by employing the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol. Nine loci exhibited polymorphism with two to 12 alleles (mean 3.9 alleles/locus) in a test population, and observed heterozygosity ranged from 0.1111 to 0.9630 (mean 0.4426). Three of the nine loci showed polymorphism in a congeneric species, the largemouth bronze gudgeon Coreius guichenoti. These loci should provide sufficient level of genetic diversity to evaluate the fine‐scale population structure of C. heterodon.     

Genetic diversity in population of largemouth bronze gudgeon (Coreius guichenoti Sauvage et Dabry) from Yangtze River determined by microsatellite DNA analysis

Largemouth bronze gudgeon (Coreius guichenoti Sauvage et Dabry 1874), one of the endemic fish species in the upper reaches of the Yangtze River in China, is a benthic and potamodromous fish that is typically found in rivers with torrential flow. Three dams in the Yangtze River, Ertan Dam, Three Gorges Dam and Gezhouba Dam, may have had vital impacts on the habitat and spawning behaviors of largemouth bronze gudgeon, and could ultimately threaten the survival of this fish. We studied the population genetic diversity of C. guichenoti samples collected at seven sites (JH, GLP, BX, HJ, MD, SDP and XB) within the Yangtze River and one of its tributaries, the Yalong River. Genetic diversity patterns were determined by analyzing genetic data from 11 polymorphic microsatellite loci. A high genetic diversity among these largemouth bronze gudgeon populations was indicated by the number of microsatellite alleles (A) and the expected heterozygosity (HE). No significant population variation occurred among GLP, BX, HJ and MD populations, but dramatic population differentiation was observed among JH and XB, two dam-blocked populations, versus other populations. Tests for bottlenecks did not indicate recent dramatic population declines and concurrent losses of genetic diversity in any largemouth bronze gudgeon populations. To the contrary, we found that dams accelerated the population differentiation of this fish.     

长江宜宾江段铜鱼属鱼类种间食物关系

采用碳、氮稳定同位素技术对2012年4-5月长江宜宾江段铜鱼和圆口铜鱼的食物组成进行了分析,并利用多元统计分析方法探讨了铜鱼和圆口铜鱼种间食物关系,包括饵料相似性指数、重叠系数及2种鱼的摄食器官形态差异对食物组成的影响.结果表明:1)铜鱼的δ13C和δ15N变化范围分别为-21.15‰～-20.31‰和9.67‰～ 10.21‰,为偏动物性的杂食性鱼类;圆口铜鱼的δ13C和δ15N分别为-23.30‰～-21.18‰和7.40‰～ 9.21‰,相对铜鱼为偏植物性的杂食性鱼类,铜鱼和圆口铜鱼均与传统肠含物分析的结果存在一定的差异;2)两种鱼的食物相似性指数和食物重叠系数分别为78.7％和55.6％;3)主成分分析(PCA)表明,铜鱼和圆口铜鱼摄食器官形态特征存在一定的差异.长江宜宾江段铜鱼和圆口铜鱼种间竞争不激烈,作为向家坝蓄水前最后一次对长江宜宾江段铜鱼和圆口铜鱼食性及种间食物关系的调查,研究结果可为分析向家坝蓄水对宜宾江段鱼类营养结构的影响提供数据参考.     

Genetic diversity in the bronze gudgeon, <Emphasis Type="Italic">Coreius heterodon</Emphasis>, from the Yangtze River system based on mtDNA sequences of the control region

The bronze gudgeon, Coreius heterodon (Bleeker), is an economically important species, which only inhabits the Yangtze River. The stock declined drastically in recent years due to dam construction, over-fishing, and pollution. Little is known about its population genetic structure. In this study, the sequences of the mitochondrial DNA (mtDNA) control regions of natural bronze gudgeon was determined for fish collected from four sites in the Yangtze River (n = 102). The molecular data were used to estimate the genetic diversity and differentiation of the bronze gudgeon. The results showed that 28 haplotypes and 22 variable sites were found, and the haplotype diversity (π) and nucleotide diversity (h) were 0.849 and 0.00257, respectively. A low level of genetic diversity exists in the bronze gudgeon. Analysis of molecular variance (AMOVA) suggests that 98.8% of the genetic variability occurred within the populations; the site of collection had little influence on diversity. Future research should focus on investigating the genetic divergence of populations in different tributaries and using additional polymorphic markers, such as microsatellite DNA, to verify the results and improve interpretation.     

长江上游圆口铜鱼幼鱼肠道内寄生小吻虫种群生态的研究

对长江上游圆口铜鱼幼鱼肠道内寄生小吻虫种群生态的研究表明,长江上游圆口铜鱼幼鱼体内小吻虫感染率为69．88％,感染强度8．18(1-47),相对密度5．72。雌鱼的感染率和感染强度均高于雄鱼,体长4．0～5．9cm的圆口铜鱼被小吻虫的感染率最高,且染虫对肥满度有显著影响。小吻虫在圆口铜鱼幼鱼种群中呈负二项分布,66％的虫体集丛分布在圆口铜鱼肠道的前段,其种群主要由5mm以下个体组成,雌虫明显多于雄虫。     

长江下游地区夜鹭种群微卫星变异及遗传多样性

利用微卫星位点对长江下游地区夜鹭3个地方种群的遗传多样性及其种群结构进行了分析。研究结果表明:除了Ah526位点外,其他7个位点在夜鹭种群中均为高度多态。在3个地方种群中,6个微卫星位点中经Bonferroni校正后南京大校场种群和芜湖四褐山种群中分别有2个及3个位点显示杂合不足,显著偏离了哈迪-温伯平衡,这可能与夜鹭繁殖后个体的扩散能力较强及长江下游地区夜鹭存在着替代型迁徙现象有关。突变-漂移平衡分析表明,长江下游地区夜鹭种群显著具有杂合过剩的位点,这表明长江下游地区夜鹭种群已偏离了突变-漂移平衡,近期可能经历了瓶颈效应,种群数量曾经下降。地方种群间Fst分析表明,长江下游地区夜鹭地方种群间遗传分化程度较低,并没有形成显著的遗传结构,在保护与管理上可以作为同一个保护单元(或管理)单元     

长江流域潜在蒸散量时空变化特征

根据1961-2011年长江流域116个气象站点的逐日气象资料,应用Penman-Monteith法计算该流域的潜在蒸散量,在此基础上使用反距离加权(IDW)插值、M-K突变检验、Morlet小波分析和R/S趋势分析等方法对该流域潜在蒸散量的时空变化特征进行研究.结果表明:近51年来长江流域潜在蒸散量年际变化倾向率为-0.34 mm· a-1,空间分布上表现为由西向东先减小后增大的趋势;从潜在蒸散量的季节变化来看,除秋季增加趋势比较明显外,其他各季均表现为不同程度的减小趋势,总体表现为夏季＞秋季＞春季＞冬季;通过M-K突变检验和小波分析发现,全年潜在蒸散量的突变发生在1980年前后,年潜在蒸散量出现了准12年左右的第一主周期和准4年左右的第二主周期;R/S分析表明,除了降水量之外,其他气候因子与潜在蒸散量的变化都与过去保持持续的趋势一致性.     

长江上游圆口铜鱼生长方程的分析

根据2005～2007年在长江上游鱼类资源调查中采集到的476尾圆口铜鱼Coreius guichenoti Sauvage et Dabry标本的数据,对其生长方程进行了分析.圆口铜鱼鳞片半径-体长的函数关系在雌雄群体间不存在显著性差异并符合方程L=85.429S0.8125 (R2=0.9635),推算体长表现出Lee氏现象;运用非线性混合模型方法,对基于4种备选生长方程(von Bertalanffy生长方程(VBG)、Richards生长方程、Gompertz生长方程和Robertson生长方程)的36种不同模型分别以生长推算数据进行拟合,并根据AIC选择最优生长模型,得到不同备选方程对圆口铜鱼生长描述的优劣顺序为:VBG、Richards、Gompertz、Robertson方程,其中最优生长模型为VBG Model 6:Lt=602.9(1-e-0.1693(t+0.024)) (雌雄群体间在0.01水平上不存在显著性差异).圆口铜鱼的生长特征指数φ=4.7891±0.01612.对于存在Lee氏现象的鱼类,在使用生长推算数据构建生长方程时,建议使用非线性混合模型以对参数值进行较合理的估计.本文为圆口铜鱼种群动态及资源保护提供了基础资料,并为不同种鱼类、同种鱼类不同生活史阶段表现出的不同生长模式的识别提供了一个范例.     

Microsatellite variation among divergent populations of stalk-eyed flies, genus Cyrtodiopsis

Microsatellite primers are often developed in one species and used to assess neutral variability in related species. Such analyses may be confounded by ascertainment bias (i.e. a decline in amplification success and allelic variability with increasing genetic distance from the source of the microsatellites). In addition, other factors, such as the size of the microsatellite, whether it consists of perfect or interrupted tandem repeats, and whether it is autosomal or X-linked, can affect variation. To test the relative importance of these factors on microsatellite variation, we examine patterns of amplification and allelic diversity in 52 microsatellite loci amplified from five individuals in each of six populations of Cyrtodiopsis stalk-eyed flies that range from 2.2 % to 11.2% mitochondrial DNA sequence divergence from the population used for microsatellite development. We find that amplification success and most measures of allelic diversity declined with genetic distance from the source population, in some cases an order of magnitude faster than in birds or mammals. The median and range of the repeat array length did not decline with genetic distance. In addition, for loci on the X chromosome, we find evidence of lower observed heterozygosity compared with loci on autosomes. The differences in variability between X-linked and autosomal loci are not adequately explained by differences in effective population sizes of the chromosomes. We suggest, instead, that periodic selection events associated with X-chromosome meiotic drive, which is present in many of these populations, reduces X-linked variation.     

Microsatellite and chloroplast DNA analyses reveal no genetic variation in a beach plant Surianana maritima on the Paracel Islands,China

Genetic variation within and among six natural populations of beach plant Suriana maritima on the Paracel Islands of China was assessed using SSR and chloroplast DNA sequence analysis. The results showed a complete absence of genetic variation between individuals either within or among populations. The cumulative consequences of a founder effect, selfing, and inbreeding may be responsible for the loss of genetic diversity in S. maritima.     

长江口北支水域营养盐的季节性变化

于2010年12月—2011年9月,2012年9月—2013年6月按季度采样对长江口北支水域氮、磷营养盐的季度变化规律、形态组成以及环境因子间相互关系进行了分析。结果显示溶解性无机氮存在形态主要是硝酸盐,占90%以上,浓度变化规律为夏秋高于春冬两季;溶解性无机氮、总氮峰值分别为3.99 mg/L及1.70 mg/L,均出现在2011年夏季,该现象与当年洪期长江流域连日降雨有关。长江径流所携带营养盐是导致北支无机氮、总磷浓度变化的主要原因。对理化因子进行相关性分析表明,盐度、pH值是营养盐最主要的限制因子。     

Genetic variation of the Chinese longsnout catfish Leiocassis longirostris in the Yangtze River revealed using mitochondrial DNA cytochrome b sequences

The mitochondrial DNA cytochrome b of 132 Leiocassis longirostris collected from 12 localities in the upper to lower reaches of the Yangtze River were amplified and partially sequenced using the PCR technique. The results showed that 27 nucleotide sites were variable along 817 bp length of homologous sequence (3.3%), base substitutions happened mostly at the third codon position. A total of 22 haplotypes were identified, which were characterized with moderate haplotype diversity (h = 0.5417 ± 0.0519), but low nucleotide diversity (π = 0.0019 ± 0.0012). Median-joining network analysis revealed star-shaped patterns with one common central haplotype (H3), whereas mismatch distribution analysis found that the Chinese longsnout catfish fitted a smooth unimodal distribution, which suggested that this species underwent population expansion following bottlenecks and/or they originated from a small number of founding individuals. The time that the total population of Chinese longsnout catfish in the Yangtze River expanded was estimated 169,000–337,000 years before present. The analysis of molecular variance (AMOVA) and phylogenetic reconstructions did not detect significant geographic structure between different river sections, especially between above and below the Gezhouba Dam and the Three Gorges Dam, which suggested that these recently developed dams might have not significantly resulted in population genetic differentiation in the Chinese longsnout catfish.     

长江口北支浮游植物群落结构周年变化特征

2010年10月至2011年9月对长江口北支水域的浮游植物进行周年调查,共采集到183种（包括变种和变型）,隶属于7门60属,其中硅藻门种类最多,有35属137种,占浮游植物总种类数的75%。周年优势种为具槽直链藻、中肋骨条藻、条纹小环藻、两栖颤藻、小伪菱形藻双楔变种、颗粒直链藻和小环藻未定种。本次调查中,季节间浮游植物的丰度差异不显著（P〉0.05）,但各月间浮游植物丰度差异显著（P〈0.05）,全年丰度在2.83×10^3～6.18×10^4cells/L之间,其中6月的丰度最高,1月的丰度最低,全年的平均丰度为1.73×10^4cells/L。Pearson相关性分析显示,浮游植物丰度与硝酸盐浓度显著正相关（P〈0.05）,与氨氮浓度极显著正相关（P〈0.01）,含氮营养盐对浮游植物的影响明显。     

Microsatellite variation and differentiation among local populations of Castanopsis species in Japan

Microsatellite variations in Castanopsis species in Japan were examined to clarify the genetic relationships among 25 local populations according to the difference in the number of layers of adaxial epidermis in the leaves. Six microsatellite loci were assayed for 629 seedlings from the populations, and these seedlings were classified into five types according to the state of the leaf epidermis. Remarkable differences in the allele frequency of the six microsatellite loci were observed among these local populations. The coefficients of genetic differentiation, R_ST, of each locus ranged from 0.209 to 0.388. An unweighted pair-group method (UPGMA) phenogram constructed on the population pairwise R_ST over the loci revealed three clusters (A–C), and six sub-clusters. These clusters reflected the differences in the occurrence frequency of seedlings in each epidermis type within a population. Our findings suggest that clusters A and C are the local populations dominated by Castanopsis sieboldii and Castanopsis cuspidata, respectively, while local populations of cluster B are composed of the two Castanopsis species and/or include many individuals derived by hybridization. The six sub-clusters were found to reflect the geographic relationship among the populations, suggesting a different process for geographic population dynamics during the postglacial period.     

钱塘江日本沼虾野生群体遗传变异的SSR分析

利用微卫星标记分析了钱塘江干流水域闻堰、富阳、场口、桐庐等7个野生日本沼虾群体的遗传多样性和遗传结构。结果表明:10个微卫星位点呈现高度多态性;闻堰、富阳、场口、新安江等中下游野生群体的遗传多样性水平有高于歙县和休宁两个上游群体遗传多样性水平的趋势。符号检验和Wilcoxon符号秩次检验的结果表明,钱塘江日本沼虾群体近期没有发生瓶颈效应,群体数量也没有下降。FST的范围介于0.0201～0.1069。分子方差分析结果显示,大部分的遗传变异(93.48%)存在于个体间,少部分遗传变异(6.52%)存在于群体之间。群体间FST及AMOVA分析表明,群体处于中等遗传分化水平;基于DA遗传距离构建的NJ聚类树显示,地理位置相邻的群体聚在一起。STRUCTURE分析413份参试的日本沼虾样本被分为2个理论种群,即上游歙县和休宁群体为一个理想种群,其余中下游的5个群体为另一个理想种群。日本沼虾的遗传多样性和遗传结构与所生存的地理位置具有相关性。     

Impact of Yangtze River Water Transfer on the Water Quality of the Lixia River Watershed,China

To improve water quality and reduce the negative impacts of sudden inputs of water pollution in the Lixia River watershed, China, a series of experimental water transfers from the Yangtze River to the Lixia River were conducted from 2 December 2006 to 7 January 2007. Water samples were collected every six days at 55 monitoring sites during this period. Eight water parameters (water temperature, pH, dissolved oxygen (DO), chemical oxygen demand (COD), potassium permanganate index (COD_Mn), ammonia nitrogen (NH₄ ⁺-N), electrical conductivity (EC), and water transparency (WT)) were analyzed to determine changes in nutrient concentrations during water transfers. The comprehensive pollution index (Pi) and single-factor (Si) evaluation methods were applied to evaluate spatio-temporal patterns of water quality during water transfers. Water quality parameters displayed different spatial and temporal distribution patterns within the watershed. Water quality was improved significantly by the water transfers, especially for sites closer to water intake points. The degree of improvement is positively related to rates of transfer inflow and drainage outflow. The effects differed for different water quality parameters at each site and at different water transfer times. There were notable decreases in NH₄ ⁺-N, DO, COD, and COD_Mn across the entire watershed. However, positive effects on EC and pH were not observed. It is concluded that freshwater transfers from the Yangtze River can be used as an emergency measure to flush pollutants from the Lixia River watershed. Improved understanding of the effects of water transfers on water quality can help the development and implementation of effective strategies to improve water quality within this watershed.     

Microsatellite diversity and population genetic structure of yellowcheek, Elopichthys bambusa (Cyprinidae) in the Yangtze River

Yellowcheek carp (Elopichthys bambusa) is the only species of genus Elopichthys. It is widely distributed in Chinese freshwaters but currently its populations have declined to threatening level. We examined the genetic diversity and population structure of E. bambusa in the Yangtze River basin. A total of nine polymorphic microsatellite markers were employed to study five populations occurring in middle and lower reaches of the river. The results revealed low-to-moderate genetic diversity. The number of alleles per locus varied between 3 and 8 with an average of 4.8. Observed heterozygosity ranged from 0.15 to a maximum of 1.00. Significant deviations (P < 0.01) from Hardy–Weinberg equilibrium were observed for all the tested locus-population combinations with clear heterozygosity deficits. AMOVA indicated that majority of the variance lies within populations (93.81%) than among the populations (7.05%). Pairwise F_ST and unbiased genetic distance pointed out significant differentiation among the samples from populations with different connections to the Yangtze River. In the UPGMA dendrogram, clustering pattern of populations indicated that most of the populations are reproductively isolated due to anthropogenic interventions. Clustering of PYL and DTL populations shows ongoing gene flow through the mainstream. The recent hydrological alterations and overfishing are major factors shaping the current genetic structure. These results can be helpful for effective management and sustainable conservation of E. bambusa populations.     

Mitochondrial DNA variation in River Usk brown trout, Salmo trutta

Mitochondrial DNA (mtDNA) polymorphism in the essentially non-anadromous River Usk brown trout Salmo trutta population was investigated by restriction analysis. Following mtDNA extraction and purification on caesium chloride density gradients, monomorphic restriction profiles were obtained with Hae III , Hind III , Sau 3AI and Xbal . However, the restriction endonucleases Ava II and HinfIl proved informative. The distribution of four composite genotypes found within the Usk system was heterogeneous, and a fifth genotype appeared exclusively in an outgroup sample from the adjacent River Wye drainage. The source of the observed genetic variation is discussed in relation to estimated divergence times for Usk mtDNA genotypes and the stocking history of the catchment.     

Genetic variation among trout in the River Neretva basin, Bosnia and Herzegovina

Mitochondrial DNA haplotypes, characteristic of the Adriatic, Danubian and Atlantic lineages of brown trout Salmo trutta and of Salmo obtusirostris were found in trout inhabiting the River Neretva basin. With the exception of the one associated with softmouth trout, haplotypes were not correlated with operational taxonomic units based on phenotype. Nuclear DNA analysis identified four genetic assemblages corresponding to S. obtusirostris , different geographically confined autochthonous S. trutta populations, introduced S. trutta and a genetically heterogeneous group located between S. obtusirostris and S. trutta in the dendrogram of individuals, indicating the existence of hybrid swarms in the Neretva basin. Genetic assemblages corresponding to Salmo marmoratus and the recently proposed Salmo cf. montenigrinus were not detected. The presence of genetic intermediates indicates that the studied taxa are not completely reproductively isolated and that genetic stability has been either anthropogenically interrupted or not yet achieved among Neretva trout. This finding should be considered in management decisions since such an unstable community must be particularly susceptible to breakdown in genetic population structure as a result of hybridization between native and non-native introduced trout stocks.