我国沿海缢蛏群体遗传结构的mtDNA-COⅠ分析

采集了我国沿海共计9个缢蛏(Sinonovacula constricta)地理群体的197个样本,分别是北部组群的3个群体:辽宁省庄河群体(ZH),天津市汉沽群体(HG),山东省海阳群体(HY);中部组群的3个群体:江苏省盐城群体(YC),上海市崇明县东滩群体(DT)和堡镇群体(BZ);以及南部组群的3个群体:浙江省宁波群体(NB),浙江省台州群体(TZ)以及福建省宁德群体(ND)。利用线粒体COⅠ标记分析了9个群体的遗传多样性和遗传分化。结果表明,在共计197个个体中检测到125个单倍型和96个变异位点,核苷酸多样性指数位于2.1764～7.4970之间,其中中部组群的群体遗传多样性指数最高。AMOVA分析结果显示,组间遗传变异量占总变异的80.27%,18.74%来自于群体内,只有0.99%来自于组内群体间。群体间遗传分化系数位于0.0219～0.8706之间,不同群体间具有一定的遗传分化,尤其是中部群体与其他群体间遗传分化值达到了0.8以上,为极高度分化。遗传距离和聚类结果显示,北部3群体和南部3群体首先聚在一起,之后与中部3群体聚类。     

Genetic evidence for multiple geographic populations of the giant mottled eel <Emphasis Type="Italic">Anguilla marmorata</Emphasis> in the Pacific and Indian oceans

Anguillid eels have been believed to have a unique catadromous life history completed within a particular ocean current system, and consequently to have extraordinary population structures, with each species comprising a single, virtually panmictic population with a species-specific spawning area far offshore. The giant mottled eel Anguilla marmorata is enigmatic in this respect because it is widely distributed from East Africa to the central South Pacific, where several different current systems exist, and apparently must have multiple spawning areas. To address this issue, the population structure was examined through the mitochondrial (mt) DNA analysis of 162 individuals collected from ten localities representing the overall distributional range. Nucleotide sequencing of a 626-bp segment in the control region of the mtDNA revealed 151 haplotypes, and these were clustered into several major groups supported by high bootstrap probabilities. Sequence differences among geographic samples revealed the existence of five geographic populations around North Pacific, Madagascar, Sumatra, Fiji, and Tahiti. Genetic differentiation among the populations in the Southern Hemisphere was supported by examination of nuclear DNA with amplified fragment length polymorphism (AFLP) analysis performed on 76 individuals from four sampling localities in the Southern Hemisphere. The distribution pattern of five populations was closely associated with the water-mass structure of oceans and major current systems. This observation suggests a hypothesis that present population differentiation in A. marmorata might have resulted from the establishment of new population-specific spawning sites in different oceanic current systems as the species colonized new areas, as its unique catadromous life history of anguillid eels.This revised version was published online in February 2005 with corrections to the repetition of the 1st authors name.     

Genetic diversity of introduced populations of the water hyacinth biological control agent Eccritotarsus catarinensis (Hemiptera: Miridae)

Genetic bottlenecks can be deleterious to populations. In biological control, agent populations may be subject to severe bottlenecks during selection, importation and while in culture. The genetic variability of two collections of the water hyacinth biological control agent Eccritotarsus catarinensis Carvalho (Hemiptera: Miridae) was measured using Inter-simple Sequence Repeats (ISSR) and mtDNA cytochrome oxidase I (COI) sequences. The first collection (Brazilian) went through a bottleneck of a single gravid female, while the second collection (Peru) originated from 1000 individuals and has been maintained at a large size in culture. Two naturalised South African populations from the Brazilian collection were also sampled (Nseleni and Mbozambo). Polymorphism for ISSR was high in the Peruvian and two naturalised samples, but much less so in the Brazilian sample. The Peruvian population was shown to be highly differentiated from the Brazilian and its naturalised populations by high values of F_ST and Nei’s genetic distance, as well as in a Multidimensional Scaling (MDS) plot and an unrooted neighbour joining tree derived from Jaccard’s coefficient of similarity. In addition, sequencing of the COI region of the mitochondrial DNA revealed only two haplotypes, one Brazilian and one Peruvian, with a 5.2% sequence divergence, suggesting that recombination and not mutation is the cause of most variation in the ISSR regions. The results suggest that substantial genetic variation may be retained or recovered after a bottleneck. This may mitigate deleterious effects that are a concern for the fate of biological control agents after release.     

Synthesis, biological, and theoretical evaluations of new 1,2,3-triazoles against the hemolytic profile of the Lachesis muta snake venom

The current treatment used against envenomation by Lachesis muta venom still presents several side effects. This paper describes the synthesis, pharmacological and theoretical evaluations of new 1-arylsulfonylamino-5-methyl-1H-[1,2,3]-triazole-4-carboxylic acid ethyl esters (8a–f) tested against the hemolytic profile of the L. muta snake venom. Their structures were elucidated by one- and two-dimensional NMR techniques (¹H, APT, HETCOR ¹J_CH and ⁿJ_CH, n = 2, 3) and high-resolution electrospray ionization mass spectrometry. The series of triazole derivatives significantly neutralized the hemolysis induced by L. muta crude venom presenting a dose-dependent inhibitory profile (IC₅₀ = 30−83 μM) with 1-(4′-chlorophenylsulfonylamino)-5-methyl-1H-[1,2,3]-triazole-4-carboxylic acid ethyl ester (8e) being the most potent compound. The theoretical evaluation revealed the correlation of the antiophidian profile with the coefficient distribution and density map of the Highest Occupied Molecular Orbitals (HOMO) of these molecules. The elucidation of this new series may help on designing new and more efficient antiophidian molecules.     

Genetic diversity and population structure of spottedtail goby (Synechogobius ommaturus) based on AFLP analysis

Larval dispersal may have an important impact on genetic structure of benthic fishes. To examine population genetic structure of spottedtail goby Synechogobius ommaturus, samples from five different locations of China and Kunsan population in Korea were analyzed by using amplified fragment length polymorphism (AFLP) technology. A total of 253 bands were identified from 91 individuals by 5 primer combinations and the percentage of polymorphic bands was 43.87%. The average gene diversity was 0.0794 ± 0.1470 and Shannon’s information index was 0.1279 ± 0.2138. The pairwise F_st values ranged from 0.022 to 0.201. The results of AMOVA analysis indicated that 90.54% of the genetic variation contained within populations and 9.46% occurred among populations. The gene flow estimates (Nm) demonstrated that different gene flow existed among populations from 0.994 to 11.114. No significant genealogical branches or clusters were recognized on the UPGMA tree. The results support the hypothesis that larval dispersal ability can be responsible for the genetic diversity and population structuring.     

云南中华按蚊的遗传变异和种群结构

为了掌握云南省各地中华按蚊种群间的遗传变异和种群结构特征,测序并分析了采自云南9个样本点5个种群组的89头中华按蚊的线粒体COII基因。结果表明这些中华按蚊种群的COII基因序列平均单倍型多样性指数和核苷酸多样性指数分别为h=0.933,π=0.00406,共有51个变异位点,占分析的739个碱基总数的6.9%;定义了39个单倍型,有2个频率最高的单倍型H1和H9,分别占个体序列数的20.2%和12.4%;系统发育分析表明单倍型与地理位置没有明显的对应关系,单倍型网络图显示大部分单倍型分布没有明显的亲缘地理格局,主要以单倍型H1、H9、H4、H33和H2为中心呈星状分布,但元江和元阳构成的种群组(YU)单倍型存在明显地域分布特征;AMOVA结果表明种群组间遗传变异为12.58%,达到显著水平(P=0.04888),地理种群组间具有明显种群遗传结构。不同地区两两种群组间的Fst值和Nm值显示大部分种群组间存在基因交流,没有形成明显的遗传分化,但YU种群组和其他种群组间缺乏明显的基因交流,这主要是因为哀牢山的阻隔,使云南东西部形成两种不同的气候,产生了明显的遗传分化;歧点分布图显示为明显单峰分布,中性检测结果均为显著负值,说明云南省的中华按蚊种群在近期经历过复杂的种群扩张事件。掌握中华按蚊遗传多样性及分化特征,对中华按蚊及疟疾控制具有重要的作用。     

Genetic structure of chukar partridge ( Alectoris chukar) populations in the Longdong Loess Plateau, China

This study used polymerase chain reaction (PCR) and dideoxy direct sequencing methods to analyze the genetic structure of the chukar partridge (Alectoris chukar) in the Longdong Loess Plateau, northwestern China. A total of 491 nucleotides of mitochondrial DNA from the control region gene were sequenced for 78 chukar partridges from eight different populations. The 24 variable positions defined 25 haplotypes. The high gene flow (Nm=3.75) implied little genetic differentiation between the eight populations. All the populations shared the haplotype C_1, which suggested that they all came from a common ancestor. The 25 haplotypes were spread through the populations, but could be clustered into two groups. The haplotype similar index between the two groups was only 0.15, with a genetic distance of 0.43%. The genetic variation was significantly different between the two groups, which had been isolated for all of recorded history. The genetic structure of chukar partridge populations in the Plateau appears to be the result of the synergistic effect of a glacier, along with debris flow and human activities since the middle of the Pleistocene.Communicated by F. Bairlein     

淮河水系日本沼虾群体遗传结构和系统演化的线粒体COI序列分析

测定了淮河水系17个日本沼虾(Macrobrachium nipponense)野生群体共248个个体的线粒体细胞色素氧化酶亚基I(COI)部分序列,获得623 bp核苷酸片段,包括48个变异位点,定义了31个单倍型,共享单倍型有12个,整体单倍型多样性和平均核苷酸多样性均处于中间水平。AMOVA分析表明,17个群体间的遗传分化系数Fst=0.041 3(P0.05),群体间遗传分化较小。Kimura 2-paramter遗传距离在五河与焦岗湖、花家湖及瓦埠湖群体间最大,为0.014,在高邮和邵伯湖群体之间最小,为0.003。MP系统树与单倍型进化网络关系图具有较高的一致性,31个单倍型被分为3个进化枝,其中一个进化枝主要以下游群体为主,另外2个进化枝主要以中游群体为主。群体中性检验、错配分析表明,淮河日本沼虾近期曾经历过种群扩张。     

Population genetic structure of striped mullet, Mugil cephalus, along the coast of China, inferred by AFLP fingerprinting

The striped mullet, Mugil cephalus, is an economically important species for both aquaculture and commercial fisheries in China. In this study, the amplified fragment length polymorphism (AFLP) technique was employed to analyze population genetic diversity and genetic distance between different populations with the aim of elucidating the population structure and gene flow of M. cephalus along the coast of China. A total of 230 fragments with 150–500 bp were identified from 118 individuals by five AFLP primer combinations. The polymorphic loci within populations varied from 46.52% to 64.78%, with an average of 53.91%, and the average heterozygosity from 0.1829 to 0.2282, with an average of 0.2074. The UPGMA phenograms of 118 individuals were constructed based on Dice similarity coefficients and four clusters were recognized. AMOVA analysis revealed that 60.7% of genetic variations were within populations and 39.3% between populations. The estimated genetic distance (φ_ST) value over all polymorphic loci across the six populations was 0.393 (p < 0.0010), indicating a strong population structuring. The pairwise φ_ST value ranged from 0.1112 to 0.5358, with an average of 0.3693. The population pairwise gene flows (average N_m = 0.73) are low. In addition, the result of the Mantel test showed that there was a significant correlation between geographic and genetic distances (r = 0.5434, p = 0.0050). It was speculated that there exist at least four distinct geographic populational subdivisions of M. cephalus along the Chinese coast. This research has provided new molecular data which will aid our understanding of the genetic structure of this species.     

人工砍伐后短柄枹栎的居群遗传重建研究

为探讨人工砍伐后短柄枹栎(Quercus glandulifera var.brevipetiolata Nakai)居群的遗传关系,采用SSR分子标记技术,对短柄枹栎天然林中的4个次生林居群的遗传多样性、遗传结构进行研究。结果表明,筛选的7对SSR引物在4个居群内共揭示了101个等位基因。砍伐后恢复20年(20YAH)的短柄枹栎居群的遗传多样性最高,而砍伐后恢复1年(1YAH)和10年(10YAH)的遗传多样性相对较低。从长远来看,试验地居民特殊的砍伐习惯不会造成短柄枹栎天然林遗传多样性的变化。     

An AFLP analysis of genetic diversity and structure of Caragana microphylla populations in Inner Mongolia steppe, China

Genetic diversity and structure of five natural populations of Caragana microphylla from the Inner Mongolia steppe were estimated using AFLP markers. Five pairs of primers generated a total of 312 bands among 90 individuals, with percentage of polymorphic bands (PPB) being 63% at the population level and 76% at the species level, respectively. The genetic diversity within populations was correlated significantly with the soil N:P ratio. AMOVA analysis revealed high genetic variations within populations (95.5%). The estimated number of migrants per generation (Nm) was 10.72, indicating a high level of gene flow among populations. There was no significant correlation (r = 0.36) between genetic distance and geographical distance. These results were discussed in terms of eco-geographical variations among populations, together with the life history traits and breeding system of the species. The knowledge obtained may have important implications for better conservation and wise use of the vegetation dominate by C. microphylla.     

Assessment of genetic diversity and population structure of Chinese wild almond, Amygdalus nana, using EST- and genomic SSRs

Amygdalus nana L., commonly known as wild almond, is an endangered wild relative of cultivated almond, which has great potential in almond crop breeding. In this study, we used microsatellite (SSR) loci derived from both expressed sequence tag (EST) and anonymous genomic sequence to explore the genetic diversity and population structure of A. nana in Xinjiang of China. Seven natural populations were collected across the whole distribution of A. nana in China, including populations from both inside (four populations) and outside (three populations) the established protected areas. A total of 22 and 19 alleles were detected from the seven pairs of EST and genomic SSR loci, respectively. Generally, the genomic SSRs showed lower levels of variation than EST-SSRs, which may partially due to the higher cross-species transferability in EST-SSRs than in genomic SSRs. The population-level genetic diversity (A = 1.84, P = 50.00%, H_o = 0.3491, H_E = 0.2271) was lower than cultivated almond and several wild fruit species with similar breeding system. Most of the genetic variation (82.16%) was partitioned within populations. In particular, the population collected from Tacheng County (outside the protected areas) had the highest levels of genetic diversity and had significantly different genetic constitution from other populations.     

Genetic diversity within and among the wild populations of Murraya koenigii (L.) Spreng., as revealed by ISSR analysis

Murraya koenigii (L.) Spreng., commonly known as curry leaf plant, is found in the different hilly regions of India. In the present study, fifty-nine accessions representing eight wild populations of M. koenigii were analyzed using thirteen ISSR primers. A total of 152 bands were amplified, out of which, 136 were polymorphic corresponding to 89.47% polymorphism across the accessions. The pairwise population genetic distances were calculated for all the populations that varied from 0.05 to 0.13 between the populations of M. koenigii. AMOVA and Nei’s genetic diversity analysis revealed higher genetic variations within populations than among the populations. The clustering of populations in the dendrogram was not in congruence with geographical affiliations. The results indicate that the ISSR method is sufficiently informative and powerful to estimate the genetic diversity in M. koenigii populations. As M. koenigii is an important wild plant genetic resource, therefore, information on genetic variability might be a potential source as breeding material for development of commercially valuable traits in M. koenigii plants.     

基于线粒体控制区的嘉陵裸裂尻鱼种群遗传结构分析

嘉陵裸裂尻鱼为青藏高原特有鱼类,近年来随自然地理气候的变迁和人类活动的影响,种群数量急剧减少。为了解嘉陵裸裂尻鱼的遗传背景以便更好的保护其遗传资源,本研究采用线粒体控制区部分序列变异,分析了嘉陵裸裂尻鱼6个地理种群的遗传结构和分布动态。在147尾个体中共发现17个变异位点,定义了14种单倍型,群体总的单倍型多样性较高为0.810,核苷酸多样性低为0.00698。AMOVA分析显示,44.29%的分子差异源于群体间,55.71%的分子差异源于群体内,群体间遗传分化极显著。Fst值统计检验表明,除宕昌群体和舟曲群体之间差异不显著外,其余两两群体之间Fst值统计检验均显著。基因流估计显示各群体间的基因流水平较高,遗传交流较频繁。Mantel test检验表明,嘉陵裸裂尻鱼种群之间遗传分化程度与地理距离存在显著相关。系统树和单倍型网络进化图显示,6个地理群体的单倍型按照嘉陵江水系和渭河水系形成两个大的类群。错配分布和中性检验表明嘉陵裸裂尻鱼群体在近期历史上群体大小保持稳定,未出现显著的种群扩张。根据本文所揭示的嘉陵裸裂尻鱼种群遗传结构特征,建议将分布在嘉陵江水系的嘉陵裸裂尻鱼作为一个整体进行保护,嘉陵裸裂尻鱼渭河种群属高度分化的单倍型类群,且遗传多样性极低,需对该种群进行优先保护。     

基于SSR标记的紫花风铃木群体遗传多样性分析

为揭示紫花风铃木(Handroanthus impetiginosus)的群体遗传变异特征,对广东省6市12个群体72份种质材料进行遗传多样性和群体遗传结构分析。结果表明,9对引物共扩增出123个等位基因位点,引物的平均多态信息量为0.754,具有较高的多态性。12个群体均具有较高的遗传多样性,群体间平均有效等位基因数为3.272个,平均Shannon指数为1.159。AMOVA分析表明群体间遗传分化程度相对较低,群体内遗传分化程度较高。群体的总体遗传分化系数为0.077,处于中等程度。基于Structure分析、主坐标分析和NJ聚类分析均可将12个群体分为2大类群,分组结果具有一定相似性,表明供试紫花风铃木群体遗传结构较为简单。这为紫花风铃木优良种质资源的利用、遗传变异和科学育种提供了理论参考。     

中国近海细鳞鯻线粒体控制区的遗传多样性

通过线粒体控制区序列的分析,研究采自中国南海及东海5个群体102尾细鳞鯻的遗传多样性。发现在962 bp序列中有205个变异位点,其中135个为简约信息位点,共定义102个单倍型。中国近海细鳞鯻总体呈现出较高的遗传多样性特征(Hd=1.000,Pi=0.022),其中博鳌最高(Hd=1.000,Pi=0.028),平潭最低(Hd=1.000,Pi=0.014)。不同地理群体间无明显分化,基因交流频繁(Fst=-0.014—0.041,P0.05);中性检验均为显著负值,推测在16.9万年—5.06万年前,即中-晚更新世出现种群扩张。系统邻接树和单倍型网络图均出现3个显著分化的谱系(谱系间Fst=0.508—0.698,P0.001;净遗传距离Da=0.024—0.031),且各谱系中均有不同地理来源的群体。3个谱系间分歧时间大约在1.07百万年—0.24百万年前,推测可能是更新世冰期边缘海的出现导致群体隔离而产生分化。谱系A(Lineage A)包含85.3%的个体,其总体遗传多样性较高(Hd=1.000,Pi=0.012),其中平潭最高(Hd=1.000,Pi=0.014),合浦最低(Hd=1.000,Pi=0.010);群体间Fst在-0.021—0.068之间,P0.005;AMOVA分析显示只有1.97%的变异来自于种群间,表明群体间也无明显分化;中性检验均为显著负值,推测在25.4万年—7.6万年前出现种群扩张。中国近海细鳞鯻主要受到中-晚更新世海侵和海退的影响而出现种群扩张使得谱系间发生二次接触,最终形成具有显著谱系结构但无地理分化的情况。     

Molecular phylogenetics and population structure of Sousa chinensis in Chinese waters inferred from mitochondrial control region sequences

Phylogenetic analyses of the genus Sousa were carried out across their geographic range and focused especially on the genetic variation patterns and population structure of Sousa chinensis in Chinese waters. The analyses were based on 287-bp of the mitochondrial control region from 122 Indo-Pacific humpback dolphins (Sousa chinensis) and two Atlantic humpback dolphins (Sousa teuszii). All specimens from China grouped together in a well-supported clade with high bootstrap (BS) and Bayesian posterior probability values (BPP), strongly suggesting that only one species of Sousa exists in China. Six haplotypes were identified in 65 individuals from Xiamen and Pearl River Estuary in China. The extremely low level of detected mtDNA genetic diversity strongly suggests a high priority in conservation of Sousa. The highly significant genetic differentiation between the two populations in Xiamen and Pearl River Estuary supports the designation of these two populations as separate management units (MUs) when designing management programs for this species.     

Genetic neighbourhood structure in a population of Picea abies L.

Summary Natural populations are currently the basic material for studying forest tree breeding, but little is known on the genotypic spatial structures in these stands. The use of gene markers, such as isozymes, leads to the determination of part of the allelic constitution of individuals. A method is presented here to estimate the degree of genetic relationship between any pair of genotypes. A French Picea abies population is analyzed by these means and a slight but significant correlation between estimated genetic relationship and topographic distance is found.     

Genetic structure of wild populations of the endangered Desert Pupfish complex (Cyprinodontidae: Cyprinodon)

Data from 10 microsatellite DNA loci were used to describe the genetic structure of the two extant species (Cyprinodon macularius and C. eremus) of the endangered Desert Pupfish complex of southwestern United States and northwestern Mexico. Variation at microsatellite loci was significantly correlated (Mantel test) with that of previous mtDNA results, both for the complex and for the relatively wide-ranging C. macularius alone. Both species showed unusually high levels of microsatellite diversity for non-marine fish (H _e = 0.84–0.93; A_R = 11.9–17.0). There was evidence (R _ST > F _ST) that the two extant populations of C. eremus have been isolated sufficiently long for mutation to contribute significantly to genetic divergence, whereas divergence among the nine assayed populations of C. macularius could be attributed to genetic drift alone. Correspondingly, 10% of the diversity in C. eremus was attributable to differences between the two populations, whereas, for C. macularius, only 2.7% was attributable to among-population variation. Within C. macularius, a small (0.8%), but statistically significant, portion was attributable to differences between populations in the Salton Sea area and those on the lower Colorado River delta. The two populations of C. eremus and five groups of populations of C. macularius are recommended as management units for conservation genetics management of the two species.     

Genetic population structure of miiuy croaker (Miichthys miiuy) in the Yellow and East China Seas base on mitochondrial COI sequences

The miiuy croaker (Miichthys miiuy) is an economically important fish species in China. However, information about population structure in this species is limited. In this study, the genetic diversity and population structure of four populations of Miichthys miiuy were investigated using a mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) segment of 599 bp. A total of 35 polymorphic sites, and 31 haplotypes were defined in 109 individuals. High levels of haplotype diversity (0.731 ± 0.047) and low nucleotide diversity (0.00278 ± 0.0019) were observed in miiuy croaker populations. The results of AMOVA and pairwise fixation index (F_ST) analysis did not indicate any significant genetic differentiation among populations obtained from four sites (P > 0.05). In addition, no significant genealogical branches or clusters were recognized in the NJ tree. Analysis of neutral evolution and mismatch distribution suggested that the miiuy croaker might have experienced a recent population expansion.