珍稀濒危植物夏蜡梅遗传多样性的ISSR分析

利用ISSR分子标记技术,对濒危植物夏蜡梅10个居群的遗传多样性进行了分析.结果表明:夏蜡梅种的遗传多样性较高,多态位点百分率为73.08%,Shannon指数为0.3097,Nei指数为0.1987;而居群水平的遗传多样性较低,多态位点百分率平均为23.65%,Shannon指数平均为0.1251,Nei指数平均为0.0839.AMOVA分子差异分析显示:居群间遗传分化程度高,57.11%的变异存在于居群间,42.89%存在于居群内,基因分化系数(G_st)为0.5779;居群间的基因流为0.3651.生境的片断化使居群间的基因流受阻,可能是导致居群间高遗传分化和居群水平低遗传多样性的主要原因.10个居群间的平均遗传距离为0.1471.利用UPG-MA法对10个居群进行聚类,结果是天台县内的2个居群、临安市内的8个居群各组成一大类群.     

Genetic structure and differentiation of four populations of Afghan Pika (Ochotona rufescens) in Iran based on mitochondrial cytochrome b gene

The population genetics of the Afghan Pika (Ochotona rufescens) was studied in Northern Khorasan Province, Iran. For prediction of the genetic differentiation of four populations, the DNA of mitochondrial cytochrome b of 32 individuals from four areas was sequenced and a Bayesian analysis based on the HKY model was constructed. In total, 15 polymorphic sites, 1125 conserved sites (98.7%) and 14 different haplotypes were found. The phylogenetic tree resulting from the Bayesian analysis and network analysis showed that all samples were clustered in two major groups and the haplotypes of the four populations did not separate geographically. An analysis of molecular variance (AMOVA) indicated that a large majority of the genetic variance was due to the variance within populations. The results of fixation indices showed significant genetic structure among populations in both methods. The pairwise F_st revealed that two northern populations have a significant genetic differentiation from two southern populations, but no significance pairwise F_st value was demonstrated between the closed populations. Nei's genetic distances between closed populations were not significant, while significant values occurred between distant populations. It seems that there is not a major discontinuity between populations of Afghan Pika based on cyt-b mitochondrial gene. However, phylogenetic analysis did not separate populations and a large majority of the genetic variance was found within populations. However, AMOVA analysis showed a significant level of genetic structure among populations (p?<?0.001) and between groups (p?<?0.5). It seems that these results suggest shallow genetic differentiation between populations of different geographic groups.     

山罗花和天柱山罗花四个居群的数值分析

对山罗花和天柱山罗花的4个居群的15项形态特征进行了数值分析。结果表明:形态性状在4个居群间均存在一定程度的变异,居群间变异系数的平均值从小到大排列为:天柱山居群(天柱山罗花)、天柱山居群(山罗花)、黄山居群(山罗花)、鹞落坪居群(山罗花);天柱山罗花与山罗花种间的形态差异已达到极显著水平,山罗花的3个居群间部分性状也具有极显著的形态差异;以形态特征为基础的Q-聚类分析可以把天柱山罗花和山罗花聚为两类,但山罗花(天柱山居群)和其他2个居群在较远处聚在一起,R-聚类分析发现了强正相关关系、弱正相关关系、弱负相关关系的性状。     

Assessment of allozyme variation among New Zealand populations of Gracilaria chilensis (Gracialiares,Rhodophyta) using starch-gel electrophoresis

New Zealand populations of Gracilaria chilensis are uniform in anatomical reproductive characteristics but vary morphologically and have been found to separate into two distinct groups with respect to agar methylation level, namely low (24–30%) and high (43–47%). To investigate the genetic variation within New Zealand populations of this species, 14 isozyme loci detected by starch-gel electrophoresis were examined in 17 wild populations from a wide range of localities, and in cultures derived from these populations. Five of these loci were polymorphic, but the genetic variation within populations was low: of the 17 populations examined, 15 were fixed at all loci (heterozygosity 0.000) and in the remaining two populations the observed heterozygosity was still low (0.004 and 0.011). The genetic distances between the populations ranged from 0.00 to 0.43. UPGMA cluster analysis separated the populations into two groups, a northern group and a group found throughout the country. Although these two groups do not correlate with the two groups based on agar methylation level at every locality, the correlation is sufficiently striking to merit further investigation.     

濒危植物资源冷杉遗传多样性研究

资源冷杉(Abies ziyuanensis)属松科(Pinaceae)冷杉属(Abies),是国家一级保护的濒危植物。利用RAPD分子标记对分布于广西资源县银竹老山和湖南省炎陵县大院的2个资源冷杉种群共54株进行了遗传多样性分析。用20个随机引物共扩增到126个位点,其中66个位点是多态性的,总的多态位点百分率为52.4％,在两个种群分别为33.6％和31。2％。Nei's基因多样性为0.312,Shannon信息指数为0.475,两个种群的遗传分化系数Gst为0.455。基于Nei's遗传距离进行了UPGMA聚类分析,结果两种群的样品彼此明显区分开来。分析结果表明资源冷杉种群内的遗传多样性较低,但两种群间的遗传分化明显。需要同时重视两分布地的资源冷杉的保护工作。     

Load of hereditary diseases in the populations of the Adyg autonomic district

Comparative analysis of the loads of hereditary diseases in two ethnically different populations coexisting in the Adyg national district was performed. The modes of inheritance of diseases studied were tested by segregational analysis. The results obtained demonstrated that the load of autosomal-recessive diseases in the populations of the Adyg national district is higher than that in Russian population, while the load of autosomal-dominant diseases is similar in two populations. This difference in the level of the loads appear to be connected with genetic structure of the populations studied. Regressional analysis of relations between loads and the level of inbreeding in the Adyg population showed the explicit interrelation between the load of autosomal-dominant diseases and the Fst correlation coefficient being 0.89.     

Divergence and gene flow between the East Sea and the Southeast Atlantic populations of North Pacific light fish Maurolicus japonicus Ishikawa

In the present study, we examined the divergence time and the magnitude of gene flow between two distantly separated populations of North Pacific light fish Maurolicus japonicus, one in the southern part of the East Sea (off Korea) and the other in the Southeast Atlantic Ocean (off Namibia). The mitochondrial 16SrDNA sequences (524 base pairs) obtained from the two populations were analyzed using the isolation with migration (IM) coalescent method as well as the conventional F _ST statistic and a phylogeographic method. A significant nonzero F _ST value (0.176, P<0.05) indicated genetic differentiation between the two populations. The low level of nucleotide diversity compared to the moderately high level of haplotype diversity implied that the populations have experienced a bottleneck followed by rapid growth in both populations. IM analysis suggested that these two populations most likely split approximately 500?C800 K years ago during the Pleistocene climatic oscillations and that gene flow has occurred unidirectionally from the Southeast Atlantic population to the East Sea population. Nested clade phylogeographic analysis supports restricted gene flow between the two populations.     

中间球海胆、光棘球海胆及杂交F1代（中间球海胆♀×光棘球海胆♂）群体遗传多样性AFLP分析

应用AFLP技术对中间球海胆、光棘球海胆及杂交F1代（中间球海胆♀×光棘球海胆♂）群体的遗传多样性进行了分析。结果表明,4对引物共扩增得到272个位点,其中269个多态位点,总的多态位点比例为98.89%。3个群体的香农多样性指数分别为：0.2331±0.1273、0.2005±0.1385和0.2625±0.1067。群体内遗传相似度分别为：0.6876±0.0523、0.6501±0.0548和0.6552±0.0553。分子方差分析（AMOVA）结果表明,变异来源有25.39%来自群体间,有74.61%来自群体内,群体内的遗传多样性比较丰富。尽管杂交海胆在表型上可以明显分成两种类型,但是通过AFLP统计的遗传距离进行的个体聚类却随机聚在一起,不能分成两个群体。     

An electrophoretic investigation of populations of Atherina boyeri Risso, 1810 and A. presbyter Cuvier, 1829 (Teleostei: Atherinidae): genetic evidence in support of the two species

The data obtained using electrophoresis strongly support the specific status of Atherina boyeri Risso, 1810 and A. presbyfer Cuvier, 1829, and thuscontradict the recently proposedsynonymyof the two species. Four populations of A. boyeri and six populations of A. presbyter were assayed for 11 enzymes and general protein using muscle and liver extracts. Eight of the 11 enzymes were shown to be polymorphic at the 95% level. Sixteen loci, encoding 40 putative alleles were consistently resolved in all 10 populations.
The two species were fixed for different alleles at the EST-3 locus. At the G3PDH locus. with the exception of two heterozygotes, all individuals of each species were also homozygous for different alleles. At the PGM locus the common allele was unique to each species.
The mean Nei's genetic distance ( ), over all loci, calculated between populations of A. boyeri (= 0.10 ± 0.06); between populations of A. presbyter ( = 0.02 0.02) and between populations of A. boyeri and A. presbyter ( = 0.42 0.09) indicated the separateness of the two species.
UPGMA cluster analysis based on genetic distances produced a dendrogram whose principal dichotomy resulted in the formation of two clusters. The ordination of populations in the UPGMA cluster analysis strongly reflected the geographic distribution of populations in both species.     

采用微卫星标记分析10个双峰驼群体的遗传变异和群体间的遗传关系

为从分子水平上对我国双峰驼(Camelus bactrianus)群体的遗传多样性、群体间遗传关系、群体遗传分化及近交情况进行全面、系统地研究,为双峰驼种质资源保护和新品种培育提供基础数据,本文利用18对微卫星引物,分析了我国9个双峰驼群体和1个蒙古双峰驼群体的遗传多样性和遗传关系。结果显示:10个群体均具有较高的遗传多样性,共检测到242个等位基因,平均等位基因数为13.44,平均有效等位基因数为4.18,平均观察杂合度(Ho)为0.5528。10个群体间存在显著的遗传分化,有9.6%的遗传变异来自群体间,90.4%的遗传变异来自群体内部的个体间。聚类分析、主成分分析和群体遗传结构分析结果都表明10个群体被分成2个明显的分支,新疆4个群体单独聚为一类,剩下的6个群体聚为一类。这一结果可能与它们的地理分布和群体间的地理屏障有关。     

Extinct Birds

A preliminary analysis of the phylogeographic pattern of the two main African populations of Lesser Flamingo Phoenicopterus minor from East and southern Africa was carried out to evaluate possible gene flow. A fragment of mitochondrial DNA encoding the NADH dehydrogenase subunit 2 gene (ND2) was sequenced in 27 specimens from these two populations and 11 haplotypes were identified. The phylogenetic analyses, based both on distance and parsimonious methods (neighbour joining and maximum parsimony), showed a homogeneous clade with a low level of genetic distance (0.26% ± 0.12 SD), which was also evidenced by the minimum spanning network method. The mismatch distribution analysis suggested a sudden demographic expansion from a single ancestral population. This latter result is also reinforced by the presence of few ancestral haplotypes, by the high level of haplotype diversity (0.83) and the low level of nucleotide diversity (0.0015–0.0017). These data support the belief of field ornithologists for restricted interchange between the two populations determined by the geographical distance between the two populations and lack of any observations of movement between them, but with evidence of changes in each population's numbers, giving the concept of a permeable geographic barrier.     

Genetic characterization and phylogeography of the wild boar Sus scrofa introduced into Uruguay

The European wild boar Sus scrofa was first introduced into Uruguay, in southern South America during the early decades of the last century. Subsequently, and starting from founder populations, its range spread throughout the country and into the neighbouring Brazilian state Rio Grande do Sul. Due to the subsequent negative impact, it was officially declared a national pest. The main aim in the present study was to provide a more comprehensive scenario of wild boar differentiation in Uruguay, by using mtDNA markers to access the genetic characterization of populations at present undergoing rapid expansion. A high level of haplotype diversity, intermediate levels of nucleotide diversity and considerable population differentiation, were detected among sampled localities throughout major watercourses and catchment dams countrywide. Phylogenetic analysis revealed the existence of two different phylogroups, thereby reflecting two deliberate introduction events forming distantly genetic lineages in local wild boar populations. Our analysis lends support to the hypothesis that the invasive potential of populations emerge from introgressive hybridization with domestic pigs. On taking into account the appreciable differentiation and reduced migration between locales in wild boar populations, management strategies could be effective if each population were to be considered as a single management unit.     

西藏牦牛线粒体DNA 的遗传多样性及系统进化分析

为从分子水平上探究西藏牦牛类群的遗传多样性、亲缘关系,本研究测定了日多牦牛、类乌齐牦牛、丁青牦牛、错那牦牛、隆子牦牛、仲巴牦牛、聂荣牦牛、申札牦牛等8 个西藏牦牛类群共328 头牦牛mtDNAD-loop区序列,分析其多态性,构建系统进化树。结果表明:本次测定的西藏牦牛mtDNA D-loop 区序列长度为 887 - 895 bp,共检测到135 个变异位点,其中单态突变位点52 个,简约信息位点83 个。在328 个个体中共检测出91 种单倍型,平均单倍型多样性(Hd)、平均核苷酸多样性(π)分别为0. 884、0.010 27,显示西藏牦牛具有丰富的遗传多样性。8 个类群间平均遗传距离为0.011;日多牦牛与错那牦牛间遗传距离最小(0. 006);类乌 齐牦牛与隆子牦牛间遗传距离最大(0.015)。系统进化分析显示西藏牦牛可分为两大类,错那牦牛是较纯的牦牛类群,其它牦牛类群在进化过程中出现相互交流的情况。     

Genetic variation of Avicennia marina (Forsk.) Vierh. (Avicenniaceae) in Vietnam revealed by microsatellite and AFLP markers

Genetic variation of Avicennia marina in the costal area of Vietnam was examined using microsatellite and AFLP markers. By using five microsatellite loci a total of 21 alleles were detected. The average number of alleles per locus per population ranged from 1.667 to 3.000. The observed heterozygosity varied from 0.180 to 0.263, with an average of 0.210 indicating relatively low level of genetic variation comparing to the previous studies on A. marina in the worldwide range. The expected heterozygosity was larger than the observed heterozygosity leading to positive inbreeding coefficients in all the six populations. Highly significant departures from Hardy-Weinberg Equilibrium were detected in four populations. AFLP analysis revealed a total of 386 loci, of which 232 (60.1%) were polymorphic. In congruent with microsatellite markers relatively low levels of genetic variation were detected at both gene and nucleotide levels (H = 0.086; pi = 0.0054). Reduced level of genetic variation was found in the central population, and in the southern populations. Both microsatellite and AFLP markers revealed large genetic differentiation (F(ST) = 0.262 and 0.338, respectively) indicating strong genetic structure among regional populations. Pairwise genetic distance by AFLP showed two populations in the north and the other two in the south are closely related each other.     

华中特有珍稀植物裸芸香的AFLP遗传多样性分析

采用选择性扩增片段多态性(AFLP)方法对华中特有单种属植物裸芸香(Psilopeganum sinense)的8个自然居群的遗传多样性进行了检测与分析。结果表明:裸芸香的遗传多样性较低,且居群内遗传多样性显著低于物种水平遗传多样性。筛选出的5对引物共得到180个位点,76个为多态位点,多态位点百分率为42.2%,8个居群多态位点百分率为:3.3%～16.7%,居群平均多态位点百分率为9.4%;8个居群Nei多样性指数为0.01987～0.06987,Shannon’s多样性指数为0.0197～0.0816。居群间分化系数Gst=0.5069,居群间基因流为0.2432,不足以维持居群间的基因交流及现有的遗传结构。AMOVA分析表明总遗传变异的13.17%存在于4个地理区域之间,50.45%存在于地理区域内的居群间,36.38%的遗传变异存在于居群内个体间。NTSYS分析表明遗传距离与地理距离不存在相关关系。UPGMA聚类结果表明长江南北两岸的居群并没有产生明显分化。最后,分析了裸芸香的濒危原因并提出了有效的保育措施。     

Genetic variation in Arabidopsis suecica and its parental species A. arenosa and A. thaliana

Random amplified polymorphic DNA (RAPD) markers were used to estimate the level of genetic variation in Swedish accessions of the allopolyploid Arabidopsis suecica and its parental species A. thaliana and A. arenosa. The results showed clear differences among the three species with respect to the level of variation. A. arenosa was highly variable, A. thaliana showed a moderate level of variation whereas A. suecica was much less variable than the two other species. An extended analysis covering 19 Swedish populations of A. suecica corroborated the low level of variation in this species, yet 16 unique phenotypes were observed. No isolation by distance was observed. When the genetic variation was partitioned among and within populations of A. suecica, the results showed that the majority of the variation (81%) occurred among populations. This result is interpreted as a strong indication that A. suecica is autogamous in nature.     

中国杯萼海桑遗传多样性的ISSR研究

杯萼海桑(Sonneratia alba J.Smith.)是海桑科红树植物,在我国分布于海南岛的东海岸.本文采用简单序列霞复区间扩增(ISSR)分子标记技术对分布于海南岛的杯萼海桑的4个天然居群和东寨港红树林自然保护区引种的一人工居群共100个个体进行了遗传变异分析.11个引物共扩增出133条带,其中103条具多态性,多态位点百分率为77.44%.在居群水平上相对较低,多态位点百分率为51.88%～65.41%,平均为57.74%.期望杂合度、香农信息指数在物种水平上分别为0.227 1和0.348 9;在居群水平上分别为0.1 83 7和0.227 5.依据Gst值,杯萼海桑绝大多数遗传变异发生在居群内的个体间(81.02%),18.98%的遗传变异发生在居群间.AMOVA分析也表明了类似的遗传结构.居群间平均遗传一致度为0.934 2.依据Nei(1972)的遗传距离对不同居群进行UPGMA聚类,将居群分为两组,来自三亚(SY)和陵水(LS)的居群聚为一类;东寨港引种栽培的人工居群(DZ)和琼海(QH)、文昌(WC)的居群聚为另一类.Mantel检验表明,遗传距离与地理距离呈极显著相关.     

Genetic variation and clonal diversity of Bromus ircutensis Kom. in the Otingdag sandy land detected by ISSR markers

Genetic variation and clonal diversity of nine populations of Bromus ircutensis Kom. from the Otingdag sandy land were investigated using Inter Simple Sequence Repeat (ISSR) markers. A total of 102 bands were amplified by using II ISSR primers chosen for the study. Among those 99% were polymorphic indicating high level of genetic variation at the species level with a mean genetic diversity (H) of 0.292 and Shannon information index (1) of 0.450. Percentage of polymorphic loci (PPL) of nine populations was 76.48% on average, which provides more evidence of considerable genetic variation at the population level. AMOVA analysis revealed that total genetic variation was higher within populations (87.06%) than between populations (12.94%), which is mainly the result of the extensive gene flow (Nm = 1.682) among B. ircutensis populations. UPGMA cluster analysis divided the nine populations into two groups. There was significant or moderate negative correlations between genetic diversity parameters (PPL, H, 1) and longitude or latitude. Mantel test also showed a significant correlation between geographical distance and genetic distance (r = 0.681, p = 0.002). Our findings indicated that distribution of B. ircutensis populations was influenced by geographical and ecological factors. Clonal diversity was also high with 108 individuals identified by 11 ISSR primers being all of different genets. Our results provide a molecular basis for sustainable management and conservation ofB. ircutensis in the study area.     

Genome-wide analysis of Hanwoo and Chikso populations using the BovineSNP50 genotyping array

Hanwoo and Chikso are classified as Korean native cattle breeds that are currently registered with the Food and Agriculture Organization. However, there is still a lack of genomic studies to compare Hanwoo to Chikso populations. The objective of this study was to perform genome-wide analysis of Hanwoo and Chikso populations, investigating the genetic relationships between these two populations. We genotyped a total of 319 cattle including 214 Hanwoo and 105 Chikso sampled from Gangwon Province Livestock Technology Research Institute, using the Illumina Bovine SNP50K Beadchip. After performing quality control on the initially generated datasets, we assessed linkage disequilibrium patterns for all the possible SNP pairs within 1 Mb apart. Overall, average r² values in Hanwoo (0.048) were lower than Chikso (0.074) population. The genetic relationship between the populations was further assured by the principal component analysis, exhibiting clear clusters in each of the Hanwoo and Chikso populations, respectively. Overall heterozygosity for Hanwoo (0.359) was slightly higher than Chikso (0.345) and inbreeding coefficient was also a bit higher in Hanwoo (??0.015) than Chikso (??0.035). The average F_ST value was 0.036 between Hanwoo and Chikso, indicating little genetic differentiation between those two breeds. Furthermore, we found potential selection signatures including LRP1B and NTRK2 genes that might be implicated with meat and reproductive traits in cattle. In this study, the results showed that both Hanwoo and Chikso populations were not under severe level of inbreeding. Although the principal component analysis exhibited clear clusters in each of the populations, we did not see any clear evidence that those two populations are highly differentiated each other.     

海南岛红树植物海桑遗传多样性的ISSR分析

海桑 (Sonneratia caseolaris)是海桑科红树植物 ,在我国仅天然分布于海南万宁、琼海、文昌等地。采用 ISSR分子标记技术对所有天然种群和海南东寨港红树林自然保护区引种的人工种群共 4个种群 86个个体进行了遗传变异分析。 11个引物共扩增出 2 39条带 ,其中 194条具多态性 ,多态位点百分率为 81.17%。在种群水平上多态位点百分率 4 0 .5 9%～ 5 0 .2 1% ,平均值为4 5 .71%。 Nei的基因多样性、Shannon信息指数在物种水平上分别为 0 .2 10 0和 0 .32 5 6 ,在种群水平上平均值分别为 0 .14 6 8和0 .2 2 10。 Nei的遗传分化系数 Gst和 AMOVA分析表明种群间已发生了较高的遗传分化。种群间的遗传一致度为 0 .90 11。估测的种群间的基因流为 0 .5 787。依据 Nei的遗传距离对不同种群进行 U PGMA聚类 ,聚类结果为横山种群 (HS)和东寨港种群(DZG)聚在一起 ,万宁种群 (WN)和琼海种群 (QH)聚为一类。Mantel检验表明遗传距离与地理距离之间有一定的正相关 ,但不显著。种群遗传多样性与环境因子间的相关性分析表明 :海桑种群遗传多样性水平与各环境因子间相关性均不显著。因东寨港引种种群的遗传多样性明显低于天然种群 ,为保护遗传多样性 ,应加强对琼海、万宁种群的就地保护和迁地保护工作。