Concordance of microsatellite and mitochondrial DNA markers in detecting genetic population structure in the boring giant clam Tridacna crocea across the Indo‐Malay Archipelago

Mitochondrial DNA (mtDNA) is a single, usually non‐recombining locus, and often uniparentally inherited. Therefore, its ability to reveal recent gene flow among populations is usually questioned. In this study, the genetic population structure of 16 populations of Tridacna crocea (n = 366) from the Indo‐Malay Archipelago (IMA) was examined with 10 microsatellite markers and compared to previous studies using mtDNA, in order to test if the revealed population structure was congruent between the two marker systems. The results showed that the genetic population structure revealed by the two marker systems was mostly congruent, with a high correlation between cytochrome c oxidase subunit I (COI) and microsatellites. The studied populations could be divided by both marker systems as follows: (i) Eastern Indian Ocean, (ii) Central IMA, and (iii) Western Pacific. Populations in the Central IMA showed high gene flow. However, populations in the Java Sea (Karimunjava, Pulau Seribu) were grouped into a separate cluster by mtDNA analysis, while this grouping was not detected by microsatellites. It was also noteworthy that there is obvious heterozygosity deficiency in most of the populations, which may be caused by null alleles, inbreeding or population expansion. Overall, these results indicate that the mitochondrial COI gene is applicable for population genetic analysis and precise recovery of connectivity patterns of giant clams. Therefore, the combination of mtDNA and nuclear DNA markers can lead to a more complete understanding of population genetics. Moreover, this study is expected to facilitate fully displaying the population genetic structure of giant clams combining with other researchers' results.     

基于微卫星标记的真鲷放流群体与增殖海域群体遗传变异比较分析

真鲷(Pagrus major)是中国沿岸海域重要的经济种类,增殖放流作为修复真鲷渔业资源、恢复自然群体的方法,现已在中国被广泛地应用。然而,将大量人工繁育的苗种投入自然海域中,可能会对自然群体造成一定程度的遗传学影响。因此,在开展真鲷增殖放流的同时,应进行遗传监测。本研究使用7对真鲷微卫星标记,对2017年于防城港沿岸海域开展的真鲷增殖放流进行遗传监测,对比分析了真鲷亲体、放流真鲷苗种以及放流后混合群体的遗传多样性。研究结果表明,真鲷亲本群体与真鲷放流群体的等位基因丰度(13.525 3,16.428 6)和期望杂合度(0.792 7,0.814 5)没有明显的差异,表明在苗种繁育过程中,没有出现遗传多样性丢失的现象。真鲷放流群体和放流后混合群体的期望杂合度(0.814 5, 0.822 8)、等位基因丰度(16.428 6, 16.755 5)相似,表明真鲷放流群体和放流后混合群体处于相同的遗传多样性水平。3个群体的多态信息含量为0.768 8～0.805 5,表明3个群体均具有较高的遗传多样性。群体间遗传分化指数(0.016 667)和遗传距离(0.265 375～0.301 9...     

基于线粒体控制区序列的黄海日本鳀(Engraulis japonicus)的群体遗传结构*

遗传多样性和群体遗传结构是研究群体动态变化的重要内容, 也是种质资源评估与保护的基础。日本鳀(Engraulis japonicus)是我国东部近海的重要鱼种, 具有重要的生态价值和经济价值。文章利用线粒体控制区全序列分析了黄海海域4个地理群体(北黄海北部、北黄海南部、南黄海北部和南黄海中部)日本鳀的遗传多样性、种群遗传结构和历史动态变化。结果显示, 131个样品检测到了126个单倍型, 且4个群体的单倍型多样性均很高, 其中北黄海南部群体的最低(0.995±0.009), 南黄海中部群体的最高(1.000±0.014)。而核苷酸多样性均较低, 为0.010±0.005 ~ 0.011±0.006。主成分判别分析(DAPC)和遗传分化系数F_st表明4个群体无明显的群体分化现象, 群体间的遗传同质性水平高, 分子方差分析(AMOVA)也显示分子变异基本来自于群体内, 并且没有明显的群体遗传结构。贝叶斯系统发育树分析发现, 黄海日本鳀有2个谱系, 谱系1和谱系2的分化时间为0.701Ma前, 可以追溯到更新世期间; 进一步中性检验和核苷酸错配分布分析表明这2个谱系可能发生过群体扩张。贝叶斯天际线图则显示黄海鳀鱼的有效群体数量在0.150Ma前发生了明显的下降。     

基于线粒体细胞色素b的秋刀鱼种群遗传结构的研究

秋刀鱼主要分布在西北太平洋亚热带到温带水域中,是一种资源量较高的上层洄游性鱼类。为了对秋刀鱼的遗传结构进行研究,2016年6月-11月,在38°38′-44°31′N,146°36′-162°26′E海域随机取145条秋刀鱼,取其肌肉与DNA、PCR以及测序后获得421 bp基于线粒体细胞色素b (Cytb)基因的DNA序列。分析结果显示,145条序列中共发现了15个单倍型,单倍型多样性指数h=0.258±0.049,核苷酸多样性π=0.000 87±0.007 56。计算得出Tajima′s D与Fu′s Fs均呈负值并且绘制的核苷酸不配对曲线呈现单峰,可得出秋刀鱼群体经历了种群扩张。Nm值表明4个采样点的秋刀鱼群体之间存在频繁的基因交流,AMOVA分析结果显示97.22%的遗传变异来自群体内,结合遗传分化系数Fst得出群体遗传分化水平较低。单倍型网络图呈现星状拓扑结构、系统发育树分枝不明显均显示地域性差异不显著。研究发现秋刀鱼群体遗传多样性较低,需对其进行合理保护。     

Microsatellites reveal fine‐scale genetic structure of the Chinese surf clam Mactra chinensis (Mollusca,Bivalvia, Mactridae) in Northern China

As a commercially important fisheries resource in East Asia, the Chinese surf clam Mactra chinensis has experienced severe population declines in the past decades, probably due to over‐exploitation. To provide scientific bases for fisheries management and artificial breeding, we investigated genetic variation and population structure of Mactra chinensis in Northern China using microsatellites. Samples collected from eight localities throughout natural habitats of the species in Northern China were genotyped. Nine microsatellites revealed high allelic diversity with 14–36 alleles per locus. Observed and expected heterozygosity varied from 0.593 to 0.945 and from 0.638 to 0.958, respectively. Pairwise F_ST values indicated that all population pairs had small but significant genetic differentiation. A Mantel test showed statistically significant correlations between genetic distance and geographical distance, indicating that genetic differentiation of the Chinese surf clam conformed to a pattern of isolation‐by‐distance. Cluster analysis using neighbor‐joining separated the eight populations into three groups. The three areas of low gene flow identified by barrier analysis corresponded with local oceanographic features, suggesting that marine currents and peninsulas play an important role in population structuring of this species.     

Assessment by microsatellite analysis of genetic diversity and population structure of Enhalus acoroides from the coast of Khanh Hoa Province, Vietnam

Seagrass beds degraded significantly since the last century on both, global and local scale. The seagrass species Enhalus acoroides (Linnaeus f.) Royle is a common species found in almost all marine ecosystems including bays, lagoons and around offshore islands in tropical regions of the West Pacific. It was shown that genetic diversity is an essential indicator of the conditions of ecosystems. In the present study, microsatellite markers were used to assess the genetic diversity and population structure of six distinct seagrass beds along the coast of the Khanh Hoa Province, Vietnam. The results indicate that the genetic diversity of the populations in the open sea is higher than in the lagoon. Seagrass beds occurring in disturbed sites show reduced genetic diversity. The fixing index value (F_ST) depicts a relatively high genetic structure among populations. Structure analysis clusters the populations into open sea and lagoon populations and cluster analysis and AMOVA indicate a significant difference between the two groups. There are low but non-significant positive correlations between geographic and genetic distances. The different habitats of the open sea and the lagoon are probably responsible for forming two groups.     

The influence of environmental variability of a coastal lagoon ecosystem on genetic diversity and structure of white seabream [Diplodus sargus (Linnaeus 1758)] populations

As coastal lagoons serve as nursery areas for some marine and estuarine fish, selective pressures of these brackish or hypersaline lagoons may influence the genetic structure of species and populations. We examined spatial and temporal genetic patterns at eight microsatellite loci in white seabream [Diplodus sargus (Linnaeus 1758)] recruits from the Mar Menor (Southeast Spain) and compared these loci with those in coastal populations from the open sea, observing a high degree of genetic diversity and spatio‐temporal genetic stability. However, the results suggest the presence of subpopulations or genetic substructures in the Mar Menor D. sargus population that could be interpreted as a homogeneous mixture of individuals from three differentiated subpopulations in the Mediterranean and evidence of the Wahlund effect. It also suggests that D. sargus adults return to their original spawning habitat, thus conserving the genetic differences among the respective populations over time. Overall, this study demonstrates the importance of the Mar Menor coastal lagoon as a nursery area for the conservation of genetic diversity of D. sargus populations.     

Genetic diversity and population structure of the golden cuttlefish,Sepia esculenta (Cephalopoda: Sepiidae) indicated by microsatellite DNA variations

The golden cuttlefish, Sepia esculenta Hoyle, 1885 (Cephalopoda: Sepiidae) is a valuable and important fishery resource for China, Japan and Korea. This fishery has experienced severe population decline largely due to overexploitation in past decades. To provide guidelines for fisheries management, we estimated genetic diversity and population structure across four locations along the coast of Japan and one location in China (a total 281 individuals) using nine microsatellite DNA loci. Sepia esculenta showed high genetic variability with mean allele richness ranging from 15.8 to 21.4, and mean heterozygosity from 0.80 to 0.90. Weak but significant genetic differentiation was present and the F_ST value was 0.020 across all five populations. The useful information obtained in this study will offer insights into how to fine‐tune conservation and fishery management measures for this species and resource in the future.     

微卫星标记在大菱鲆(Scophthalmus maximus L.)家系系谱印证中的应用研究

用8个微卫星标记对大菱鲆7个人工选育家系进行了系谱鉴别和遗传多样性研究。8个微卫星位点的平均多态信息含量为0.6721,平均杂合度为0.7206。8个微卫星位点在7个家系分析中,共检测到40个等位基因,每个位点的等位基因数在38个之间,每个位点平均有5个等位基因。根据已知亲本及子代基因型,成功的推断出了7个家系中缺失亲本的基因型。在双亲未知的情况下8个微卫星位点累积排除概率是97.07%,已知单亲时累积排除概率达99.63%。用UPG-MA法对7个家系的137个子代个体进行了聚类分析,90.5%同一家系的子代个体能完全聚类到一起,分类结果与系谱来源基本一致。微卫星标记可以为大菱鲆混养家系进行亲权鉴定和系谱构建提供技术支持。     

形态学和SNP标记分析马氏珠母贝杂交子代及其亲本群体的遗传结构

马氏珠母贝是重要的海水养殖贝类, 为了探究繁育亲本及其子代的遗传结构和关系, 本研究运用多元性形态学和SNP标记对马氏珠母贝母本深圳群体、父本海南群体和其杂交子代F1的外部形态和分子遗传结构进行分析。结果发现, 3个群体的综合判别率为72%, F1和母本群体的形态差异最小, 父本群体与母本、F1的形态差异较大。采用HRM法 (high resolution melting) 应用4个SNP位点对这3个群体进行分型, 3个群体的平均观测杂合度H_o和期望杂合度H_e分别为0.2110~0.2879和0.3317~0.4685, F1的杂合度高于两个亲本; 平均多态信息含量PIC值为0.2643~0.3556, 呈现中等程度遗传多样性。F1与母本之间的基因流N_m最大(7.7701), 遗传距离最小(0.0546), 亲缘关系最近; 两个亲本之间的N_m最小(1.9662), 遗传距离最大(0.1759)。rs8位点可以判别两个亲本群体, 可作为特异性的标记。该结果可以为马氏珠母贝群体遗传结构鉴别、育种群体管理提供指导。     

Study on genetic diversity and resource conservation of amphioxus (Branchiostoma balcheri Gray) population

1 Introduction Branchiostom a belcheri G ray (am phioxus) is aprecious m arine species listed in the nationalprotectedanim als ofsecond class (H uang etal., 1999). Itbe-longs to the subphylum cephalochordata ofthe phylumvertebrata. A m phioxus is the ancestor of vertebrates5×108 a ago, and is a typical transitionalsam ple ofevolution from invertebrates to vertebrates. The re-search of am phioxus,therefore,is ofgreatim portanceboth for anim al taxonom y and organic evolution(N ozakiand G or…     

尼罗罗非鱼Oreochromis niloticus、奥利亚罗非鱼O.aureus和红罗非鱼O.sp.群体遗传多样性的比较

用9对微卫星引物对尼罗罗非鱼Oreochromis niloticus、奥利亚罗非鱼O.aureus和红罗非鱼O.sp.群体的遗传变异进行了比较研究。在3个群体109个个体中共检测到60个等位基因,3个群体的平均等位基因数分别为4.11、1.33和3.44,平均观测杂合度分别为0.528、0.056和0.491,平均期望杂合度分别为0.644、0.091和0.526,平均多态信息含量分别为0.580、0.077和0.466。杂合子偏离度D值分别为0.148、0.222和0.044,表明3个罗非鱼群体存在不同程度的杂合子缺失。卡方检验表明3个群体的大部分位点偏离Hardy-Weinberg平衡,存在遗传漂变现象。群体间遗传分化显著(遗传分化指数FST在0.329到0.656之间,P<0.01)。尼罗罗非鱼和红罗非鱼群体间的遗传距离最小(0.47)。上述分析表明,尼罗罗非鱼的遗传多样性最高,奥利亚罗非鱼的遗传多样性最低,群体间分化显著。表明尼罗罗非鱼和红罗非鱼尚具有一定的选育潜力,而奥利亚罗非鱼遗传多样性低,不利于选择育种,需要引进新的种群。     

基于线粒体控制区的中国近海竹荚鱼种群遗传结构和种群历史动态分析

竹荚鱼(Trachurus japonicus)是中国近海主捕鱼种之一, 在海洋食物网中扮演了重要角色, 然而环境污染和过度捕捞导致其出现种群数量衰退以及个体趋于小型化等现象。为了解中国近海竹荚鱼的种群遗传格局, 文章以线粒体DNA控制区为遗传标记研究了东海大陆架、福建近海和南海北部湾竹荚鱼群体的遗传结构以及种群历史动态。结果表明, 中国近海竹荚鱼整体呈现高单倍型多态性(H_d=0.998±0.001)和高核苷酸多态性(π=0.01259±0.00041)的遗传多样性特征。单倍型网络图呈现为星形辐射状的单一谱系, 利用最大似然法构建的系统进化树也未发现谱系分化。不同海区地理群体的分子方差分析显示东海群体和南海北部湾群体间无遗传分化, 遗传变异主要来源于群体内部(99.39%)。中性检验和核苷酸歧点分布分析结果暗示各海区竹荚鱼群体(东海、南海北部湾)以及整个群体均经历过近期的种群扩张。中国近海竹荚鱼群体呈现为遗传均匀的种群结构, 可以作为一个单一的种群加以管理, 人类高强度捕捞压力尚未影响其种群恢复潜力。     

马氏珠母贝家系遗传结构的微卫星分析

利用6个微卫星位点研究了9个马氏珠母贝(Pinctada fucata)养殖家系的遗传结构,为后续育种工作提供了指导。从60对引物中筛选出6对能够稳定扩增且多态性较好的引物。6个微卫星位点在9个家系中共检测到17个等位基因,每个位点等位基因数(A)为2~4个,平均2.833个。6个位点在9个家系上的有效等位基因数(Ne)平均值为2.030~2.632,平均杂合度观测值(Ho)为0.4306~0.6354,平均杂合度期望值(He)为0.4380~0.5962。家系间遗传分化系数(FST)为0.0749。采用NJ法进行聚类分析显示,9个家系分为明显的两支,根据遗传距离计算结果, F7和F9家系之间的遗传距离最近, F11与F12家系遗传距离最远。结果表明,9个家系的遗传多样性和遗传分化处于中等水平,可以考虑F11与F12家系杂交,以期获得较好的杂种优势, F11自交培育出遗传稳定的优良家系。     

方斑东风螺3个选育世代遗传多样性和遗传结构的微卫星分析

采用12个多态性微卫星标记对方斑东风螺(Babylonia areolata)泰国选育系TF₄~TF₆连续3代选育群体的遗传多样性与遗传结构进行了分析。3个群体的多态信息含量分别为0.730、0.717和0.708,均高于0.5,表现出较高的多态性。平均等位基因数(A)、有效等位基因数(A_e)、观测杂合度(H_o)、期望杂合度(H_e)和Shannon’s信息指数(I)的变化范围分别为11.667~12.583、6.334~6.915、0.658~0.672、0.737~0.787和1.837~2.003,整体呈降低趋势,但差异并不显著(P>0.05)。分子方差分析结果显示,群体间的遗传变异仅占总变异的0.95%;群体间的遗传分化系数(F_st)介于0.00569~0.01324,处于低等分化水平(F_st<0.05)。主坐标分析和STRUCTURE分析结果显示,3个群体呈现出相似的遗传背景和遗传结构。以上研究结果表明,经过连续多代的人工选育,方斑东风螺选育群体保持着较高的遗传多样性水平,遗传变异和遗传分化水平较低,遗传结构趋于稳定,仍具有较高的遗传选育潜力。