Isolation and characterization of 49 polymorphic microsatellite loci for Decapterus maruadsi using SLAF-seq,and cross-amplifi cation to related species

Decapterus maruadsi is a commercially important species in China, but has been heavily exploited in some areas. There is a growing need to develop microsatellites promoting its genetic research for the adequate management of this ?shery resources. The recently developed speci?c-locus ampli?ed fragment sequencing(SLAF-seq) is an effcient and high-resolution method for genome-wide microsatellite markers discovery. In this study, 28 905 microsatellites(mono-to hexa-nucleotide repeats) were identi?ed using SLAF-seq technology, of which di-nucleotide was the most frequent(13 590, 47.02%), followed by mono-nucleotide(8 138, 28.15%), tri-nucleotide(5 727, 19.81%), tetra-nucleotide(1 104, 3.82%), pentanucleotide(234, 0.81%), and hexa-nucleotide(112, 0.39%). One hundred and thirty-two microsatellite loci(di-and tri-nucleotide) were randomly selected for ampli?cation and polymorphism, of which 49 were highly polymorphic and well-resolved. The average number of alleles per locus was 13.63, ranging from 4 to 25, and allele sizes varied between 110 bp and 309 bp. The observed heterozygosity( Ho) and expected heterozygosity( He) ranged from 0.233 to 1.000 and from 0.374 to 0.959, with mean values of 0.738 and0.836, respectively. The polymorphism information content(PIC) ranged from 0.341 to 0.941(mean=0.806).However, 12 loci deviated from Hardy-Weinberg equilibrium. Furthermore, transferability tests were also successful in validating the utility of the developed markers in ?ve phylogenetically related species of family Carangidae. A total of 48 microsatellite markers were successfully cross-ampli?ed in Decapterus macarellus, Decapterus macrosoma, Decapterus kurroides, Trachurus japonicus, and Selaroides leptolepis.The present microsatellites provided the ?rst known set of microsatellite DNA markers for D. maruadsi,D. macarellus, D. kurroides, and D. macrosoma, and would be useful for further population genetic and molecular phylogeny studies as well as help with the ?sheries management formulation and implementation of the understudied species.     

Development of microsatellite loci for two Agabus diving beetle species from the pooled DNA and testing their utility in mountain lake populations

Diving beetles (Dytiscidae) are the most speciose water beetle group, occurring on all continents except Antarctica. They inhabit various lotic and lentic habitats and play an important role in ecosystem functioning. In this study, we developed functional polymorphic microsatellites for two widely distributed species from one of the most diversified dytiscid genus Agabus: Agabus bipustulatus (Linnaeus, 1767) and Agabus cf. guttatus from the Agabus guttatus group sensu Foster and Bilton (1997). For microsatellites development, pooled DNA and NGS pyrosequencing were used. Microsatellites are still very useful genetic markers for studying recent population changes, but for dytiscids, highly diversified and ecologically important group of freshwater invertebrates, only 8 microsatellite loci are available for one North American species. To test utility of the developed markers, we used several populations of alpine lakes, situated in the Tatra Mountains (Western Carpathians). From the 60 tested markers, 13 loci for Agabus bipustulatus and 8 loci for A. cf. guttatus showed polymorphism. The number of alleles per locus varied from 2 to 10 and no significant linkage disequilibrium was observed. Observed/expected heterozygosity varied from 0/0.077 to 1/0.834 within populations of A. cf. guttatus and from 0/0.056 to 1/0.837 within populations of A. bipustulatus. The significant deviation from HWE was probably caused by presence of null alleles or undetected biological processes. Bayesian cluster analysis revealed differences in the cluster proportions, confirming applicability of the developed markers for future studies of population structure of both Agabus species.     

Timing,magnitude and geochemistry of major Southeast Asian volcanic eruptions: identifying tephrochronologic markers

We review the current knowledge about Southeast Asian volcanoes and their eruption histories, and focus on identifying tephrochronologic markers representing major explosive eruptions in order to further future palaeoclimate and volcanological studies. Forty-one volcanic edifices in Southeast Asia have been classified as large calderas by Whelley et al. (2015) and thus have, or are likely to have, produced large explosive eruptions with a Volcanic Explosivity Index (VEI) of 6–8. Unfortunately, only 20 such eruptions have known ages, spanning from 1.2 Ma to 1991 ad , and fewer have geochemical data that can be used for tephrostratigraphic correlations. Volcanic products from different geodynamic regions and different sources can generally be distinguished on major element plots (e.g. K₂O versus CaO) of matrix glass composition. However, the distinction of multiple eruptions from the same source often requires additional data such as trace element compositions of matrix glass and/or mineral compositions. Biotite, but also magnetite compositions (MgO and TiO₂ content in particular) appear to be very discriminating. Up to nine tuffs in addition to the three to four Toba tuffs can be utilised as widespread tephrochronologic markers and span a range from 1.2 to 1.6 Ma to recent. As only a few Holocene major eruptions have been well characterised and dated, many large calderas are still unstudied, and many distal tephra layers are still lacking a source, more tephrochronologic markers can certainly be defined in the future.     

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（0.265 375~0.301 915）的结果显示群体间的遗传分化微弱,未形成明显的遗传分化。因此,可认为本研究中真鲷增殖放流未对放流后混合群体造成明显的遗传学影响。本研究为今后真鲷增殖放流遗传监测提供了理论参考依据。     

有害藻华的宏条形码分析:机会与挑战

宏条形码分析（metabarcoding analysis）是通过对野外样本的分子标记（即条形码）进行PCR扩增、测序,并利用测序结果分析野外样本物种组成、物种相对丰度,及其时空动态变化。这项在近20年里逐步发展起来的分子技术,得益于DNA测序技术的快速发展,包括测序通量的提升和测序成本的降低,以及生物信息学分析方法的快速开发。基于可操作分类单元（operational taxonomic units,OTUs）分析方法,特别是最近的扩增子序列变异（amplicon sequence variants,ASVs）方法的开发,极大促进了宏条形码分析的应用。在世界及我国的海洋生态领域,宏条形码分析的应用还处于起步阶段。随着分析方法的日趋成熟,可适用于不同应用领域的分子标记不断增加,以及参考数据库的不断完善,宏条形码分析将释放出广阔的应用潜力。可以预期,宏条形码分析将在系统分析我国近岸海域有害藻华物种（及其他浮游生物物种）的组成和相对丰度中起关键作用,通过发现新物种,辨别隐存种,跟踪物种的生物地理学,进而帮助解析有害藻华暴发机理。     

东海赤潮高发区表层沉积物中部分脂类标记物的分布与来源

通过对2005年和2006年东海赤潮高发区表层沉积物部分脂类标记物（正构烷烃、脂肪酸等）的分析,初步探讨了表层沉积物有机物的来源。沉积物中正构烷烃的碳优势指数Icp值及姥鲛烷／植烷的质量比（Pr／Ph）普遍较低,而n-C16,n-C18的质量分数较高。分析表明,石油烃是东海赤潮高发区表层沉积物脂肪烃的主要成分。来源于细菌、海洋微藻和陆生高等植物的脂肪酸如直链饱和脂肪酸、支链饱和脂肪酸、不（多不）饱和脂肪酸等在2005～2006年间的组成和分布比较稳定：直链脂肪酸含量普遍较高,其次为支链脂肪酸和单不饱和脂肪酸,多不饱和脂肪酸含量相对较少。利用生物标记物分析表明,海洋自生生物源（细菌、海洋微藻等）是沉积物中脂肪酸的主要来源,陆源脂肪酸对东海赤潮高发区表层沉积物的贡献较小。     

4种养殖扇贝的群体遗传多样性及特异性AFLP标记研究

应用AFLP技术对我国4种主要养殖扇贝进行了遗传分析.虾夷扇贝、海湾扇贝、华贵栉孔扇贝、栉孔扇贝4种养殖扇贝群体中,种内遗传相似度依次分别为0.841 5,0.786 3,0.719 0和0.673 1,香侬氏指数分别为43.52,58.87,80.16和92.83,栉孔扇贝和华贵栉孔扇贝的遗传多样性水平明显高于海湾扇贝和虾夷扇贝;AFLP标记共享位点分布表明,在4种扇贝中栉孔扇贝与华贵栉孔扇贝之间的共享位点最多,同时4种扇贝的种间遗传相似度也以栉孔扇贝和华贵栉孔扇贝之间为最高(0.769 5),海湾扇贝和虾夷扇贝之间为最低(0.662 6),揭示所研究的几种扇贝中栉孔扇贝和华贵栉孔扇贝的遗传关系最近(遗传距离为0.262 1);找到了21个种内特异性AFLP标记和种间共享标记,可用于种质鉴定和分子辅助分类.     

皱纹盘鲍杂交F1代与亲本的RAPD标记及分离方式分析

应用RAPD标记技术对皱纹盘鲍杂交家系JC的双亲及3个F₁个体进行了分析,对JC家系在皱纹盘鲍遗传连锁图谱构建中的应用前景进行了初步评估,并分析了RAPD分子标记在JC家系F₁代中的分离方式及该家系的1对亲本及其子代个体的遗传结构.7条随机引物共扩增出41个分子标记,其中24个为多态性,占总数的58.5%;有14个分离标记可用于遗传连锁作图,有7个符合孟德尔独立分配定律,占总数的17.1%.2个标记与子代个体大小有一定的相关性,但其连锁关系仍有待于进一步研究.父母本之间的遗传距离为0.384 4,父本与子代间的距离为0.137 2,母本与子代间的距离为0.127 3;父本提供的分离标记在子代中的显性频率为0.47,母本为0.55.双亲之间的遗传距离较远,杂交产生的JC-F₁群体具有较高的杂合度(0.201 6),该结果初步表明皱纹盘鲍杂交家系JC的子1代即可作为作图群体应用于皱纹盘鲍的连锁图谱构建.     

不同地理品系卤虫的同工酶变异初步研究

利用聚丙烯酰胺凝胶电泳方法，对国内外不同生态地区的孤雌生殖和两性生殖卤虫进行了酯酶（ＥＳＴ）、四唑氧化酶（ＴＯ）和碱性磷酸酶（ＡＬＰ）同工酶变异分析。指出不同地理品系卤虫有其独特的ＥＳＴ和ＴＯ标志酶带；孤雌生殖卤虫具有与两性生殖卤虫显著不同的ＴＯ基本带型和ＡＬＰ标志带区。这些结果为卤虫地理品系的纯度鉴定，以及两种生殖方式卤虫的分类和鉴别提供了生化指标。     

EST-SSR标记的开发及其在南黄海浒苔研究中的应用

Ulva species can grow rapidly in nutrient-rich habitats causing green tides and marine fouling. A more complete understanding of the reasons behind these outbreaks is urgently required. Accordingly, this study attempts to use microsatellite markers based expressed sequence tag（EST） to analyze the genetic variation of several Ulva prolifera populations in the South Yellow Sea of China. Two hundred and thirty-eight SSRs were identified from 8 179 unique ESTs（6 203 newly sequenced and 1 976 downloaded from NCBI database） and 37 primer pairs were successfully designed according to the ESTs; 11 pairs were selected to detect the genetic diversity and relationship of 69 attached U. prolifera samples and 13 free-floating samples collected from coastal and off-coast areas of the South Yellow Sea. The results of cross-species transferability showed that six of the 11 EST-SSR primers could give good amplification in other five Ulva species and the average allele number was 4.67. Genetic variation analysis indicated that all 82 U. prolifera samples were clearly divided and most samples collected from the same site clustered together as a group in the dendrogram tree produced by unweighted pair-group mean analysis（UPGMA） method and the cluster results showed some consistency with the geographical origins. In addition, 13 free-floating samples（except HT-001-2） were grouped as a single clade separated from the attached samples.