基于线粒体Cytb基因全序列的松江鲈群体遗传结构分析
POPULATION GENETIC STRUCTURE OF ROUGHSKIN SCULPIN TRACHIDERMUS FASCIATUS BASED ON THE MITOCHONDRIAL CYTb SEQUENCE
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摘要: 对松江鲈(Trachidermus fasciatus Heckel)中国沿海7个群体和日本有明海群体的线粒体Cytb基因全序列进行了测定、分析。结果显示: 47个个体共检测到31个单倍型, 8个群体均呈现出较高的单倍型多样性(0.60-1.00)和较低的核苷酸多样性(0.0005-0.0041)的特点。AMOVA分析结果及单倍型邻接关系树和单倍型网络关系图均显示松江鲈分为中国和日本两个世系, 而中国世系的7个群体未呈现出明显的地理遗传结构。基于核苷酸Kimura双参数替代模型计算得出的中国和日本两个世系的净遗传距离, 再参照其他硬骨鱼类线粒体Cytb基因2%/Ma(百万年)的分歧速率, 推测松江鲈中日两个世系间分化时间约为41万年前。对中国世系进行群体历史动态分析, 中性检验结果均为负值且显著, 核苷酸不配对分布呈单峰型, 表明松江鲈中国世系曾发生过群体扩张, 其扩张时间大约为12万年前。Abstract: Roughskin sculpin, Trachidermus fasciatus is a catadromous fish, and it is distributed along the coast of Northwest Pacific. The fish population has been greatly decreased in recent years due to degradation of habitats, water pollution and dam construction. In order to protect the fish population, it is necessary to study genetic structure of the fish population, which is very important for fishery management and conservation. Forty seven individuals used in this study were collected from 8 sampling locations in the coast of China and Japan, i.e., Hangzhou Bay (HZB), Wendeng (WD), Rongcheng (RC), Dongying (DY), Qinhuangdao (QHD), Dalian (DL), Dandong (DD) and Ariake Sea. The mitochondrial cytochrome b (Cytb) gene sequence of T. fasciatus was amplified by polymerase chain reaction (PCR) technology and sequenced on an automatic sequencer with both forward and reverse primers. The sequences were analyzed by using some software, which included Dnastar, Arlequin3.1, Mega4.0, Modeltest3.7 and Paup4.0. The results were as follows: the Cytb sequence of each specimen was 1141 bp and used for genetic diversity analysis. There was neither insertion nor deletion found among 38 mutations of nucleotide acids and 31 haplotypes were found among 47 individuals from 8 sampling sites. All 8 populations were characterized by high haplotype diversity (0.60-1.00) and low nucleotide diversity (0.0005-0.0041). The analysis result of molecular variance (AMOVA), median-networks and NJ phylogenetic trees showed that there was large genetic differentiation between those two regions, while there was no genetic variance among populations of the Chinese lineage. Net average genetic distance between two lineages was 0.82%. Applying divergence rate of Cytb gene sequence, the divergence of lineage China and Japan occurred about 410000 years ago. The mismatch distribution of pairwise nucleotide and the negatively selective neutrality test suggest that a recent population expansion had occurred in Chinese lineages, and the time was estimated to be about 120000 years before present (during the late Pleistocene). Two distinct lineages found in T. fasciatus were probably related to the Pleistocene coastal glaciations and the long geographical distance. Dispersal ability, coastal currents and the population expansion may be responsible for the homegeneity among the Chinese populations.
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Keywords:
- Trachidermus fasciatus /
- Cytb gene /
- Complete sequence /
- Genetic structure /
- Population expansion
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