|关键词||小黄鱼 日本鳗鲡 群体遗传结构 群体基因组 本地适应性|
|摘要||小黄鱼（Larimichthys polyactis）和日本鳗鲡（Anguilla japonica）是中国乃至东亚地区非常重要的海洋经济鱼类，然而受全球气候变化及过度捕捞等人类活动的影响，中国沿海的渔业资源正面临全面衰退的严峻现状，该两种海洋鱼类也不例外，尤其是日本鳗鲡已经被世界自然保护联盟红色名录收录，状态定为“濒危”。群体遗传学（population genetics）可以用来检测物种的遗传变异水平和群体遗传结构，探讨各种进化因素的影响机制，以及阐明种群适应环境的遗传学机制，为渔业资源的管理和保护提供重要的理论依据。前期关于小黄鱼和日本鳗鲡的群体遗传学研究由于受到遗传标记种类及数目的限制，基于不同类型的遗传标记所获得的研究结果存在一定的分歧甚至相互矛盾。因此，为了更好的保护和利用这两种重要的海洋渔业资源，亟需通过更加精细的分子遗传标记对这两种海洋鱼类群体遗传特征进行解析。在本研究中，我们分别基于较高密度的微卫星位点和基于简化基因组测序技术（RAD-seq）筛选的全基因组层面的SNP位点，对小黄鱼和日本鳗鲡进行了群体遗传结构和本地适应性方面的研究。|
|其他摘要||The small yellow croaker（Larimichthys polyactis ）and the Japanese eel（Anguilla japonica）are two of the most economically important marine fishery species in China and East Asian countries, however, the abundance of these species had severely decreased due to overfishing as well as other anthropogenic factors. Especially for the Japanese eel, the abundance of Japanese eel had sharply decreased more than 90% since 1970s, and in March 2014, the Japanese eel was included in the IUCN（International Union for the Conservation of Nature）Red List of Threatened Species, with a current status as ‘endangered’（http://www.iucnredlist.org/details/166184/0）.Population genetics can be used to detect the genetic structure of marine fish, thereby providing important insights into the sustainable management and utilization of fisheries resources. Limited source of markers has somehow constrained genetic studies of L. polyactis and A. japonica, and previous studies based on various types of genetic markers have obtained discrepant or even conflicting results. Hence, it is urgently needed to assess population genetic structure, genetic diversity, and possible regions of genome under selection for L. polyactis and A. japonica, in order to better manage and conserve these two species.|
The main results are as follows:
1. Seventeen polymorphic microsatellite loci were developed and characterized for L. polyactis using magnetic beads enrichment procedure. The number of alleles per locus ranged from 4 to 21, and the observed and expected heterozygosities varied from 0.4583-0.9167 and 0.7154-0.9566, respectively. Two loci showed significant deviations from Hardy–Weinberg equilibrium, most likely because of null alleles. These highly polymorphic nuclear markers would be useful for studies of genetic diversity and population genetic structure of the highly exploited L. polyactis
2. Using fifteen microsatellites markers, we noted a non-significant decrease in genetic diversity between different time periods, and no obvious change in allelic richness was observed. Measures of population structure indicated substantial temporal genetic changes according to population differentiation tests（FST）, the PCoA, STRUCTURE and the AMOVA analysis. To our knowledge, this is the first study that showed the temporal genetic variation of the L. polyactis. The temporal genetic variation of L. polyactis populations might be attributed to genetic drift, fishing-induced or ecological changes for this species.
3. Fifteen microsatellite loci were used to estimate genetic diversity and population structure of fifteen samples along China coast. High genetic diversity and low genetic differentiation among populations were detected with all microsatellites. No evidence of isolation by distance and recent genetic bottleneck events was detected. However, outlier analyses indicated that the locus Lpol03 might be under directional selection, which showed a strong homology with Grid2 gene encoding the glutamate receptor δ2 protein（GluRδ2）. Based on Lpol03, two distinct clusters were identified by both STRUCTURE and PCoA analyses, suggesting that there were two overwintering aggregations of L. polyactis, and these results provided new perspectives on the population genetic structure and migratory routine of L. polyactis.
4. Based on restriction site-assosciated DNA（RAD）sequencing technology, we analyzed 264 Japanese eel（Angullia japonica）individuals from eleven geographic locations. A total of 4,149,717,848 Raw Reads were generated after sequencing, and 45,552,012 SNPs were called using SAMTOOLS. After the quality filtering, a total of 37,700 SNPs were retained, the identified 37,700 SNPs were widely distributed across the draft genome of the Japanese eel. The overall low genetic differentiation found（FST=0.002012, P > 0.05）indicated that most of the genome is homogenized by gene flow. Results of ADMIXTURE revealed that all individuals were grouped into a single cluster when using all the SNPs. While the results of DAPC and NETVIEW suggested that there might some substructure for the 11 populations, which might be attributed to genetic drift for this species.
5. We tested for local selection by searching for increased population differentiation using FST-based outlier tests and by testing for significant associations between allele frequencies and environmental variables, and a total of 355 outlier SNPs were detected. Functional categorization of the annotated sequences involved in signaling, response to stimulus, metabolic process, biological regulation, catalytic activity and development process, etc.. The KEGG pathway analysis showed some of putative targets of local selection, including genes in several important pathways such as Wnt signaling pathway, Oocyte meiosis, calcium signaling pathway and MAPK signaling pathway.
These results will be useful to inform conservation and management decisions for these two species.
|刘炳舰. 小黄鱼和日本鳗鲡群体遗传结构及本地适应性研究[D]. 北京. 中国科学院大学,2017.|