|关键词||日本鳗鲡 群体遗传结构 本地适应性 微卫星 单核苷酸位点多态性|
探究生物不同地理群体的遗传结构，不仅可以加深对生物多样性的认识，也是合理有效管理生物资源的基础。目前对于日本鳗鲡（Anguilla japonica）群体遗传结构的研究大多基于中性遗传标记，本研究采用与基因相关的微卫星标记和基于全基因组扫描筛选的离散SNP标记开展研究，从新的角度解析日本鳗鲡的群体遗传结构。除了群体遗传结构的解析，适应性进化也是近几十年来进化生态学研究的热点。本地适应性是指本地群体的某些特征，使其相较于外来群体可更好地适应本地环境。一直以来都普遍认为，适应性进化是一个缓慢的过程，需要经过很长时间的积累，因此它可能不会对当前的生态过程造成影响。然而近年来发现，适应性进化可以发生在几个世代的时间尺度内。鳗鲡属鱼类随机交配的特征使它们成为研究微时间尺度上本地适应性问题理想的材料。欧洲鳗鲡（Anguilla anguilla）、美洲鳗鲡（Anguilla rostrata）的研究均已证明，尽管鳗鲡是随机交配物种，依然可以检测到其对本地环境适应的遗传学信号。对日本鳗鲡的本地适应性进行研究，将加深对于单一世代时间尺度内适应性进化的认识，也有助于深入理解全球气候变化对海洋鱼类的影响。从二十世纪八十年代开始，日本鳗鲡的种群衰退不断加剧。玻璃鳗（Glass eel）、黄鳗（Yellow eel），以及银鳗（Silver eel）的野生群体资源量均出现了严重衰退。在2016年公布的IUCN濒危物种红色名录中，日本鳗鲡已经被列为“濒危”。目前对于日本鳗鲡种群资源的保护已经迫在眉睫。解析日本鳗鲡的群体遗传结构将为其种群资源的管理和保护提供科学依据，而阐明日本鳗鲡对本地环境的适应机制有助于深入理解日本鳗鲡种群衰退的机制。
|其他摘要||Figuring out the genetic population structure within species can help understand the importance of biodiversity, and is also the basis on which we can accomplish scientific management of biological resources. Previous studies on the genetic population structure of the Japanese eel (Anguilla japonica) were based on neutral markers; our study aimed to dig this issue from a new perspective, using gene-associated microsatellite markers and outlier SNP markers resulted from whole-genome scan instead. Local adaptation of the genus Anguilla is another hot scientific issue. Populations can evolve traits that confer a Darwinian fitness advantage in their local habitat, due to the interaction between genotype and their local conditions. The process and the resulting pattern are termed “local adaptation”. It has long been accepted that adaptive evolution requires the accumulation of signature of natural selection for many generations, and it is too slow to influence contemporary ecological dynamics, which we now know is not always true. Evolution can happen within a few generations. Freshwater eels, of the genus Anguilla, are ideal materials for the study of contemporary local adaptation owing to their panmixic features. The case studies on the American eel (Anguilla rostrata) and European eel (Anguilla anguilla) detected signatures of local adaptation happening within single-generation time scale, which lighted the road for other Anguilla eels. We extended the study to the Japanese eel, the results would advance our understanding on local adaptation that happens within single-generation time scale and provide some clues on how to deal with the globally changing environment. The resource of the Japanese eel has been declining since 1980s. The wild population of glass eel, yellow eel and silver eel has decreased dramatically. The Japanese eel was ranked as “Endangered” by the IUCN red list published in 2016. Figuring out the population structure of the Japanese eel is the basis of scientific management and protection, and a good understanding of the local adaptation can help understand the mechanism of the fluctuation of the Japanese eel resource.|
The main results of the study are as follows:
1. Developing gene-associated microsatellite markers
We developed gene-associated microsatellite markers for the Japanese eel. A total of 24 loci were polymorphic. The 24 loci were polymorphic in all sampled localities. Among these loci, a total of 18 loci were developed based on the genes under selection in North Atlantic eels (European eel and American eel), and the other 6 loci were developed from transcript sequence randomly selected from database. The average number of alleles per locus across populations ranged from 4.846 to 29.231. Observed and expected mean heterozygosities per sample across loci ranged from 0.675 and 0.746 to 0.716 and 0.769, respectively. Twenty-nine out of 312 cases showed significant departure from HWE after Bonferroni correction (α= 0.05, K = 13). No linkage disequilibrium was detected after Bonferroni correction (α= 0.05, K = 276). Eight loci showed evidence of null alleles in more than three samples (not in all samples).
2. Developing SNP markers
Twelve glass eels from each of the two populations were chosen for RAD-Seq (Restriction site-associated DNA sequencing). After quality filtering, the reads were sorted according to their unique index sequences and aligned to the draft genome of the Japanese eel using BWA version 0.5.9. SNP calling was conducted using a conservative Bayesian approach as implemented in the package SAMTOOLS. We identified 73,557 putative SNPs in total. ARLEQUIN version 3.5 were utilized to detect SNPs potentially affected by diversifying selection between the two geographic localities DD and SS. We detected 250 outlier SNPs with FST value located above the 99.5% quantile of simulated distribution, among which 85 loci could find annotation match using BLAST2GO. We then performed KASPar (KBiosciences Competitive Allele-Specific PCR genotyping system) genotyping for 373 specimens from 12 populations in 96 loci (85 outlier loci with annotation match + 11 outlier SNPs without annotation match).
3. Genetic analysis based on the gene-associated microsatellite markers
The global insignificant FST value of -0.001 (95% CI: -0.002 < FST < 0.000) indicated that there was no significant genetic differentiation among these samples. None of the pairwise FST values were significant after FDR correction (α= 0.05, K = 78). In STRUCTURE analysis, the optimal value of ΔK occurred at K = 5. However, all samples showed similar patterns when K = 5, suggesting no genetic structure. Mantel test showed no significant pattern of IBD among 13 geographic samples (R2 = 4.634e-03, P = 0.6233). All measures of differentiation were accordant with a panmixic scenario.
4. Detecting signatures of local adaptation based on SNP markers
The appearance of several significant FST values indicated that adaptive genetic divergence should exist among different geographic populations of the Japanese eel. The STRUCTURE results showed that the 12 populations could be divided into 2 groups: Group I (MA, MY and MJ) and Group II (populations from Mainland China). And the clustering results were confirmed by DAPC analysis.
The locus AVPY01361442_1313 and locus AVPY01361442_1313 were found to be significantly associated with environmental parameters by both BAYENV2 software and SAMBADA software. The locus AVPY01361442_1313 was associated with SMC6 gene, and locus AVPY01361442_1313 was associated with taar13c gene. The function of DNA repair played by SMC6 gene might be a way of dealing with the unstable external environment to keep the chromosome in a stable state. And taar13c gene might play a role in the diamine sensing, which affects the response to diamine of glass eels of the Japanese eel; however, to further understand the function of taar13c gene, more experiments on odor-driven behavior of glass eels are needed.
The present study confirmed the hypothesis of panmixia and detected the signature of local adaptation in the Japanese eel. Based on outlier SNPs, we detected the adaptive divergence between island-source populations and continent-source populations. The results of the study could provide basic data needed by scientific management and protection on the Japanese eel resource.
|于磊. 日本鳗鲡（Anguilla japonica）群体遗传结构及本地适应性机制研究初探[D]. 北京. 中国科学院大学,2017.|
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