51. Population structure, demographic history and local adaptation of the grass carp
- Author
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Jianjun Fu, Gen Hua Yue, Yubang Shen, Le Wang, Jiale Li, Xiaoyan Xu, and School of Biological Sciences
- Subjects
0106 biological sciences ,Carps ,Genotyping Techniques ,lcsh:QH426-470 ,Demographic history ,Evolution ,lcsh:Biotechnology ,Population ,SNP ,Aquaculture ,Balancing selection ,Population structure ,Polymorphism, Single Nucleotide ,01 natural sciences ,Evolution, Molecular ,03 medical and health sciences ,lcsh:TP248.13-248.65 ,Genetic variation ,Genetics ,Animals ,Selection, Genetic ,education ,Selection (genetic algorithm) ,Demography ,030304 developmental biology ,Local adaptation ,0303 health sciences ,Genetic diversity ,education.field_of_study ,Diversity ,Genome ,biology ,Biological sciences [Science] ,biology.organism_classification ,Grass carp ,lcsh:Genetics ,Genetic Loci ,Evolutionary biology ,Grass Carp ,Research Article ,010606 plant biology & botany ,Biotechnology - Abstract
Background Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture. Results We used 43,310 SNPs to infer the population structure, evidence of local adaptation and sources of introduction. The overall genetic differentiation of this species was low. The native populations were differentiated into three genetic clusters, corresponding to the Yangtze, Pearl and Heilongjiang River Systems, respectively. The populations in Malaysia, India and Nepal were introduced from both the Yangtze and Pearl River Systems. Loci and genes involved in putative local selection for native locations were identified. Evidence of both positive and balancing selection was found in the introduced locations. Genes associated with loci under putative selection were involved in many biological functions. Outlier loci were grouped into clusters as genomic islands within some specific genomic regions, which likely agrees with the divergence hitchhiking scenario of divergence-with-gene-flow. Conclusions This study, for the first time, sheds novel insights on the population differentiation of the grass carp, genetics of its strong ability in adaption to diverse environments and sources of some introduced grass carp populations. Our data also suggests that the natural populations of the grass carp have been affected by the aquaculture besides neutral and adaptive forces. Electronic supplementary material The online version of this article (10.1186/s12864-019-5872-1) contains supplementary material, which is available to authorized users.
- Published
- 2019