Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences
This study was performed by using D-loop region sequences to investigate genetic diversity and population structure across eight representative groups of M. nipponense from south to north China. Eight populations comprising a total of 144 individuals were from Songhua River (SHJ), Yellow River (HH),...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-04-01
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| Series: | Aquaculture Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352513422000825 |
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| author | Wenyi Zhang Sufei Jiang Khamis Rabii Salumy Zhongya Xuan Yiwei Xiong Shubo Jin Yongsheng Gong Yan Wu Hui Qiao Hongtuo Fu |
| author_facet | Wenyi Zhang Sufei Jiang Khamis Rabii Salumy Zhongya Xuan Yiwei Xiong Shubo Jin Yongsheng Gong Yan Wu Hui Qiao Hongtuo Fu |
| author_sort | Wenyi Zhang |
| collection | DOAJ |
| description | This study was performed by using D-loop region sequences to investigate genetic diversity and population structure across eight representative groups of M. nipponense from south to north China. Eight populations comprising a total of 144 individuals were from Songhua River (SHJ), Yellow River (HH), Yangtze River (YZ), Pearl River (ZJ), Weishan Lake (WSH), Taihu Lake (TH), Bosten Lake (BH) and Wanquan River (WQH). The 1130-bp D-loop region exhibited a higher content of A + T (79.04%) than C + G (20.95%). In addition, 239 variable sites and 73 haplotypes were detected. The population haplotype diversity (h) were ranked as follows: WQH (0.9810) > YZ (0.9571) > WSH (0.9429) > ZJ (0.8901) > SHJ (0.8791) > HH (0.8693) > TH (0.8667) > BH (0.3684); the nucleotide diversity (π) were ranked as: WQH (0.0607) > YZ (0.0299) > SHJ(0.0236) > WSH(0.0221) > TH(0.0132) > ZJ(0.0131) > HH(0.0118) > BH(0.0011). The pairwise FST values reached highly significant level (P < 0.01). The gene flow (Nm) results revealed abundant gene exchange between WSH and TH (11.057), HH (7.226) and ZJ (6.255). The maximum likelihood (ML) phylogenetic tree showed that 73 haplotypes were divided into two main branches. Only the haplotypes of the BH population clustered together, indicating the low genetic diversity of this population, whereas a high diversity was observed in other populations. Network results were consistent with phylogenetic tree results. The analysis of mismatch distribution showed that all eight populations presented multimodal distribution. Fu’s Fs test and Tajima’s D tests were applied to determine the population expansion. All eight populations showed non-significant negative values, which suggests that the M. nipponense population in China did not experience population expansion. |
| first_indexed | 2024-12-22T20:42:34Z |
| format | Article |
| id | doaj.art-dfbb4beccd0942c69e046ddbde4a32f2 |
| institution | Directory Open Access Journal |
| issn | 2352-5134 |
| language | English |
| last_indexed | 2024-12-22T20:42:34Z |
| publishDate | 2022-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Aquaculture Reports |
| spelling | doaj.art-dfbb4beccd0942c69e046ddbde4a32f22022-12-21T18:13:18ZengElsevierAquaculture Reports2352-51342022-04-0123101086Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequencesWenyi Zhang0Sufei Jiang1Khamis Rabii Salumy2Zhongya Xuan3Yiwei Xiong4Shubo Jin5Yongsheng Gong6Yan Wu7Hui Qiao8Hongtuo Fu9Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, People’s Republic of ChinaKey Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, People’s Republic of ChinaWuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, People’s Republic of ChinaWuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, People’s Republic of ChinaKey Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, People’s Republic of ChinaKey Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, People’s Republic of ChinaKey Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, People’s Republic of ChinaKey Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, People’s Republic of ChinaKey Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, People’s Republic of China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, People’s Republic of China; Corresponding authors at: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, People’s Republic of China.Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, People’s Republic of China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, People’s Republic of China; Corresponding authors at: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, People’s Republic of China.This study was performed by using D-loop region sequences to investigate genetic diversity and population structure across eight representative groups of M. nipponense from south to north China. Eight populations comprising a total of 144 individuals were from Songhua River (SHJ), Yellow River (HH), Yangtze River (YZ), Pearl River (ZJ), Weishan Lake (WSH), Taihu Lake (TH), Bosten Lake (BH) and Wanquan River (WQH). The 1130-bp D-loop region exhibited a higher content of A + T (79.04%) than C + G (20.95%). In addition, 239 variable sites and 73 haplotypes were detected. The population haplotype diversity (h) were ranked as follows: WQH (0.9810) > YZ (0.9571) > WSH (0.9429) > ZJ (0.8901) > SHJ (0.8791) > HH (0.8693) > TH (0.8667) > BH (0.3684); the nucleotide diversity (π) were ranked as: WQH (0.0607) > YZ (0.0299) > SHJ(0.0236) > WSH(0.0221) > TH(0.0132) > ZJ(0.0131) > HH(0.0118) > BH(0.0011). The pairwise FST values reached highly significant level (P < 0.01). The gene flow (Nm) results revealed abundant gene exchange between WSH and TH (11.057), HH (7.226) and ZJ (6.255). The maximum likelihood (ML) phylogenetic tree showed that 73 haplotypes were divided into two main branches. Only the haplotypes of the BH population clustered together, indicating the low genetic diversity of this population, whereas a high diversity was observed in other populations. Network results were consistent with phylogenetic tree results. The analysis of mismatch distribution showed that all eight populations presented multimodal distribution. Fu’s Fs test and Tajima’s D tests were applied to determine the population expansion. All eight populations showed non-significant negative values, which suggests that the M. nipponense population in China did not experience population expansion.http://www.sciencedirect.com/science/article/pii/S2352513422000825Macrobrachium nipponenseMitochondrial DNA D-loopGenetic diversityGenetic structure |
| spellingShingle | Wenyi Zhang Sufei Jiang Khamis Rabii Salumy Zhongya Xuan Yiwei Xiong Shubo Jin Yongsheng Gong Yan Wu Hui Qiao Hongtuo Fu Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences Aquaculture Reports Macrobrachium nipponense Mitochondrial DNA D-loop Genetic diversity Genetic structure |
| title | Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences |
| title_full | Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences |
| title_fullStr | Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences |
| title_full_unstemmed | Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences |
| title_short | Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences |
| title_sort | comparison of genetic diversity and population structure of eight macrobrachium nipponense populations in china based on d loop sequences |
| topic | Macrobrachium nipponense Mitochondrial DNA D-loop Genetic diversity Genetic structure |
| url | http://www.sciencedirect.com/science/article/pii/S2352513422000825 |
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