{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T15:30:11Z","timestamp":1789659011502,"version":"4.0.1"},"reference-count":35,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:00:00Z","timestamp":1789084800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"This research was supported by grants from Central Public-interest Scientific In-stitution Basal Research Fund CAFS","award":["No. 2023TD39"],"award-info":[{"award-number":["No. 2023TD39"]}]},{"name":"the earmarked fund for China Agriculture Research System","award":["CARS-47-07"],"award-info":[{"award-number":["CARS-47-07"]}],"id":[{"id":"https:\/\/ror.org\/03p5eky76","id-type":"ROR","asserted-by":"crossref"}]},{"award":["CARS-47-07"],"award-info":[{"award-number":["CARS-47-07"]}],"id":[{"id":"https:\/\/ror.org\/03p5eky76","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>This study evaluated the genetic diversity and population structure of wild M. nipponense populations in the Pearl River Basin based on mitochondrial DNA (mtDNA) D-loop sequences. A total of 14 wild populations were collected from the West River, North River, and Pearl River Delta, and genetic diversity and population differentiation were assessed using haplotype analysis, analysis of molecular variance (AMOVA), pairwise FST, and principal component analysis (PCA). A total of 351 variable sites were identified. The overall haplotype diversity (h) and nucleotide diversity (\u03c0) were 0.947 and 0.03665, respectively, indicating high genetic diversity across the Pearl River Basin. Significant genetic differentiation was detected among populations (FST = 0.3785, p-value &lt; 0.001), with 37.85% of genetic variation occurring among populations. PCA revealed distinct genetic relationships among populations, supporting the presence of population genetic structure within the Pearl River Basin. Populations from Tian\u2019e County, Xilin County, Dahua Yao Autonomous County, and other upper tributaries of the West River exhibited distinct genetic characteristics compared with populations from Zhaoqing City, Guiping City, Guangzhou City, and the middle and lower reaches of the West River and the Pearl River estuary. Among the 14 populations, those from Zhaoqing City, Guiping City, and Guangzhou City exhibited relatively high genetic diversity and distinctive genetic characteristics. These findings suggest that the complex hydrological structure and historical connectivity of the Pearl River Basin have contributed to the observed population genetic structure. The genetically diverse populations identified in this study represent valuable wild germplasm resources for the conservation and selective breeding of M. nipponense.<\/jats:p>","DOI":"10.3390\/ani16182869","type":"journal-article","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T14:39:24Z","timestamp":1789137564000},"page":"2869","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genetic Diversity and Population Structure of Wild Macrobrachium nipponense in the Pearl River Basin: A Treasury of Germplasm for Aquaculture and Conservation"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-6042-4149","authenticated-orcid":false,"given":"Hao","family":"Dong","sequence":"first","affiliation":[{"name":"Key Laboratory of Mariculture & Stock Enhancement in North China\u2019s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-1869-4414","authenticated-orcid":false,"given":"Xiaofan","family":"Fang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Mariculture & Stock Enhancement in North China\u2019s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-0631-6288","authenticated-orcid":false,"given":"Yuefan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Mariculture & Stock Enhancement in North China\u2019s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6550-9268","authenticated-orcid":false,"given":"Shubo","family":"Jin","sequence":"additional","affiliation":[{"name":"Key Laboratory of Mariculture & Stock Enhancement in North China\u2019s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China"},{"name":"Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China"},{"name":"Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenyi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China"},{"name":"Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiwei","family":"Xiong","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Qiao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Mariculture & Stock Enhancement in North China\u2019s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China"},{"name":"Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China"},{"name":"Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sufei","family":"Jiang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Mariculture & Stock Enhancement in North China\u2019s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China"},{"name":"Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China"},{"name":"Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1051\/alr\/2024003","article-title":"Genetic structure of Macrobrachium nipponense, an important farmed freshwater shrimp in China, in the Three Gorges Reservoir","volume":"37","author":"Wang","year":"2024","journal-title":"Aquat. Living Resour."},{"key":"ref_2","first-page":"245","article-title":"Report on a collection of freshwater shrimps (Crustacea: Decapoda: Caridea) from the Philippines, with descriptions of four new species","volume":"54","author":"Cai","year":"2006","journal-title":"Raffles Bull. Zool."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1080\/24701394.2017.1350953","article-title":"Genetic diversity analysis of the oriental river prawn (Macrobrachium nipponense) in Huaihe River","volume":"29","author":"Cui","year":"2018","journal-title":"Mitochondrial DNA Part A"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1111\/j.1365-2109.2011.03085.x","article-title":"Current status and prospects of farming the giant river prawn (Macrobrachium rosenbergii) and the oriental river prawn (Macrobrachium nipponense) in China","volume":"43","author":"Fu","year":"2012","journal-title":"Aquac. Res."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1093\/gigascience\/giaa160","article-title":"A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense","volume":"10","author":"Jin","year":"2021","journal-title":"GigaScience"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/j.aquaculture.2003.08.002","article-title":"Artificial interspecific hybridization between Macrobrachium nipponense Macrobrachium hainanense and their isozyme analysis","volume":"232","author":"Fu","year":"2004","journal-title":"Aquaculture"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"5069","DOI":"10.1007\/s11033-023-08402-8","article-title":"Genetic diversity and population structure of wild Macrobrachium nipponense populations across China: Implication for population management","volume":"50","author":"Jiang","year":"2023","journal-title":"Mol. Biol. Rep."},{"key":"ref_8","first-page":"73","article-title":"Genetic Structure and Phylogeography of Natural Macrobrachium nipponense Populations in Huaihe River Based on Mitochondrial COI Sequence","volume":"47","author":"Jiang","year":"2012","journal-title":"Chin. J. Zool."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"101086","DOI":"10.1016\/j.aqrep.2022.101086","article-title":"Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences","volume":"23","author":"Zhang","year":"2022","journal-title":"Aquac. Rep."},{"key":"ref_10","first-page":"e00876","article-title":"Genetic diversity and structure of the round-tailed paradise fish (Macropodus ocellatus): Implications for population management","volume":"21","author":"Zhang","year":"2020","journal-title":"Glob. Ecol. Conserv."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1111\/1755-0998.12953","article-title":"Finding stories in noise: Mitochondrial portraits from RAD data","volume":"19","author":"Stobie","year":"2019","journal-title":"Mol. Ecol. Resour."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1017\/S0025315418000929","article-title":"Mitochondrial D-loop DNA analyses of Norway lobster (Nephrops norvegicus) reveals genetic isolation between Atlantic and East Mediterranean populations","volume":"99","author":"Gallagher","year":"2019","journal-title":"J. Mar. Biol. Assoc. U. K."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"4235","DOI":"10.4238\/2012.September.20.1","article-title":"Genetic variation based on microsatellite analysis of the oriental river prawn, Macrobrachium nipponense from Qiandao Lake in China","volume":"11","author":"Ma","year":"2012","journal-title":"Genet. Mol. Res."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1111\/j.1749-7345.2011.00492.x","article-title":"Genetic variation in wild and cultured populations of the freshwater prawn, Macrobrachium nipponense, in China","volume":"42","author":"Ge","year":"2011","journal-title":"J. World Aquac. Soc."},{"key":"ref_15","first-page":"77","article-title":"Fauna Sinica: Invertebrata. Crustacea, Decapoda, Palaemonoidea","volume":"Volume 44","author":"Li","year":"2007","journal-title":"Fauna Sinica: Invertebrata"},{"key":"ref_16","unstructured":"Sambrook, J., and Russell, D. (2001). Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press. [3rd ed.]."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e7007","DOI":"10.7717\/peerj.7007","article-title":"Maternal ancestry analyses of red tilapia strains based on D-loop sequences of seven tilapia populations","volume":"7","author":"Jiang","year":"2019","journal-title":"PeerJ"},{"key":"ref_18","unstructured":"Hall, T.A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95\/98\/NT. Nucleic Acids Symposium Series, Oxford University Press."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1111\/j.1755-0998.2010.02847.x","article-title":"Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows","volume":"10","author":"Excoffier","year":"2010","journal-title":"Mol. Ecol. Resour."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1007\/BF01731581","article-title":"A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences","volume":"16","author":"Kimura","year":"1980","journal-title":"J. Mol. Evol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: A practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. Ser. B-Stat. Methodol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1111\/2041-210X.12410","article-title":"POPART: Full-feature software for haplotype network construction","volume":"6","author":"Leigh","year":"2015","journal-title":"Methods Ecol. Evol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Ou, H.D., Cai, S.R., Fan, W., Qiu, J.L., Mu, X.L., Zhou, T., Yang, X.K., and Picco, L. (2024). Sustaining the Pearl River: A Critical Review of Changes in Fluvial Geomorphological Processes and the Driving Forces in the Pearl River Basin. Water, 16.","DOI":"10.3390\/w16071001"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1111\/age.12752","article-title":"Genetic diversity analysis of French goat populations reveals selective sweeps involved in their differentiation","volume":"50","author":"Oget","year":"2019","journal-title":"Anim. Genet."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"20172589","DOI":"10.1098\/rspb.2017.2589","article-title":"Genetic diversity, inbreeding and cancer","volume":"285","author":"Ujvari","year":"2018","journal-title":"Proc. R. Soc. B-Biol. Sci."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"739816","DOI":"10.1016\/j.aquaculture.2023.739816","article-title":"Whole-genome resequencing reveals genetic diversity and signatures of selection in mono-female grass carp (Ctenopharyngodon idella)","volume":"575","author":"Zhang","year":"2023","journal-title":"Aquaculture"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Lin, M.H., Liang, X.F., Lu, K., Zeng, M., Gao, J.J., Dou, Y.Q., Kuang, Y.L., and Zhang, Q.W. (2025). Genetic Diversity in Three Sinipercine Fishes Based on Mitochondrial D-Loop and COX1 Sequences. Fishes, 10.","DOI":"10.3390\/fishes10060264"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Iko, R., Gao, Z.J., Jiang, S.F., Xiong, Y.W., Zhang, W.Y., Qiao, H., Jin, S.B., and Fu, H.T. (2025). Genetic Diversity and Population Structure of Macrobrachium nipponense Populations in the Saline-Alkaline Regions of China. Animals, 15.","DOI":"10.3390\/ani15020158"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.bse.2013.01.007","article-title":"Genetic variation and Phylogeography of Sinibrama macrops (Teleostei: Cyprinidae) in Qiantang River Basin, China","volume":"49","author":"Zhao","year":"2013","journal-title":"Biochem. Syst. Ecol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1080\/24701394.2016.1278533","article-title":"Population structure and genetic diversity of Sinibrama macrops from Ou River and Ling River based on mtDNA D-loop region analysis, China","volume":"29","author":"Zhao","year":"2018","journal-title":"Mitochondrial DNA Part A"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1292","DOI":"10.1080\/23802359.2021.1906172","article-title":"Genetic diversity of Gymnocypris chilianensis (Cypriniformes, Cyprinidae) unveiled by the mitochondrial DNA D-loop region","volume":"6","author":"Wang","year":"2021","journal-title":"Mitochondrial DNA Part B-Resour."},{"key":"ref_33","first-page":"173","article-title":"Genetic Structure of Spinibarbus caldwelli Based on mtDNA D-Loop","volume":"10","author":"Yuan","year":"2019","journal-title":"Agric. Sci."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2240","DOI":"10.1080\/23802359.2021.1878963","article-title":"Gene variation and population structure of Pampus chinensis in the China coast revealed by mitochondrial control region sequences","volume":"6","author":"Sun","year":"2021","journal-title":"Mitochondrial DNA Part B-Resour."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Fang, D.A., Luo, H., He, M., Mao, C.C., Kuang, Z., Qi, H.F., Xu, D.P., Tan, L.F., and Li, Y.D. (2022). Genetic Diversity and Population Differentiation of Naked Carp (Gymnocypris przewalskii) Revealed by Cytochrome Oxidase Subunit I and D-Loop. Front. Ecol. Evol., 10.","DOI":"10.3389\/fevo.2022.827654"}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/18\/2869\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T04:11:39Z","timestamp":1789531899000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/18\/2869"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,11]]},"references-count":35,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ani16182869"],"URL":"https:\/\/doi.org\/10.3390\/ani16182869","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,11]]}}}