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Population genomics of the peripheral freshwater fish Polynemus melanochir (Perciformes, Polynemidae) in a changing Mekong Delta

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Abstract

The Mekong River is a vital fisheries resource supporting millions of people in mainland Southeast Asia. However, numerous threats have the potential to negatively impact fish populations in this region including overfishing, pollution, climate change and increased urban, agriculture and upstream hydropower development. Although a few studies have examined the population genetic structure of fishes within the upper Mekong River, no known studies have explored that of fishes within the Mekong Delta (MD). Here, we examine the population structure of an important food fish within the MD, Polynemus melanochir, using a panel of 1735 single nucleotide polymorphisms (SNPs) generated by restriction site-associated DNA (RAD) sequencing across eight locations on the Tien (Mekong) and Hau (Bassac) Rivers in Vietnam. Pairwise FST values, principal component analysis and Structure analysis all indicate high levels of gene flow among the sites sampled across the MD. In contrast to the lack of genetic structure, high levels of relatedness were found, including 26 putatively related pairs, as well as an effective population size (Ne) of less than 500 across the MD. While panmixia indicates that fragmentation of this population is not presently an important threat, a low Ne estimate suggests this species may not be resilient to long-term environmental changes in the MD. The reliance on P. melanochir as a food resource may be contingent on management and mitigation of low effective population sizes.

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Acknowledgements

We thank the many people from the communities of the Mekong River Delta who helped us collect tissues from fish markets and team members of Biodiversity and Conservation, Institute for Biotechnology and Environment, Nha Trang University for project support. We are very grateful to Christopher Bird and Sharon Furiness Magnuson who provided help and advice in sequencing and data analysis. We thank Min Dong, Wirawan Purwanto, Terry Stilwell and John Pratt of the Old Dominion University High Performance Computing Facility for computational assistance. This project was funded by the United States Agency for International Development supported Partnerships for Enhanced Research Project 2–7 under USAID Cooperative Agreement AID-OAA-A-11-00012 and project OISE-0730256 sponsored by the United States National Science Foundation.

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Authors and Affiliations

  1. Department of Biology, Institute of Biotechnology and Environment, Nha Trang University, 02 Nguyen Dinh Chieu, Nha Trang, Vietnam

    B. T. Dang, Q. H. D. Vu & O. T. Truong

  2. Faculty of Biology – Biotechnology, University of Science, Vietnam National University Ho Chi Minh City, 227 Nguyen Van Cu Str., Dist. 5, Ho Chi Minh City, Vietnam

    Q. H. D. Vu & T. L. Tran

  3. Department of Biological Sciences, Old Dominion University, Norfolk, VA, 23529-0266, USA

    E. E. Biesack, A. S. Ackiss, B. L. Stockwell & K. E. Carpenter

  4. Department of Software Engineering, IT Faculty, Nha Trang University, 02 Nguyen Dinh Chieu, Nha Trang, Vietnam

    T. V. Doan

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Dang, B.T., Vu, Q.H.D., Biesack, E.E. et al. Population genomics of the peripheral freshwater fish Polynemus melanochir (Perciformes, Polynemidae) in a changing Mekong Delta. Conserv Genet 20, 961–972 (2019). https://doi.org/10.1007/s10592-019-01189-x

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