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Partnerships for enhanced engagement in research (PEER) SCIENCE
Cycle 2 (2012 Deadline)

Conservation genetics for improved biodiversity and resource management in a changing Mekong Delta

PI:  Dang Thuy Binh (Nha Trang University)
U.S. Partner: Kent E. Carpenter (Old Dominion University)
Project Dates: August 2013 to January 2016

 Vietnam3
The project team commences its DNA labwork (Photo courtesy Dr. Binh).

The study of the genetics of populations is a valuable tool in investigating the origins of the extreme biodiversity of southeast Asia. The National Science Foundation (NSF) Partnerships for International Research and Education (PIRE) project “Origins of high marine biodiversity in the Indo-Malay-Philippine Archipelago” has extended phylogeographic studies to Vietnam and Thailand to better understand mechanisms of speciation in the marine realm of this region. This PEER Science project leverages and extends this investigation into the estuarine and freshwater biomes of the most prominent and extremely biodiverse hydrological feature of southeast Asia, the Mekong Delta. Connectivity of populations across and within the Mekong Delta is shaped by the complex and dynamic physical processes of the Mekong River Basin. The outflow of the basin will potentially serve as a barrier to gene flow of marine populations distributed along the coast of Vietnam similar to what has been observed for the Amazon River (Rocha et al. 2002). Also similar to the Amazon system, the complex branches and hydrography of the Mekong Delta provide both potential barriers and environmental gradients that would influence gene flow and natural selection of vertebrate populations (e.g. Cooke et al. 2012, Hollatz 2011) within the Mekong Delta. This PEER project aims to examine fine-scale population connectivity of three fish species (marine, estuarine, and freshwater) across the Mekong Delta using advanced genomic methodologies. This will initiate a long-term research program to investigate processes that promote lineage diversification across the delta and provide a basis to examine genetic adaptation of populations to the changing conditions of the delta caused by increasing effects of damming, development, agriculture and climate change.
 
This PEER Science project should produce valuable information about the connectivity of aquatic populations within and across the mouth of the Mekong Delta that can be used for improved environmental governance, such as delineating management zones and formulating strategies for biodiversity conservation. Furthermore, one species to be studied is considered Near Threatened on the International Union for Conservation of Nature Red List (IUCN 2012), and the population information gained in this study will be applicable to its conservation and biodiversity conservation in general in the Mekong Delta. As for capacity building, the project will provide training to Vietnamese researchers and give them a solid foundation for applying their new methods and skills to most pressing environmental concern in Vietnam: threats to the biodiversity and resources of the Mekong Delta.
 
Summary of Recent Activities
 
The summer of 2014 saw Dr. Binh and team members attend multiple workshops and trainings in line with both PEER and project objectives. In June, Dr. Binh and her team attended a weeklong training hosted by the University of De La Salle titled Applied Bioinformatics in the Study of Genetic Diversity and Conservation. During this training, team members presented their PEER work to a group of international molecular geneticists. The team also learned about new opportunities in the application of genetic diversity and conservation and was taught technical skills in next generation sequencing and bioinformatics. This training had direct implications for the project and the group has practiced bioinformatics using Bioperl Software to read FASTQ files and to run in internal applications.
  

Vietnam 1
Dr. Carpenter and students preparing for an expedition on the water (Photo courtesy Dr. Binh).

Vietnam 2
Dr. Carpenter at a fish market examining the local catch in search of species (Photo courtesy Dr. Binh).

 
The second training took place at Old Dominion University and was attended by Dr. Binh and her PhD student, Ha Quyen for two weeks. At ODU, they conducted ezrad techiniques for new generation sequencing and participated in courses on fish ichthyology and bioinformatics. Additionally, the teams collaborated in successfully troubleshooting lab equipment that has allowed for the acquisition of greater gene libraries. Dr. Binh hopes to be able to send her teams samples out for sequencing and receive the resulting data by the end of this year.

While on her trip to the United States, Dr. Binh initiated future partnership agreements between Nha Trang University, ODU, and MSU. This has resulted in further collaboration between the institutions that should hopefully see a student exchange in 2015. Furthermore, Dr. Binh hopes to continue develop her team’s sequencing capacity in the near future by upgrading her equipment and installing better optimized software.

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