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Cycle 6 (2017 Deadline)

Riverscape Genetics to Inform Natural History of Exploited Fishes in the Lower Mekong River Basin 

PI: Dang Thuy Binh (, Institute for Biotechnology and Environment, Nha Trang University (NTU); with co-PIs Chheng Phen(, Inland Fisheries Research and Development Institute (IFReDI); Latsamy Phounvisouk (, Living Aquatic Resources Research Center (LARReC); Chaiwut Grudpan (, Ubon Ratchathani University (UBU); and Mie Mie Kyaw (, University of Mandalay
U.S. Partner: Jeffrey Williams, Smithsonian Institution
Project Dates: December 2017 - November 2020

Project Facebook Page:

Project Overview:

Riverscape genetics, or the influence of hydrographic features on the genetics and ecology of lentic and lotic populations, is a young discipline (Selkoe et al. 2016). There have been several temperate riverscape studies with a few tropical studies, being limited mostly to the Amazon and Australia. Very little is known about the population genetics of fishes in the Mekong River Basin (MRB), which is characterized by complicated hydrographic features, including wide seasonal fluctuations in flow (Mekong River Commission 2005, Chea et al. 2016) and numerous changes experienced and expected with more than 350 hydropower dams built, under construction, and planned (Winemiller et al. 2016). This PEER project will support the completion of population genetic studies of 14 species across 26 MRB locations from Myanmar to the Vietnam delta. This will augment information on 2 species collected and analyzed during the PI’s project in PEER Cycle 2, add new localities to species initiated in a project on which she was co-PI in PEER Cycle 3, and add an additional 6 species not already initiated in previous PEER projects. Advanced genomic analyses will continue to be conducted on data collected using restriction site-associated DNA (RAD) data. These analyses will provide important information on the population structure, effective population size, and directionality of gene flow to substantially add to our knowledge of the natural history of Mekong River fishes. The extent of collection sites throughout the Lower Mekong Basin and the number of species in this study provide the basis for the first ever comparative riverscape genetic analysis of fishes of tropical Southeast Asia.

To ensure that the scientific information to be developed is available to and useful for resource managers, outreach will take place in conjunction with all field and annual meeting activities throughout this project. This will include seminars followed by roundtable discussions to introduce and understand how these analyses can be used and the consequences of disrupting the present population structure. The outreach efforts will target resource managers and development planners in governmental, intergovernmental, non-governmental, and academic institutions in the region, with particular emphasis on those involved in hydropower development projects. This project will also build on the need to create stronger regional collaborations for a better knowledge base to inform decision making by solidifying collaborations initiated during the PEER Cycle 3 project. This will be done by expanding the work done by collaborators in each of the four Lower Mekong Basin existing partner countries (Cambodia, Laos, Thailand, and Vietnam) and expanding this to Myanmar by including for the first time a collection component in that country. This new PEER project will add the University of Mandalay, Myanmar, to the network and will aim to build the advanced genomic capacity of all collaborative institutions to the level currently enjoyed at Nha Trang University.

6-435 Partner Visit at Lake6-435 Siem Reap Meeting
The team pauses for a picture during sample collection at Tonle Sap Lake.Participants of kick-off meeting in Siem Reap, Cambodia (photo courtesy of Dr. Binh).

Summary of Recent Activities:

Following are the status updates on work by each of the partners involved for the first quarter of 2020:
  • Vietnam: No field sampling was conducted. Instead team members focused on using DNA barcodes to check fish specimens. Despite painstaking analysis and comparison with sequences obtained earlier in the project and in PEER project 3-100, the researchers found great differences with some of the specimens collected in Laos, so misidentification is suspected. 
  • Cambodia: No field sampling was conducted. Team members at IFReDI re-extracted the DNA of some fish samples to supplement the original 48 samples per population. They completed DNA extraction and quantification of the amount of extracted DNA for six populations (sites). All extracted samples were loaded into sample plates for further work.
  • Myanmar: Dr. Mie Mie and colleagues traveled to the Shan State Regional Government Office, Taunggyi City, Southern Shan State, Myanmar (March 14-17, 2020) to get official permission for sampling. Dr. Mie Mie also conducted training for students every Friday on fish taxonomy, sampling, and preservation of samples for DNA work. She also gave a talk at the Third Myanmar-Korea Conference, held at Dagon University, Yangon, January 14-15, 2020. She spoke on the topic of Environmental DNA (eDNA): Monitoring and management of fisheries and water resources in Paunglaung River and Mekong River.
  • Thailand: As part of their sampling efforts, Dr. Chaiwut and his team from UBU collected 50 individuals of the species Mekongina and 60 individuals of Scaphognatops from the Mekong Mainstream site (Ubon Ratchathani) but failed to fulfill their target on Probarbus. In the case of Pangasius krempfi, they made contact with the key person in the habitat site of interest and also at the local fish landing site for that species from the large Vietnamese community in Thailand, Nakorn Panom Province. They hope to complete this target species in the next quarter, and they will also schedule an intensive survey in the Chi sampling site, which still lacks sufficient tissue samples. In addition, the UBU researchers organized a full-day workshop with key regional stakeholders in the Thai Mekong region. The workshop included 30 participants from the Thailand Department of Fisheries, including the head of the provincial fisheries station, scientists, NGO representatives, and students. The PI and his colleagues presented the core activities of PEER project 6-435 with regard to preservation of fish biodiversity in the Lower Mekong Basin. The keynote speaker was Professor Tauntong Jutagate, who delivered remarks on the effect of dam construction and global warming in the basin. This workshop successfully concluded with a discussion session for all participants, which was covered by Thai Television broadcasting station Thai PBS and aired February 12, 2020:
  • Laos: Dr. Mee and colleagues collected all their target species on the Mekong River at Paksan, Bolykhamsay Province, Central Laos. All fish samples were processed in the lab at LARReC following standard protocols for genetic work. Dr. Mee also met with two lecturers from the China Agricultural University of Beijing and one lecturer and 13 students from Laos National University. The purpose of this meeting was to discuss genetic work and future collaboration. In addition, Dr. Mee is writing a set of genetic implementation guidelines for the Lao PDR in the Lao language, including fish sampling, DNA collection and extraction, and next generation sequencing theory.
As for future plans, during the second and third quarters of 2020, all partners will focus on completing all remaining sampling at their study sites, and the partners in Cambodia and Thailand will prepare samples for genetic analysis. While also working with her team at Nha Trang University on data analysis, Dr. Binh will be recruiting a PhD student, as well as at least one Master’s student from each partner. Dr. Phen at IFReDI will be identifying potential stakeholders and preparing for outreach activities, and all partners will collaborate on the organization of the third annual project meeting. It was to have been held at UBU in Thailand in July 2020, but it has been postponed indefinitely due to the current COVID-19 pandemic and associated travel and social distancing restrictions. The pandemic has also disrupted transfers of samples among the partners. U.S. partner Chris Bird’s lab at Texas A&M University is handling the DNA sequencing on the project, and with that institution temporarily shut down, Dr. Binh and her colleagues have been unable to access the resulting data.

Following is a link to an article published in 2019 by the project team, entitled “Cryptic lineages and a population dammed to incipient extinction? Insights into the genetic structure of a Mekong River catfish,” which can be found in the Journal of Heredity, esz016,

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