Partnerships for enhanced engagement in research (PEER) SCIENCE Cycle 3 (2014 Deadline)
Building a Mekong River genetic biodiversity research network
PI: Vu Ngoc Ut (firstname.lastname@example.org), Can Tho University, with co-PIs Dang Thuy Binh, Nha Trang University; Chheng Phen, Inland Fisheries Research and Development Institute (IFReDI); So Nam, Mekong River Commission; Latsamy Phounvisouk, Living Aquatic Resources Research Centre; and Chaiwut Grudpan, Ubon Ratchathani University
U.S. Partner: Kent Carpenter, Old Dominion University Project Dates: December 2014 to June 2018
The Next Generation Sequencing workshop was held at NTU, October 16-24, 2015.
The Mekong River Basin (MRB) represents a global hotspot of aquatic biodiversity, second only to the Amazon River in terms of total fish species richness. The purpose of this project will be to initiate a network of scientists working in the MRB whose coordinated action will lead to a systematic sampling of populations and species to provide a set of robust tests of biogeographic origins of MRB biodiversity through advanced genomics and comparative phylogeography. Specifically, the research team will aim to examine a set of synchronously diverging co-distributed taxa to determine whether the genetic connectivity or barriers to gene flow are determined by processes relating to ecological (relatively recent) or evolutionary (geological) time scales. Directionality of gene flow will be tested to determine if connectivity is predominantly governed by larval dispersal through prevailing fluvial flow, or whether fish movement patterns potentially reverse this natural tendency. Shared phylogeographic patterns among taxa will be examined together with both present ecological and geological processes to corroborate likely causality in a natural experimental framework.
A significant developmental impact of this project will be the establishment of a network of scientists, managers, and conservationists interested in using genetics to better understand and manage the biodiversity of the MRB. The primary partner will be the Mekong River Commission, which previously initiated population genetic data collection for important species, and the aim will be to strengthen and expand this initiative. The implementation of the project will forge and strengthen long-term collaborative research ties through mutual design and implementation of a comparative population genetic project. Since most of the participants do not have extensive experience in next-generation sequencing and advanced genomic analysis, another proximate development impact will be training of aquatic researchers across the MRB in this methodology. Population genetic data will be systematically collected as a result of the establishment of the network, and data will be analyzed for information relative to resource management and biodiversity conservation. The data will also be used as the basis for establishing a long-term genetic monitoring system for aquatic resources and integrity of genetic biodiversity. The benefits of the collected data will include: 1) the ability to estimate and monitor effective population size of exploited stocks; 2) evaluation of spatial stock structure for fisheries management, for assessment of fragmentation due to damming, and to enhance adaptive mitigation and management in anticipation of hydrological changes from climate change and damming; 3) baseline information on genetic variability collected during this study will allow monitoring of genetic integrity that may be influenced by fishing, stock enhancement (release of hatchery reared individuals), and accidental release from aquaculture; 4) baseline information on genetic variability collected during this study that will allow monitoring of genetic variation as potential for biological adaptation and resilience to changing environmental conditions; and 5) establishment of a genetic data repository in collaboration with the Mekong River Commission for data sharing.
Dr. Ut and his team visit the fish market to collect samples (photo credit: Dr. Binh).
Summary of Recent Activities
By the end of December 2017, the partners at Can Tho University (CTU), Nha Trang University (NTU), Ubon Ratchathani University (UBU), and the Inland Fisheries Research and Development Institute (IFReDI) had completed their sample collection activities on this project. Due to spoilage of some of the samples they originally collected, the Living Aquatic Resources Research Center (LARReC) still needs to collect some more samples (of Macrognathus siamennsis and Pangasius krempfi) and send them to CTU for analysis. Sample processing and analysis have continued. At NTU, the samples received from Thailand have been processed, and the samples collected by NTU have been completely analyzed and sent to the lab of U.S. co-partner Chris Bird at Texas A&M University for sequencing. CTU has sent a sample library on one of the five species they collected to Texas for sequencing, and they continue processing the rest of the samples. At IFReDI, progress on sample analysis has been slow for two reasons: (1) the time required for staff to adapt to the new EzRAD method and (2) problems in purchasing the analytical kits they need. The kits are not sold in Cambodia, and importing them from Vietnam takes more time. As a result, IFReDI has only processed 20 samples for DNA extraction to continue with EzRAD analysis.
The partners involved in this multi-country project had planned to complete all the analysis and obtain the results in time to convene a final workshop by the end of June 2018. However, the delays in sample collection and processing and the need to send the material to Texas for sequencing means that another six-month extension may be required.