Partnerships for enhanced engagement in research (PEER) SCIENCE Cycle 3 (2014 Deadline)
Building a Mekong River genetic biodiversity research network
PI: Vu Ngoc Ut (email@example.com), 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
Fifteen participants representing all six southeast Asian partners in this multinational project convened for their third annual meeting June 21-22, 2017, in Pakse, Laos. Representatives of each partner institution reported on their activities and progress and discussed possible solutions for challenges related to sample collection and analysis. Plans were also made for completing the project by June 2018 under a no-cost extension to be requested.
During the second quarter of 2017, sample analysis was continuously conducted at Nha Trang University (NTU), Can Tho University (CTU), and the Inland Fisheries Research and Development Institute (IFReDI). NTU has completed most of its samples and sent the DNA libraries to Texas A&M University for sequencing analysis. CTU has been working on analyzing its samples, and researchers there have mastered all the complicated steps required for use of the EzRAD technique. IFReDI has completed DNA extraction and quantification on agarose gel but has encountered some problems with sample analysis and interpretation, so further training is required. Most of the sample collection has been completed at NTU, IFReDI, and the Living Aquatic Resources Research Center (LARReC) but is continuing at CTU for the last two species (Pangasius macronema and Labeo chrysophekadion) at two sites in the Hau and Tien Rivers. Because many of their samples were damaged or spoiled, LARReC must re-collect some of the species (L. chrysophekadion, P. larnaudii, P. macronema, and P. krempfi) later this summer. IFReDI will collect P. conchophilus from Kratie (at least 30 specimens) to send to NTU for complete analysis of this species.
As for additional upcoming plans, CTU researchers will complete analysis of samples collected by CTU and LARReC in December 2017, while NTU is responsible for analyzing samples from Ubon Ratchathani University and IFReDI will finish their sample analysis after getting extra training at NTU. All partners have agreed that the final workshop on this project will be held at Ubon Ratchathani University at the end of June 2018.