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 (August 2018 for LARReC portion only, and September 2018 for CTU portion only)
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
As of April 2018, all partners had completed their sample collection efforts except for Dr. Grudpan and his team at Ubon Ratchathani University in Thailand, who still lack specimens of Macromachus sianensis and have been unable to obtain specimens of Pangasius krempfi in the Mun River. Therefore, Dr. Binh and her colleagues are NTU are still awaiting those missing samples at so they can complete analyzing all species from Thailand. Dr. Ut and his team at CTU are still awaiting receipt of a few more specimens of P. krempfi and M. sianensis from Laos that have been held up in shipment. However, NTU finished analyzing all samples received and sent the DNA libraries to Dr. Chris Bird’s lab at Texas A&M University in February 2018, receiving the results in March. CTU has prepared five sets of DNA libraries to be sent to Texas as well. Sample analysis at IFReDI is in progress but has been slow. Dr. Phen and his team have completed DNA extraction on 30 samples and are preparing EzRAD libraries.
The PI, co-PIs, and key members of this project are preparing to hold their final workshop June 13-14 in Siem Riep, Cambodia. NTU is currently conducting data analysis of 6-7 target species, including 3 species that cover sampling locations in the lower Mekong Delta (P. conchophilus, Ompok bimaculatus, and Trichopodus trichopterus), 2 species represented only in sampling locations in Thailand (Pangasius lanaudi and P. macronema). CTU is processing the complete data set for M. sianensis and has shared it with NTU for presentation at the coming workshop.