The Next Generation Sequencing workshop was held at NTU, October 16-24, 2015.
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
Dr. Binh and her colleagues continued working during July - September 2017 on two joint publications, one on Polynemus melanochir (almost ready for submission as of October 2017) and the other on Boesemania microlepis (first draft complete). On the outreach side, thanks to some PEER supplemental funding received last year, the researchers are collaborating with a local TV station to create a video about their work. The finished video is expected to be released in October or November. Meanwhile, other supplemental funding is allowing the group to conduct an expanded multi-national sample collection and data analysis campaign focused in the Sekong (3S) Basin. Dr. Binh and her group are focusing on sampling in the Vietnamese Highland Mekong (Serepok and Sesan Rivers), with U.S. partner Dr. Kent Carpenter accompanying them on some of the field work. The Sekong Basin sample collection and genetic analysis efforts are designed to help produce policy suggestions regarding the master plan for dams in the area. Dr. Binh and Dr. Carpenter have worked together to submit their recommendations to the Natural Heritage Institute (n-h-i.org), which is coordinating the policy input. Besides the ongoing analytical and publication drafting efforts, Dr. Binh and her team also plan some additional sampling in Laos and Thailand in the final quarter of 2017. On the sequencing and analysis side, U.S. co-partner Dr. Chris Bird and his team at Texas A&M University have almost finished all the sequencing and have send the results to Dr. Binh and Dr. Carpenter for analysis by their groups. A no-cost extension is being issued through June 2018 to allow the researchers time to complete their work.
Dr. Carpenter and students preparing for an expedition on the water (Photo courtesy Dr. Binh).
Dr. Carpenter at a fish market examining the local catch in search of species (Photo courtesy Dr. Binh).