Population subdivision in Siamese mud carp Henicorhynchus siamensis in the Mekong River basin: implications for management

Evidence for population genetic structure in two exploited Mekong River fishes across a natural riverine barrier

Impacts of urban development on aquatic populations are often complex and difficult to ascertain, but population genetic analysis has allowed researchers to monitor and estimate gene flow in the context of existing and future hydroelectric projects. The Lower Mekong Basin is undergoing rapid hydroelectric development with around 50 completed and under-construction dams and 95 planned dams. The authors investigated the baseline genetic diversity of two exploited migratory fishes, the mud carp Henicorhynchus lobatus (five locations), and the rat-faced pangasiid catfish, Helicophagus leptorhynchus (two locations), in the Lower Mekong Basin using the genomic double digest restriction site-associated DNA (ddRAD) sequencing method. In both species, fish sampled upstream of Khone Falls were differentiated from those collected at other sites, and N_e estimates at the site above the falls were lower than those at other sites. This was the first study to utilize thousands of RAD-generated single nucleotide polymorphisms to indicate that the Mekong's Khone Falls are a potential barrier to gene flow for these two moderately migratory species. The recent completion of the Don Sahong dam across one of the only channels for migratory fishes through Khone Falls may further exacerbate signatures of isolation and continue to disrupt the migration patterns of regionally vital food fishes. In addition, H. lobatus populations downstream of Khone Falls, including the 3S Basin and Tonle Sap system, displayed robust connectivity. Potential obstruction of migration pathways between these river systems resulting from future dam construction may limit dispersal, which has led to elevated inbreeding rates and even local extirpation in other fragmented riverine species.

Cryptic Lineages and a Population Dammed to Incipient Extinction? Insights into the Genetic Structure of a Mekong River Catfish

An understanding of the genetic composition of populations across management boundaries is vital to developing successful strategies for sustaining biodiversity and food resources. This is especially important in ecosystems where habitat fragmentation has altered baseline patterns of gene flow, dividing natural populations into smaller subpopulations and increasing potential loss of genetic variation through genetic drift. River systems can be highly fragmented by dams built for flow regulation and hydropower. We used reduced-representation sequencing to examine genomic patterns in an exploited catfish, Hemibagrus spilopterus, in a hotspot of biodiversity and hydropower development—the Mekong River basin. Our results revealed the presence of 2 highly divergent coexisting genetic lineages which may be cryptic species. Within the lineage with the greatest sample sizes, pairwise FST values, principal component analysis, and a STRUCTURE analysis all suggest that long-distance migration is not common across the Lower Mekong Basin, even in areas where flood-pulse hydrology has limited genetic divergence. In tributaries, effective population size estimates were at least an order of magnitude lower than in the Mekong mainstream indicating these populations may be more vulnerable to perturbations such as human-induced fragmentation. Fish isolated upstream of several dams in one tributary exhibited particularly low genetic diversity, high amounts of relatedness, and a level of inbreeding (GIS = 0.51) that has been associated with inbreeding depression in other outcrossing species. Our results highlight the importance of assessing genetic structure and diversity in riverine fisheries populations across proposed dam development sites for the preservation of these critically important resources.

Taxonomy, Ecology and Population Genetics of Opisthorchis viverrini and Its Intermediate Hosts

There have been considerable advances in our understanding of the systematics and ecology of Opisthorchis viverrini; however, this new knowledge has not only clarified but also complicated the situation. We now know that what was once considered to be a single species is, in fact, a species complex, with the individual species being confined to specific wetland areas. There is also a strong genetic association between the members of the O. viverrini species complex and their Bithynia snail intermediate hosts. Although this does not negate data collected before the recognition of this situation, it does lead to the caveat that regional and temporal variations in data collected may be related to the species examined. The advances in ecology have generally been spatially limited and have led, in part, to contradictory results that may well be related to nonrecognition of the species studied. It may also be related to natural temporal and spatial variation related, for example, to habitat characteristics. To understand the variation present, it will be necessary to conduct long-term (several years at least) sampling projects after defining the genetic characteristics of O. viverrini sensu lato and its Bithynia snail intermediate hosts.

Integrative Taxonomy of Southeast Asian Snail-Eating Turtles (Geoemydidae: Malayemys) Reveals a New Species and Mitochondrial Introgression

Based on an integrative taxonomic approach, we examine the differentiation of Southeast Asian snail-eating turtles using information from 1863 bp of mitochondrial DNA, 12 microsatellite loci, morphology and a correlative species distribution model. Our analyses reveal three genetically distinct groups with limited mitochondrial introgression in one group. All three groups exhibit distinct nuclear gene pools and distinct morphology. Two of these groups correspond to the previously recognized species Malayemys macrocephala (Chao Phraya Basin) and M. subtrijuga (Lower Mekong Basin). The third and genetically most divergent group from the Khorat Basin represents a previously unrecognized species, which is described herein. Although Malayemys are extensively traded and used for religious release, only few studied turtles appear to be translocated by humans. Historic fluctuations in potential distributions were assessed using species distribution models (SDMs). The Last Glacial Maximum (LGM) projection of the predictive SDMs suggests two distinct glacial distribution ranges, implying that the divergence of M. macrocephala and M. subtrijuga occurred in allopatry and was triggered by Pleistocene climate fluctuations. Only the projection derived from the global circulation model MIROC reveals a distinct third glacial distribution range for the newly discovered Malayemys species.

Potential effects of hydroelectric dam development in the Mekong River basin on the migration of Siamese mud carp (Henicorhynchus siamensis and H. lobatus) elucidated by otolith microchemistry

The migration of Siamese mud carp (Henicorhynchus siamensis and H. lobatus), two of the most economically important fish species in the Mekong River, was studied using an otolith microchemistry technique. Fish and river water samples were collected in seven regions throughout the whole basin in Thailand, Laos and Cambodia over a 4 year study period. There was coherence between the elements in the ambient water and on the surface of the otoliths, with strontium (Sr) and barium (Ba) showing the strongest correlation. The partition coefficients were 0.409–0.496 for Sr and 0.055 for Ba. Otolith Sr-Ba profiles indicated extensive synchronized migrations with similar natal origins among individuals within the same region. H. siamensis movement has been severely suppressed in a tributary system where a series of irrigation dams has blocked their migration. H. lobatus collected both below and above the Khone Falls in the mainstream Mekong exhibited statistically different otolith surface elemental signatures but similar core elemental signatures. This result suggests a population originating from a single natal origin but bypassing the waterfalls through a passable side channel where a major hydroelectric dam is planned. The potential effects of damming in the Mekong River are discussed.

Analysis of genome survey sequences and SSR marker development for Siamese Mud Carp, Henicorhynchus siamensis, using 454 pyrosequencing

Siamese mud carp (Henichorynchus siamensis) is a freshwater teleost of high economic importance in the Mekong River Basin. However, genetic data relevant for delineating wild stocks for management purposes currently are limited for this species. Here, we used 454 pyrosequencing to generate a partial genome survey sequence (GSS) dataset to develop simple sequence repeat (SSR) markers from H. siamensis genomic DNA. Data generated included a total of 65,954 sequence reads with average length of 264 nucleotides, of which 2.79% contain SSR motifs. Based on GSS-BLASTx results, 10.5% of contigs and 8.1% singletons possessed significant similarity (E value < 10(-5)) with the majority matching well to reported fish sequences. KEGG analysis identified several metabolic pathways that provide insights into specific potential roles and functions of sequences involved in molecular processes in H. siamensis. Top protein domains detected included reverse transcriptase and the top putative functional transcript identified was an ORF2-encoded protein. One thousand eight hundred and thirty seven sequences containing SSR motifs were identified, of which 422 qualified for primer design and eight polymorphic loci have been tested with average observed and expected heterozygosity estimated at 0.75 and 0.83, respectively. Regardless of their relative levels of polymorphism and heterozygosity, microsatellite loci developed here are suitable for further population genetic studies in H. siamensis and may also be applicable to other related taxa.

Phylogeography of the Mekong mud snake (Enhydris subtaeniata): the biogeographic importance of dynamic river drainages and fluctuating sea levels for semiaquatic taxa in Indochina

During the Cenozoic, Southeast Asia was profoundly affected by plate tectonic events, dynamic river systems, fluctuating sea levels, shifting coastlines, and climatic variation, which have influenced the ecological and evolutionary trajectories of the Southeast Asian flora and fauna. We examined the role of these paleogeographic factors on shaping phylogeographic patterns focusing on a species of semiaquatic snake, Enhydris subtaeniata (Serpentes: Homalopsidae) using sequence data from three mitochondrial fragments (cytochrome b, ND4, and ATPase-2785 bp). We sampled E. subtaeniata from seven locations in three river drainage basins that encompassed most of this species' range. Genetic diversities were typically low within locations but high across locations. Moreover, each location had a unique suite of haplotypes not shared among locations, and pairwise φ(ST) values (0.713-0.998) were highly significant between all location pairs. Relationships among phylogroups were well resolved and analysis of molecular variance (AMOVA) revealed strong geographical partitioning of genetic variance among the three river drainage basins surveyed. The genetic differences observed among the populations of E. subtaeniata were likely shaped by the Quaternary landscapes of Indochina and the Sunda Shelf. Historically, the middle and lower Mekong consisted of strongly dissected river valleys separated by low mountain ranges and much of the Sunda Shelf consisted of lowland river valleys that served to connect faunas associated with major regional rivers. It is thus likely that the contemporary genetic patterns observed among populations of E. subtaeniata are the result of their histories in a complex terrain that created abundant opportunities for genetic isolation and divergence yet also provided lowland connections across now drowned river valleys.

Strong population genetic structure and its management implications in the mud carp Cirrhinus molitorella, an indigenous freshwater species subject to an aquaculture and culture-based fishery

This study investigated population genetic structure and diversity of mud carp Cirrhinus molitorella, a species widely used in aquaculture and culture-based fisheries in China and Mekong River riparian countries. Seven newly developed and one published microsatellite DNA markers were used to analyse samples from six wild locations, four hatchery broodstocks and one farmed site from the Mekong, Red and Pearl Rivers. Significant genetic structure was detected in C. molitorella, with isolation-by-distance being a strong force in the Mekong. Pair-wise F(ST) , Fisher's exact tests for population differentiation, permutation tests and individual-based structure analysis all support the recognition of a sample originating from Toul Krasaing Lake (Cambodia) and one between Kratie and Stung Treng (Cambodia) as distinct from the remainder of the sampled range. Samples from the main upper Mekong and the Nam Khan River were significantly differentiated, but on a time scale inferred to be short (i.e. by genetic drift, not sufficient for evolution of new microsatellite alleles). The Mekong stock of C. molitorella was strongly differentiated from those from the Red and Pearl Rivers, inferred to be on an evolutionary time scale. Finer-scale sampling is warranted to further improve the understanding of genetic interactions among fish from the Mekong and its tributaries. Detailed studies on the ecology of C. molitorella (e.g. migration pathways and preferred spawning habitats) would provide useful information to explain the patterns of genetic structure detected here, and deepen insights about evolutionary distinctiveness of the population units.