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Iranawati, Feni (2014) an Assessment of the Geographical Scale of Recurrent Gene flow in Wild Populations of Two Species of Mekong River Carps (Henicorhynchus Spp.)

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Iranawati, Feni (2014) an Assessment of the Geographical Scale of Recurrent Gene flow in Wild Populations of Two Species of Mekong River Carps (Henicorhynchus Spp.) This may be the author’s version of a work that was submitted/accepted for publication in the following source: Iranawati, Feni (2014) An assessment of the geographical scale of recurrent gene flow in wild populations of two species of Mekong River carps (Henicorhynchus spp.). PhD thesis, Queensland University of Technology. This file was downloaded from: https://eprints.qut.edu.au/71217/ Notice: Please note that this document may not be the Version of Record (i.e. published version) of the work. Author manuscript versions (as Sub- mitted for peer review or as Accepted for publication after peer review) can be identified by an absence of publisher branding and/or typeset appear- ance. If there is any doubt, please refer to the published source. An assessment of the geographical scale of recurrent gene flow in wild populations of two species of Mekong River Carps (Henicorhynchus spp.) Feni Iranawati Earth, Environmental and Biological Sciences Science and Engineering Faculty Queensland University and Technology Brisbane, Australia This dissertation is submitted in fulfilment of requirements for the degree of Doctor of Philosophy March 2014 Keywords Mekong River, freshwater fish, mud carp, microsatellite DNA, population structure, biogeography, gene flow, fisheries management, genetic diversity, drainage evolution, Indochina, Khorat Plateau, Tonle Sap Lake, SSR marker, Bayesian analysis, Neighbour joining network. i Abstract The Mekong is the most productive river fishery in the world, and such as, the Mekong River Basin (MRB) is very important to very large human populations across the region as a source of revenue (through fishing and marketing of aquatic resources products) and as the major source for local animal protein. Threats to biodiversity in the MRB, either to the fishery sector itself or to other sectors are a major concern, even though currently, fisheries across this region are still very productive. If not managed properly however, fish population declines will cause significant economic impact and affect livelihoods of local people and will have a major impact on food security and nutrition. Biodiversity declines will undoubtedly affect food security, income and socio- economic status of people in the MRB that depend on aquatic resources. This is an indicator of unsustainable development and hence should be avoided. Genetic diversity (biodiversity) that can be measured using techniques based on DNA markers; refers to variation within and among populations within the same species or reproductive units. In a population, new genetic variation is generated by sexual recombination contributed by individuals with mutations in genes and chromosomes. Over time, populations of a species that are not reproducing together will diverge as differential impacts of selection and genetic drift change their genetic attributes. For mud carp (Henicorhynchus spp.), understanding the status of breeding units in the MRB will be important for their long term persistence, sustainability and for implementing effective management strategies. Earlier analysis of stock structure in two economically important mud carp species (Henicorhynchus siamensis and H. lobatus) in the MRB completed with mtDNA markers identified a number of populations of both species where gene flow had apparently been interrupted or reduced but applying these data directly to management unit identification is potentially compromised because information was only available about female dispersal patterns. The current study aimed to address this problem and to fully assess the extent of current gene flow (nDNA) and reproductive exchange among selected wild populations of two species of carp (Henicorhynchus spp.) of high economic importance in the MRB using combined ii mtDNA and nDNA markers. In combination, the data can be used to define effective management units for each species. In general, nDNA diversity for H. lobatus (with average allelic richness (A) 7.56 and average heterozygosity (Ho) 0.61) was very similar to that identified for H. siamensis (A = 6.81 and Ho = 0.75). Both mud carp species show significant but low FST estimates among populations as a result of lower genetic diversity among sampled populations compared with genetic diversity within populations that may potentially mask any ‘real’ population structure. Overall, population genetic structure patterns from mtDNA and nDNA in both Henicorhynchus species were largely congruent. Different population structures however, were identified for the two Henicorhynchus species across the same geographical area. Apparent co-similarity in morphology and co-distribution of these two relatively closely related species does not apparently imply parallel evolutionary histories. Differences in each species population structure likely reflect historical drainage rearrangement of the Mekong River. The data indicate that H. siamensis is likely to have occupied the Mekong system for much longer than has H. lobatus in the past. Two divergent stocks were identified for H. lobatus in the MRB below the Khone Falls while a single stock had been evident in the earlier mtDNA study. This suggests that the two Henicorhynchus species may possess different life history traits and that different patterns of gene flow has likely influenced modern genetic structure in these close congeners. In combination, results of the earlier mtDNA and the current study have implications for effective management of both Henicorhynchus species across the MRB. Currently, both species are essentially treated as a single management unit in this region. This strategy may be appropriate for H. lobatus as a single stock was evident in the main stream of the MRB, but may not be appropriate for H. siamensis as more than a single stock was identified across the same range for this species. Management strategies should consider this difference to conserve overall biodiversity (local discrete populations) and this will include maintaining natural habitat and migration pathways, provision of fish sanctuaries (refuges) and may also require close monitoring of any stock declines, a signal that may require effective recovery strategies. iii Table of Content Keywords ...................................................................................................................... i Abstract ....................................................................................................................... ii Table of Content ........................................................................................................ iv List of Tables ............................................................................................................. vii List of Figures .......................................................................................................... viii Statement of Original Authorship ............................................................................ x Acknowledgements: .................................................................................................. xi Chapter 1: General introduction .............................................................................. 1 1.1. Population structure and gene flow ................................................................. 2 1.2. Gene flow estimation ....................................................................................... 5 1.3. Phylogeography and genetic structures of freshwater species ........................ 7 1.4. Microsatellite markers used for estimating population differentiation ......... 13 1.5. Importance to conservation and management ............................................... 15 1.6. Biology and previous studies of Henicorhynchus spp. ................................. 18 1.7. Current study ................................................................................................. 22 Chapter 2: Materials and Methods ......................................................................... 25 2.1. Rapid development of nDNA genetic markers for Henicorhynchus spp. using 454 pyrosequencing ....................................................................................... 26 2.1.1. Methods ................................................................................................ 26 2.1.2. Results and Discussion ......................................................................... 29 2.2. Sample collection and general statistical data analyses employed ................ 37 2.2.1. Sample collection ................................................................................. 37 2.2.2. Sample identification ............................................................................ 37 2.2.3. Diversity ............................................................................................... 38 2.2.4. Population structure .............................................................................. 39 Chapter 3: Patterns of genetic structure in H. siamensis ..................................... 43 3.1. Introduction ................................................................................................... 43 iv 3.2. Methods ......................................................................................................... 48 3.2.1. Sample Information .............................................................................. 48 3.2.2. Genotyping ........................................................................................... 49 3.2.3. Data Analysis ......................................................................................
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