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Species Lists, Dna Barcodes, and Images for Ornamental Fish

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Species Lists, Dna Barcodes, and Images for Ornamental Fish DEVELOPING MONITORING TOOLS FOR TOMORROW’S INVASIVES: SPECIES LISTS, DNA BARCODES, AND IMAGES FOR ORNAMENTAL FISH YI YOUGUANG NATIONAL UNIVERSITY OF SINGAPORE 2014 DEVELOPING MONITORING TOOLS FOR TOMORROW’S INVASIVES: SPECIES LISTS, DNA BARCODES, AND IMAGES FOR ORNAMENTAL FISH YI YOUGUANG (B.Sc. (Hons 2nd Upper), NUS) A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF BIOLOGICAL SCIENCES NATIONAL UNIVERSITY OF SINGAPORE 2014 DECLARATION I hereby declare that this thesis is my original work and it has been written by me in its entirety. I have duly acknowledged all the sources of information which have been used in the thesis. This thesis has also not been submitted for any degree in any university previously. ___________________ YI YOUGUANG 31 March 2014 ACKNOWLEDGEMENTS I would like to thank the PI and colleagues in the Evolutionary Biology Laboratory for providing valuable help and resources, and consultation during my course of research. I especially like to thank Miss Amrita for providing valuable assistance in bioinformatics to make many of my research analyses possible. I will like to thank Dr Ang Yuchen for providing valuable opinion on the aesthetics and effective data presentation in this thesis. Both Amrita, Jayanthi and Yuchen have made substantial contributions in providing the computational scripts and species page templates needed for mass production of ornamental fish species pages. I would like to thank Amrita, Yuchen and Kathy for editing and doing spell check for the thesis. I would like to thank Jayanthi for contributing her computer for data analysis. I will like to thank my supervisor Prof. Rudolf Meier for his patients and valuable consultations, and Dr Tan Heok Hui from the Raffles Museum of Biodiversity Research (RMBR) for providing his taxonomic expertise in fish identification, specimens and network in the ornamental trade to obtain specimens, and valuable photography tips. I Table of Contents Summary……………………………..………………………………….…IV List of Tables………………..……………………………………………...V List of Figures……………………………………………………..……….VI Publications included in this thesis……………………………………...VII 1. Introduction: DNA barcoding: current applications and future developments………………………………………………………..1-18 1.1. Introduction to DNA barcoding and its applications…….........…2 1.2. Establishing what are the species in the trade…………..………8 1.3. DNA barcoding for monitoring invasive species………..……….9 1.4. References for chapter I………………………..........................13 2. Chapter II: Tracking a moving target: ornamental fish in the pet trade......................................................................................019-057 2.1. Introduction………………………………….…………………….25 2.2. Materials and Methods…………….…………………..…………22 2.3. Results………………………….………………………………….29 2.3. Discussions…………………………………………………….….38 2.4. References for chapter II…………………………...……...…….44 Appendix I……………………………………………………...……….49 3. Chapter III: Testing the effectiveness of COI barcodes for the identification of native and invasive freshwater diversity of Singapore………………………………..………………....……050-089 3.1. Introduction………………………………………………….…….53 3.2. Materials and Methods………...…………………………………58 3.3. Results…………………….……………………………………….66 3.4. Discussions………………….…………………………………….73 3.5. Conclusions……………………………………………………….79 II 3.6. References………………………………………………………...81 Appendix II……………………………………………………………...87 4. Chapter IV: A comprehensive DNA barcode database for freshwater Aquarium fish: a pragmatic option to increase species coverage…………………………………………...…………….090-134 4.1. Introduction………………………………………….…………….93 4.2. Materials and Methods……………………………………...……98 4.3. Results………………………………….………………………..110 4.4. Discussions……………………………………………………...116 4.5. Conclusions……………………………………………………...128 4.6. References……………………………………………………….129 5. Chapter V: Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade (Publication)……………………135-147 6. Chapter: VI: Conclusions………………………...………..…...148-152 III Summary Ornamental fish are a major source of invasive species in freshwater habitats. In order to control and monitor introductions, it is important to know which species are in the trade and to develop identification tools for these species. Here I first study the species diversity in the trade by comparing two published lists with trade data for Singapore (2009-2011). I establish that a very large number of species (4769) are being traded, the lists and trade data are inconsistent, many species in Singapore’s trade are wild-caught, and that new species are continuously added. I then image and generate DNA barcodes for 1448 specimens belonging to 554 species of which 334 species had not previously been barcoded. The images are used to build an online image database for ornamental fish while the DNA barcodes are used for testing species-specificity at three levels; local, global, and systematic. First, I establish whether DNA barcodes can be used for identifying the 89 of the 105 freshwater fish species living in Singapore. An identification efficiency of 77% to 89% indicates that COI can be used to allocate specimen to species at an island scale. I then determine identification success rates of DNA barcodes at a global scale based on all my data and all available COI sequences in Genbank. An identification efficiency of 77% to 91% indicates that COI can be used to allocate specimen to species at a global scale. Lastly, I collaborate with colleagues in New Zealand to test whether DNA barcodes are diagnostic for cypriniform fishes. An identification IV efficiency of 90% to 99% is established for the 172 ornamental cyprinid fish species sampled. Results indicate that COI can be used effectively for identifying fish at local, global and systematic level. Lists of tables Table 2.3.1.I. Species distribution within families for ornamental fish recorded from the Singapore trade………………..…………………………32 Table 3.3.2.I Primers utilized for amplification of fish cox1 and cytb…….60 Table 3.4.3.I: Identification efficiency for the different methods of assigning species to specimen………………………...…………………………………69 Table 4.I. Identification efficiencies determined for COI dataset of ornamental fish in the Singapore trade……………………………….…...112 Table 4.II. Identification efficiencies of ornamental fish COI upon querying against global fish COI database ………………………………………….113 Table 4.III.Identification efficiency determined for the global fish COI dataset…………………………………………………….…………………..113 V Lists of figures Figure 2.3.1.1: Freshwater fish recorded in the global ornmental trade from 2006-2012……………………………………………...…………………29 Figure 2.3.1.2: Freshwater fish recorded in the Singapore ornamental trade from 2007 to 2012……………………………………………………………………………..30 Figure 2.3.2.1: Regional distribution of aquarium fish in the Singapore trade……………………………………………………………………………..31 Figure 2.3.2.3: Distribution of wild-caught and captive-captive-bred species according to supplier countries……………………………………..34 Figure 2.3.3.1: The status of species identification in Qian Hu fish farm..37 Figure. 3.4.1. The optimal cutoff point for the BCM.…….…………………66 Figure 3.4.2. Percentage of sequences identified using BRONX at different score thresholds………………………………...…………………...67 Figure 3.4.3.1: Identification efficiency for the different methods of assigning species to specimen………………………….……………………69 Figure 4.2.6.2.2. Percentage of sequences 1) correctly identified 2) incorrectly identified and 3) unidentified for the Global COI dataset at various score thresholds for BRONX…………………………………..…..107 Figure 4.3.1. Species coverage of freshwater aquarium fish in Genbank.………………………………………………………………………110 Figure 4.3.3. Publication trends of publications associated with environmental genomics (eDNA) & fish DNA barcoding..……………….114 Figure 4.4.1: Exemplar presentation of habitus images……………...….122 Figure 4.4.2: A visual guide to using the visual specimen database (specimen browser) website………………………….…………………..…125 Figure 4.4.3: A visual guide to using the visual specimen database (specimen comparator) website………………………………………….…126 VI Publication in this thesis 1. Collins, R. A., K. F. Armstrong, R. Meier, Y. Yi, S. D. J. Brown, R. H. Cruickshank, S. Keeling and C. Johnston (2012). "Barcoding and Border Biosecurity: Identifying Cyprinid Fishes in the Aquarium Trade." Plos One 7(1). VII CHAPTER I __________ General Introduction 1 1.1. Introduction to DNA barcoding and its applications One of the main problems faced by biologists today is the taxonomic impediment; there are simply too many species, but too few taxonomists to discover, describe and identify all the specimens that are collected by applied biologists such as those interested in bio- protection (Ball & Armstrong, 2008; Bleeker et al., 2008; Chown et al., 2008), conservation biologists (Blaxter, 2006; Holmes et al., 2009; Logan et al., 2008) and scientists identifying food items (Logan et al., 2008; Yancy et al., 2008). They all agree that there are too few taxonomic experts thus creating an imbalance between needs and availability of taxonomic expertise (Tautz et al., 2003). One solution that is promoted by Hebert (2003) under the name “DNA barcoding” is to use 650bp piece of cytochrome oxidase I (COI) to identify and delimit species; i.e., DNA barcoding has been proposed as a remedy for resolving the taxonomic impediment (Hebert et al., 2003a; Hebert et al., 2003b). Hebert (2003) assumes that inter- and intraspecific distances are non-overlapping constituting a barcoding gap; a senario which makes
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