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Download the File COMPARISON OF MITOCHONDRIAL AND NUCLEAR GENETIC VARIATION OF COMMON ACARTIA SPECIES IN THE SAN FRANCISCO ESTUARY A Thesis submitted to the faculty of San Francisco State University AS In partial fulfillment of the requirements for 3 G the Degree Master of Science In Biology: Ecology, Evolution, and Conservation Biology by KeChaunte Amrie Johnson San Francisco, California December 2017 Copyright by KeChaunte Amrie Johnson 2017 CERTIFICATION OF APPROVAL I certify that I have read COMPARISON OF MITOCHONDRIAL AND NUCLEAR GENETIC VARIATION OF COMMON ACARTIA SPECIES IN THE SAN FRANCISCO ESTUARY by KeChaunte Amrie Johnson, and that in my opinion this work meets the criteria for approving a thesis submitted in partial fulfillment of the requirement for the degree Master of Science in Biology: Ecology, Evolution and Conservation Biology at San Francisco State University. C. Sarah Cohen, Ph.D. Professor, Biology Wim Kimmerer, Ph.D. Eric Routman, Ph.D. Professor, Biology COMPARISON OF MITOCHONDRIAL AND NUCLEAR GENETIC VARIATION OF COMMON ACARTIA SPECIES IN THE SAN FRANCISCO ESTUARY KeChaunte Amrie Johnson San Francisco, California 2017 Delineation of Acartia spp. is essential to assess the biodiversity of copepods in marine ecosystems. Previous phylogenetic analyses show lack of monophyly for A.tonsa and A.hudsonica. Reported average DNA sequence divergence among some Acartia spp. includes >16% for mitochondrial cytochrome oxidase c (COI) and 13%-25% for 18S rRNA. We investigated the genetic diversity of SFE Acartia in comparison to other Acartia spp. sequences from Genbank. Copepods were collected from the SFE across a range of temperatures and salinities and sequenced at COI and nuclear 18S loci for Bayesian phylogenetic comparison. We found £23% COI divergence and >35% 18S divergence among paired comparisons of A. tonsa, A. hudsonica and A. californiensis. Acartia hudsonica SFE haplotypes clustered more closely with northeast Pacific coast (-25% COI divergence) than with northeast Atlantic (-30% divergence) samples. Acartia californiensis from SFE showed <13% divergence in comparison with Genbank haplotypes. SFE and Atlantic coast A. tonsa were -15% 18S and 31-33% COI divergent. These results support high sequence divergence among Acartia species. Further analysis of additional loci is needed to understand the phylogenetic and population structure of SFE Acartia species relative to other populations. I certify that the Abstract is a correct representation of the content of this thesis. Date ACKNOWLEDGEMENTS I would like to thank members of the Cohen Lab and the Kimmerer Lab for help with sample collections. I would also like to thank members of the Cohen Lab for gene lab and data analysis training. I would like to thank Eric Routman, Wim Kimmerer and Frank Cipriano for helpful discussion. This work was conducted at the RTC Gene Lab, supported by the SFSU NIH RISE Fellowship (KJ), RTC NSF FSML Grant No. 0435044 (CSC), the Koret Foundation, Col. John Kern, RTC, the Biology Department, and the SFSU College of Science and Engineering. Funding was provided by SFSU IRA (KJ), RTC Bay Scholarship (KJ), CSU COAST funding (KJ), and CSC start-up funds, SFSU. TABLE OF CONTENTS List of Tables.......................................................................................................................... vii List of Figures........................................................................................................................ viii List of Appendices...................................................................................................................ix Introduction................................................................................................................................ 1 Method....................................................................................................................................... 4 COI Amplification........................................................................................................5 18S rDNA Amplification............................................................................................. 5 Sequencing Reactions.................................................................................................. 6 Population Genetic Analysis........................................................................................6 Phylogenetic Analysis..................................................................,............................... 6 Results........................................................................................................................................ 7 Phylogenetic Analysis of 18S and C O I......................................................................8 Genetic Differentiation Across the 18S clades and COI clades...............................9 Discussion................................................................................................................................ 10 18S Phylogenetic Analysis is Concordant with Monophyly.................................. 11 COI Phylogenetic Analysis Shows Highly Divergent Polyphyletic Clades.......... 11 Mixed COI Clades Contain Multiple Acartia Species.............................................12 Discordance Explanations.......................................................................................... 13 Population Genetic Analysis Suggest a Population Expansion.............................. 16 Conclusion............................................................................................................................... 16 Reference................................................................................................................................. 15 Appendices...............................................................................................................................40 LIST OF TABLES Table Page 1. SFE samples and NCBI reference sequences........................................................ 27 2. 18S and COI primer sets and references................................................................ 30 3. Mean pairwise divergence among 18S clades....................................................... 31 4. Summary of COI statistics of Acartia species....................................................... 31 5. Plankton tow log for SFE........................................................................................ 32 6. Clade composition for 18S and COI phylogenetic analysis.................................. 32 7. Estimates of evolutionary divergence over sequence pairs between COI clades. 37 LIST OF FIGURES Figures Page 1. Map of SFE sampling locations................................................................................... 38 2. Map of sampling locations for NCBI references........................................................39 3. Phylogenetic reconstructions of 18 S and COI............................................................40 viii LIST OF APPENDICES Appendix Page 1. 18S Bayesian Phylogenetic Reconstruction...............................................................41 2. COI Bayesian Phylogenetic Reconstruction............................ 42 1 Introduction Estuarine and Bay habitats provide useful models for studying cryptic species and speciation events due to fluctuating environmental factors such as salinity, temperature, pH and overall water quality (Miller 1983; Bilton et al. 2002; Caudill and Bucklin 2004; Vanelslander et al 2009; Vieira et al. 2015). Cryptic species often are found to co-occur in estuarine ecosystems that may restrict gene flow; ultimately creating genetically distinct populations divergent from their currently recognized species designation (Bilton et al. 2002). Early indicator organisms such as copepods are ideal study organisms in estuaries due to their vast abundance, broad distribution, and position in the marine food changes (Raisudden et al. 2007; Alexander et al. 2015; Sun et al. 2015; Vieira et al. 2015; Menendez et al. 2015). The biological and ecological cryptic diversity of the Calanoid copepod genus Acartia is likely due to estuarine environmental variability (Sullivan and McManus 1986; Bilton et al. 2002; Sullivan et al. 2007). Acartia is a highly abundant and economically important copepod that is often the subject of estuarine ecological and population genetic studies. Acartia species are integral to the oceanic food chain as grazers on phytoplankton, and as a major food source for fish (Mauchline 1998; Turner and Tester 1989). Acartia species are involved in the cycling of nutrients and energy in marine ecosystems forming a link between primary and tertiary production (Turner and Tester 1989; Mauchline 1998; Miller and Roman 2008) Acartia have a broad range of salinity and temperature tolerance which results in Acartia species co-occuring within a single estuary (Ueda 1987; Sullivan et al. 2007; Danilo et al. 2008). Acartia species are broadly distributed in the coastal waters of the world’s continents. Acartia hudsonica occurs along the Atlantic and Pacific coasts of North America (Bradford 1976) and Japan (Ueda 1986), while A.californiensis is restricted to the North American Pacific coast from Yaquina Bay, Oregon to the Gulf of California (Frolander et al. 1973; Pace 1978; Hutchinson, 1981; Ambler et al. 1985; Razouls et al. 2005-2017). Acartia tonsa has been reported from North and South American, Asian, African and European coastal areas (Mauchline 1998). Many cryptic species of Acartia are found in temperate
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