Fgenetic V ARTATION AMONG GEOGRAPHTCALL Y ISOLATED POPULATIONS of the COMMERCIALLY IMPORT ANT SEA CUCUMBER
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fGENETIC V ARTATION AMONG GEOGRAPHTCALL Y ISOLATED POPULATIONS OF THE COMMERCIALLY IMPORT ANT SEA CUCUMBER. ISOSTICHOPUS FUSCUS. IN THE EASTERN PACIFI<j A thesis submitted to the faculty of San Francisco State University In partial fulfillment of The requirements for The degree Master of Science In Marine Science by Heather Renee Lohr San Francisco. California May.2003 Copyright by Heather Renee Lohr 2003 GENETIC VARIATION AMONG GEOGRAPHICALLY ISOLATED POPULATIONS OF THE COMMERCIALLY IMPORTANT SEA CUCUMBER ISOSTICHOPUS FUSCUS, IN THE EASTERN PACIFIC Heather Renee Lohr San Francisco State University 2003 Understanding population genetic structure of commercially exploited species can aid in the careful exploitation of animal resources while preserving sustainable genetic diversity in natural populations. The mitochondrial control region and cytochrome oxidase subunit I of the sea cucumber, Isostichopus foscus, were explored for intraspecific variation among different subpopulations from the Galapagos Archipelago, mainland Ecuador, and the Gulf of California, Mexico to estimate the level of gene flow among these populations. Pairwise F st values revealed little genetic differentiation and high levels of gene flow between populations from Galapagos Islands and Ecuador (F,, = 0.026, Nm = 18.81). Comparisons of Mexico with Galapagos Islands and Ecuador indicate higher genetic differentiation and little migration (F51 = 0.550, Nm = 0.41; F,, = 0.475, Nm = 0.55 respectively). Phylogenies of control region sequences show Galapagos and Ecuadorian individuals interspersed throughout a single clade and most Mexican sequences grouping into a second clade. These results indicate gene flow between Galapagos Islands and Ecuador either currently or in recent evolutionary history. a correct representation of the content of this thesis. ~Joh DJr.~/ ACKNOWLEDGEMENTS I would like to thank Dr. Jon Geller for his guidance and support over the past few years. I am grateful to Jon for giving me the opportunity to complete a thesis that passes my own personal "so who cares" test. This project involved tons of troubleshooting and Jon was always supportive in letting me do what was necessary in order to get it completed. I am indebted to Dr. Bob Vrijenhoek for his time spent discussing my thesis and assistance in helping me to understand my results. I also thank Dr. Tom Niessen for his critical review of my manuscript. Thanks to Dr. Simona Bartl, Laurie Fitzgerald, Jason Cope, Laurie McConnico, Shannon Johnson, Christy Schnitzler, Chad King, Matt Levey, and Matt Forrest for help and support in all forms from lab to field. Thanks especially to Laurie Fitzgerald for holding my hand while I learned the ways of the lab and for always answering every single question. To Jason Cope for an endless number of discussions of statistical software as I would never have been able to run Arlequin without him. Thanks to MLML and everyone at the labs; I am grateful in more ways than I can ever say. Thanks to Toni Roberts, Dr. Kenneth Coale, and Donna Kline. for their endless support and to Joan Parker and her library staff for always getting in papers faster than I could read them. Finally, I want to thank my family for their unconditional love and support throughout. This project was funded in part by Earl H. and Ethel M. Meyers Oceanographic and Marine Biology Trust, PAD! Project A.W.A.R.E .• and PADI Foundation. v TABLE OF CONTENTS List of Tables ...................................................................... VII List of Figures ..................................................................... viii List of Appendices ................................................................ IX Introduction ........................................................................ 1 Methods ............................................................................ 4 Data analysis .......................................................... 6 Genetic diversity ...................................................... 7 Population structure .................................................. 7 Results .............................................................................. 8 Sequence data and phylogenetic analysis ......................... 8 Genetic diversity ...................................................... 10 Genetic structure ...................................................... 10 Discussion .......................................................................... 12 History of the Galapagos Islands fishery ......................... 12 Clarification of taxonomic uncertainty using COl .............. : 14 Genetic structure and geographical connections ................. 15 Conclusions ........................................................... 17 References .......................................................... · · · · · · · · · · · · · · ·· 19 VI LIST OF TABLES Table Page 1. Sample ID, geographic location, and sequences obtained from I. fuscus individuals .................................................. 24 2. Genbank ID, sequence position, and references for COl sequence fragments from sea cucumber sequences .......................... 26 3. Control region genetic diversity measures and Tajima's test of neutrality ............................................................... 27 4. Control region pairwise F 51 values from L foscus populations ..... 28 5. Control region genetic distance measures within and among populations of L foscus from Galapagos Archipelago .......... 29 6. Control region genetic distance measures within and among populations of L fuscus from different regions .................. 30 7. COl genetic distance measures within and among populations of L fuscus from different regions ................................... 31 8. Pairwise distance matrix for fragment of COl gene for groups of sea cucumber sequences.............................................. 32 9. Analysis of variance (AMOVA) from control region sequences from three I. fuscus populations..................................... 33 10. Analysis of variance (AMOVA) from control region sequences from two I. .fitscus regions ..................................·......... 34 Vll LIST OF FIGURES Figure Page 1. Neighbor-joining phylogram of L fuscus control region sequences 35 2. Neighbor-joining bootstrap tree of L fuscus control region sequences. 36 3. Maximum parsimony best tree of L fitscus control region sequences. 3 7 4. Maximum likelihood phylogram of L fuscus control region sequences .................................... ~........................ 38 5. Neighbor-joining phylogram of sea cucumber COl sequences ..... 39 6. Neighbor-joining bootstrap tree of sea cucumber COl sequences ... 40 7. Maximum parsimony best tree of sea cucumber COl sequences .... 41 8. Maximum likelihood phylogram of sea cucumber COl sequences. 42 Vlll LIST OF APPENDICES Appendix Page ]. Mitochondrial control region sequence alignment for I. fuscus ..... 43 2. Mitochondrial COl sequence alignment for I. foscus and various other sea cucumbers................................................. 53 IX Introduction: Poor management of animal resources. lack of incentive for conservation, and lack of collaboration all affect sustainable exploitation of animal species (Rosser & Mainka 2002). Over-exploitation has been identified as the major threat to 1/3 of bird and mammal species currently in danger of extinction (Rosser & Mainka 2002). Habitat fragmentation or human disturbance resulting in species decline can lead to deleterious genetic changes, which may affect fitness and adaptive potential of individuals (Sherwin & Moritz 2000). A goal in conservation is to avert or remedy the decline of genetic variation; monitoring and understanding population genetic structure can aid in managing careful exploitation of resources and preserving sustainable genetic diversity in populations of commercially important species (Sherwin & Moritz 2000). Isostichopus fuscus (Ludwig 1875) is a commercially important shallow water species of sea cucumber in the eastern Pacific ranging from the northern Gulf of California, Mexico south to Ecuador (Herrero-Perezrul et al. 1998, 1999). Of the 1100 species of sea cucumbers in the world, only I 0- 20 are commercially harvested; fisheries off the coast of Ecuador and in the Galapagos Islands are comprised of only I. .fi1scus (Jenkins & Mulliken 1999). This sea cucumber is large, 19- 25 em in length, and abundant on. rocky coral bottoms (Herrero-Perezrul et al. 1999). Its shallow distribution and sedentary lifestyle make it an easy target for collection in large numbers by divers. Recent intense commercial fishing pressures on this animal resulting in an end of season decrease in CPUE (catch per unit effort), raised questions I of the stability and sustainability of the Galapagos Islands sea cucumber population (Conand & Byrne 1993, Conand 1997). Isostichopus foscus, like most other holothurians, reproduces by mass spawning of gametes and has a pelagic larval period (Herrero-Perezrul et al. 1999). It is often assumed that an animal with a long-lived pelagic larval stage must have high dispersal capabilities and a high level of gene flow among populations (Scheltema 1986, Scheltema et al. 1996); however, there are many barriers to gene flow or survival of colonizing larvae (Gartner-Kepkay et al. 1983, Hedgecock 1986, Scheltema 1986, Palumbi 1994, 1995, Edmands et al. 1996, Geller 1998). Barriers to dispersal may be physical, such as sharp temperature changes or current patterns (Hedgecock