Appendix 3: Example Thesis Proposal

Transcription

1 Appendix 3: Example Thesis Proposal Progress Report PHYLOGENETIC AND BIOGEOGRAPHIC ANALYSES OF THE GREATER ANTILLEAN AND MIDDLE AMERICAN CICHLIDAE Prosanta Chakrabarty Department of Ecology and Evolutionary Biology Museum of Zoology, Fish Division Ann Arbor, MI Achieved Candidacy: Winter 2003 Years in PhD Program: 4 th year begins Fall 2004 Proposed Date of Completion: 5 th year/winter Term 2006 A dissertation proposal submitted for the yearly meeting of the following thesis committee: Dr. William L. Fink (Chairman) Dr. Gerald R. Smith (EEB member) Dr. Diarmaid Ó Foighil (EEB member) Dr. Daniel C. Fisher (Cognate member) Chapter I: Chapter II: Chapter III: Chapter IV: CICHLIDBIOGEOGRAPHY:COMMENT AND REVIEW (published) TAXONOMIC REVIEW OF HISPANIOLAN CICHLIDS (to be submitted 09/04) RELATIONSHIPS AND BIOGEOGRAPHY OF ANTILLEAN CICHLIDS (in prep.) TOTALEVIDENCE PHYLOGENETIC ANALYSIS OF MIDDLE AMERICAN CICHLIDS (in prep.) TIME LINE FOR THESIS COMPLETION POSSIBLE APPENDICES CHAPTERS BUDGET SOURCES OF FUNDING BIBLIOGRAPHY A Guide to Academia: Getting into and Surviving Grad School, Postdocs, and a Research Job, First Edition. Prosanta Chakrabarty. C 2012 John Wiley & Sons, Inc. Published 2012 by John Wiley & Sons, Inc. 131

2 132 Appendix 3: Example Thesis Proposal Progress Report Publications Activities and accomplishments since last meeting (Winter Term 2003) Chakrabarty, P. (2004) Cichlid biogeography: comment and review. Fish and Fisheries 5 (2): Chakrabarty, P. (accepted pending revisions) Testing past conjectures regarding the morphological diversity of rift lake cichlids. Copeia Pikitch, E.K., Doukakis, P., Lauck, L., Chakrabarty, P. (in review) Sturgeon and paddlefish fisheries of the world: conservation strategies for the future. Fish and Fisheries (submitted August 2003) Published Abstracts Chakrabarty, P. (2004) Abstract: Relationships and biogeography of Antillean Cichlids. In: Stevenson, D. W., Abstracts of the 22 nd Annual Meeting of the Willi Hennig Society. Cladistics 20 (2004): Conference Presentations Chakrabarty, P Relationships of Antillean cichlids and biogeographic consequences. Annual Meeting of the American Society of Ichthyologists and Herpetologists, Manaus, Brazil (26 June 1 July 2003). Chakrabarty, P Relationships and Biogeography of Antillean Cichlids. Willi Hennig Society; Hennig XXII (20 24 July 2003). Chakrabarty, P Systematics and historical biogeography of the Neotropical cichlid genus Nandopsis. Annual Meeting of the American Society of Ichthyologists and Herpetologists, Norman, Oklahoma (26 31 May 2004). Field Experience Winter 2004 January 4 14, Dominican Republic, collecting freshwater and marine spp.10 localities, for morphological and molecular analyses Grants 2003 Rackham Travel Grant, $ 900 for travel to ASIH 2003 EEB Travel Grant, for the amount of $ 100 for presenting at Hennig XXII 2003 Rackham Discretionary Fund, for $ 1250 for research equipment 2004 Rackham Travel Grant, $ 400 for travel to ASIH Museum of Zoology Hinsdale Scholarship Award $2,247 for research 2004 EEB Block Grant/Okkelberg Award $1,257 for research

3 Appendix 3: Example Thesis Proposal 133 Chapter I: CICHLIDBIOGEOGRAPHY:COMMENT AND REVIEW (1) The distribution of the Cichlidae reflects a pattern congruent with the break-up of Gondwana. (2) Current molecular clock estimates and the known fossil record underestimate the age of Cichlidae. Phylogenetic analyses dealing with disjunct distributions (distributions that require marine dispersal or vicariant events) are reviewed for the Cichlidae. The most corroborated relationship between clades across a Gondwanan disjunction is the sister relationship between Indian and Malagasy cichlids. The minimum age of the Cichlidae as implied by the fossil record is at odds with the timing of the Cretaceous break of the Indian- Madagascar landmass. All well sampled phylogenies for this group fit a pattern reflecting Gondwanan break-up. Grounds for strictly dispersalist hypotheses are not well founded for any cichlid disjunct distribution, leaving vicariance alternatives as the only explanation. Status: Published Chakrabarty, P Cichlid biogeography: comment and review. Fish and Fisheries 5: Chapter II: TAXONOMIC REVIEW OF HISPANIOLAN CICHLIDS (1) Nandopsis vombergae is a junior synonym of Nandopsis haitiensis. (2) Cichlasoma woodringi is a member of the genus Nandopsis. Nandopsis vombergae (Ladiges 1938) is one of three described cichlid species from Hispaniola. This species, known only from its holotype, is a junior synonym of the widespread island species Nandopsis haitiensis (Tee-Van 1935). The holotype lacks apomorphies that could be used to discriminate it from N. haitiensis. Meristic counts are equivalent, and a Principal Components Analysis (PCA) was unable to discriminate between these two species. The Miocene fossil, Cichlasoma woodringi Cockerell 1928 closely resembles Nandopsis haitiensis; however, poor preservation precludes an adequate assessment of its status as a distinct species. Diagnostic characters of Nandopsis are also described for the first time.

4 134 Appendix 3: Example Thesis Proposal Status: ready for submission to American Museum Novitates in 09/04 Chapter III: RELATIONSHIPS AND BIOGEOGRAPHY OF ANTILLEAN CICHLIDS (1) The phylogeny of the Greater Antillean cichlids recovers a pattern that is congruent with either (a) an Early Oligocene landbridge connecting South America to the Greater Antilles (b) a vicariance event between these islands and Middle America in the Mesozoic (c) or marine dispersal Geological reconstructions proposed for the Greater Antilles fit into two major categories, each with different biogeographic consequences. One category of reconstructions suggests that an Early Oligocene landbridge connected the Greater Antillean islands to northern South America (Iturralde- Vinent and MacPhee 1999). The other suggests a period of coalescence in the Mesozoic of some of the Antillean islands with portions of Central America (Rosen 1975). A molecular phylogenetic analysis based on nuclear and mitochondrial genes that includes the endemic cichlid faunas of the Greater Antilles, as well as from South and Central America, results in a phylogeny that is congruent with the later reconstruction. Status: in prep., data has been collected, presented at ASIH 2003, Hennig 2003 Chapter IV: TOTALEVIDENCE PHYLOGENETIC ANALYSIS OF MIDDLE AMERICAN CICHLIDS (1) The eight sections of Cichlasoma are monophyletic C. (Amphilophus) C. (Archocentrus) C. (Herichthys) C. (Nandopsis) C. (Paraneetroplus) C. (Theraps) C. (Thorichthys) C. (insertae sedis) The majority of the nearly 100 species of Middle American cichlids were placed in the catch-all genus Cichlasoma (Regan ). When

5 Appendix 3: Example Thesis Proposal 135 Figure A3.1 Preliminary phylogenetic analysis of Middle American cichlids. Geographically South American species that are nested within the Middle American group are optimized as Middle American cichlids, making this group monophyletic. Kullander (1983) restricted Cichlasoma to a dozen South American species, the Middle American forms (now recognized as Cichlasoma ) were left without generic placement. Little work has been done to determine phylogenetic relationships of the Middle American cichlids. Miller (1966, 1976) placed many of the Middle American cichlids into eight sections of Cichlasoma ; however, these sections are informal assemblages of species that share similarities in trophic morphology. A preliminary molecular analysis finds that the Middle American cichlids form a clade that is sister to the Cuban cichlids and that none of the Cichlasoma sections are monophyletic (Fig. A3.1). A phylogeny will be constructed for the Middle American cichlids using mitochondrial genes COI (Folmer et al. 1994) and 16S (Koucher et al. 1989), nuclear genes TMO4C4 (Streelman and Karl 1997), Histone H3 (Colgan et al. 1998), S7 (Chow and Hazama 1998), MN32-2 (Buonaccorsi et al. 1999) and Sactin (McDowell and Graves 2002) as well as over 100 morphological characters from external features, oral jaw ligaments, neurocranial frontal pores, swimbladder extensions and the pharyngeal apophysis. Status: This chapter is incomplete and will require collection of wild caught specimens and additional molecular work and morphological. See budget and timeline for details. Time Line for Thesis Completion Fall 2004: Funding as Teaching Assistant Submit Chapter II to American Museum Novitates Send in revision of possible appendices chapter to Copeia Reapply for NSF Doctoral Dissertation Improvement Grant Apply for Rackham Predoctoral Fellowship Award Continue morphological work for Chapter IV

6 136 Appendix 3: Example Thesis Proposal Winter 2005: Funding as Research Assistant Possible collection trip to Nicaragua, Mexico or Cuba Submit Chapter III for Molecular Phylogenetics and Evolution Complete molecular work for Chapter IV Continue morphological work for Chapter IV Spring/Summer 2005 Present Phylogeny of Middle American cichlids at ASIH Complete morphological work for Chapter IV Fall 2005 Write up Chapter IV and submit Write up dissertation and submit Apply for NSF Postdoctoral Fellowship Winter 2006 Defend dissertation Possible Appendices Chapters A B C Chakrabarty, P. (accepted pending revisions) Testing past conjectures regarding the morphological diversity of rift lake cichlids. Copeia Pikitch, E.K., Doukakis, P., Lauck, L., Chakrabarty, P. (in review) Sturgeon and paddlefish fisheries of the world: conservation strategies for the future. Fish and Fisheries Fink, W.L. and Chakrabarty, P. (in prep.) Phylogeny of the piranha genus Sarrasalmus. Budget Laboratory Work (estimated for 150 taxa) Quantity Total Price DNA extraction Qiagen Dneasy kit (50 columns) 2 $ ml microcentrifuge tubes 10 cases $ 130 Micropippette tips ($55 per rack of 1000) 10 $ 550 Polymerase Chain Reaction Platinum Taq Polymerase (50 units@ $53.63 ea) 10 $ 540

7 Appendix 3: Example Thesis Proposal 137 DNA purification QIAQuick gel extraction kit (250 columns) 5 $ 1,674 Sequencing Fees Sequencing Core lane fees (8 lanes per $3/lane) 1200 $ 3,600 Purchasing of Voucher specimens $ 10 average per specimen (50 to 70 specimens, plus shipping) $ 400 Conferences ASIH 2005 (Tampa, Florida) Evolution/SSB 2005 (University of Alaska, Fairbanks) ASIH 2006 (New Orleans, Louisiana) Cost: $2000 Potential Field Work Cuba (Transport, lodging, food) Nicaragua (Transport, lodging, food) Mexico (Transport, lodging, food) Cost per trip: $ 2000 TOTAL $10,994 Sources of Funding for Research: Rackham Block Grant, Rackham Discretionary Funds, Hinsdale-Walker Grants, National Science Foundation Dissertation Improvement Grant, American Society of Ichthyology and Herpetology Gaige Award