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Christine Chessler

A Brief Molecular Phylogeny focused on Twenty-Nine Species within the Testudinidae Family using Mitochondrial Cytochrome b Gene. Christine Chessler. Introduction. Family Testudinidae Land-based tortoises Widely distributed & recognized Majority in Africa & Asia Few in America & Europe

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Christine Chessler

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  1. A Brief Molecular Phylogeny focused on Twenty-Nine Species within the Testudinidae Family using Mitochondrial Cytochrome b Gene Christine Chessler

  2. Introduction • Family Testudinidae • Land-based tortoises • Widely distributed & recognized • Majority in Africa & Asia • Few in America & Europe • Evolved ~200 mya from the Anapsid reptiles • Only living reptile grouping to retain Anapsid skull structure • Earliest fossils found in Asia • Members classified by: • High-domed shells • Exceptions exist. • Stout scaly limbs • Terrestrial

  3. Introduction • Researchers feel their phylogenetic relationships are controversial due to : • Limited taxonomic sampling • Studies focusing on only a subset within a family • IE: Gopherus • IE: Geochelone

  4. General Objective • I initially wanted to know more about where exactly the gopher tortoise “fit” phylogenetically among the tortoise family. • However, as I researched the existing phylogeny, I also wanted to address where the specific clades were situated among Testudinidae and also which clade the gopher tortoise fit within. • Identify synapomorphies shared within clade members • Lastly, I wanted to group each clade based on their known geographical locations to see if the clades “made sense” given the biogeography of each of the species.

  5. Materials & Methods • Sequence Selection • NCBI Nucleotide Database & BLAST • Gene chosen: Cytochrome b; partial cds • 29 species selected within Testudinidae (set organism parameters in search) + 1 outgroup species (Deirochelys reticularia) • Sequence Alignment • Seaview v.4 with MAFFT v.6.240-2 (einsi setting) • Construction Programs Utilized • RAxML v.7.0.4 (100 bootstraps, ML tree) • FigTree v.1.3.1

  6. Results & Conclusions

  7. Conclusions • Synapomorphies present to link individuals into their respective clades: • Clade #1 (green; Manouria and Gopherus ) • No synapomorphies? Mental glands? • Clade #4 (pink; Geochelone sp. + Pyxis + Dipsochelys) • Pyxis, G.yniphora and G.radiata relationship has been supported by the synapomorphy of an indistinct fenestra postotica • G.radiata and G. yniphora have been observed to both possess a ventral ridge on the maxilla-premaxilla suture and keels on the supraocciptal crest. • Clade #5 (blue; Indotestudo + Testudo + Malacocherus ) • the processus inferior parietalis meeting the quadrate and partially covering the prootic • a ventral tip of the processus interfenestralis, in addition to the presence of sutures between this process and the surrounding bones. • What about the other clades…and those with low(er) boot strap values?

  8. What does the biogeography reveal? • Clade #1 (green; Manouria and Gopherus) • Represent the divergence between the Asian and N. American lines • Crossing the Bering Strait in the Eocene • Clade #2 (yellow; Geochelone sp. + Homopus + Chersine) • Endemic to Africa • Clade #3 (purple; some species within the Geochelone sp + Kinixys clade) • “state of taxonomic confusion for the past 30 years” • Westward sea currents to S.America? • Clade #4 (pink; Geochelone sp. + Pyxis + Dipsochelys) • Dispersed from Africa to the Indian Ocean area/Madagascar by way of sea currents

  9. Possible Modifications • Obtain better bootstrap values to validate relationships? • More sequences/more species in analysis • Use different gene? • Some relationships (Geochelone sp.) are continually muddled and skewed due to inadequate knowledge on which are sub-species, individual species, or all the same species originating from one population…

  10. References • Alderton, D. 1988. Turtles and Tortoises of the World. New York, NY: Facts on File. • Ashton, R.E., and Ashton, P.S. 2008. The Natural History and Management of the Gopher Tortoise. Malabar, FL: Krieger Publishing Company. • BLAST: Basic Alignment Search Tool. http://blast.ncbi.nlm.nih.gov/Blast.cgiRetrieved 20 April 2010. • Buhlmann, K.A., Gibbons, J.W., and Jackson, D.R. 2008. Deirochelys reticularia (Latreille 1801) – chicken turtle. In: Rhodin, A.G.J., Pritchard, P.C.H., van Dijk, P.P., Saumure, R.A., Buhlmann, K.A., and Iverson, J.B. (Eds.). Conservation Biology of Freshwater Turtles and Tortoises: A Compilation Project of the IUCN/SSC Tortoise and Freshwater Turtle Specialist Group. Chelonian Research Monographs No. 5, pp. 014.1-014.6, doi:10.3854/crm.5.014.reticularia.v1.2008, http://www.iucn-tftsg.org/cbftt/. • Caccone, A., Gentile, G., Gibbs, J.P., Fritts, T.H., Snell, H.L., Betts, J., and Powell, J. R. 2002. Phylogeography and history of giant Galapagos tortoises. Evolution 56, 2052-2066. • Gouy M., Guindon S. & Gascuel O. 2010. SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27:221-224. • Katoh,K., Misawa,K., Kuma,K., and Miyata,T. 2002. MAFFT: a novel method for multiple sequence alignment based on fast Fourier transform. Nucleic Acid Res.,30:3059-3066 • Krenz, J.G., Naylor, G.J.P., Shaffer-Bradley, H., and Janzen, F.J. 2005. Molecular phylogenetics and evolution of turtles. Molecular Phylogenetics and Evolution 37: 178-191. • Lamb, T. and Lydeard, C. 1994. A molecular phylogeny of the Gopher tortoises, with comments on familial relationships within the Testudinoidea. Molecular Phylogenetics and Evolution, 3, 283-291. • Le, M., Raxworthy, C.J., McCord, W.P., and Mertz, L. 2006. A molecular phylogeny of tortoises (Testudines: Testudinidae) based on mitochondrial and nuclear genes. Molecular Phylogenetics and Evolution, 40, 517-531. • Palkovacs, E. P., Marschner, M., Ciofi,C., Gerlach, J., and Caccone, A. 2003. Are the native giant tortoises from the Seychelles really extinct? A genetic perspective based on mtDNA and microsatellite data. Molecular Ecology 12, 1403-1413. • NCBI: National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/ Retrieved 20 April 2010. • Rambaut, A. 2009. FigTree 1.3.1. http://tree.bio.ed.ac.uk/software/figtree Retrieved 20 April 2010. • Stamatakis, A. 2006. RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models. Bioinformatics22:2688–2690. • The Reptile Database. Retrieved from J.Craig.Venter Institute at http://jcvi.org/reptiles/families/testudinidae.php Retrieved 21 April 2010.

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