A Brief Molecular Phylogeny focused on Twenty-Nine Species within the Testudinidae Family using Mito...
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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

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

Christine Chessler


Introduction

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


Introduction1

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


General objective

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.


Materials methods

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


Results conclusions

Results & Conclusions


Conclusions

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?


Christine chessler

  • 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


Possible modifications

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…


References

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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