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

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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

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

 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

   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

Conclusions

 Synapomorphies present to link individuals into their respective clades: 

Clade #1

 (green; Manouria and Gopherus ) No synapomorphies? Mental glands?

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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?

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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

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Obtain better bootstrap values to validate relationships?

  More sequences/more species in analysis Use different gene?

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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

       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.cgi

Retrieved 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/.

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 The Reptile Database. Retrieved from J.Craig.Venter Institute at http://jcvi.org/reptiles/families/testudinidae.php

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