A Brief Molecular Phylogeny focused on
Twenty-Nine Species within the Testudinidae
Family using Mitochondrial Cytochrome b
Gene
Christine Chessler
Introduction
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Family Testudinidae
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Land-based tortoises
Widely distributed &
recognized
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Evolved ~200 mya from the
Anapsid reptiles
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Majority in Africa & Asia
Few in America & Europe
Only living reptile grouping to
retain Anapsid skull structure
Earliest fossils found in Asia
Members classified by:
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High-domed shells
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Exceptions exist.
Stout scaly limbs
Terrestrial
Introduction
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Researchers feel their
phylogenetic relationships
are controversial due to :

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Limited taxonomic
sampling
Studies focusing on only a
subset within a family

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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.
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Identify synapomorphies shared within clade members
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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
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Sequence Selection
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NCBI Nucleotide Database & BLAST
Gene chosen: Cytochrome b; partial cds
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29 species selected within Testudinidae (set organism
parameters in search) + 1 outgroup species (Deirochelys
reticularia)
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Sequence Alignment
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Seaview v.4 with MAFFT v.6.240-2 (einsi setting)
Construction Programs Utilized
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RAxML v.7.0.4 (100 bootstraps, ML tree)
FigTree v.1.3.1
Results & Conclusions
Conclusions
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Synapomorphies present to link individuals into their respective
clades:
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Clade #1 (green; Manouria and Gopherus )
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Clade #4 (pink; Geochelone sp. + Pyxis + Dipsochelys)
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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 )
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No synapomorphies? Mental glands?
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?
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Clade #1 (green; Manouria and Gopherus)
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Clade #2 (yellow; Geochelone sp.
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Represent the divergence between the Asian and
N. American lines
 Crossing the Bering Strait in the Eocene
+ Homopus + Chersine)
Endemic to Africa
Clade #3 (purple; some species within the Geochelone sp +
Kinixys clade)
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“state of taxonomic confusion for the past 30
years”
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Westward sea currents to S.America?
Clade #4 (pink; Geochelone sp.
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+ 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?
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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
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Ashton, R.E., and Ashton, P.S. 2008. The Natural History and Management of the
Gopher Tortoise. Malabar, FL: Krieger Publishing Company.
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BLAST: Basic Alignment Search Tool. http://blast.ncbi.nlm.nih.gov/Blast.cgi
Retrieved 20 April 2010.
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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.
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Le, M., Raxworthy, C.J., McCord, W.P., and Mertz, L. 2006. A molecular phylogeny of tortoises (Testudines:
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517-531.
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Palkovacs, E. P., Marschner, M., Ciofi,C., Gerlach, J., and Caccone, A. 2003. Are the native giant tortoises
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NCBI: National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/
Retrieved 20 April 2010.
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Rambaut, A. 2009. FigTree 1.3.1. http://tree.bio.ed.ac.uk/software/figtree
Retrieved 20 April 2010.
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Stamatakis, A. 2006. RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic
Analyses with Thousands of Taxa and Mixed Models. Bioinformatics 22:2688–2690.
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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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