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The complete mitochondrial genome of an agamid lizard from the Afro-Asian subfamily agaminae and the phylogenetic position of Bufoniceps and Xenagama.

Museum of Vertebrate Zoology, 3101 Valley Life Science Building, University of California, Berkeley, CA 94720, USA.
Molecular Phylogenetics and Evolution (Impact Factor: 4.02). 07/2006; 39(3):881-6. DOI: 10.1016/j.ympev.2005.08.020
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Available from: James A Schulte II, Jan 25, 2014
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    • "Published sequences of Xenagama taylori, Takydromus tachydromoides, Calotes versicolor, and Chlamydosaurus kingii (Macey et al. 2006; Amer and Kumazawa 2007; Kumazawa 2007; Ujvari and Madsen 2008; Gen- Bank accession numbers DQ008215, AB080237, AB183287, and EF090421, respectively) were used to design 12 pairs of specific primers. "
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    ABSTRACT: The complete mitochondrial genome of the Yarkand toad-headed agama Phrynocephalus axillaris, the first complete mitogenome from the genus Phrynocephalus, was determined. The total length of this complete mitogenome is 17,937 bp, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 control regions (CRs). The overall base composition of the H-strand is 36.4% A, 26.0% T, 25.4% C, and 12.3% G. The gene arrangement and composition of the mitogenome are similar to those of other Agaminae lizards, albeit with one CR existing between the tRNA ( Thr ) gene and tRNA ( Pro ) gene and another CR containing 17 copies of 77-bp tandem repeats inserting between the tRNA ( Phe ) and 12S rRNA. The complete mitogenome sequence of P. axillaris provided fundamental data for resolving phylogenetic and genetic problems related to this species and genus Phrynocephalus.
    Mitochondrial DNA 01/2013; 24(3). DOI:10.3109/19401736.2012.752477 · 1.70 Impact Factor
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    • "Guo and Wang (2007) proposed a mid-Late Miocene origin of Phrynocephalus, with diversification from the Late Miocene from a Central Asian origin. However, their study included very few Central Asian species and excluded the more basal species P. interscapularis (see Macey et al., 2006), which occurs in the sand deserts of Turkmenistan, southern Kazakhstan and Uzbekistan. Both Pang et al. (2003) and Wang and Fu (2004) showed that there is considerable phylogeographic structuring across China in the Phrynocephalus versicolor species complex, including P. przewalskii, P. frontalis and P. guttatus . "
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    ABSTRACT: The Central Asian agamid lizards are ecologically and morphologically diverse, occurring across a broad range of desert environments in this biogeographically important region. It is probable that past climatic shifts have significantly influenced the diversification patterns and distributions of the agamid lizards of this region. To assess this within a phylogenetic framework we sequenced a approximately 1200 bp region of mitochondrial DNA and a approximately 1200 bp nuclear gene (RAG-1), incorporating both inter- and intraspecific sampling across Central Asian agamids. Our topology and divergence time estimates support an Eocene origin of the Agaminae subfamily on the Indian subcontinent, coinciding with the collision of India into Eurasia. The onset of aridification in Central Asia during the Late Oligocene, resulting from the retreat of the Paratethys Sea and the intensified uplift of the Tibetan-Himalayan complex, probably played an important role in the diversification of Phrynocephalus, one of the three genera studied. Intensification of aridity and geologic events in the Plio-Pleistocene and Quaternary glacial cycling probably had a significant influence on intraspecific diversification patterns within Phrynocephalus.
    Molecular Phylogenetics and Evolution 06/2009; 53(1):99-112. DOI:10.1016/j.ympev.2009.05.011 · 4.02 Impact Factor
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    • "1.—(A) Gene organization of Calotes versicolor mtDNA shown linearly with columns which approximate sizes of individual genes, in which the inversion of the trnP gene is highlighted. (B) Gene organization around the CR for Xenagama taylori (Macey et al. 2006) in which the trnP gene is translocated from the 5#end to the 3#end of the CR. (C) Gene organization around the CR for Agama impalearis in which the trnF gene is translocated from the 3#end to the 5#end of the CR. "
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    ABSTRACT: A complete mitochondrial DNA (mtDNA) sequence was determined for the lizard Calotes versicolor (Reptilia; Agamidae). The 16,670-bp genome with notable shorter genes for some protein-coding and tRNA genes had the same gene content as that found in other vertebrates. However, a novel gene arrangement was found in which the proline tRNA (trnP) gene is located in the light strand instead of its typical heavy-strand position, providing the first known example of gene inversion in vertebrate mtDNAs. A segment of mtDNA encompassing the trnP gene and its flanking genes and the control region was amplified and sequenced for various agamid taxa to investigate timing and mechanism of the gene inversion. The inverted trnP gene organization was shared by all South Asian draconine agamids examined but by none of the other Asian and African agamids. Phylogenetic analyses including clock-free Bayesian analyses for divergence time estimation suggested a single occurrence of the gene inversion on a lineage leading to the draconine agamids during the Paleogene period. This gene inversion could not be explained by the tandem duplication/random loss model for mitochondrial gene rearrangements. Our available sequence data did not provide evidence for remolding of the trnP gene by an anticodon switch in a duplicated tRNA gene. Based on results of sequence comparisons and other circumstantial evidence, we hypothesize that inversion of the trnP gene was originally mediated by a homologous DNA recombination and that the de novo gene organization that does not disrupt expression of mitochondrial genes has been maintained in draconine mtDNAs for such a long period of time.
    Molecular Biology and Evolution 07/2007; 24(6):1330-9. DOI:10.1093/molbev/msm054 · 14.31 Impact Factor
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