MBE Advance Access published online on March 10, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh069
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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1 Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan; Department of Cell Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
* To whom correspondence should be addressed. E-mail: nokada{at}bio.titech.ac.jp.
Although turtles (order Testudines) constitute one of the major reptile groups, their phylogenetic relationships remain largely unresolved. Hence, we attempted to elucidate their phylogeny using the SINE (short interspersed repetitive element) method, in which the sharing of a SINE at orthologous loci is indicative of synapomorphy. First, a detailed characterization of the tortoise polIII/SINE was conducted using ten species from eight families of hidden-necked turtles (suborder Cryptodira). Our analysis of 382 SINE sequences newly isolated in the present study revealed two subgroups, namely Cry I and II, that were distinguishable according to diagnostic nucleotides in the 3' region. Furthermore, four (IA-ID) and five (IIA-IIE) different SINE types were identified within Cry I and II subgroups, respectively, based on features of insertions/deletions located in the middle of the SINE sequences. The relative frequency of occurrence of the subgroups and the types of SINEs in this family were highly variable among different lineages of turtles, suggesting active differential retroposition in each lineage. Further application of the SINE method using the most retrotranspositionally active types, namely IB and IC, challenged the established phylogenetic relationships of Bataguridae and its related families. The data for 11 orthologous loci demonstrated a close relationship between Bataguridae and Testudinidae, as well as the presence of the three clades within Bataguridae. Although the SINE method has been used to infer the phylogenies of a number of vertebrate groups, it has never been applied to reptiles. The present study represents the first application of this method to a phylogenetic analysis of this class of vertebrates, and provides detailed information on the SINE subgroups and types. This information may be applied to the phylogenetic resolution of relevant turtle lineages. Key Words:
tortoise, turtle, phylogeny, SINE, retroposon
© 2004 Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved.
Original Articles
First Application of the SINE (Short Interspersed Repetitive Element) Method to Infer Phylogenetic Relationships in Reptiles: An Example from the Turtle Superfamily Testudinoidea
2 Department of Cell Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
3 Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
4 Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
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