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Biogeography Revealed by Mariner-Like Transposable Element Sequences via a Bayesian Coalescent Approach

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Abstract

Genetic diversity of natural populations is useful in biogeographical studies. Here, we apply a Bayesian method based on the coalescent model to dating biogeographical events by using published DNA sequences of wild silkworms, Bombyx mandarina, and the domesticated model organisms B. mori, both of which categorized into the order of Lepidoptera, sampled from China, Korea, and Japan. The sequences consist of the BmTNML locus and the flanking intergenic regions. The BmTNML locus is composed of cecropia-type mariner-like element (MLE) with inverted terminal repeats, and three different transposable elements (TE), including L1BM, BMC1 retrotransposons, and BmamaT1, are inserted into the MLE. Based on the genealogy defined by TE insertions/deletions (indels), we estimated times to the most recent common ancestor and these indels events using the flanking, MLE, and indels sequences, respectively. These estimates by using MLE sequences strongly correlated with those by using flanking sequences, implying that cecropia-type MLEs can be used as a molecular clock. MLEs are thought to have transmitted horizontally among different species. By using a pair of published cecropia-type MLE sequences from lepidopteran insect, an emperor moth, and a coral in Ryukyu Islands, we demonstrated dating of horizontal transmission between species which are distantly related but inhabiting geographically close region.

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Acknowledgments

We would like to thank Drs. Hideaki Maekawa and Yuichi Kawanishi for their helpful discussions and comments to this study. S.N. has been supported in part by a Grant-in-Aid for the Japan Society for the Promotion of Science (JSPS) Research fellow (24-3234). Y.N. and S.M. has been supported by KAKENHI 19658023.

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Authors and Affiliations

  1. Department of Mathematical Analysis and Statistical Inference, The Institute of Statistical Mathematics, 10-3 Midori-cho, Tachikawa, Tokyo, 190-8562, Japan

    Shigeki Nakagome & Shuhei Mano

  2. Functional Genomics Group, Center of Molecular Biosciences (COMB), Tropical Biosphere Research Center, University of the Ryukyus, 1 Nishihara, Okinawa, 903-0213, Japan

    Yumiko Nakajima

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  1. Shigeki Nakagome
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  2. Yumiko Nakajima
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  3. Shuhei Mano
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Correspondence to Shuhei Mano.

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Nakagome, S., Nakajima, Y. & Mano, S. Biogeography Revealed by Mariner-Like Transposable Element Sequences via a Bayesian Coalescent Approach. J Mol Evol 77, 64–69 (2013). https://doi.org/10.1007/s00239-013-9581-0

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  • DOI: https://doi.org/10.1007/s00239-013-9581-0

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