THE TEMPO AND MODE OF EVOLUTION OF TRANSPOSABLE ELEMENTS AS REVEALED BY MOLECULAR PHYLOGENIES RECONSTRUCTED FROM MOSQUITO GENOMES |
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| Authors: | Claudio J Struchiner Eduardo Massad Zhijian Tu José M C Ribeiro |
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| Institution: | 1. ENSP/FIOCRUZ and IMS/UERJ, Av. Brasil, 4365, Rio de Janeiro, Braxil 21040 360;2. E‐mail: stru@fiocruz.br;3. FM/USP, Av. Dr. Arnaldo, 455, S?o Paulo, Braxil 01246 903;4. E‐mail: edmassad@dim.fm.usp.br;5. Department of Biochemistry, Virginia Polytechnic Institute and State University, 309 Engel Hall, Blacksburg, Virginia 24061;6. E‐mail: jaketu@vt.edu;7. Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, 12735 Twinbrook Parkway, Room 2E32D, National Institutes of Health, Rockville, Maryland 20852;8. E‐mail: jribeiro@niaid.nih.gov |
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| Abstract: | Although many mathematical models exist predicting the dynamics of transposable elements (TEs), there is a lack of available empirical data to validate these models and inherent assumptions. Genomes can provide a snapshot of several TE families in a single organism, and these could have their demographics inferred by coalescent analysis, allowing for the testing of theories on TE amplification dynamics. Using the available genomes of the mosquitoes Aedes aegypti and Anopheles gambiae, we indicate that such an approach is feasible. Our analysis follows four steps: (1) mining the two mosquito genomes currently available in search of TE families; (2) fitting, to selected families found in (1), a phylogeny tree under the general time‐reversible (GTR) nucleotide substitution model with an uncorrelated lognormal (UCLN) relaxed clock and a nonparametric demographic model; (3) fitting a nonparametric coalescent model to the tree generated in (2); and (4) fitting parametric models motivated by ecological theories to the curve generated in (3). |
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| Keywords: | Demography reconstruction genomes population dynamics transposable element |
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