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Patterns of DNA-Sequence Divergence Between Drosophila miranda and D. pseudoobscura

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Abstract

Contrary to the classical view, a large amount of non-coding DNA seems to be selectively constrained in Drosophila and other species. Here, using Drosophila miranda BAC sequences and the Drosophila pseudoobscura genome sequence, we aligned coding and non-coding sequences between D. pseudoobscura and D. miranda, and investigated their patterns of evolution. We found two patterns that have previously been observed in comparisons between Drosophila melanogaster and its relatives. First, there is a negative correlation between intron divergence and intron length, suggesting that longer non-coding sequences may contain more regulatory elements than shorter sequences. Our other main finding is a negative correlation between the rate of non-synonymous substitutions (d N) and codon usage bias (F op), showing that fast-evolving genes have a lower codon usage bias, consistent with strong positive selection interfering with weak selection for codon usage.

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Acknowledgments

This study was conducted as part of the GENACT Project, funded by the Marie Curie Host Fellowships for Early Stage training to SMP, as part of the 6th Framework Programme of the European Commission. Brian Charlesworth was supported by the Royal Society. BAC sequencing and Daniel L. Halligan were funded by a Wellcome Trust and BBSRC grant to Peter D. Keightley and Brian Charlesworth. We thank Dr. Mark Dorris for isolating BACs and Dr. Jane Rogers at the Wellcome Trust Sanger Institute for organizing their sequencing. We also thank two anonymous reviewers for helpful comments on the manuscript.

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  1. Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, UK

    Sophie Marion de Procé, Daniel L. Halligan, Peter D. Keightley & Brian Charlesworth

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  1. Sophie Marion de Procé
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  2. Daniel L. Halligan
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  3. Peter D. Keightley
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Correspondence to Sophie Marion de Procé.

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Marion de Procé, S., Halligan, D.L., Keightley, P.D. et al. Patterns of DNA-Sequence Divergence Between Drosophila miranda and D. pseudoobscura . J Mol Evol 69, 601–611 (2009). https://doi.org/10.1007/s00239-009-9298-2

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