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View full-text article in PMC

. 2005 Oct 21;1(4):e44. doi: 10.1371/journal.pgen.0010044

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Copyright: © 2005 Malik and Henikoff.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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We have chosen non-overlapping sets of the Drosophila species to do a pair-wise analysis of dN compared to dS. We present a sliding window analysis (window size 150 base pairs, slide of 50 base pairs) of dS and the dN/dS ratio (y-axis) plotted against nucleotide position (x-axis). Under neutrality, a dN/dS ratio of 1 is expected (dashed lines). We present a comparison of (A) D. melanogaster versus D. simulans, (B) D. yakuba versus D. teissieri, (C) D. erecta versus D. orena, (D) D. paralutea A versus D. lutescens A, and (E) D. paralutea B versus D. prostipennis B. In all these comparisons except (D), at least one window where dN/dS significantly exceeds 1 is seen (indicated by asterisks; significance tested by simulations in the K-estimator program [43]).