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. 2011 Mar 3;7(3):e1001319. doi: 10.1371/journal.pgen.1001319

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Mailund et al. 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 credited.

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For the two species system, we have one or two left and one or two right nucleotides. One when the left or right nucleotides have found their MRCA (open circles) and two otherwise (filled circles). Left nucleotides can be linked with right nucleotides or not.