The Dd2 clone tree.

<p>(see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004812#pgen.1004812.s001" target="_blank">S1 Fig</a>. for 3D7/HB3/W2 clone trees). Cloning by limiting dilution randomly selects one individual parasite, possibly with one or more mutations. Note that mutations observed in a progeny sample occurred within the parental generation, at some point after the preceding clonal dilution. In this Dd2 clone tree, clones Dd2_(A)1a (A-branch) and Dd2_(B)1b (B-branch) were arbitrarily selected for further clonal dilutions. As described in the main text, a double recombination event between <i>Dd2var34</i> and <i>Dd2var45</i> genes created a new chimeric <i>var</i> named <i>var34/45/34</i> in clone Dd2_(A)1a. All subsequent subclones framed in red also showed <i>var34/45/34</i>, while two subclones (Dd2_(A)4l & 4m) had lost it, two subclones in orange showed extra recombinations involving <i>var34/45/34</i> and three subclones in green had lost the original <i>Dd2var34</i> copy. *denotes limiting dilution date.