Figure 1

Protein family occurrence profiles. Profiles are listed in decreasing order of abundance. Symbols indicate the species in which the protein families are present: a, L. acidophilus (genome size 2.0 Mbp, 1659 protein families); d, L. delbrueckii (genome size 1.9 Mbp, 1849 protein families); j, L. johnsonii (genome size 2.0 Mbp, 1630 protein families); p, L. plantarum (genome size 3.3 Mbp, 2630 protein families); s, L. sakei (genome size 1.9 Mbp, 1731 protein families). *, profiles equally compatible with any tree topology. The inset highlights four couples of profiles compatible with the monophyly of the acidophilus complex.: (p.,s.) vs. (a.,d.,j.) equally compatible with any of the three tree topologies depicted in Fig. 2, (a.,d.) vs (j.,p.,s.), (a.,j.) vs. (d.,p.,s.), (d.,j.) vs. (a.,p.,s.) compatible with a single gain or loss event in topology Ta, Tb and Tc, respectively.