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Figure 4 | BMC Evolutionary Biology

Figure 4

From: Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract

Figure 4

Phylogenetic reconstruction from simulated datasets. Two replicate datasets were simulated under the hypothesis of a unique topology common to all proteins and used in phylogenetic reconstruction. Upper panel: the underlying topology is Ta for all proteins. Lower panel: the underlying topology is Tb. The number of proteins supporting each of the three possible tree topologies Ta, Tb, and Tc (cf Fig. 3) is indicated as a function of the confidence threshold applied in tree reconstruction for individual proteins. Simulations used a JTT model of protein evolution and respected the particular length, site rate heterogeneity and global evolutionary speed of each protein family.

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