FIG 4.

Strain phylogenies show longitudinal intraindividual strain similarities. RAxML phylogenies of StrainPhlAn MLSAs for each of the four species considered. Tree branches are colored by lactase persistence genotype. Columns of colors at each node reference family IDs, with multiple samples from the same individual and their twin having the same color. Samples are labeled by family ID, then by twin ID within the family. Identical labels imply samples from different time points of the same individual (i.e., intraindividual sample). Twin IDs marked with “X” imply that only a single twin had representation on the tree or that the individual had no twin in the data set. Scales show patristic distances while circle sizes represent RAxML bootstrap support of each division.