Fig. 2: Genetic changes within species are statistically associated with shifts in taxonomic composition over time.

Species relative abundances over time in three example hosts experiencing strain replacement events (a), evolutionary modification events (b), and no genetic changes (c). Species are shown if they had a relative abundance > 2% in one of the hosts in at least one timepoint; all other species are grouped together in the “Other” category. Species experiencing replacement and modification events are indicated by the triangles. d Distribution of Jensen-Shannon distances over time (Methods) for communities that experienced at least one replacement (Rep, n = 13) or modification event (Mod, n = 58), or no genetic changes (None, n = 123). Symbols denote individual data points, while boxes show the median and inter-quartile range; the JS distances between ~1000 random pairs of hosts are shown at right for comparison. e, f For each of the communities in (d), the fraction of the Jensen-Shannon divergence explained by fold changes greater than a given amount (f, Methods), as well as the fraction of this amount explained by positive vs negative changes (e). Colors indicate the Rep, Mod, and None categories in (d). g The number of abundant species that went extinct in each of the communities in (d) (Methods). Colors are the same as (e).