Conclusion
We found that gut microbiome tracks host evolution in multiple independent translocations in the wild. By studying multiple stages of this co-evolution, we revealed that the gut microbiome rapidly diverges from that of source populations – with shifts in gut morphology and environment changes – and inconsistently converges with LP native populations. We argue that lack of parallel convergence does not preclude a role for the microbiome in guppy evolution; in fact, microbiomes may provide a consistent nutritional advantage to guppies introduced to low-resource environments, provided there is the sufficient richness to filter from. In contrast to much of our knowledge of host-microbiome evolution based on macro-evolutionary patterns, our study offers an unprecedented view of host-microbiome co-evolution in real-time in wild populations.