Evidence of phylosymbiosis in A. mexicanus
We next tested if the differences in microbiome composition we observed between laboratory reared surface fish and cavefish mirror the evolutionary history of A. mexicanus. The A. mexicanusphylogeny defines two lineages; fish from the Pachón and Tinaja caves and Rascón River form a monophyletic clade referred to as the “old lineage” and fish from the Molino Cave and Río Choy River form a monophyletic clade referred to as the “new lineage” (Figure 1H ). Based on whole genome sequencing data, old and new lineages split as long as 257K generations ago with instances of secondary contact . Molino cavefish split from Río Choy Surface fish around 163k generations ago, and Pachón and Tinaja cavefish split more recently around 116k generations ago . We generated dendrograms of interspecific relatedness using the microbiota profiles of laboratory reared Pachón, Tinaja, and Molino cavefish and Río Choy surface fish. We found that the topology of the microbiota tree matches the topology of the host phylogeny (Figure 3D ). The trees similarly define two lineages; Molino cavefish and Río Choy surface fish form a monophyletic clade that is separate from Pachón and Tinaja cavefish. Our results suggest that phylosymbiosis can occur in the same species that consists of distinct populations that diverged less than 300K generations ago and adapted to dramatically different habitats.