Genomic and microbiome data support a hypothesis of hybrid speciation in endangered brown lemurs
The gut microbiome is shaped by host ecology and evolution, but the relative influences of each remain unresolved in natural hybrid zones where species boundaries are permeable. We investigated these dynamics using a hybrid zone formed between two species of brown lemur in southeastern Madagascar, Eulemur rufifrons and E. cinereiceps. These hybrids occupy a novel ecological niche and were previously proposed as a hybrid species, though this had never been tested with genome-wide data. Here, we combined low-coverage host genomes derived from fecal DNA with 16S rRNA gut microbiome profiles across a 180-kilometer transect. Population genomic analyses recovered two population clusters connected by a hybrid zone biased towards E. rufifrons ancestry. Though our data did not support a hypothesis of hybrid speciation, the hybrid zone was dominated by later-generation crosses. Hybrid microbiomes were compositionally intermediate between parental species, but more closely resembled E. rufifrons, mirroring patterns of genomic ancestry. Microbiome beta diversity was significantly correlated with host genomic distance after accounting for geography and ecology. In contrast, predicted microbial functional profiles were broadly conserved across host taxa. Together, these findings demonstrate that phylosymbiosis can emerge in the face of interspecific gene flow, providing new insight into host-microbiome dynamics during the early stages of speciation.