Genomic and microbiome data support a hypothesis of hybrid speciation in endangered brown lemurs

Hybridization poses both challenges and opportunities for biodiversity, with outcomes that can erode species integrity or generate novel lineages. In Madagascars brown lemurs (genus Eulemur), a hybrid species formed by E. rufifrons x E. cinereiceps has been proposed, but never tested with genome-wide data. To test this hybrid speciation hypothesis, we combined low-coverage host genomes derived from fecal DNA with gut microbiome profiling across a 180-kilometer transect spanning the hybrid zone. Population genomic, phylogenetic, and demographic analyses reveal that a distinct hybrid lineage originated [~]44,000 years ago, followed by extensive backcrossing with E. rufifrons beginning [~]22,000 years ago. This process has led to genomic swamping and the apparent loss of genetically "pure" E. rufifrons in southeastern Madagascar, while E. cinereiceps has remained largely distinct. Gut microbiome divergence mirrored these patterns, with hybrids more closely resembling E. rufifrons than E. cinereiceps, although predicted microbial functions were largely conserved across all three lineages. Overall, we interpret our results as a hologenomic signal of nascent speciation followed by collapse. Our findings suggest that hybridization in Eulemur is both more widespread and evolutionarily complex than previously recognized, with major implications for conservation: interspecific gene flow may serve as a key mechanism promoting primate adaptation during periods of rapid environmental change. SIGNIFICANCE STATEMENTHybridization is widespread across primates, yet hybrid speciation remains rare. The few cases that exist illuminate how complex evolutionary scenarios can give rise to new species, ecological niches, and genetic combinations. Here we leveraged genomic and gut microbiome data from wild brown lemurs across southeastern Madagascar to test whether a proposed hybrid species originated from Eulemur rufifrons and E. cinereiceps. Our analyses reveal that a distinct hybrid lineage formed [~]44,000 years ago and later mixed extensively with E. rufifrons, reshaping the genetic landscape of the region. These findings show that hybridization has played a creative and persistent evolutionary role in lemurs. Understanding these processes can improve conservation strategies by highlighting the importance of maintaining habitat connectivity and natural gene flow.