Black, A. N. | Search bioRxiv

bioRxiv2025

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.

evolutionary biology↗

bioRxiv2023

Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish

Foskett Spring in Oregons desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the daces recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the populations surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate the phenomenon of persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5,000 within Foskett Spring, though Ne in the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevadas Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace just 600 years ago, much more recently than previously suspected and coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.

genetics↗