Genomic and cytogenetic evidence for divergence and speciation in geladas

BACKGROUND: Chromosomal rearrangements can play an important role in shaping patterns of genomic divergence and speciation, yet their evolutionary context is still largely unclear, as such events are rare and challenging to identify in recent evolutionary history. Geladas (Theropithecus gelada) provide a unique system to investigate this process, as a novel fission on chromosome 7 has resulted in polymorphic karyotypes among gelada populations. RESULTS: We integrate new cytogenetic data from ten animals together with whole-genome sequencing from 149 individuals spanning all three extant gelada populations (northern, central, and southern). We report additional cytogenetic evidence consistent with fixation of a chromosomal fission on chromosome 7 in northern geladas, and the absence of the fission in the central population. Phylogenetic analyses reveal that the southern lineage diverged first, prior to the split between northern and central geladas, strongly suggesting that the southern population retains the ancestral karyotype. Demographic modeling further refines the timing of the northern-central split, indicating a more recent divergence (~ 160 thousand years ago) than previously estimated. We detect elevated genetic differentiation between the northern and central populations and reduced nucleotide diversity in the northern lineage on chromosome 7, which is consistent with historically suppressed recombination. These results suggest that the fission on chromosome 7 may have contributed to regional divergence by promoting recombination suppression in heterokaryotypes. CONCLUSIONS: By combining cytogenetics with population genomes, these findings highlight the role of chromosomal evolution in shaping localized genomic differentiation, and its potential for reinforcing reproductive isolation. Our results also suggest that northern geladas may represent an incipient species.