The chromosomes of the babirusa, a species considered to have diverged from an ancestor of the pig during the Miocene epoch, about 12–26 million years ago, were studied to determine the sites of recent rearrangements during evolution of the domestic pig. It is shown that there is a pericentric inversion of the entire short arm on pig chromosome 1, compared to its counterpart in the babirusa (chromosome 15). We also present evidence suggesting that pig chromosome 3 was derived by a telomere-centromere fusion of two ancestral chromosomes homoeologous to babirusa chromosomes 12 and 17. Likewise, we conclude that pig chromosome 6 was most likely derived by a telomere-telomere fusion of ancestral chromosomes homoeologous to babirusa chromosomes 6 and 14. The detection of interstitial hybridization signals from presumptive subtelomeric repeats in the same chromosome region as the evolutionary fusion points on pig chromosomes 3 and 6 indicates that the fusion sites may still contain elements that are otherwise restricted to the telomere regions of pig chromosomes.

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