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Multiple, independent fixations of one rRNA copy can produce an rRNA phylogenetic tree that is incongruent with the species tree. A-B: two copies of the rRNA repeat unit accumulate differences in nucleotide sequence and in gene order. C: speciation occurs and one rRNA repeat unit copy is fixed within each new species. D-E: each rRNA repeat unit copy is fixed twice, independently, resulting in an rRNA gene tree that is incongruent with the species tree.
