Genome comparisons indicate recent transfer of Ri-like between sister species and .

endosymbionts may be acquired by horizontal transfer, by introgression through hybridization between closely related species, or by cladogenic retention during speciation. All three modes of acquisition have been demonstrated, but their relative frequency is largely unknown. and its sister species harbor , denoted Suz and Spc, very closely related to Ri, identified in California populations of . However, these variants differ in their induced phenotypes: Ri causes significant cytoplasmic incompatibility (CI) in , but CI has not been detected in or . Our draft genomes of Suz and Spc contain full-length copies of 703 of the 734 single-copy genes found in Ri. Over these coding sequences, Suz and Spc differ by only 0.004% (i.e., 28 of 704,883 bp); they are sisters relative to Ri, from which each differs by 0.014%-0.015%. Using published data from , wasps and bees to calibrate relative rates of versus host nuclear divergence, we conclude that Suz and Spc are too similar-by at least a factor of 100-to be plausible candidates for cladogenic transmission. These three Ri-like , which differ in CI phenotype in their native hosts, have different numbers of orthologs of genes postulated to contribute to CI; and the CI loci differ at several nucleotides that may account for the CI difference. We discuss the general problem of distinguishing alternative modes of acquisition, focusing on the difficulties posed by limited knowledge of variation in absolute and relative rates of molecular evolution for host nuclear genomes, mitochondria, and .