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Background  Chemically mediated prezygotic barriers to reproduction likely play an important role in speciation. In facultatively sexual monogonont rotifers from the  Brachionus plicatilis  cryptic species complex, mate recognition of females by males is mediated by the Mate Recognition Protein (MRP), a globular glycoprotein on the surface of females, encoded by the  mmr-b  gene family. In this study, we sequenced  mmr-b  copies from 27 isolates representing 11 phylotypes of the  B. plicatilis  species complex, examined the mode of evolution and selection of  mmr-b , and determined the relationship between  mmr-b  genetic distance and mate recognition among isolates.    Results  Isolates of the  B. plicatilis  species complex have 1–4 copies of  mmr-b , each composed of 2–9 nearly identical tandem repeats. The repeats within a gene copy are generally more similar than are gene copies among phylotypes, suggesting concerted evolution. Compared to housekeeping genes from the same isolates,  mmr-b  has accumulated only half as many synonymous differences but twice as many non-synonymous differences. Most of the amino acid differences between repeats appear to occur on the outer face of the protein, and these often result in changes in predicted patterns of phosphorylation. However, we found no evidence of positive selection driving these differences. Isolates with the most divergent copies were unable to mate with other isolates and rarely self-crossed. Overall the degree of mate recognition was significantly correlated with the genetic distance of  mmr-b.Conclusions  Discrimination of compatible mates in the  B. plicatilis  species complex is determined by proteins encoded by closely related copies of a single gene,  mmr-b . While concerted evolution of the tandem repeats in  mmr-b  may function to maintain identity, it can also lead to the rapid spread of a mutation through all copies in the genome and thus to reproductive isolation. The  mmr-b  gene is evolving rapidly, and novel alleles may be maintained and increase in frequency via asexual reproduction. Our analyses indicate that mate recognition, controlled by MMR-B, may drive reproductive isolation and allow saltational sympatric speciation within the  B. plicatilis  cryptic species complex, and that this process may be largely neutral.

The mate recognition protein gene mediates reproductive isolation and speciation in the Brachionus plicatilis cryptic species complex