| Summary: | <p>Abstract</p> <p>Background</p> <p>The S-RNases of the Solanaceae are highly polymorphic self-incompatibility (S-) alleles subject to strong balancing selection. Relatively recent diversification of S-alleles has occurred in the genus <it>Physalis </it>following a historical restriction of S-allele diversity. In contrast, the genus <it>Solanum </it>did not undergo a restriction of S-locus diversity and its S-alleles are generally much older. Because recovery from reduced S-locus diversity should involve increased selection, we employ a statistical framework to ask whether S-locus selection intensities are higher in <it>Physalis </it>than <it>Solanum</it>. Because different S-RNase lineages diversify in <it>Physalis </it>and <it>Solanum</it>, we also ask whether different sites are under selection in different lineages.</p> <p>Results</p> <p>Maximum-likelihood and Bayesian coalescent methods found higher intensities of selection and more sites under significant positive selection in the 48 <it>Physalis </it>S-RNase alleles than the 49 from <it>Solanum</it>. Highest posterior densities of dN/dS (ω) estimates show that the strength of selection is greater for <it>Physalis </it>at 36 codons. A nested maximum likelihood method was more conservative, but still found 16 sites with greater selection in <it>Physalis</it>. Neither method found any codons under significantly greater selection in <it>Solanum</it>. A random effects likelihood method that examines data from both taxa jointly confirmed higher selection intensities in <it>Physalis</it>, but did not find different proportions of sites under selection in the two datasets. The greatest differences in strengths of selection were found in the most variable regions of the S-RNases, as expected if these regions encode self-recognition specificities. Clade-specific likelihood models indicated some codons were under greater selection in background <it>Solanum </it>lineages than in specific lineages of <it>Physalis </it>implying that selection on sites may differ among lineages.</p> <p>Conclusions</p> <p>Likelihood and Bayesian methods provide a statistical approach to testing differential selection across populations or species. These tests appear robust to the levels of polymorphism found in diverse S-allele collections subject to strong balancing selection. As predicted, the intensity of selection at the S-locus was higher in the taxon with more recent S-locus diversification. This is the first confirmation by statistical test of differing selection intensities among self-incompatibility alleles from different populations or species.</p>
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