Areas of hybridization between related species have become fertile ground for studying the evolutionary process at the genetic level. To fully exploit the opportunities offered by hybrid zones, we need a reliable index of the hybridity of individual organisms. We have developed maximum likelihood methods for the analysis of molecular and morphological marker data, both for codominant and dominant markers and for qualitative and quantitative morphological traits. In simulation studies, we looked at the effects of marker number, marker diagnosticity, linkage and allelic dominance relations on these estimates and their support limits (confidence levels). In addition, for dominant markers, we examined the degree to which violation of Hardy-Weinberg equilibrium in the parental populations biases estimates. We tested the predictions of the simulation study by analysis of a large data set (304 hybrid individuals) from a natural hybrid zone between Helianthus annuus and Helianthus bolanderi , for which we screened microsatellite (codominant molecular), AFLP (dominant molecular) and morphological marker traits. Comparisons of hybrid indices based on these three kinds of markers generally confirm our earlier simulation conclusions. Over most of the range of possible hybrid index values,a given number of codominant markers give significantly, but not dramatically, better confidence intervals than dominant markers. For most hybrid zone studies, about 50 dominant or 30-40 codominant markers would produce acceptable confidence intervals, assuming that they are non-diagnostic but do show significant differences in frequency between the parental populations. The hybrid index estimates are also very robust to deviations of FIS from 0. The codominant microsatellite-based hybrid index scores were significantly better predictors of morphology-based hybrid index scores (R2=0.65) than were the AFLP hybrid index scores R2=0.34). Surprisingly, the codominant index was a poorer predictor of the AFLP index than it was of the morphology based index.We are currently investigating whether these discrepancies have a methodological or biological explanation.

Key words: Helianthus annuus, Helianthus bolanderi, Hybrid index, Hybrid zone, microsatellite, Molecular markers