Neutral genetic markers are useful for identifying species hybrids in natural populations, especially when used in conjunction with statistical methods like the one implemented in the software NewHybrids. Here, a short description of the extension of NewHybrids to dominant markers is given. Subsequently, an extensive series of simulations of amplified fragment length polymorphism (AFLP) data is performed to evaluate the prospects for hybrid identification with (possibly non-diagnostic) dominant markers. Distinguishing between F1's and F2's is shown to be difficult, possibly requiring upwards of 100 AFLP markers to be done accurately. Discriminating between pure-bred and non-pure (hybrid) individuals, however, is shown to be much easier, requiring perhaps as few as 10 dominant markers, even from relatively weakly diverged species.
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