Table 2. Evidence for introgression or shared ancestral polymorphism.

Support for introgression	Support for ancestral polymorphism	Biological reason
Species are know to hybridize under greenhouse conditions and in the wild	Species cannot hybridize under greenhouse conditions, and/or little evidence of hybridization in the wild	Strength of reproductive barrier dictates potential for hybridization and introgression
Tightly linked genes show similar patterns of gene flow between species	Lack of correlation between allelic states at linked genes	Recombination less likely between linked genes, and introgressed linkage blocks are likely to be maintained
Different patterns of genetic distances between species at different loci, with the greatest degree of divergence between loci contributing to species-level differences	Equal divergence across different loci	Selection pressures different for different loci, with strong diversifying selection at loci underlying species-specific traits
Populations in sympatry or parapatry show less genetic divergence than those that occur in allopatry	Equivalent levels of divergence across species range	Where introgression occurs a cline of shared genes may be expected between species
Phylogenetic incongruency between uniparentally and biparentally inherited markers	Congruency between the phylogeny derived from uniparentally inherited markers and the maximum clade credibility tree from biparentally inherited markers	Uniparentally inherited markers (thus with a low effective population size) are particularly susceptible to introgression

Data from Willyard et al. (2009); Yatabe et al. (2007) and Donnelly et al. (2004).