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Background  Intra-specific and intra-individual polymorphism is frequently observed in nuclear markers of  Ilex  (Aquifoliaceae) and discrepancy between plastid and nuclear phylogenies is the rule in this genus. These observations suggest that inter-specific plastid or/and nuclear introgression played an important role in the process of evolution of  Ilex . With the aim of a precise understanding of the evolution of this genus, two distantly related sympatric species collected in Tenerife (Canary Islands),  I. perado  and  I. canariensis , were studied in detail. Introgression between these two species was previously never reported. One plastid marker (the  atpB-rbcL  spacer) and two nuclear markers, the ribosomal internal transcribed spacer (ITS) and the nuclear encoded plastid glutamine synthetase ( nepGS ) were analyzed for 13 and 27 individuals of  I. perado  and  I. canariensis , respectively.    Results  The plastid marker is intra-specifically constant and correlated with species identity. On the other hand, whereas the nuclear markers are conserved in  I. perado , they are highly polymorphic in  I. canariensis . The presence of pseudogenes and recombination in ITS sequences of  I. canariensis  explain this polymorphism. Ancestral sequence polymorphism with incomplete lineage sorting, or past or recent hybridization with an unknown species could explain this polymorphism, not resolved by concerted evolution. However, as already reported for many other plants, past or recent introgression of an alien genotype seem the most probable explanation for such a tremendous polymorphism.    Conclusions  Data do not allow the determination with certitude of the putative species introgressing  I. canariensis , but  I. perado  is suspected. The introgression would be unilateral, with  I. perado  as the male donor, and the paternal sequences would be rapidly converted in highly divergent and consequently unidentifiable pseudogenes. At least, this study allows the establishment of precautionary measures when nuclear markers are used in phylogenetic studies of genera having experienced introgression such as the genus  Ilex .

Are both sympatric species Ilex perado and Ilex canariensis secretly hybridizing? Indication from nuclear markers collected in Tenerife.