Contrasting nuclear‐plastidial phylogenetic patterns in the recently diverged Iberian <i>Phlomis crinita</i> and <i>P. lychnitis</i> lineages (Lamiaceae)

Abstract Systematic and evolutionary relationships within the diploid Western Mediterranean Phlomis crinita/lychnitis complex remain controversial apparently due to hybridization and introgression. This study examines patterns of sequence variation in the nuclear ribosomal DNA (ITS region) and three non‐coding plastid DNA regions ( trnH ‐ psbA , trnT ‐ trnL and atpB ‐ rbcL ) in this complex in an aim to clarify whether hybridization, introgression or lineage sorting resulting from recent diversification is mainly responsible for poorly understood relationships. Information recovered from nuclear and chloroplast markers was found to be strongly incongruent. Phylogenetic analysis of inferred nuclear ITS ribotypes is consistent with previous morphometric and taxonomic results in distinguishing two sister lineages, P . crinita s.l. and P . lychnitis . In addition, the high number of additive polymorphisms detected in ITS sequences suggests the sharing of ancestral variability and local patterns of gene flow within the complex. In contrast, the pattern of chloroplast haplotype variation is geographic rather than taxonomic, which might be caused by low mutation rates combined with frequent instances of interspecific hybridization. To integrate the apparently discordant plastid and nuclear evidence, we suggest that both lineage sorting and horizontal transfer have been involved. Even though pinpointing cases due to either phenomenon is difficult, the available data provide evidence of two sister lineages where hybridization events can be identified despite the inheritance of ancestral polymorphisms.

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