Cephalaria squamiflora is a chamaephyte restricted to rupicolous habitats in islands of the Western (Balearic Islands, Sardinia) and Eastern Mediterranean (Crete and few Aegean islands). Four narrowly distributed races (subspp. squamiflora, mediterranea, ebusitana, balearica) have been described to encompass the morphological variation within the species. We have used nuclear ribosomal ITS and cpDNA sequences to assess how the patterns of molecular differentiation are related to taxonomic and geographic boundaries. Extensive intragenomic ITS variation was detected in samples from all territories, the average sequence divergence among cloned ribotypes was 1.339%. The parsimony network of cloned ITS sequences suggests a split between Eastern and Western Mediterranean accessions. Chloroplast DNA sequences showed five distinct haplotypes, only one of which was shared between islands (Majorca and Sardinia). Both nuclear and cpDNA markers supported the monophyly of the C. squamiflora complex and identified a highly structured pattern of molecular variation composed by sister monophyletic lineages that mirror major biogeographic units (Western and Eastern Mediterranean). The molecular evidence supports the hypotheses that vicariance events linked to the geological history of the region or dispersal across the Mediterranean may explain the distribution of the complex.
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