Israeli Oncocyclus irises: Phylogenetic relationships and evolutionary history

<p><em>Oncocyclus</em> is a large group of bearded irises with poorly known phylogeny and evolutionary history. In Israel, <em>Iris </em>sect. <em>Oncocyclus </em>comprises eight species belonging to three aggregates. We used a combination of approaches to resolve the phylogenetic relationships of these species and indicate the evolutionary forces responsible for their origin. We sequenced the whole chloroplast genomes of species and integrated a phylogenetic tree with results of genetic (AFLP) divergence, degree of reproductive isolation, and species distribution modeling. Our findings suggest that quantitative and even qualitative morphological characters, such as flower color, are unreliable diagnostic traits for <em>Oncocyclus</em> taxonomy; that some recognized species comprise more than one species; and that group evolution did not involve the origin of distinct flower aggregates. A lack of pre-zygotic reproductive isolation agrees with the very low variability of the <em>Oncocyclus</em> plastome, suggesting that Israeli <em>Oncocyclus</em> species are very young. Homoploid hybridization followed or preceded by long periods of geographic isolation, and local selection likely contributed to speciation in <em>Oncocyclus</em>. In the group evolutionary history, importance of homoploid hybridization and local selection differed among species, but limited gene flow played a crucial role for all species. </p>