Original AFLP data matrixthis file has the following structure: - data for individuals are in rows, and loci are in columns - additionally, there are two columns in the beginning giving the population (pop), and species (species) of each individual; pop is either the population identifier [aga1 = aga-1, aga3 = aga-3, hyb1 = hyb-1, hyb2 = hyb-2, pha1 = pha-1, pha3 = pha-3] or indicates individuals repeated for error estimation [con (control) = individuals repeated on each plate, with A-E as part of the identifier indicating the plate; test = individuals repeated on a different plate] - the last row (quality) gives an indication of the peak quality for each locus (separation from other peaks, clarity of peak) [A - very good, B - good, C - bad, X - extremely bad; intermediate categories, e.g. A-B for between A and B are used as well; generally A and B are good for use]ORIGINAL_AFLP_data.csvsimulated hybrids (R objects)7-zip archive containing the originally simulated hybrid populations; (sim.hyb.RData, sim.parent.RData) to use it copy the contents to /R/hybsimoriginal_data_R_hybsim.7zoriginal introgress results7-zip archive containing the original simulation results from introgress; (introgress.RData, sim.introgress.RData, introgress.test.l.locus.RData) to use it copy the contents to /R/introgressoriginal_data_R_introgress.7zoriginal Structure results7-zip archive containing the results from the structure runs for the original data; to use copy to /R/structure/resultsoriginal_results_structure.7zStructure results (simulations)7-zip archive containing the results from the structure runs for the simulated hybrids; to use copy to /R/structure/results_simoriginal_results_structure_sim.7zR and Structure scriptsScripts.7z

An increasing number of studies of hybridization in recent years have revealed that complete reproductive isolation between species is frequently not finalized in more or less closely related organisms. Most of these species do, however, seem to retain their phenotypical characteristics despite the implication of gene flow, highlighting the remaining gap in our knowledge of how much of an organism's genome is permeable to gene flow, and which factors promote or prevent hybridization. We used AFLP markers to investigate the genetic composition of three populations involving two interfertile Rhododendron species: two sympatric populations, of which only one contained hybrids, and a further hybrid-dominated population. No fixed differences between the species were found, and only 5.8% of the markers showed some degree of species differentiation. Additionally, 45.5% of highly species-differentiating markers experienced significant transmission distortion in the hybrids, which was most pronounced in F1 hybrids, suggesting that factors conveying incompatibilities are still segregating within the species. Furthermore, the two hybrid populations showed stark contrasting composition of hybrids; one was an asymmetrically backcrossing hybrid swarm, while in the other, backcrosses were absent, thus preventing gene flow.