A hypothetical scenario of Hieracium speciation based on all available (including non-molecular) evidence is depicted. These patterns can be best explained by a rapid diversification of the genus with ancestral polymorphism and incomplete lineage sorting. Both cpDNA and sqs trees showed basal polytomies as well as merging or splitting of species groups of non-hybrid taxa. The ETS tree was considered as the best approximation of the species tree. The same crown groups of species were recognizable in each dataset, but basal relationships were strongly incongruent among cpDNA, sqs and ETS trees. The power of the different markers to detect hybridization varied, but they largely agreed on particular hybrid and allopolyploid origins. Both gene trees were compared with previous results based on the multicopy external transcribed spacer (ETS) of the nuclear ribosomal DNA. Part of the highly variable gene for squalene synthase ( sqs) was applied as a low-copy nuclear marker.
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Sequences of the trnV- ndhC and trnT- trnL intergenic spacers were combined for phylogenetic analyses of cpDNA. To investigate the particular strengths and limitations of chloroplast DNA (cpDNA), low-copy nuclear and multicopy nuclear markers for elucidating the evolutionary history of such groups, we focus on Hieracium s.str., a predominantly apomictic genus combining the above-mentioned features.
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Phylogeny reconstruction based on multiple unlinked markers is often hampered by incongruent gene trees, especially in closely related species complexes with high degrees of hybridization and polyploidy.