## 3 Results  
### Phylogenetic Analysis  
The phylogenetic relationships of the 45 _Crepis_ species and _Lapsana communis_ were inferred from analyses of their nrITS sequences and four plastid regions (_rpl32-trnL_, _ndl_/C-trnV_, _rps16-trnK_ and _trnT-psb_D). A total of 61 nrITS and 244 cpDNA sequences (61 sequences per each of the four chloroplast markers) were analysed. Three species, _Picris hieracioides_, _Lactuca serriola_, and _Sonchus oleraeus_, were used as the outgroups. The length of the isolated nrITS regions among the analysed species ranged from 540 to 598 bp. The final alignment was 668 bp long (including gaps) with 241 Characters that were parsimony informative. Only one ribotype of the nrITS was amplified for all of the studied accessions. The total length of the analysed concatenated plastid DNA regions ranged from 2948 to 3577 bp (the data for the individual chloroplast markers are listed in Table S5). The concatenated alignment of the cpDNA was 5693 bp long (including gaps) with 720 characters that were parsimony informative.  
Two major well-supported clades (nrITS BS100 and cpDNA BS100) corresponding to the evolutionary lineages of _Lagoseris_ and _Crepis_ s.s. (Figure 1) were consistently recovered in both the nrITS and cpDNA ML analyses. _Crepis_ s.s., which contained most of the analysed species, was monophyletic in both of the nrITS and cpDNA analyses; however, the nrITS- and cpDNA-tree topologies differed in their branching patterns. The clades that were recovered in the cpDNA marker analyses were labelled with Roman numerals(clades I-IV) and the subclades with Roman numerals and lower-case letters (subclades IVa-IVc). The clades in the nrITS phylogenetic analyses were labelled with Arabic numerals (clades 1-4) and the subclades were labelled with Arabic numerals and lower-case letters (subclades 4a-4c). Four clades were distinguished in _Crepis_ s.s. in all of the analyses. Clade 1 (BS81), which was recovered in the nrITS data analysis, included five perennial European species and the central Asian _C. lynta_. This group of species was monophyletic in the nrITS phylogeny, but not in the cpDNA analysis in which the species were placed in two highly supported clades instead: clade I (BS99) and clade II (BS100; Figure 1). The second monophyletic clade 2 (BS96), which was recovered in the nrITS analysis, comprised nine, mostly annual _Crepis_ species, with the exception of the perennial _C. sibirica_. These species were placed in subclade IVb (BS97) in the cpDNA tree together with _C. setosa_ (Figure 1). Six European and/or Middle East perennial species, which were recovered in clade 3 (BS96) of the nrITS tree, were placed in subclade IVa (BS100) in the cpDNA phylogeny. Nearly half of the analysed _Crepis_ s.s. species were placed in clade 4 in the nrITS phylogeny. Three highly supported subclades could be distinguished within this clade: (i) subclade 4a (BS90), which consisted of species that are native to North America; (ii) subclade 4b (BS86), which comprised C. _biennis_, _C. setosa_, and _C. nicaensis_; and (iii) subclade 4c, which comprised both annual and perennial species from Europe and North Africa (from Algeria to Morocco). However, in the cpDNA phylogeny, the North American species together with _C. tectorum_, _C. nigrescens_, _C. nicaensis_, and _C. biennis_ formed the monophyletic clade III (BS100).  
Three main evolutionary lineages were distinguished in the phylogenetic tree that resulted from the analysis of the newly obtained nrITS sequences and previously published data (species of _Askellia_. _Lagoseris_ and _Crepis_ s.s.; Figure S1; Table S3; [22]). Among the species of _Crepis_ s.s., five main clades were identified, in congruence with earlier reports [22; 23].