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Parmelioid lichens are a diverse and ubiquitous group of foliose lichens. Generic delimitation in parmelioid lichens has been in a state of flux since the late 1960s with the segregation of the large, heterogeneous genus Parmelia into numerous smaller genera. Recent molecular phylogenetic studies have demonstrated that some of these new genera were monophyletic, some were not, and others, previously believed to be unrelated, fell within single monophyletic groups, indicating the need for a revision of the generic delimitations. This study aims to give an overview of current knowledge of the major clades of all parmelioid lichens. For this, we assembled a dataset of 762 specimens, including 31 of 33 currently accepted parmelioid genera (and 63 of 84 accepted genera of Parmeliaceae). We performed maximum likelihood and Bayesian analyses of combined datasets including two, three and four loci. Based on these phylogenies and the correlation of morphological and chemical characters that characterize monophyletic groups, we accept 27 genera within nine main clades. We re-circumscribe several genera and reduce Parmelaria to synonymy with Parmotrema. Emodomelanelia Divakar & A. Crespo is described as a new genus (type: E. masonii). Nipponoparmelia (Kurok.) K.H. Moon, Y. Ohmura & Kashiw. ex A. Crespo & al. is elevated to generic rank and 15 new combinations are proposed (in the genera Flavoparmelia, Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A short discussion of the accepted genera is provided and remaining challenges and areas requiring additional taxon sampling are identified. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships of Adenocarpus species were assessed by sequence analyses of the ITS and 3' end of ETS (nrDNA) regions and the trnL-trnF intergenic spacer (cpDNA). The nrDNA analysis recovered four main clades within Adenocarpus. Clades 1-3 comprise morphological and molecularly well-differentiated species that occur in the western Mediterranean realm. Clade 4 comprises three distinctive endemic species from the Canary Islands, an endangered Algerian endemic, and a set of species close to A. complicatus with distinct geographical areas but with little molecular variation between taxa. The latter species are centred in the Iberian Peninsula but also distributed along the Mediterranean basin (from the Iberian Peninsula to Turkey). The phylogenetic position of A. mannii, a morphologically distinctive species with a unique afro-tropical distribution, is not unequivocally resolved, being sister to clade 3 in the ETS tree but to clade 4 in the ITS tree. Rates of evolution and ages of divergence of major groups were estimated using nonparametric rate smoothing with a fixed calibration point of 41.2 Ma and constraining the node of the separation of Anarthrophyllum and Mediterranean Genisteae at a minimum age of 13.6 and a maximum of 25.8 Ma. The estimated ages indicate that the diversification of Adenocarpus and first separation of two lineages may have occurred during the onset and the wake of the profound Middle Miocene cooling episode. One of the lineages separated rapidly into two groups (clades 1 and 2) while the second one led to clade 3, A. mannii and clade 4. Clades 1, 2 and 3 differentiated into the present species soon after these major events whereas clade 4 radiated much later, during the Pliocene. [ABSTRACT FROM AUTHOR]

The tribe Genisteae includes genera of great ecological importance in Mediterranean countries because they are dominant elements of many plant communities. Genetic variation and diversification patterns in Stauracanthus (Genisteae) provide information relevant for the study of the processes of diversification in relation to the environmental history of the western Mediterranean. Nineteen populations of S. boivinii and S. genistoides were assessed by 11 chloroplast microsatellite markers, revealing 44 haplotypes. Both species had different haplotypes and contrasting patterns of karyological, morphological, and genetic variation. In the minimum spanning tree of the haplotypes, AMOVA analysis, and nested clade analysis, S. boivinii had high levels of differentiation and restricted gene flow among populations. Allopatric differentiation occurred between the Moroccan and Iberian populations of S. genistoides, although S. genistoides subsp. spectabilis and subsp. vicentinus had high levels of differentiation among populations (FST), whereas S. genistoides subsp. genistoides had a low FST. Genetic patterns are discussed in relation to the Messinian salinity crisis (MSC): hard conditions drove plants to refuge habitats along the Atlantic coast and higher altitude areas in the Moroccan mountains (S. genistoides subsp. spectabilis and S. boivinii). After the MSC, S. boivinii underwent polyploidization and expansion, whereas S. genistoides expanded and continued diversifying into S. genistoides subspp. genistoides and vicentinus. [ABSTRACT FROM AUTHOR]

Genetic distances among populations and phylogenetic hypothesis concerning origin and diversification of Cytisus purgans s.l. are inferred by analysis of the ITS and ETS regions (nrDNA) and the trnL-trnF intergenic spacer (cpDNA). Cytisus purgans s.I., a shrub of western Mediterranean mountains, consists of two evolutionary units: C. balansae (Boiss.) Ball (Morocco, Algeria, southern Spain) and C. oromediterraneus Rivas Mart. & al. (France, Portugal, Andorra, central and northern Spain). The two units are related to different cytisus groups, in Bayesian and Maximum Parsimony analyses, and may be genetically unrelated, their morphological similarities being the result of convergence. However, the incongruence in the position of both species in the ITS tree and the ETS and trnL-trnF trees suggests an alternative explanation. Genetic differentiation could be due to lineage sorting of allelic polymorphism in the ITS region of the common ancestor, and the morphological similarities the result of morphological parallelism. Cytisus balansae conserves ITS sequences related to old Cytisus taxa; rapid radiation may have led to a western Mediterranean lineage in which C. oromediterraneus originated. [ABSTRACT FROM AUTHOR]

Genetic variation in 27 populations of Ulex species from southern Spain and northern Morocco (Betic-Rif arc) was assessed using 11 chloroplast microsatellite (cpSSR) markers, which revealed 47 different haplotypes. These nonrecombinant, haploid markers allow measurement of genetic variation in closely related species of Ulex where molecular phylogenetic analyses have not provided a clear view of interspecific relationships. Discriminant analysis indicates that the haplotypes are useful to differentiate among species, and analysis of molecular variance (AMOVA) shows high levels of differentiation among populations. The minimum spanning tree (MST), that represents the connections between the haplotypes, suggests that the eastern Rifean U. africanus haplotypes are more genetically related than those from southern Spain. The latter may have lost genetic diversity while colonizing new habitats, eventually differentiating into U. baeticus and U. scaber. Hybridization between these populations, followed by polyploidization, may have originated the tetraploids (U. congestus and U. borgiae) that colonized new habitats associated with acidic rocks. Separate groupings of U. scaber populations may indicate multiple origins from different stocks. Diversification in this group of Ulex species could be related to the opening of the Alboran Sea by Middle Miocene, when the populations from Morocco and Spain became isolated from each other. [ABSTRACT FROM AUTHOR]