Molecular Phylogeny of the genus Thymus (Lamiaceae)

Yohannes B. Mekonnen 1, Mika Bendiksby 1, 2, Brita Stedje 1

1
Natural History Museum, University of Oslo, 0318, Norway
2
NTNU University Museum, Norwegian University of Science and Technology, 7491
Trondheim, Norway

The genus Thymus is one of the most taxonomically complex genus regarding species
delimitation due to its high level of polymorphism as a result of hybridization, presence of
polyploidy, diploidy/aneuploidy and gynodioecy. A number of studies have been conducted on
its essential oil compositions and medicinal application. However, less is known about its
genetic diversity and molecular phylogeny. In this study: DNA sequence data from four regions
(chloroplast: trnK intron, trnL-F and rps16; nuclear: ITS) in total 98 accessions, representing
42 species of the genus and 19 outgroup species (7 Origanum, 8 Thymbra, and the monotypic
genera Pentapleura, Zataria, Saccocalyx, and Argantoniella) were used to construct the
evolutionary history, test previous hypotheses of classification which was based on mainly
morphological characters. Therefore, this study aimed to conduct a more conclusive study by
including a greater number of species.

Using maximum parsimony (MP) and Bayesian analysis phylogenetic reconstructions based on
nuclear and chloroplast sequence data were incongruent, consequently the data were analyzed
separately. Two major lineages were resolved with a strong support on the plastid and less on
the ITS dataset: the ‘‘Thymbra” and ‘‘Thymus + Origanum” groups. The first contains members
of Thymbra. The second lineage further splits into two clades with strong support on both
datasets. In the first clade Origanum were resolved as monophyletic on both dataset as a sister
to the Thymus group on the ITS and it appeared as sister to Argantoniella, Saccocalyx and three
Thymus species (T. saturejoides, T. caespititius and T. riatarum) on the plastid dataset. Thymus
is revealed as paraphyletic since Argantoniella and Saccocalyx imbedded in both the plastid
and ITS and Origanum in the plastid dataset only. Two major clades resolved in the Thymus
group on the ITS dataset: Argantoniella, Saccocalyx and T. saturejoides, T caespititius and T.
riatarum comprise one group and separated from the rest. Regarding the bulk of the Thymus
group, there is incongruence between the ITS and plastid dataset and neither of them were able
to adequately resolve the relationships among the Thymus species; this may be due to
incomplete lineage sorting, by recent and ancient hybridization and chloroplast capture.