The Lichenologist 48(3): 209–227 (2016) © British Lichen Society, 2016 doi:10.1017/S0024282915000572 Phylogenetic relationships among reindeer lichens of North America Sarangi N. P. ATHUKORALA, Raquel PINO-BODAS, Soili STENROOS, Teuvo AHTI and Michele D. PIERCEY-NORMORE Abstract: Cladonia is one of the largest lichen-forming ascomycete genera. It was formerly divided into ten sections, three of which, Crustaceae (Cladina), Tenues, and Impexae, are called the reindeer lichens. While previous studies have elucidated the relationships between species and sections, they often examined only one or a few specimens of each species in the analysis. This study examined the monophyly of selected members of sections Crustaceae, Tenues, and Impexae and their relationships in the genus Cladonia using the internal transcribed spacer region of the nuclear ribosomal DNA (ITS rDNA) and the mitochondrial small subunit gene of the mitochondrial ribosomal DNA (mtSSU). The phylogenetic tree contained four clades, two representing species in section Impexae, one representing species that belong to sections Crustaceae and Tenues, and one clade with C. arbuscula and related species. Five of 22 species, C. pycnoclada, C. stellaris, C. evansii, C. ciliata and C. subtenuis, showed monophyly in the phylogenetic tree; some of these 5 species have been shown previously to be monophyletic. The thallus branching pattern was interpreted as an important heritable character using the mtSSU network. Three duplets of paraphyletic species were further examined using ITS rDNA haplotype networks and AMOVA analysis. The results for the species duplets showed some mixing of haplotypes but the AMOVA analysis provided support for species separation within the duplets. While the evidence supports distinct species, further study is needed to conclusively show separate species in these duplets. Keywords: AMOVA, Cladina, haplotype network, ITS rDNA, monophyly, mtSSU, phylogeny Accepted for publication 12 December 2015 Introduction Cladonia is the largest genus in the lichen- forming fungal family Cladoniaceae, consist- ing of c. 459 accepted species (T. Ahti, August 2015, unpublished data). Based on morphology and secondary chemistry, Ahti (2000) divided the neotropical species of Cladonia into seven taxonomic sections and three sections were recognized in the segregate genus Cladina (Ahti 2000). The division was applicable to most species in the world. The group called Cladina (known as reindeer lichens) is most abundant in the coniferous belt of the Northern Hemisphere and in the Nothofagus regions in the Southern Hemisphere, but is also known in sandy areas of the south-eastern United States and elsewhere, as well as at high altitudes in many mountain ranges. While the lack of competitive ability of lichens with plants is well known, the reindeer lichens have adapted better than almost all other lichens to the terrestrial niches uninhabited by vascular plants and bryophytes. Some species, such as Cladonia arbuscula, C. rangiferina, C. stygia and C. stellaris, are important components of northern ecosystems where they provide vast areas of ground cover (Auclair & Rencz 1982; Shaver & Chapin 1991) and form a major component of the winter food for caribou and reindeer (Svihus & Holand 2000; den Herder et al. 2003). Knowledge of their species status would inform ecosystem management and maintenance of biodiversity. S. N. P. Athukorala and M. D. Piercey-Normore (corresponding author): Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada, R3T 2N2. Email: Michele.Piercey- Normore@umanitoba.ca R. Pino-Bodas, S. Stenroos and T. Ahti: Botanical Museum, Finnish Museum of Natural History, P.O. Box 7, FI-00014 University of Helsinki, Finland.