Variability of Nuclear SSU-rDNA Group Introns Within Septoria Species: Incongruence with Host Sequence Phylogenies Nicolas Feau, 1,2 Richard C. Hamelin, 2 Louis Bernier 1 1 Centre dÕe´tude de la foreˆt, Universite´ Laval, Que´bec G1K 7P4, Canada 2 Service canadien des foreˆts, Ressources naturelles Canada, Centre de foresterie des Laurentides, 1055 du PEPS, P.O. Box 3800, Que´bec G1V 4C7, Canada Received: 21 December 2005 / Accepted: 29 January 2007 [Reviewing Editor: Debashish Bhattacharya] Abstract. We report structural features and distri- bution patterns of 26 different group I introns located at three distinct nucleotide positions in nuclear small subunit ribosomal DNA (SSU-rDNA) of 10 Septoria and 4 other anamorphic species related to the teleo- morphic genus Mycosphaerella. Secondary structure and sequence characteristics assigned the introns to the common IC1 and IE groups. Intron distribution patterns and phylogenetic relationships strongly suggested that some horizontal transfer events have occurred among the closely related fungal species sampled. To test this hypothesis, we used a compar- ative approach of intron- and rDNA-based phylog- enies through MP- and ML-based topology tests. Our results showed two statistically well-supported major incongruences between the intron and the equivalent internal transcribed spacer (ITS) tree comparisons made. Such absence of a co-evolutive history between group I introns and host sequences is discussed rel- atively to the intron structures, the mechanisms of intron movement, and the biology of the Mycosp- haerella pathogenic fungi. Key words: Group I introns — Fungi — Septoria — Pseudocercospora — Mycosphaerella — Small subunit ribosomal DNA — Horizontal transfer — RNA secondary structure Introduction The coelomycetous anamorphic genus Septoria rep- resents more than 2000 described fungal species including important pathogens of crops and trees. Based on morphological and molecular studies, Septoria spp. appear unequivocally linked to the te- leomorphic genus Mycosphaerella (Dothideales) (Verkley and Priest 2000; Verkley et al. 2004). More than 30 anamorphic genera have been associated with Mycosphaerella and recent molecular studies have underlined the difficulty in using morphological characters for generic and specific definition among these anamorphs (Crous et al. 2000, 2001; Verkley and Priest 2000; Verkley et al. 2004). Host specificities also have appeared inadequate to delimit species and reconstruct phylogenetic relationships among ana- morphs within Mycospaherella. This is in disagree- ment with the co-evolutionary concept usually expected between parasites and host species (Feau et al. 2006; Crous et al. 2004). Under these phylogenetic investigations, the small (SSU) and large (LSU) subunits of the nuclear ribo- somal DNA (rDNA) gene have been sequenced in a wide variety of fungal taxa, but to date very little is known about nuclear rDNA size variation among species within the Mycosphaerella genus. In a recent survey of the 3¢ end of the SSU-rDNA region in Septoria spp., we noted length polymorphisms in four Septoria species (Feau et al. 2006). Sequence align- ments revealed that 484–500 nucleotides (nt) inser- tions were all located at the same rDNA position corresponding to base 1506 of the SSU-rDNA gene Correspondence to: Louis Bernier; email: Louis.Bernier@rsvs. ulaval.ca J Mol Evol (2007) 64:489–499 DOI: 10.1007/s00239-005-0309-7