The complete or nearly complete large-subunit rRNA (LSU rRNA) sequences were determined for representatives of several algal groups such as the chlorarachniophytes, cryptomonads, haptophytes, bacillariophytes, dictyochophytes and pelagophytes. Our aim was to study the phylogenetic position and relationships of the different groups of algae, and in particular to study the relationships among the different classes of heterokont algae. In LSU rRNA phylogenies, the chlorarachniophytes, cryptomonads and haptophytes seem to form independent evolutionary lineages, for which a specific relationship with any of the other eukaryotic taxa cannot be demonstrated. This is in accordance with phylogenies inferred on the basis of the smallsubunit rRNA (SSU rRNA). Regarding the heterokont algae, which form a wellsupported monophyletic lineage on the basis of LSU rRNA, resolution between the different classes could be improved by combining the SSU and LSU rRNA data. Based on a concatenated alignment of both molecules, the phaeophytes and the xanthophytes are sister taxa, as well as the pelagophytes and the dictyochophytes, and the chrysophytes and the eustigmatophytes. All these sister group relationships are highly supported by bootstrap analysis and by different methods of tree construction.Keywords : heterokont algae, cryptophytes, chlorarachniophytes, haptophytes, large-subunit rRNA (LSU rRNA)
INTRODUCTIONGenerally, on the basis of pigmentation, three main eukaryotic algal groups have been discerned, namely the chlorophytes or green algae (characterized by the presence of chlorophyll a and b), the rhodophytes or red algae (chlorophyll a and phycobilins), and the chromophytes or yellow-brown algae (chlorophyll a and c, and absence of chlorophyll b). The latter group, which is polyphyletic, is further subdivided into four taxa, namely the cryptophytes, the haptophytes, the dinoflagellates and the heterokont algae, on the basis of pigmentation and plastid ultrastructure, flagellar apparatus and small-subunit rRNA (SSU rRNA). phylogenies (Whatley, 1989 ; Bhattacharya et al., 1992 ;Leipe et al., 1994 ; Cavalier-Smith et al., 1994a ;Medlin et al., 1995).The cryptophytes or cryptomonads (Gillot, 1990) are unicellular biflagellated organisms for which the evolutionary history is unclear and controversial. In previous studies, they have been phylogenetically positioned with chlorobionts (Eschbach et al., 1991), other chromophytes (Cavalier-Smith et al., 1994a), glaucocystophytes (Bhattacharya et al., 1995a ;Ragan & Gutell, 1995 ;Van de Peer et al., 1996a) and Acanthamoeba (McFadden, 1993). The haptophytes or prymnesiophytes (Green et al., 1990) are unicellular flagellate cells, characterized by a filiform organelle associated with the flagella, called the haptonema. Also for this group of organisms, the phylogenetic status is rather unclear (Daugbjerg & Andersen, 1997a ; and references therein). The heterokont algae, also referred to as 'stramenochromes ' (Leipe et al., 1994) and 'Ochrista' (Cavalier-Smith et al., 1994b), consist A....