-Within the leptosporangiate ferns, chloroplast DNA (cpDNA) structural mutations have been identified by physical mapping. Earlier work revealed that members of four disparate higher fern families all possess cpDNAs that share the same set of complex rearrangements in the inverted repeat. cpDNA lacks these rearrangements. We have examined the chloroplast genomes of additional ferns and determined that Polypodium and the schizaeaceous ferns share the rearrangements previously found in Cyathea, Pteridium, Adiantum, and Polystichum. Two additional cpDNA structural types also have been identified. A partial duplication and relocation of the gene chlL usually occurs with the other gene rearrangements found in higher ferns but may be lacking in the heterosporous water fern, Marsilea. Also, a structural type lacking any of these complex rearrangements, but still different from Osmunda, occurs in Gleichenia cpDNA. The phylogenetic implications of these findings conflict, at least in part, with previously proposed evolutionary hypotheses. Numerous pteridologists have offered detailed hypotheses of fern evolutionary relationships (reviewed in Smith, 1995; Pichi Sermolli, 1974). These scenarios, for the most part, have been intuitive attempts at generating phylogenetic hypotheses. Unfortunately, there is little consensus on the basic structure of the proposed trees (Fig. 1). Searching for markers to characterize major lineages, we have examined chloroplast genome structure in some ferns representating groups commonly regarded as pivotal in the analysis of higher-level fern phylogeny. Land plant chloroplast genomes share many features of basic organization, gene content and gene order (Palmer, 1991). Although instances of structural change are relatively uncommon (reviewed in Downie and Palmer, 1992; Palmer, 1991; Palmer et al., 1988), where present these mutations can serve as important phylogenetic markers. For example, the lycopsids, Lycopodium, Selaginella, and Isoetes, share with the bryophytes the same orientation of a 30-kb region. All other vascular plant cpDNAs, including Psilotum, Equisetum, and the eusporangiate ferns Botrychium and Marattia, possess the derived, inverted gene order (Raubeson and Jansen, 1992a) indicating that the lycopsids are the basal extant lineage of vascular land plants. Other examples of phylogenetically-informative structural changes include an inversion marking the Barnadesiinae as the basal lineage of Asteraceae (Jansen and Palmer, 1987), a loss of one copy of the IR linking members of a subtribe of legumes (Lavin, Doyle, and Palmer, 1990), and a separate IR loss event supporting the monophyly of conifers (Raubeson and Jansen, 1992b). Current address: Department of Biological Sciences, Central Washington University, Ellensburg, WA 98926-7537. This content downloaded from 157.55.39.35 on Tue, 30 Aug 2016 06:31:28 UTC All use subject to http://about.jstor.org/terms AMERICAN FERN JOURNAL: VOLUME 85 NUMBER 4 (1995) Pterldlum Polystlchum Adlantum Polystichum Adiantum Polypodlum / Pterldum tree ferns tree terns Schlzaeaceae Polypodlum Glelchenia Schlzaeaceae Glelchenla | Osmunda HOLTTUM, 1973 MICKEL, 1974 Adiantum tree ferns Pterldlum Pterldlum Polystichum Polystichum tree ferns