FUNCTIONAL CONSTRAINTSAND rbcL EVIDENCE FORLAND PLANT PHYLOGENY'ABSTRACTVictor A. Albert,2'3 Anders Backlund,2 K&Bremer,2 Mark W. Chase,*James R. Manhart, Brent D. Mishler,*and Kevin C. Nixon7 Although the proportion of "functional" DNA in eukaryotic genomes is both debatable and subject to defimost sequences gathered for phylogenetic purposes are indisputably functional. For example, patterns of varare likely to be strongly constrained in ribosomal RNAs because of their structural and catalytic roles in prtranslation, and in protein-coding genes, because of protein function itself. Although seemingly obvious, these conare usually ignored by workers producing gene trees. We have examined the extent of functional constraints inplant rbcL sequences. Not only do rbcL sequences appear to change with essentially clocklike regularity, but nuclecbased cladograms imply that approximately 97.5% of codon changes on internal branches are functionally ne(i.e., synonymous or functionally labile). From this perspective, rbcL evolution appears to be strongly constrainefunction. Transforming nucleotide data into ad hoc string recognitions alters the size of the unit character suffieito highlight "blocks" of conservative information that may or may not be functionally constrained. Simultancladistic analysis of ail available evidence will highlight the proportion of congruent information, despite difunctional constraints among the characters analyzed. We demonstrate the strength of this approach using difforms of the saine rbcL evidence (i.e., nucleotides, strings, or amino acids) in combination with the seed-plantof Nixon et al. Diversification of the major clades of extant landplants probably dates from the Silurian to Creta-ceous. During the Silurian-Devonian, liverworts,hornworts, mosses, and tracheophytes formed dis-tinct lineages. Differentiation of the tracheophyteclades, notably angiosperms and other seed plants,began by the Devonian. The estimation of land-plant phylogeny, a research goal spanning over400 million years of cladogenesis and extinction,is no simple task. For example, many groups lackstrong morphological similarities that might suggestpatterns of relationship. Recent years have seen an explosion of interestin molecular information, with its promise of easilyinterpreted similarities for bridging otherwise largephenotypic gaps. In particular, the plastidgene (which encodes the large subunit of RuBribulose-1,5-bisphosphate carboxylase/oxyg(a primary enzyme in carbon fixation) hassequenced extensively, with primary emphaithe angiosperms (Clegg, 1993; Chase et al.,Arguing from expected synonymous substitper site under a particular rate assumption,(1993) suggested that rbcL sequences shophylogenetically informative for the time in400-100 million years before present. Wehere that this and similar assertions are incoiFrom direct estimation of total substtutiooptimized on cladograms; see Albert et al., 11993; Albert & Mishler, 1992 Albert et al., We thank Steve Farris and Peter Engstrdm for ideas, advice, and discussion, Diana Lipscomb, Bruneand Mick Richardson for comments on an earlier draft of the manuscript, Bill Crepet, Else Marie Friis,Stevenson for permission to use unpublished versions of their data matrix produced in collaboration with 1Bil Anderson for last-minute discussion of Malpighiaceae biogeography. Ail interpretations are, of coue,The program for constructing random strings was written by Karl-Kinig Konigsson and Rolf Staflin. Supthe Swedish Natural Science Research Council (to VAA, AB, and KB) and the U.S. National Science F(BSR-8906496 to MWC, BSR-8906126 to JRM, BSR-9107484 to BDM) is gratefully acknowledged. Lathanks the symposium organizers, travel arrangement staff, and editorial office of the Missouri Botanical Ctheir courteous and patient assistance. 2 Department of Systematic Botany, Uppsala University, Villavigen 6, S-752 36 Uppsala, Sweden. 3 Present and corresponding address: Department of Physiological Botany, Uppsala University, Vll36 Uppsala, Sweden. SLaboratory of Molecular Systematics, Royal Botanical Gardens, Kew, Richmond, Surrey TW9 3Kingdom. Department of Biology, Texas A&M University, College Station, Texas 77843, U.S.A. University and Jepson Herbaria and Department of Integrative Biology, University of CalfornCalifornia 94720, U.S.A. SL. H. Bailey Hortorium, Cornell University, Ithaca, New York 14853, U.S.A.ANN. MISSOURI BOT. GARD. 81: 534-567. 1994.