Victor A. Albert

PARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR-JOINING

Abstract— Because they are designed to produced just one tree, neighbor‐joining programs can obscure ambiguities in data. Ambiguities can be uncovered by resampling, but existing neighbor‐joining programs may give misleading bootstrap frequencies because they do not suppress zero‐length branches and/or are sensitive to the order of terminals in the data. A new procedure, parsimony jackknifing, overcomes these problems while running hundreds of times faster than existing programs for neighbor‐joining bootstrapping. For analysis of large matrices, parsimony jackknifing is hundreds of thousands of times faster than extensive branch‐swapping, yet is better able to screen out poorly‐supported groups.

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Coffee, tea, and chocolate converge Caffeine has evolved multiple times among plant species, but no one knows whether these events involved similar genes. Denoeud et al. sequenced the Coffea canephora (coffee) genome and identified a conserved gene order (see the Perspective by Zamir). Although this species underwent fewer genome duplications than related species, the relevant caffeine genes experienced tandem duplications that expanded their numbers within this species. Scientists have seen similar but independent expansions in distantly related species of tea and cacao, suggesting that caffeine might have played an adaptive role in coffee evolution. Science, this issue p. 1181; see also p. 1124 The genetic origins of coffee’s constituents reveal intriguing links to cacao and tea. Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.

Homoplasy Increases Phylogenetic Structure

According to currently accepted theories, rapidly evolving nucleotide sites are phylogenetically less informative than more slowly evolving ones, especially for recognizing more ancient groupings. For this reason third codon positions are often regarded as less reliable than first and second positions as indicators of phylogeny. Analysis of the largest nucleotide matrix treated to date—2538 rbc L sequences covering all major lineages of green plants—shows the opposite: although rapidly evolving and highly homoplastic, third positions contain most of the phylogenetic structure in the data. Frequency of change should thus be used with caution as a criterion for weighting or selecting characters.

Functional Constraints and rbcL Evidence for Land Plant Phylogeny

Although the proportion of «functional» DNA in eukaryotic genomes is both debatable and subject to definition, most sequences gathered for phylogenetic purposes are indisputably functional. For example, patterns of variation are likely to be strongly constrained in ribosomal RNAs because of their structural and catalytic roles in protein translation, and in protein-coding genes, because of protein function itself. Although seemingly obvious, these concerns are usually ignored by workers producing gene trees. We have examined the extent of functional constraints in land-plant rbcL sequences. Not only do rbcL sequences appear to change with essentially clocklike regularity, but nucleotide-based cladograms imply tbat approximately 97.5% of codon changes on internal branches are functionally neutral (i.e., synonymous or functionally labile)

Floral gene resources from basal angiosperms for comparative genomics research

BackgroundThe Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and under intensive comparative genomic investigation, are separated by at least 125 million years of evolutionary time, and cannot in isolation provide a comprehensive perspective on structural and functional aspects of flowering plant genome dynamics. Here we discuss new genomic resources available to the scientific community, comprising cDNA libraries and Expressed Sequence Tag (EST) sequences for a suite of phylogenetically basal angiosperms specifically selected to bridge the evolutionary gaps between model plants and provide insights into gene content and genome structure in the earliest flowering plants.ResultsRandom sequencing of cDNAs from representatives of phylogenetically important eudicot, non-grass monocot, and gymnosperm lineages has so far (as of 12/1/04) generated 70,514 ESTs and 48,170 assembled unigenes. Efficient sorting of EST sequences into putative gene families based on whole Arabidopsis/rice proteome comparison has permitted ready identification of cDNA clones for finished sequencing. Preliminarily, (i) proportions of functional categories among sequenced floral genes seem representative of the entire Arabidopsis transcriptome, (ii) many known floral gene homologues have been captured, and (iii) phylogenetic analyses of ESTs are providing new insights into the process of gene family evolution in relation to the origin and diversification of the angiosperms.ConclusionInitial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage-specific gene duplication and functional divergence, and analyses of adaptive molecular evolution. Since not all genes in the floral transcriptome will be associated with flowering, these EST resources will also be of interest to plant scientists working on other functions, such as photosynthesis, signal transduction, and metabolic pathways.

Phylogenetics of the slipper orchids (Cypripedioideae, Orchidaceae): Nuclear rDNA ITS sequences

Cypripedioideae (Orchidaceae) have been the subject of numerous taxonomic treatments with conflicting interpretations of relationships among the five genera and the 150–170 species. We have produced nuclear ribosomal ITS nucleotide sequences for nearly 100 slipper orchid species and used parsimony analysis to investigate their relationships. Our results demonstrate that each genus, as currently circumscribed, is monophyletic (Mexipedium andSelenipedium being represented by a single taxon). LikerbcL data, ITS sequences placeMexipedium sister toPhragmipedium. Relationships at the sectional level inPaphiopedilum are largely as described byCribb. However, the division ofPaphiopedilum into subgg.Brachypetalum andPaphiopedilum is not supported; subg.Brachypetalum is paraphyletic to subg.Paphiopedilum. Phragmipedium species are divided into the same three major clades as in the taxonomic scheme ofMcCook. The plicate-leaved genera,Cypripedium andSelenipedium, are successive sister groups to the rest of the subfamily, confirming generally held opinions that they display plesiomorphic characters compared to the conduplicate-leaved genera. A survey of karyotypes in the context of the ITS tree reveals a general trend toward increased chromosome number, probably brought about by centric fission. These data also accord with a previously suggested biogeographic hypothesis of a widespread Northern Hemisphere distribution, followed by range fragmentation due to Miocene cooling.

Conifer homologues to genes that control floral development in angiosperms

A set of MADS-box genes in flowering plants encode transcription factors that control both flower meristem formation and organ identity in the developing flower. In this report we present the first documentation of the presence of MADS-box genes in a non-flowering seed plant, and indeed from a plant bearing truly unisexual reproductive axes. A MADS-box-specific screening of a cDNA library from immature female strobili of the conifer Norway spruce, Picea abies (L.) Karst, resulted in cDNA clones that correspond to three different deficiens-agamous-like (dal) genes, dall, dal2 and dal3. In addition to the MADS box, the spruce genes contain a second sequence element conserved among angiosperm genes, the K box, which is located downstream to the MADS box. A phylogenetic analysis of the nucleotide sequences confirms common ancestry of the gene superfamily. dall is related to agl2, agl4 and agl6 from Arabidopsis thaliana, all genes with unknown functions, and is expressed in vegetative as well as reproductive shoots on the adult spruce tree. dal2 is sister to angiosperm genes that control the identity of sexual organs, and is expressed only in the developing male and female strobili. dal3 is related to the vegetatively expressed tomato gene tm3 and is transcribed in both vegetative and reproductive shoots. These results strongly suggest that the functional and structural complexity within the MADS-box superfamily of reproduction-control genes is an ancestral property of seed plants and not a novelty in the angiosperm lineage.

GEG Participates in the Regulation of Cell and Organ Shape during Corolla and Carpel Development in Gerbera hybrida

The molecular mechanisms that control organ shape during flower development are largely unknown. By using differential hybridization techniques, a cDNA designated GEG (for Gerbera hybrida homolog of the gibberellin [GA]–stimulated transcript 1 [GAST1] from tomato) was isolated from a library representing late stages of corolla development in Gerbera. GEG expression was detected in corollas and carpels, with expression spatiotemporally coinciding with flower opening. In corollas and styles, GEG expression is temporally correlated with the cessation of longitudinal cell expansion. In plants constitutively expressing GEG, reduced corolla lengths and carpels with shortened and radially expanded stylar parts were found, with concomitant reduction of longitudinal cell expansion in these organs. In addition, in styles, an increase in radial cell expansion was detected. Taken together, these observations indicate a regulatory role for the GEG gene product in determining the shape of the corolla and carpel. The deduced amino acid sequence of the GEG gene product shares high similarity with previously characterized putative cell wall proteins encoded by GA-inducible genes, namely, GAST1, GIP (for GA-induced gene of petunia), and the GASA (for GA-stimulated in Arabidopsis) gene family. Our studies suggest that GEG, the expression of which can also be induced by application of GA3, plays a role in phytohormone-mediated cell expansion.

A trnL-F cpDNA sequence study of the Condamineeae-Rondeletieae-Sipaneeae complex with implications on the phylogeny of the Rubiaceae.

DNA sequences from the chloroplast trnL-F region of 154 Rubiaceae and 11 outgroup taxa were analyzed cladistically. An emphasis was placed on the tribes Rondeletieae, Sipaneeae, and Condamineeae. Sipaneeae are not close to Rondeletieae and belong in the Ixoroideae. There is no support for a widely distributed Rondeletieae in a broad sense. Instead, Rondeletieae sensu stricto form an almost entirely Antillean clade. Support was found for the separation of Arachnothryx, Rogiera, Roigella, and Suberanthus from Rondeletia. The Guettardeae as well as Gonzalagunia are found close to a complex formed by Arachnothryx, Javorkaea, and Rogiera. Condamineeae, in a strict sense, belongs in the Ixoroideae. A number of Rondeletieae genera should be transferred to Condamineeae or other parts of Ixoroideae. Support is found for an emended tribe Naucleeae, comprising several genera with spherical pseudanthia. For the first time, tribal or subfamilial affiliation based on molecular sequence data is suggested for Allenanthus, Blepharidium, Chione, Coutaportla, Dolichodelphys, Mazaea, Neobertiera, Neoblakea, Phialanthus, Phyllacanthus, Phyllomelia, Schmidtottia, and Suberanthus.

Character-State Weighting for Cladistic Analysis of Protein-Coding DNA Sequences

Nucleotide data are a restricted character system complex enough to confound phylogenetic analyses yet simple enough to permit establishment of probability models for sequence change and corresponding character-state weighting schemes. We have previously developed a general method for weighting DNA data that is here elaborated for protein-coding sequences. Included in the present model are corrections for (i) multiple substitution events, (ii) transition/transversion bias, and (iii) differential proportions of changes occurring at first, second, and third codon positions. This model is shown to be generally consistent for all phylogenetically useful data