Jeff J. Doyle

Gene trees and species trees : molecular systematics as one-character taxonomy

Reconstruction of phylogenies from molecular data has become an important and increasingly common approach in systematics. The product of such studies is a gene tree, hypoth- esizing relationships among genes or genomes. This gene tree may be fundamentally incongruent with the true species phylogeny, due to various biological phenomena such as introgression, lineage sorting, or mistaken orthology. In such circumstances all of the gene tree characters defining the relationships of molecular taxa (haplotypes) may be necessarily correlated, and the gene or genome may behave as a single species tree character. In these circumstances robustness of the gene hypoth- esis is meaningless as a measure of confidence in the species phylogenetic hypothesis. Incongruence between a phylogenetic hypothesis based on numerous, presumably independent, non-molecular characters and a single gene tree should not be assumed to be due to noise in non-molecular data. As with other characters, a character phylogeny, in this case a gene tree, can be tested best by a parsimony analysis in which other characters are included. If independence of molecular characters is assumed, then each is an equivalent phylogenetic hypothesis, as is each non-molecular character, leading to the suggestion that direct combination is appropriate. Swamping becomes an issue when a large molecular data set may be behaving as a single character. To alleviate this problem, a gene tree may be treated as a single multistate character, either ordered or unordered, and included with non-molecular data to obtain a globally parsimonious result. An example is given using published molecular and non-molecular data from the Asteraceae.

Molecular systematics of plants II

Preface. Part I: Molecules and genomes in plant systematics. Chloroplast DNA and the study of plant phylogeny: present status and future prospects - M T Clegg and G Zurawski Use of chloroplast DNA rearrangements in reconstructing plant phylogeny - S R Downie and J D Palmer Mitochondrial DNA in plant systematics: applications and limitations - J D Palmer Ribosomal RNA as a phylogenetic tool in plant systematics - R K Hamby and E A Zimmer Evolution of the NOR and 5S DNA loci in the Triticeae - R Appels and B Baum Part II: Molecular approaches to plant evolution Intraspecific chloroplast DNA variation: systematic and phylogenetic implications - D E Soltis, P S Soltis and B G Milligan Molecular data and polyploid evolution in plants - P S Soltis, J J Doyle and D E Soltis Molecular systematics and crop evolution - J Deobley Part III: Model studies of phylogenetic relationships Contributions of molecular data to polyploid evolution in plants - P S Soltis, J J Doyle and D E Soltis Molecular systematics and crop evolution - J Deobley Contributions of molecular data to papilionoid legume systematics - J J Doyle, M Levin and A Bruneau Chloroplast DNA variation in the asteraceae: phylogenetic and evolutionary implications - R K Jansen, H J Michaels, R S Wallace, K-J Kim, S C Keeley, L E Watson and J D Palmer Chloroplast DNA restriction site variation and the evolution of the annual habit in North American Coreopsis (Asteraceae) - D J Crawford, J D Palmer and M Kobayashi Molecular systematics of onagraceae: examples from Clarkia and Fuschia - K J Systema and J E Smith Floral morphology and chromosome number in the subtribe oncidiinae (Orchidaceae): evolutionary insights from a phylogenetic analysis of the chloroplast DNA restriction site variation - M W Chase and J D Palmer Part IV: Theoretical perspectives The suitability of molecular and morphological evidence in reconstructing plant phylogeny -M J Donaghue and M J Sanderson Character-site weighting for restriction site data in phylogenetic reconstruction, with an example from chloroplast DNA - V A Albert, B D Mishler and M W Chase Polymorphism, hybridization and variable evolutionary rate in molecular phylogenies - K Ritland and J E Eckenwalder Index.

Phylogenetic Incongruence: Window into Genome History and Molecular Evolution

The field of systematic biology has been revitalized and transformed during the last few decades by the confluence of phylogenetic thinking with ready access to the tools of molecular biology. Indeed, the title of this volume and the fact that it is already in its second edition offers ample testimony to the impact that molecular approaches have had on efforts to reconstruct the phylogenetic history of plants. Concomitant with the proliferation of molecular tools has been a growing awareness that reliance on a single data set may often result in insufficient phylogenetic resolution or misleading inferences. Accordingly, it is an increasingly widespread practice to apply multiple data sets to a common group of taxa. One of the consequences of analyzing multiple data sets is that the phylogenies inferred may differ from each other in one or more details. This phylogenetic incongruence is not rare; to the contrary, it is almost the rule rather than the exception, being evident to varying degrees.

Evolutionary Genetics of Genome Merger and Doubling in Plants

Polyploidy is a common mode of evolution in flowering plants. The profound effects of polyploidy on gene expression appear to be caused more by hybridity than by genome doubling. Epigenetic mechanisms underlying genome-wide changes in expression are as yet poorly understood; only methylation has received much study, and its importance varies among polyploids. Genetic diploidization begins with the earliest responses to genome merger and doubling; less is known about chromosomal diploidization. Polyploidy duplicates every gene in the genome, providing the raw material for divergence or partitioning of function in homoeologous copies. Preferential retention or loss of genes occurs in a wide range of taxa, suggesting that there is an underlying set of principles governing the fates of duplicated genes. Further studies are required for general patterns to be elucidated, involving different plant families, kinds of polyploidy, and polyploids of different ages.

The Rest of the Iceberg. Legume Diversity and Evolution in a Phylogenetic Context

Most readers of a special issue of Plant Physiology on legumes will be familiar with only a handful of species, primarily pea ( Pisum sativum ) and the various economically important “beans” such as soybean ( Glycine max ), and of course, the model legumes Medicago truncatula and Lotus japonicus

DNA Protocols for Plants

This procedure has been used with success on a wide variety of plant groups and even some animals. The method is used to isolate total genomic DNA (nuclear, chloroplast, and mitochondrial). It is a rapid, inexpensive method that is suitabie for use in conjunction with other protocois, such as isolation of DNA enriched for cpDNA. it is also easy to scale down for use in population sampling, using 0.01g or less of fresh tissue. Other applications include isolation of DNA from herbarium specimens (Doyle & Dickson, 1987. Taxon 36:715–722), and isolation of RNA. A brief word on the history of the protocol is in order. This procedure was modified by us (Doyle and Doyle, 1987. Phytochemical Bulletin 19:11–15) for use with fresh plant tissue from a method of Saghai-Maroof et al. (1984, PNAS USA 81:8014–8019) who used lyophilized tissue. They in turn had developed their procedure from earlier protocols. We were recently asked to publish a slightly modified version of our procedure (Doyle and Doyle, 1990 Focus 12:13–15). We recently learned from Brian Taylor (Texas A&M University, USA) that he had published a virtually identical procedure for fresh tissue, also in Focus, in 1982 (Taylor & Powell, Focus 4:4–6) of which we (and apparently the editors of Focus!) were entirely unaware. It is indeed a useful procedure, thus independently confirmed.

The Charophycean green algae as model systems to study plant cell walls and other evolutionary adaptations that gave rise to land plants.

The Charophycean green algae (CGA) occupy a key phylogenetic position as the evolutionary grade that includes the sister group of the land plants (embryophytes), and so provide potentially valuable experimental systems to study the development and evolution of traits that were necessary for terrestrial colonization. The nature and molecular bases of such traits are still being determined, but one critical adaptation is thought to have been the evolution of a complex cell wall. Very little is known about the identity, origins and diversity of the biosynthetic machinery producing the major suites of structural polymers (i. e., cell wall polysaccharides and associated molecules) that must have been in place for land colonization. However, it has been suggested that the success of the earliest land plants was partly based on the frequency of gene duplication, and possibly whole genome duplications, during times of radical habitat changes. Orders of the CGA span early diverging taxa retaining more ancestral characters, through complex multicellular organisms with morphological characteristics resembling those of land plants. Examination of gene diversity and evolution within the CGA could help reveal when and how the molecular pathways required for synthesis of key structural polymers in land plants arose.

HecA, a member of a class of adhesins produced by diverse pathogenic bacteria, contributes to the attachment, aggregation, epidermal cell killing, and virulence phenotypes of Erwinia chrysanthemi EC16 on Nicotiana clevelandii seedlings

Erwinia chrysanthemi is representative of a broad class of bacterial pathogens that are capable of inducing necrosis in plants. The E. chrysanthemi EC16 hecA gene predicts a 3,850-aa member of the Bordetella pertussis filamentous hemagglutinin family of adhesins. A hecA∷Tn7 mutant was reduced in virulence on Nicotiana clevelandii seedlings after inoculation without wounding. Epifluorescence and confocal laser-scanning microscopy observations of hecA and wild-type cells expressing the green fluorescent protein revealed that the mutant is reduced in its ability to attach and then form aggregates on leaves and to cause an aggregate-associated killing of epidermal cells. Cell killing also depended on production of the major pectate lyase isozymes and the type II, but not the type III, secretion pathway in E. chrysanthemi. HecA homologs were found in bacterial pathogens of plants and animals and appear to be unique to pathogens and universal in necrogenic plant pathogens. Phylogenetic comparison of the conserved two-partner secretion domains in the proteins and the 16S rRNA sequences in respective bacteria revealed the two datasets to be fundamentally incongruent, suggesting horizontal acquisition of these genes. Furthermore, hecA and its two homologs in Yersinia pestis had a G+C content that was 10% higher than that of their genomes and similar to that of plant pathogenic Ralstonia, Xylella, and Pseudomonas spp. Our data suggest that filamentous hemagglutinin-like adhesins are broadly important virulence factors in both plant and animal pathogens.

Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome

BACKGROUND The study of plant populations is greatly facilitated by the deployment of chloroplast DNA markers. Asymmetric inheritance, lower effective population sizes and perceived lower mutation rates indicate that the chloroplast genome may have different patterns of genetic diversity compared to nuclear genomes. Convenient assays that would allow intraspecific chloroplast variability to be detected are required. RESULTS Eukaryote nuclear genomes contain ubiquitous simple sequence repeat (microsatellite) loci that are highly polymorphic in length; these polymorphisms can be rapidly typed by the polymerase chain reaction (PCR). Using primers flanking simple mononucleotide repeat motifs in the chloroplast DNA of annual and perennial soybean species, we demonstrate that microsatellites in the chloroplast genome also exhibit length variation, and that this polymorphism is due to changes in the repeat region. Furthermore, we have observed a nonrandom geographic distribution of variations at these loci, and have examined the number and location of such repeats within the chloroplast genomes of other species. CONCLUSIONS PCR-based analysis of mononucleotide repeats may be used to detect both intraspecific and interspecific variability in the chloroplast genomes of seed plants. The analysis of polymorphic microsatellites thus provides an important experimental tool to examine a range of issues in plant genetics.

rbcL and Legume Phylogeny, with Particular Reference to Phaseoleae, Millettieae, and Allies

Abstract A parsimony analysis was conducted on 319 rbcL sequences, comprising 242 from 194 genera of Leguminosae and 77 from other families. Results support earlier conclusions from rbcL and other molecular data that a monophyletic Leguminosae is part of a Fabales that includes Polygalaceae, Surianaceae, and the anomalous rosid genus Quillaja. Within legumes, results of previous analyses were also supported, such as the paraphyletic nature of Caesalpinioideae and monophyly of Mimosoideae and Papilionoideae. Most new data (74 sequences) were from Papilionoideae, particularly Phaseoleae, Millettieae, and allies. Although the overall topology for Papilionoideae was largely unresolved, several large clades were well-supported. The analysis contained a large sample of Phaseoleae and Millettieae, and not surprisingly showed both tribes to be polyphyletic, though with all taxa except Wisteria and allied Millettieae belonging to a single well supported clade. Within this clade was a strongly supported group that included Phaseoleae subtribes Erythrininae, Glycininae, Phaseolinae, Kennediinae, and Cajaninae, with only the last two being monophyletic. Desmodieae and Psoraleeae were also part of this clade. The monophyletic Phaseoleae subtribes Ophrestiinae and Diocleinae grouped with most Millettieae in a clade that included a group similar to the core Millettieae identified in other studies. All but one of the remaining Millettieae sampled formed an additional clade within the overall millettioid/phaseoloid group. Communicating Editor: Aaron Liston