Anne Bruneau

PLANT O-METHYLTRANSFERASES : MOLECULAR ANALYSIS, COMMON SIGNATURE AND CLASSIFICATION

Comparative analysis of the predicted amino acid sequences of a number of plant O-methyltransferase cDNA clones show that they share some 32–71% sequence identity, and can be grouped according to the different compounds they utilise as substrates. Five highly conserved regions are proposed as a signature for plant O-methyltransferases, two of which (regions I and IV) are believed to be involved in S-adenosyl-L-methionine and metal binding, respectively. The glycine-rich signature regions include a 36 amino acid domain which is located in the mid-terminal section of the carboxy terminus of most O-methyltransferase sequences. Cladistic analysis of the amino acid sequences suggests that plant O-methyltransferases may have arisen from common ancestral genes that were driven by different structural and/or functional requirements, and whose descendants segregated into different biochemical species. A comprehensive classification of plant O-methyltransferases is proposed following the guidelines of the Commission of Plant Gene Nomenclature.

Phylogenetic Relationships in the Caesalpinioideae (Leguminosae) as Inferred from Chloroplast trnL Intron Sequences

Abstract The basal subfamily Caesalpinioideae of the Leguminosae generally is subdivided into four or five tribes, but their monophyly remains questionable. Recent cladistic analyses based on morphological characters and chloroplast rbcL sequences suggest conflicting hypotheses of relationships among tribes and subtribal groupings and of the identification of the basal Caesalpinioideae. Our phylogenetic analysis of the chloroplast trnL intron for 223 Caesalpinioideae, representing 112 genera, plus four Papilionoideae, 12 Mimosoideae and three outgroup taxa, provides some well-supported hypotheses of relationships for the subfamily. Our analysis concurs with the rbcL studies in suggesting that a monophyletic Cercideae is sister to the remainder of the Leguminosae. Among the other tribes of Caesalpinioideae, only the broadly circumscribed Detarieae (including Amherstieae or Macrolobieae) is also supported as monophyletic. The Detarieae s.l. occurs as sister to all Leguminosae, excluding Cercideae. Cassieae subtribes Dialiinae and Labicheinae together are sister to the remaining Leguminosae, which includes a monophyletic Papilionoideae, a paraphyletic Mimosoideae, and several monophyletic groups that correspond to previously defined generic groups or subtribes in the Caesalpinioideae. The trnL intron analysis suggests that basal legumes are extremely diverse in their floral morphology, and that presence of simple, actinomorphic flowers may be a derived feature in a number of lineages in the family. Communicating Editor: Matt Lavin

Phylogenetic patterns and diversification in the caesalpinioid legumesThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Subfamily Caesalpinioideae is a paraphyletic grade of 171 genera that comprises the first branches of the Leguminosae and from which are derived the monophyletic subfamilies Mimosoideae and Papilionoideae. We have sequenced the chloroplast matK gene, and the trnL and 3′-trnK introns for 153 genera of caesalpinioid legumes. Parsimony and Bayesian phylogenetic analyses of these data support the monophyly of several major groups within the caesalpinioid legumes: the Cercideae, Detarieae, Detarieae s. str., Prioria, Amherstieae, Dialiinae, Cassia, Caesalpinia, Peltophorum, and Tachigali clades. Relationships among the first branching lineages of the legumes are not well supported, with Cercideae, Detarieae, and the genus Duparquetia alternatively resolved as sister group to all of the legumes. The division of certain large genera (e.g., Caesalpinia s. l., Bauhinia s. l.) into segregate genera generally is supported by our molecular data. Using 18 well-documented fossils as calibration points, fixing the stem ...

Incorporating Allelic Variation for Reconstructing the Evolutionary History of Organisms from Multiple Genes: An Example from Rosa in North America

Allelic variation within individuals holds information regarding the relationships of organisms, which is expected to be particularly important for reconstructing the evolutionary history of closely related taxa. However, little effort has been committed to incorporate such information for reconstructing the phylogeny of organisms. Haplotype trees represent a solution when one nonrecombinant marker is considered, but there is no satisfying method when multiple genes are to be combined. In this paper, we propose an algorithm that converts a distance matrix of alleles to a distance matrix among organisms. This algorithm allows the incorporation of allelic variation for reconstructing the phylogeny of organisms from one or more genes. The method is applied to reconstruct the phylogeny of the seven native diploid species of Rosa sect. Cinnamomeae in North America. The glyceralgehyde 3-phosphate dehydrogenase (GAPDH), the triose phosphate isomerase (TPI), and the malate synthase (MS) genes were sequenced for 40 individuals from these species. The three genes had little genetic variation, and most species showed incomplete lineage sorting, suggesting these species have a recent origin. Despite these difficulties, the networks (NeighborNet) of organisms reconstructed from the matrix obtained with the algorithm recovered groups that more closely match taxonomic boundaries than did the haplotype trees. The combined network of individuals shows that species west of the Rocky Mountains, Rosa gymnocarpa and R. pisocarpa, form exclusive groups and that together they are distinct from eastern species. In the east, three groups were found to be exclusive: R. nitida-R. palustris, R. foliolosa, and R. blanda-R. woodsii. These groups are congruent with the morphology and the ecology of species. The method is also useful for representing hybrid individuals when the relationships are reconstructed using a phylogenetic network.

Evolution and homology of bird pollination syndromes in Erythrina (Leguminosae)

Erythrina L. (Leguminosae: Phaseoleae) is a pantropical genus of over 100 species, all of which are either hummingbird or passerine pollinated. Phylogenetic hypotheses based on morphological and chloroplast DNA restriction site characters suggest that shifts from passerine to hummingbird pollination have occurred a minimum of four times in the genus. In hummingbird-pollinated species the inflorescences are held upright, the flowers are arranged radially along the axis, and the narrow standard petal is conduplicately folded to form a pseudotube. In most of the passerine-pollinated species, the inflorescences are held horizontally, the flowers are secund, and the standard petal is open so that the nectar and androecium are easily visible and accessible. Nectar amino acid concentrations and sucrose to hexose ratios are closely associated with pollination mode. Despite the general resemblance in flower and inflorescence morphology among species with the same pollination type, homology assessment reveals that petal morphology and size, and calyx and pollen morphology differ. Morphological characters, even if comprising modifications associated with adaptive pollination systems, therefore provide useful phylogenetic information.

A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny

The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or cladebased classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

Polyploid and hybrid evolution in roses east of the Rocky Mountains

This study investigates the impact of hybridization and polyploidy in the evolution of eastern North American roses. We explore these processes in the Rosa carolina complex (section Cinnamomeae), which consists of five diploid and three tetraploid species. To clarify the status and origins of polyploids, a haplotype network (statistical parsimony) of the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) nuclear gene was estimated for polyploids of the complex and for diploids of section Cinnamomeae in North America. A genealogical approach helped to decipher the evolutionary history of polyploids from noise created by hybridization, incomplete lineage sorting, and allelic segregation. At the diploid level, species west of the Rocky Mountains are distinct from eastern species. In the east, two groups of diploids were found: one consists of R. blanda and R. woodsii and the other of R. foliolosa, R. nitida, and R. palustris. Only eastern diploids are involved in the origins of the polyploids. Rosa arkansana is derived from the blanda-woodsii group, R. virginiana originated from the foliolosa-nitida-palustris group, and R. carolina is derived from a hybrid between the two diploid groups. The distinct origins of these polyploid taxa support the hypothesis that the three polyploids are separate species.

Population genetic consequences of extreme variation in sexual and clonal reproduction in an aquatic plant

Most plants combine sexual reproduction with asexual clonal reproduction in varying degrees, yet the genetic consequences of reproductive variation remain poorly understood. The aquatic plant Butomus umbellatus exhibits striking reproductive variation related to ploidy. Diploids produce abundant viable seed whereas triploids are sexually sterile. Diploids also produce hundreds of tiny clonal bulbils, whereas triploids exhibit only limited clonal multiplication through rhizome fragmentation. We investigated whether this marked difference in reproductive strategy influences the diversity of genotypes within populations and their movement between populations by performing two large‐scale population surveys (n = 58 populations) and assaying genotypic variation using random amplified polymorphic DNA (RAPDs). Contrary to expectations, sexually fertile populations did not exhibit higher genotypic diversity than sterile populations. For each cytotype, we detected one very common and widespread genotype. This would only occur with a very low probability (< 10−7) under regular sexual recombination. Compatibility analysis also indicated that the pattern of genotypic variation largely conformed to that expected with predominant clonal reproduction. The potential for recombination in diploids is not realized, possibly because seeds are outcompeted by bulbils for safe sites during establishment. We also failed to find evidence for more extensive movement of fertile than sterile genotypes. Aside from the few widespread genotypes, most were restricted to single populations. Genotypes in fertile populations were very strongly differentiated from those in sterile populations, suggesting that new triploids have not arisen during the colonization of North America. The colonization of North America involves two distinct forms of B. umbellatus that, despite striking reproductive differences, exhibit largely clonal population genetic structures.

Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead

Ten years after DNA barcoding was initially suggested as a tool to identify species, millions of barcode sequences from more than 1100 species are available in public databases. While several studies have reviewed the methods and potential applications of DNA barcoding, most have focused on species identification and discovery, and relatively few have addressed applications of DNA barcoding data to ecology. These data, and the associated information on the evolutionary histories of taxa that they can provide, offer great opportunities for ecologists to investigate questions that were previously difficult or impossible to address. We present an overview of potential uses of DNA barcoding relevant in the age of ecoinformatics, including applications in community ecology, species invasion, macroevolution, trait evolution, food webs and trophic interactions, metacommunities, and spatial ecology. We also outline some of the challenges and potential advances in DNA barcoding that lie ahead.

Phylogenetic Relationships in the Genus Rosa: New Evidence from Chloroplast DNA Sequences and an Appraisal of Current Knowledge

Abstract The genus Rosa (roses) comprises approximately 190 shrub species distributed widely throughout the temperate and subtropical habitats of the northern hemisphere. Despite numerous recent studies examining phylogenetic relationships in the genus, relationships remain obscure due to problems such as poor identification of garden specimens, hybridization in nature and in the garden, and low levels of chloroplast and nuclear genome variation. Phylogenetic analyses of non-coding chloroplast sequences from the trnL-F region and psbA-trnH intergenic spacer for 70 taxa show slightly more variation than previous analyses of the genus. Bayesian and parsimony analyses suggest that subg. Rosa can be divided into two large clades, each with low internal resolution. One comprises species from sections Carolinae, Cinnamomeae and Pimpinellifoliae p.p., whilst the other consists of all of the remaining sections of subg. Rosa (Banksianae p.p., Bracteatae, Caninae, Indicae, Laevigatae, Rosa, Synstylae and Pimpinellifoliae p.p.). A fairly complete sampling of field-collected North American taxa has been incorporated in this analysis. Analyses indicate that migration into North America occurred at least twice within this primarily Old World genus. Most North American taxa, except R. setigera and R. minutifolia, fall into a single clade that includes Asian and European taxa. Analyses also are consistent with the notion that cultivated commercial roses have a relatively narrow genetic background. Six of the seven primary taxa believed to be involved in the creation of domesticated roses are found within the same large clade that mostly includes Asian and European taxa.