Showing papers in "Taxon in 2007"

A proposal for a standardised protocol to barcode all land plants

Abstract: Chase, M. W., Cowan, R. S., Hollingsworth, P. M., van den Berg, C., Madrinan, S., Petersen, G., Seberg, O., Jorgsensen, T., Cameron, K. M., Carine, M., Pedersen, N., Hedderson, T. A. J., Conrad, F., Salazar, G. A., Richardson, J. E., Hollingsworth, M. L., Barraclough, T. G., Kelly, L., Wilkinson, M. (2007). A proposal for a standardised protocol to barcode all land plants. Taxon, 56, (2), 295-299.

Autopolyploidy in angiosperms: Have we grossly underestimated the number of species?

Abstract: Many species comprise multiple cytotypes that represent autopolyploids, or presumed autopolyploids, of the basic diploid cytotype. However, rarely has an autopolyploid been formally named and considered to represent a species distinct from its diploid progenitor (Zea diploperennis and Z. perennis represent a rare example). The major reasons why autopolyploids have not been named as distinct species are: (1) tradition of including multiple cytotypes in a single named species; and (2) tradition and convenience of adhering to a broad morphology-based taxonomic (or phenetic) species concept. As a result, plant biologists have underrepresented the distinct biological entities that actually exist in nature. Although it may seem "practical" to include morphologically highly similar cytotypes in one species, this practice obscures insights into evolution and speciation and hinders conservation. However, we do not suggest that all cytotypes should be named; each case must be carefully considered. A number of species comprising multiple cytotypes have been thoroughly investigated. Drawing on the literature, as well as our own experience with several autopolyploids (Tolmiea menziesii, Galax urceolata, Chamerion angustifolium, Heuchera grossulariifolia, Vaccinium corymbosum), we reassess the traditional view of plant autopolyploids as mere cytotypes. When considered carefully, many "unnamed" autopolyploids fulfill the requirements of multiple species concepts, including the biological, taxonomic, diagnosability, apomorphic, and evolutionary species concepts. Compared to the diploid parent, the autopolyploids noted above possess distinct geographic ranges, can be distinguished morphologically, and are largely reproductively isolated (via a diversity of mechanisms including reproductive and ecological isolation). These five autopolyploids (and probably many others) represent distinct evolutionary lineages; we therefore suggest that they be considered distinct species and also provide a system for naming them.

Fern phylogeny inferred from 400 leptosporangiate species and three plastid genes

Abstract: In an effort to obtain a solid and balanced approximation of global fern phylogeny to serve as a tool for addressing large-scale evolutionary questions, we assembled and analyzed the most inclusive molecular dataset for leptosporangiate ferns to date. Three plastid genes (rbcL, atpB, atpA), totaling more than 4,000 bp, were sequenced for each of 400 leptosporangiate fern species (selected using a proportional sampling approach) and five outgroups. Maximum likelihood analysis of these data yielded an especially robust phylogeny: 80% of the nodes were supported by a maximum likelihood bootstrap percentage ≥ 70. The scope of our analysis provides unprecedented insight into overall fern relationships, not only delivering additional support for the deepest leptosporangiate divergences, but also uncovering the composition of more recently emerging clades and their relationships to one another.

An ITS phylogeny of tribe Senecioneae (Asteraceae) and a new delimitation of Senecio L.

Abstract: Senecioneae is the largest tribe ofAsteraceae, comprised ofca. 150 genera and 3,000 species. Approximately one-third of its species are placed in Senecio, making it one of the largest genera of flowering plants. Despite considerable efforts to classify and understand the striking morphological diversity in Senecioneae, little is known about its intergeneric relationships. This lack ofphylogenetic understanding is predominantly caused by conflicting clues from morphological characters, the large size ofthe tribe, and the absence of a good delimitation of Senecio. Phylogenetic analyses of nrITS and plastid DNA sequence data were used to produce a hypothesis of evolutionary relationships in Senecioneae and a new, monophyletic, delimitation of Senecio. The results of separate and combined phylogenetic analyses of the two datasets were compared to previous taxonomic treatments, morphological and karyological data, and biogeographic patterns. These studies indicate that the subtribal delimitation of Senecioneae needs to be revised to reflect exclusively monophyletic subtribes. This would involve abolishing subtribes Adenostylinae, Blennospermatinae, and Tephroseridinae and recognizing subtribes Abrotanellinae, Othonninae, and Senecioninae. Moreover, Tussilagininae may need to be split into three or four subtribes: Brachyglottidinae, Chersodominae, Tussilagininae, and perhaps Doronicinae. On the intergeneric level, these phylogenies provide new insights into evolutionary relationships, resulting in a first approximation of a comprehensive phylogeny for the tribe. Most species currently assigned to Senecio form a well supported clade. Thus, a new delimitation of Senecio is proposed, which involves transferring the species ofAetheolaena, Culcitium, Hasteola, locenes, Lasiocephalus, and Robinsonia to Senecio and removing several Senecio groups that are only distantly related to the core of Senecio. Area optimization analyses indicate a strong African influence throughout the evolutionary history of Senecioneae, predominantly in subtribes Senecioninae and Othonninae.

Multiple meanings and modes: on the many ways to be a generalist flower

Abstract: The concept of a generalist flower appears to mean different things to different people, depending upon their background and training We assess the different meanings of generalist flowers with respect to the ecological "set and setting" of pollination, and then we discuss notions of ecological, functional and phenotypic generalization These ideas are explored in more detail using examples from our own published and unpublished studies on the pollination ecology of Daucus carota, Hedera helix, and Chamerion angustifolium, and from the published work of other researchers Finally we relate these ideas and clarified definitions of "generalist" and "specialist" flowers to the pollination syndrome concept

Towards a phylogenetic nomenclature of Tracheophyta

Abstract: This is an abbreviated version of a paper that appears in full in the Electronic supplement to Taxon. Phylogenetic definitions are provided for the names of 20 clades of vascular plants (plus 33 others in the electronic supplement). Emphasis has been placed on well-supported clades that are widely known to non-specialists and/or have a deep origin within Tracheophyta or Angiospermae. These treatments follow the draft PhyloCode and illustrate the application ofphylogenetic nomenclature in a variety of nomenclatural and phylogenetic contexts. Phylogenetic nomenclature promotes precision in distinguishing crown, apomorphy-based, and total clades, thereby improving communication about character evolution and divergence times. To make these distinctions more transparent without increasing the number of entirely different names that must be learned, the following naming conventions (which have been adopted in the most recent draft of the PhyloCode) are employed here: widely known names are applied to crown clades, and the corresponding total clade (i.e., crown plus stem) is named "Pan-X", where "X" is the name of the crown (e.g., Pan-Spermatophyta for the total clade of plants that share more recent ancestry with extant seed plants than with any other crown clade). If a name "X" that is based etymologically on an apomorphy is applied to the crown, the name "Apo-X" is applied to the clade for which this trait is synapomorphic (e.g., Apo-Spermatophyta for the clade originating from the first plant with seeds). Crown clade names can be defined by three kinds of definitions, two of which are used here: standard node-based and branch-modified node-based. The latter is particularly useful when outgroup relationships of a crown clade are better known than basal relationships within the clade. Criteria and approaches used here to choose among competing preexisting names for a clade, to select a definition type, to choose appropriate specifiers, and (in some cases) to restrict the use of a name to certain phylogenetic contexts may be widely applicable when naming other clades. The phylogenetic definitions proposed here should help focus future discussions of the PhyloCode on real definitions rather than simplified hypothetical ones.

Concordance trees, concordance factors, and the exploration of reticulate genealogy

Abstract: Reticulate evolution, whether due to lateral gene transfer, introgression, incomplete lineage sorting, or hybrid speciation, is a ubiquitous phenomenon, yet systematists have few tools for analyzing and summarizing the resulting genealogical discordance. Here I argue that a primary concordance tree, a tree built from clades that are true of a plurality of the genome, provides a useful summary of the dominant phylogenetic history for a group of organisms. Residual historical signals can also be extracted in the form of secondary, tertiary, etc. concordance trees, which are built from clades that are present in the genome but contradict clades on the primary concordance tree. Clades on concordance trees can be annotated with their concordance factor (CF), the proportion of the genome for which the clade is true. Concordance trees can potentially be estimated either from population histories or from multilocus molecular datasets. In the latter case one can use the recently developed Bayesian concordance analysis to obtain point estimates and credibility intervals on CF's. I argue that the concepts of concordance trees and concordance factors inform the debate on how to integrate information from multiple independent datasets and help clarify the nature of the boundary between reticulate and divergent genealogy.

The openness of a flower and its number of flower-visitor species

Abstract: Using a sample of 1,403 flowering plant species, we tested the hypothesis that flower openness and flower-visitor aeneralization level of a plant species correlate positively. The "flower-visitor generalization level" L. of a flo, vering plant species n, here defined as number of flower-visiting animal species attracted to the flowers of n in a aiven study site, varied enormously among plant species. Its frequency distribution was extremely skewed. Within a study site, L also increased with number of flower-visitor species A. In order to correct for this, ve expressed L relatively, as the proportion of the total flower-visitor fauna in a study site that visited a gyiv-en plant species (relative generalization level, L/A). We listed the top-10 most generalized species (both according to L and LIA) in the "world", i.e., out of our sample of 1,403 plant species. Flower openness is defined as accessibilitv to the interior of the flower. We placed the blossom classes of Facgri & van der Pijl along a aradient, albeit not very well defined, of decreasing flower openness (dish-bowl, bell-funnel, head-brush, tube. aullet. flag) and tested for any relationship to their generalization level. The classes differed slightly but significantly in their level of L/A. Tube, bell-funnel, and dish-bowl had the highest generalization level and flaLy. uullet. and head-brush the lowest. Thus, flower openness and generalization level were not correlated. We discuss other factors influencing generalization level such as accessibility to pollen and nectar, morphology and behavior of visitor, and species diversity of the different functional types of visitors.

Suprageneric phylogenetics of Myrteae, the generically richest tribe in Myrtaceae (Myrtales)

Abstract: To clarify relationships within the predominantly Neotropical and exclusively fleshy-fruited Myrteae (49 genera and c. 2,500 species), we provide a phylogenetic hypothesis for evolutionary relationships between 31 of these genera by analyzing nuclear ITS and ETS ribosomal DNA, and plastid psbA-trnH and matK DNA sequences from 75 Myrteae species and 13 outgroup taxa using parsimony and Bayesian inference. Four morphological characters are epitomized on the resulting trees, and biogeographical analyses are also performed. Myrteae are monophyletic, comprising seven clades plus two isolated taxa of unclear relationships. Morphological characters exhibit homoplasy, although in combination are useful for clade diagnosis. Biogeographical analyses are inconclusive regarding the ancestral area of the tribe, but South American colonization before northern radiation via the Andes appears likely. The largest genera, Eugenia and Myrcia s.1., have western and south-eastern South American origins, respectively.

Evolution of leafy liverworts (Jungermanniidae, Marchantiophyta): estimating divergence times from chloroplast DNA sequences using penalized likelihood with integrated fossil evidence

Abstract: Based on chloroplast DNA sequences we develop a phylogenetic hypothesis of the diversification of liverworts (Marchantiophyta) with an extant diversity of about 6,000 species. Divergence time estimates obtained using penalized likelihood with integrated fossil evidence suggest a Late Ordovician origin of Marchantiophyta, a separation ofHaplomitriopsida from the remainder of liverworts in the Early Devonian, a split of Jungermanniopsida and Marchantiopsida in the Late Devonian, and a separation of Metzgeriidae and Jungermanniidae in the Late Carboniferous. Leafy liverworts (Jungermanniidae) with an extant diversity of ca. 4,500 species split into Porellales and Jungermanniales in the Early-Middle Permian. Our data provide evidence for a diversification of Jungermanniidae in the Triassic-perhaps coinciding with the recovery of terrestrial vegetation from the Perm/Trias extinction-and an enhanced diversification in the Cretaceous and Early Tertiary. The latter diversification events may coincide with the establishment of modern rainforests in the Late Cretaceous to Early Tertiary that were dominated by derived groups ofangiosperms. In addition, the Late Mesozoic and Early Tertiary diversification of leafy liverworts may have also been influenced by drastic changes in the geographical structure of the land masses and the global climate.

A taxonomic nightmare comes true: phylogeny and biogeography of glassworts (Salicornia L., Chenopodiaceae)

Abstract: In this study we analysed ETS sequence data of 164 accessions belonging to 31 taxa of Salicornia, a widespread, hygrohalophytic genus of succulent, annual herbs of Chenopodiaceae subfam. Salicornioideae, to investigate phylogenetic and biogeographical patterns and hypothesise about the processes that shaped them. Furthermore, our aim was to understand the reasons for the notorious taxonomic difficulties in Salicornia. Salicornia probably originated during the Miocene somewhere between the Mediterranean and Central Asia from within the perennial Sarcocornia and started to diversify during Late Pliocene/Early Pleistocene. The climatic deterioration and landscape-evolution caused by orogenetic processes probably favoured the evolution and initial diversification of this annual, strongly inbreeding lineage from the perennial Sarcocornia that shows only very limited frost tolerance. The further diversification of Salicornia was promoted by at least five intercontinental dispersal events (2 x to South Africa, at least 3 x to North America) and at least two independent polyploidization events resulting in rapidly expanding tetraploid lineages, both of which are able to grow in lower belts of the saltmarshes than their diploid relatives. The diploid lineages of Salicornia also show rapid and effective range expansion resulting in both widespread genotypes and multiple genotypes in a given area. Reproductive isolation through geographical isolation after dispersal, inbreeding, and comparatively young age might be responsible for the large number of only weakly differentiated lineages. The sequence data show that the taxonomic confusion in Salicornia has two major reasons: (1) in the absence of a global revision and the presence of high phenotypic plasticity, the same widespread genotypes having been given different names in different regions, and (2) striking morphological parallelism and weak morphological differentiation led to the misapplication of the same name to different genotypes in one region.

Pollination drops, pollen, and insect pollination of Mesozoic gymnosperms

Abstract: Recent focus on plant-insect associations during the angiosperm radiation from the last 30 million years of the Early Cretaceous has inadvertently de-emphasized a similar but earlier diversification that occurred among gymnosperms. The existence of gymnosperm-insect associations during the preangiospermous Mesozoic is evidenced by mouthparts capable of reaching and imbibing pollination drops or similar fluids, availability of pollen types consistent with entomophily, and opportunities for related consumption of pollen, seeds, and reproductively associated tissues in major seed-plant groups, namely seed ferns, conifers, cycads, bennettitaleans, and gnetaleans. Based on stereotypical plant damage, head-adherent pollen, gut contents, wing structure, mouthpart morphology and insect damage to plant reproductive organs, the likely nectarivores, pollinivores and pollinators were orthopterans, phasmatodeans, webspinners, sawflies and wasps, moths, beetles, mecopteroids, and true flies. These associations are ranked from possible to probable although the last three insect clades provide the strongest evidence for pollinator activity. We document two mid Cretaceous examples of these associations-cycadeoideaceous bennettitaleans and beetles and a cheirolepidiaceous conifer and flies-for which there are multiple lines of evidence for insect consumption of plant reproductive tissues but also pollination mutualisms. These data highlight the independent origin of a major phase of plant-insect pollinator-related associations during the mid Mesozoic that served as a prelude for the separate, iterative and later colonization of angiosperms.

Genetic and epigenetic alterations after hybridization and genome doubling

Abstract: Hybridization and polyploidization are now recognized as major phenomena in the evolution of plants, promoting genetic diversity, adaptive radiation and speciation. Modern molecular techniques have recently provided evidence that allopolyploidy can induce several types of genetic and epigenetic events that are of critical importance for the evolutionary success of hybrids: (1) chromosomal rearrangements within one or both parental genomes contribute toward proper meiotic pairing and isolation of the hybrid from its progenitors; (2) demethylation and activation of dormant transposable elements may trigger insertional mutagenesis and changes in local patterns of gene expression, facilitating rapid genomic reorganisation; (3) rapid and reproducible loss of low copy DNA sequence appears to result in further differentiation of homoeologous chromosomes; and (4) organ-specific up- or down-regulation of one of the duplicated genes, resulting in unequal expression or silencing one copy. All these alterations also have the potential, while stabilizing allopolyploid genomes, to produce novel expression patterns and new phenotypes, which together with increased heterozygosity and gene redundancy might confer on hybrids an elevated evolutionary potential, with effects at scales ranging from molecular to ecological. Although important advances have been made in understanding genomic responses to allopolyploidization, further insights are still expected to be gained in the near future, such as the direction and nature of the diploidization process, functional relevance of gene expression alterations, molecular mechanisms that result in adaptation to different ecologies/habitats, and ecological and evolutionary implications of recurrent polyploidization.

Evolution and temporal diversification of western European polyploid species complexes in Dactylorhiza (Orchidaceae)

Abstract: Patterns of polyploid evolution in the taxonomically controversial Dactylorhiza incarnata/maculata groups were inferred genetically by analyzing 399 individuals from 177 localities for (1) four polymorphic plastid regions yielding aggregate haplotypes and (2) nuclear ribosomal ITS allele frequencies. Concordance between patterns observed in distributions of plastid haplotypes and ITS alleles renders ancestral polymorphism an unlikely cause of genetic variation in diploids and allopolyploids. Combining the degree of concerted evolution in ITS alleles (thought to reflect gene conversion) with inferred parentage provides support for a quadripartite classification of western European allopolyploid dactylorchids according to their respective parentage and relative dates of origin. The older allotetraploids that generally exhibit only one parental ITS allele can be divided into those derived via hybridization between the divergent complexes we now call D. incarnata s.l. and D. fuchsii (e.g., D. majalis) and those derived via hybridization between D. incarnata s.l. and D. maculata (e.g., D. elata). Similarly, the younger allotetraploids that maintain evidence of both parental ITS alleles can be divided into those derived from hybridization between D. incarnata s.l. and D. fuchsii, or perhaps in some cases a diploid species resembling D. saccifera (e.g., D. praetermissa, D. purpurella, D. traunsteineri s.l., D. baltica), and those derived from hybridization between the D. incarnata s.l. and D. maculata groups (e.g., D. occidentalis, D. sphagnicola). Older allotetraploids are inferred to have passed through glacially induced migration bottlenecks in southern Eurasia, whereas at least some younger allotetraploids now occupying northern Europe are inferred to have originated post-glacially and remain sympatric with their parents, a scenario that is largely in agreement with the morphology and ecology of these allotetraploids. ITS conversion is in most cases biased toward the maternal parent, eventually obscuring evidence of the original allopolyploidization event because plastid haplotypes also reflect the maternal contribution. Gene flow appears unexpectedly low among allotetraploids relative to diploids, whereas several mechanisms may assist the gene flow observed across ploidy levels. There is good concordance between (1) the genetically delimited species that are required to accurately represent the inferred evolutionary events and processes and (2) morphologically based species recognized in certain moderately conservative morphological classifications previously proposed for the genus. Further research will seek to improve sampling, especially in eastern Eurasia, and to develop more sensitive markers for distinguishing different lineages within (1) the remarkably genetically uniform D. incarnata group (diploids) and (2) locally differentiated populations of (in some cases unnamed) allotetraploids. (Less)

Generalist flowers and phytophagous beetles in two tropical canopy trees : resources for multitudes

Abstract: In the Republic of Panama, phytophagous beetles were collected by hand and beating from superficially similar generalist blossoms of Nectandra umbrosa (Lauraceae) and Tapirira guianensis (Anacardiaceae), two phylogenetically distant Neotropical canopy trees. Beetles were sorted into three functional groups (guilds): general flower visitors, species developing in buds, and seed predators. Out of a total of 1,564 collected specimens belonging to 177 beetle species, 55 species or 31% were identifiable to specific epithet. These small- to medium-sized beetles belonged to four families: Cerambycidae, Chrysomelidae, Brentidae, and Curculionidae. A total of 723 beetles representing 121 species, and 841 beetles representing 121 species were recorded from N. umbrosa and T. guianensis, respectively. Of the beetles collected, 65 species were common to both trees, which equates to a similarity index value of 0.46 (Jaccard) or 0.34 (Sorensen). With respect to functional groups, there was no significant difference in the number of beetle species between the two tree species. Overall, beetle abundance patterns on flowers of the two trees are similar in terms of phytophagous beetle subfamily dominance. There are differences however, significantly more leaf beetles (Cryptocephalinae, Eumolpinae, Galerucinae) were collected per hour on T. guianensis than on N. umbrosa. Moreover, among beetles shared between the two tree species, Baridinae weevils showed a tendency to be more abundant on N. umbrosa. Nearly three-quarters of the flower feeders (72%) were shared between the two trees. The large overlap in beetle species between the two plant species suggests that the fauna is fairly general in terms of host use. We discuss the possible significance of our results to phytophagous beetle and host plant evolution. The combined effects of large species numbers, high abundance and broad diet breadth across generalist flowers of tropical canopy trees suggests that small- to medium-sized beetles play a crucial role in maintenance of species biodiversity and forest ecosystem function.

Molecular insights into the phylogeny of the leafy liverwort family Lophoziaceae Cavers

Abstract: Delimitation and classification of the large, cosmopolitan liverwort family Lophoziaceae is controversial. Many recent workers have included it in Jungermanniaceae, and even in its strictest sense, internal classification has varied widely among different treatments. We analyse variation in DNA sequences of the chloroplast rps4 gene and the trnG intron to provide resolution of phylogenetic relationships in the leafy liverworts with emphasis on the various elements usually placed in Lophoziaceae. The following conclusions are drawn. Lophoziaceae is not closely related to Jungermanniaceae. Lophoziaceae, and perhaps also Cephaloziellaceae, should be included in Scapaniaceae unless many small families are recognised. Delavayella and Blepharidophyllum are excluded from Scapaniaceae. Jamesonielloideae is a family of its own (Jamesoniellaceae) sister to Adelanthaceae (or a subfamily of Adelanthaceae). The genus Anastrophyllum should be split into Anastrophyllum and Sphenolobus. Lophozia is polyphyletic and the genera Isopaches and Schistochilopsis, and perhaps Obtusifolium, should be recognised while L. sudetica could be transferred to Barbilophozia. Barbilophozia s.str. is monophyletic while Orthocaulis is polyphyletic with the four sampled species appearing in 3 different clades; their relationships are poorly resolved. Lophozia silvicola Buch is clearly separated from L. ventricosa and Jamesoniella oenops from J. colorata at species level.

Phylogenetic relationships among Pteridaceae, including Brazilian species, inferred from rbcL sequences

Abstract: Phylogenetic relationships among Pteridaceae were established using rbcL sequences, parsimony and posterior probabilities. The analyses involved 38 Pteridaceae species native in Brazil (12 of them endemic) and 81 species of Dennstaedtiaceae, Lindsaeaceae, Saccolomataceae (outgroups) and Pteridaceae. The resultant phylogeny comprehends five main clades: Platyzomatoideae-Pteridoideae-Taenitoideae; Ceratopteris-Acrostichum; Adiantoideae-vittarioids; Cheilanthoideae; Coniogramme-Cryptogramma-Llavea. The cladograms support the most recent classification of Pteridaceae and demonstrate the paraphyly of Cheilanthoideae and the unnaturalness of Ceratopteridoideae, Platyzomatoideae, Pteridoideae, and Taenitidoideae as traditionally defined. Adiantoideae can only be recognized if combined with the vittarioids. Several genera of Pteridaceae appear to be paraphyletic (e.g., as Cheilanthes, Doryopteris, Pellaea, Pteris), and new generic affinities suggested by consistent internal clades are proposed.

Neglecting evolution is bad taxonomy

Abstract: Hörandl • Neglecting evolution is bad taxonomy TAXON 56 (1) • February 2007: XX–XY \" Nothing in biology makes sense except in the light of evolution \" T. Dobzhansky (1973). In a recent letter to the editor, Ebach & al. (2006) argue for monophyly as a sole criterion for grouping of taxa. Since their argumentation does not address the main points of previous advocates of paraphyletic taxa, I would like to (1) respond to their letter, and (2) provide a brief outline of strength and weaknesses of different concepts of classifications, and (3) give a plea for the here proposed evolutionary classification (in the sense of Mayr & Bock, 2002). Ebach & al. (2006) wonder why the theoretical issues of paraphyly, that have been intensively discussed in the late 1970s and 1980s, are nowadays raised again. This is simply because in the meantime extensive empirical data resulting from cladistic and molecular phylogenetic studies have been accumulated, and the resulting classifications provide an empirical \" test \" of usefulness of Hennigian principles. have expressed the opinion that a concept of strict monophyly results in unsatisfactorily classifications. The difficulties of including extinct taxa have been outlined by palaeon-tologists (see e. The reasons are (1) conceptual problems, (2) frequently observed discrepancies with pre-cladistic classifications, and the (3) nomenclatural consequences (e.g., Stevens, 2006). I will address here the first two items; the third one and some thoughts on practicability will be presented in a forthcoming paper. Conceptual problems of Hennigian classifications. — Accepting paraphyly is not just a result of \" inaccurate \" definitions, as seen by Ebach & al. (2006). In the past, several definitions of monophyly and paraphyly have been proposed (reviews e.g., Wiley 1981; Reif, 2005a). Hennig (1966) and almost all later authors include two components in the definition of a monophyletic group: common ancestry and inclusiveness (all descendants of a common ancestor). The former is an evolutionary component , the latter just a logical one. This has been best recognized by Ashlock (1971) who defines \" monophyly \" in a broader sense, i.e., solely by common ancestry, and subdivides it into holophyletic = inclusive groups (\" A ho-lophyletic group is a monophyletic group that contains all of the descendants of the most recent common ancestor of that group (= monophyly of Hennig) \" and paraphyletic = non-inclusive-groups (\" a paraphyletic group is a mono-phyletic group that does not contain all …

Genetic diversity at chloroplast microsatellites (cpSSRs) and geographic structure in endangered West Mediterranean firs (Abies spp., Pinaceae)

Abstract: We investigated patterns of genetic variation within and among the eight extant populations of the genus Abies in the western Mediterranean Basin. Using six chloroplast microsatellite (cpSSR) loci, a total of 22 alleles and 34 haplotypes was found among 225 individuals. The analyzed populations showed high levels of genetic diversity (mean H e = 0.84). Two clearly separated main groups corresponding to the three Spanish and the five Moroccan populations, respectively, were distinguished. A phylogeographic signal was evident and a Mantel test revealed a strong positive correlation between geographic and genetic distances of the eight populations. Analysis of Molecular Variance (AMOVA) assigned 85% of the total genetic variation to differences between continents. Within each continent, populations were remarkably little differentiated with the exception of one highly divergent Moroccan stand; the origin of this divergence requires further investigation. Our results document a strong effect of the Strait of Gibraltar on Abies differentiation in this region, whereas the high diversity within and the low differentiation among populations on each side point to a certain level of pollen-mediated gene flow among the extant stands. On the other hand, our analysis indicates that the population formerly assigned to the species A. tazaotana is, in fact, genetically very close to most A marocana stands. We discuss implications of the observed population structures for conservation and management of West Mediterranean Abies taxa.

Molecular phylogeny of Planchonella (Sapotaceae) and eight new species from New Caledonia

Abstract: We present a hypothesis of phylogenetic relationships in Planchonella (Sapotaceae, Chrysophylloideae) using nrDNA (ITS) data analysed with parsimony jackknifing and Bayesian inference. Results from these two approaches yield similar majority-rule consensus trees. Planchonella (formerly included in Pouteria) is a monophyletic genus of trees and shrubs with 60 species currently recognised. They are distributed in Australia (13 spp.), New Caledonia (32 spp.), the Pacific islands (10 spp.), and New Guinea (5 spp.), but more molecular research is needed in order to identify all members in New Guinea and Malesia. Three strongly supported clades and several subclades were recovered by our analysis. Two clades are restricted to New Caledonia. Within these are eight recently discovered species that are described here (P. crenata, P. glauca, P. latihila, P. luteocostata, P. mandjeliana, P. povilana, P. roseoloba, P. rufocostata), each with a conservation assessment. Our molecular phylogeny shows that some of these taxa, initially believed to be conspecific or closely related, represent separate lineages that deserve species rank. Two of these species are restricted to areas with near-future mining activities, which is why urgent conservation assessments are needed. Several subspecies or varieties of P. myrsinifolia and P. cotinifolia are recognised in Australia. Neither of these two species is monophyletic in its present circumscription, and for this reason P. cotinifolia var. pubescens is given species rank here as P. pubescens. We also amend the generic description of Planchonella, a genus best distinguished on a character combination of stamens positioned just below (rarely in) the tube orifice, a multi-seeded fruit, and foliaceous cotyledons embedded in endosperm.

Hybridization in Macaronesian Sideritis (Lamiaceae) : evidence from incongruence of multiple independent nuclear and chloroplast sequence datasets

Abstract: With 23 suffrutescent to woody perennial species distributed in diverse ecological zones, Sideritis subgenus Marrubiastrum constitutes one of the largest plant radiations in the Macaronesian archipelagos. In an earlier study, we investigated the evolution of Sideritis in Macaronesia using chloroplast restriction site (RFLP) data, but inferences were limited by the lack of a nuclear marker. A second study used sequence data to determine the continental origin of the Macaronesian group, but that study included only seven island taxa in a much larger sampling of continental taxa. For the present study, we generated new datasets from sequences of the nuclear ribosomal DNA internal transcribed spacers (ITS) and two plastid regions (trnL intron, trnT-trnL intergenic spacer) in order to reconstruct relationships among all extant island taxa using both nuclear and chloroplast data. Relationships based upon plastid data suggest that there may be a geographical component to cpDNA variation. Individual phylogenies reconstructed from the nuclear and chloroplast sequence data were incongruent, and differing placements of taxa were well supported in each of the two datasets. This incongruence has enabled us to identify several instances of potential cytoplasmic introgression, suggesting that hybridization may have been important in the evolution of Sideritis in Macaronesia. Because the ITS phylogeny concurs with current taxonomic circumscriptions in the Macaronesian subgenus, we reassess patterns of diversification based upon the nuclear tree.

A phylogeny and new classification for Mesembryanthemoideae (Aizoaceae)

Abstract: We present a phylogeny for Mesembryanthemoideae (Aizoaceae) based on sampling of nearly all species and subspecies of the subfamily and analysis ofcptrnL-F, rbcL-atpB, rps16, nrITSl and morphology. The larger genera Phyllobolus and Mesembryanthemum are not monophyletic. Although some clades can be circumscribed with morphological (often homoplasious) synapomorphies, several clades are impossible to characterise morphologically. We recognise a single genus, Mesembryanthemum, in Mesembryanthemoideae. The genera Aptenia, Aridaria, Aspazoma, Brownanthus, Caulipsolon, Dactylopsis, Phyllobolus, Prenia, Psilocaulon, Sceletium, and Synaptophyllum are reduced to synonymy. Mesembryanthemum, which now consists of 101 species without recognised sections, can be distinguished by several uniquely derived morphological characters. Mesembryanthemum longipapillosum, which had recently been reduced to synonymy, is reinstated.

Classification of a large and widespread genus of Neotropical trees, Guatteria (Annonaceae) and its three satellite genera Guatteriella, Guatteriopsis and Heteropetalum

Abstract: Guatteria (Annonaceae) is with ca. 265 species one of the largest genera of Neotropical trees together with Inga and Ocotea. Use of Guatteria in evolutionary studies has been hampered by taxonomic problems caused by lack of morphological variability in the genus. This study focuses on molecular phylogenetic relationships within Guatteria and its satellites Guatteriopsis, Guatteriella and Heteropetalum, and implications of these relationships for classification and character evolution. Results show that Guatteriopsis, Guatteriella and Heteropetalum should be merged with Guatteria. Heteropetalum may be recognized at subgeneric level because of its aberrant morphology and Guatteriopsis and Guatteriella might be given sectional status. Most of the currently recognised sections in Guatteria are probably non-monophyletic. A completely new infrageneric classification of Guatteria would be premature, however, due to the lack of molecular and morphological synapomorphies to define the sections. Synapomorphies defining Guatteria s.str. probably evolved after divergence of several early branching lineages.

Floristics of the angiosperm flora of Sub-Saharan Africa: an analysis of the African Plant Checklist and Database

Abstract: The African Plant Checklist and Database Project (APCD) provides botanists with the first angiosperm checklist and database for Sub-Saharan Africa. This was achieved by merging the existing datasets for Southern and Tropical Africa. The checklist is published as a one-off hardcopy publication. The database, with all attached additional information, is freely accessible via the internet and will be regularly updated. The APCD, for the first time, gives accurate statistics for the angiosperm flora of Sub-Saharan Africa. There are 50,136 current taxa (representing approximately 44,830 species) in the database, plus an additional 393 taxa where there are discrepancies in genus concept between the two original datasets. Taxa are classified into 274 families and 3,802 current genera. Several other important statistics can also be drawn from the database. Furthermore, by pointing out problems and discrepancies in taxonomic opinion, the APCD highlights taxa where further research is necessary. The APCD will be an invaluable tool to botanists working on the African flora. It also has an important role to play in greater projects such as the Global Plant Checklist Project and has already emerged as a nomenclatural standard for the African Plants Initiative.

Phylogeny of the Cyphomandra clade of the genus Solanum (Solanaceae) based on ITS sequence data

Abstract: About 13 major clades can be recognized within the genus Solanum (Solanaceae) based on chloroplast DNA sequence data. One of these is the Cyphomandra clade, which includes about 50 neotropical species. These have traditionally been placed into two or three sections: S. section Pachyphylla (formerly recognized as the genus Cyphomandra), S. section Cyphomandropsis, and S. section Glaucophyllum (monotypic and sometimes placed in S. section Cyphomandropsis). Phylogenetic relationships among 61 accessions of 35 species of the Cyphomandra clade are investigated using sequence data from the nuclear ITS region analyzed by parsimony and Bayesian inference. The Cyphomandra clade forms a monophyletic group, but the ITS data are equivocal as to the monophyly of sections Pachyphylla and Cyphomandropsis. Four well-supported groups of species can be recognized within the Cyphomandra clade; these conform in part to species groups proposed on the basis of morphology. The distribution of self-incompatible and self-compatible breeding systems is mapped onto the ITS cladogram, and patterns of evolution of enlarged anther connectives, osmophores, and volatile composition are discussed in light of hypothesized phylogenetic relationships.

Polyphyly of Polycarpon (Caryophyllaceae) inferred from DNA sequence data.

Abstract: A phylogenetic study of the genus Polycarpon was made using DNA sequence data from the chloroplast rpsl6 intron and nuclear RPB2 regions. Polycarpon as currently recognised is shown to be polyphyletic. The South American species P. coquimbense and P. suffruticosum are more closely related to Haya obovata (Socotra) and Polycarpaea spicata (paleotropical) than to the remaining species of Polycarpon, and the widespread tropical species P. prostratum is nested with Macaronesian species of Polycarpaea. All three should therefore be excluded from Polycarpon. The remaining species, the P. tetraphyllum group, has its main diversity in the Mediterranean region. It is a polyploid complex with morphologically very similar taxa mostly separated only by partially overlapping characters. The members of this group form a strongly supported, but largely unresolved clade. It is proposed that they are all included in a widely circumscribed P. tetraphyllum. The dehiscence of the capsules in P. tetraphyllum, by valves that elastically roll inwards and finally throw out the seeds, is unique in Caryophyllaceae and provides a strong synapomorphy for Polycarpon in this new restricted sense.

The systematics of Knoxieae (Rubiaceae)—molecular data and their taxonomic consequences

Abstract: The tribe Knoxieae consists of genera formerly included in (at least) four tribes of the Rubiaceae (the coffee family). Apart from Knoxia itself, which is mainly Indomalesian, the group is from Africa and Madagascar. Most genera are herbaceous or shrubby, but small trees are also present. They generally have fimbriate, colleter-tipped stipules and five-merous flowers with unequal calyx lobes. We present a molecular phylogeny of the group (based on two chloroplast markers, rps16 and trnT-F, and the nuclear ITS) and discuss the morphological support for the resulting groups and the taxonomic consequences of the phylogeny. Two hundred and sixty-one new sequences from 90 species have been obtained. Of the 19 genera of the Knoxieae, all but three (two monotypic and one with two species) are represented. The genera Calanda, Chlorochorion, Neopentanisia, and Paraknoxia are merged with Pentanisia. Pentas is shown to be not monophyletic and is split into the new genera Phyllopentas, Dolichopentas, and Rhodopentas. We also suggest the Pentas subgenera Megapentas and Chamaepentadoides be included in Chamaepentas. The genus Carphalea is also shown to be not monophyletic and for the African members of the genus (section Dirichletia) the name Dirichletia should be used. Placopoda is suggested to be merged with Dirichletia. Triainolepis is enlarged to include Paratriaina and Thyridocalyx. The tribal position of Lathraeocarpa is discussed. Twenty-nine new combinations for species and seven for infraspecific taxa are made. A key to the genera of Knoxieae is provided.

Paraphyly of Paederieae, recognition of Putorieae and expansion of Plocama (Rubiaceae-Rubioideae)

Abstract: This thesis deals with phylogenetic relationships at different taxonomic levels. All the plants studied are or have been included in the order Gentianales, which comprises about 17 200 species. The phylogenies are based on parsimony analyses of nucleotide sequence data (DNA) from different regions in the chloroplast genome, but morphological characteristics have also been studied. Analyses of sequence data from the genes rbcL and ndhF provide the interfamilial structure of the order Gentianales, shown to comprise the families Apocynaceae (incl. Asclepiadaceae), Gelsemiaceae, Gentianaceae, Loganiaceae, and Rubiaceae. Exclusion of certain genera from the Loganiaceae is confirmed and their phylogenetic positions are clarified. Some of these genera remain within the Gentianales, while others belong to other orders. Exclusion of the tribe Buddlejeae from the Loganiaceae is confirmed, and a monophyletic group formed by Buddleja, Emorya, Gomphostigma, and Nicodemia is recognized and placed in the Lamiales. The Loganiaceae s.str. forms, after these exclusions, a strongly supported monophyletic group comprising 13 genera. The tribe Paederieae in the family Rubiaceae is analysed using sequence data from the regions rbcL gene, rps16 intron, and the regions trnT-F, and is shown to be paraphyletic. These results lead to a new circumscription of Paederieae comprising the genera Leptodermis, Paederia, Serissa, and Spermadictyon. The tribe Putorieae is reestablished with the single genus Plocama, including 34 species. Aitchisonia, Choulettia, Crocyllis, Gaillonia, Jaubertia, Pseudogaillonia, Pterogaillonia, and Putoria are reduced to synonyms of Plocama based on the molecular analyses and morphological studies. The Mediterranean species of the re-circumscribed Plocama, previously segregated as the genus Putoria, are revised. Two species, Plocama calabrica and P. brevifolia, are recognized, their synonymics are established, and seven lectotypes are selected.