Using phylogeny to investigate the origins of the Cape flora: the importance of taxonomic, gene and genome sampling strategies

Phylogenetic methods hold great promise for the reconstruction of the transition from precursor to modern flora and the identification of underlying factors which drive the process. The phylogenetic methods presently used to address the question of the origin of the Cape flora of South Africa are considered here. The sampling requirements of each of these methods, which include dating of diversifications using calibrated molecular trees, sister pair comparisons, lineage through time plots and biogeographical optimizations are reviewed. Sampling of genes, genomes and species are considered. Although increased higher-level studies and increased sampling are required for robust interpretation, it is clear that much progress is already made. It is argued that despite the remarkable richness of the flora, the Cape flora is a valuable model system to demonstrate the utility of phylogenetic methods in determining the history of a modern flora.

Molecular characterization of Iranian wheat stripe virus shows its taxonomic position as a distinct species in the genus Tenuivirus

The full lengths of three genome segments of Iranian wheat stripe virus (IWSV) were amplified by reverse transcription (RT) followed by polymerase chain reaction (PCR) using a primer complementary to tenuivirus conserved terminal sequences. The segments were sequenced and found to comprise 3469, 2337, and 1831 nt, respectively. The gene organization of these segments is similar to that of other known tenuiviruses, each displaying an ambisense coding strategy. IWSV segments, however, are different from those of other viruses with respect to the number of nucleotides and deduced amino acid sequence for each ORF. Depending on the segment, the first 16-22 nt at the 5' end and the first 16 nt at the 3' end are highly conserved among IWSV and rice hoja blanca virus (RHBV), rice stripe virus (RSV) and maize stripe virus ( MStV). In addition, the first 15-18 nt at the 5' end are complementary to the first 16-18 nt at the 3' end. Phylogenetic analyses showed close similarity and a common ancestor for IWSV, RHBV, and Echinochloa hoja blanca virus (EHBV). These findings confirm the position of IWSV as a distinct species in the genus Tenuivirus.

Phylogenomics of eukaryotes: Impact of missing data on large alignments

Resolving the relationships between Metazoa and other eukaryotic groups as well as between metazoan phyla is central to the understanding of the origin and evolution of animals. The current view is based on limited data sets, either a single gene with many species (e.g., ribosomal RNA) or many genes but with only a few species. Because a reliable phylogenetic inference simultaneously requires numerous genes and numerous species, we assembled a very large data set containing 129 orthologous proteins (similar to30,000 aligned amino acid positions) for 36 eukaryotic species. Included in the alignments are data from the choanoflagellate Monosiga ovata, obtained through the sequencing of about 1,000 cDNAs. We provide conclusive support for choanoflagellates as the closest relative of animals and for fungi as the second closest. The monophyly of Plantae and chromalveolates was recovered but without strong statistical support. Within animals, in contrast to the monophyly of Coelomata observed in several recent large-scale analyses, we recovered a paraphyletic Coelamata, with nematodes and platyhelminths nested within. To include a diverse sample of organisms, data from EST projects were used for several species, resulting in a large amount of missing data in our alignment (about 25%). By using different approaches, we verify that the inferred phylogeny is not sensitive to these missing data. Therefore, this large data set provides a reliable phylogenetic framework for studying eukaryotic and animal evolution and will be easily extendable when large amounts of sequence information become available from a broader taxonomic range.

Multivariate relationships between groundwater chemistry and toxicity in an urban aquifer

Multivariate statistical methods were used to investigate file Causes of toxicity and controls on groundwater chemistry from 274 boreholes in an Urban area (London) of the United Kingdom. The groundwater was alkaline to neutral, and chemistry was dominated by calcium, sodium, and Sulfate. Contaminants included fuels, solvents, and organic compounds derived from landfill material. The presence of organic material in the aquifer caused decreases in dissolved oxygen, sulfate and nitrate concentrations. and increases in ferrous iron and ammoniacal nitrogen concentrations. Pearson correlations between toxicity results and the concentration of individual analytes indicated that concentrations of ammoinacal nitrogen, dissolved oxygen, ferrous iron, and hydrocarbons were important where present. However, principal component and regression analysis suggested no significant correlation between toxicity and chemistry over the whole area. Multidimensional Scaling was used to investigate differences in sites caused by historical use, landfill gas status, or position within the sample area. Significant differences were observed between sites with different historical land use and those with different gas status. Examination of the principal component matrix revealed that these differences are related to changes in the importance of reduced chemical species.

Phylogenetic relationships of the Fox (Forkhead) gene family in the Bilateria

The Forkhead or Fox gene family encodes putative transcription factors. There are at least four Fox genes in yeast, 16 in Drosophila melanogaster (Dm) and 42 in humans. Recently, vertebrate Fox genes have been classified into 17 groups named FoxA to FoxQ [Genes Dev. 14 (2000) 142]. Here, we extend this analysis to invertebrates, using available sequences from D. melanogaster, Anopheles gambiae (Ag), Caenorhabditis elegans (Ce), the sea squirt Ciona intestinalis (Ci) and amphioxus Branchiostoma floridae (Bf), from which we also cloned several Fox genes. Phylogenetic analyses lend support to the previous overall subclassification of vertebrate genes, but suggest that four subclasses (FoxJ, L, N and Q) could be further subdivided to reflect their relationships to invertebrate genes. We were unable to identify orthologs of Fox subclasses E, H, I, J, M and Q1 in D. melanogaster, A. gambiae or C. elegans, suggesting either considerable loss in ecdysozoans or the evolution of these subclasses in the deuterostome lineage. Our analyses suggest that the common ancestor of protostomes and deuterostomes had a minimum complement of 14 Fox genes. (C) 2003 Elsevier B.V. All rights reserved.

Multiple domestications and their taxonomic consequences: the example of Phaseolus vulgaris

The evolutionary history of P. vulgaris is important to those working on its genetic resources, but is not reflected in its infraspecific taxonomy. Genetic isolation of wild populations between and also within Middle and South America has resulted in morphological and molecular differentiation. Populations from northern and southern ends of the range are assigned to different gene pools, though intermediates occur in intervening areas. Chloroplast haplotypes suggest three distinct lineages of wild beans and several intercontinental dispersals. The species was domesticated independently in both Middle and South America, probably several times in Middle America. This, together with further differentiation under human selection, has produced distinct races among domesticated beans. The informal categories of wild versus domesticated, gene pool, and race convey the evolutionary picture more clearly than the formal categories provided by the Codes of Nomenclature for wild or cultivated plants.

Correlation-type structure activity relationships for the kinetics of gas-phase RO2 self-reactions and reaction with HO2

Structure activity relationships (SARs) are presented for the gas-phase reactions of RO2 with HO2, and the self- and cross-reactions of RO2. For RO2+HO2 the SAR is based upon a correlation between the logarithm of the measured rate coefficient and a calculated ionisation potential for the molecule R-CH=CH2, R being the same group in both the radical and molecular analogue. The correlation observed is strong and only for one RO2 species does the measured rate coefficient deviate by more than a factor of two from the linear least-squares regression line. For the self- and cross-reactions of RO2 radicals, the SAR is based upon a correlation between the logarithm of the measured rate coefficient and the calculated electrostatic potential (ESP) at the equivalent carbon atom in the RH molecule to which oxygen is attached in RO2, again R being the same group in the molecule and the radical. For cases where R is a simple alkyl-group, a strong linear correlation observed. For RO2 radicals which contain lone pair-bearing substituents and for which the calculated ESP<-0.05 self-reaction rate coefficients appear to be insensitive to the value of the ESP. For RO2 of this type with ESP>-0.05 a linear relationship between log k and the ESP is again observed. Using the relationships, 84 out of the 85 rate coefficients used to develop the SARs are predicted to within a factor of three of their measured values. A relationship is also presented that allows the prediction of the Arrhenius parameters for the self-reactions of simple alkyl RO2 radicals. On the basis of the correlations, predictions of room-temperature rate coefficients are made for a number of atmospherically important peroxyl-peroxyl radical reactions. (C) 2003 Elsevier Ltd. All rights reserved.

Synthesis of heterosulfamates. Search for structure-taste relationships

Thirty one new sodium heterosulfamates, RNHSO3Na, where the R portion contains mainly thiazole, benzothiazole, thiadiazole and pyridine ring structures, have been synthesized and their taste portfolios have been assessed. A database of 132 heterosulfamates ( both open-chain and cyclic) has been formed by combining these new compounds with an existing set of 101 heterosulfamates which were previously synthesized and for which taste data are available. Simple descriptors have been obtained using (i) measurements with Corey-Pauling-Koltun (CPK) space- filling models giving x, y and z dimensions and a volume VCPK, (ii) calculated first order molecular connectivities ((1)chi(v)) and (iii) the calculated Spartan program parameters to obtain HOMO, LUMO energies, the solvation energy E-solv and V-SPART AN. The techniques of linear (LDA) and quadratic (QDA) discriminant analysis and Tree analysis have then been employed to develop structure-taste relationships (SARs) that classify the sweet (S) and non-sweet (N) compounds into separate categories. In the LDA analysis 70% of the compounds were correctly classified ( this compares with 65% when the smaller data set of 101 compounds was used) and in the QDA analysis 68% were correctly classified ( compared to 80% previously). TheTree analysis correctly classified 81% ( compared to 86% previously). An alternative Tree analysis derived using the Cerius2 program and a set of physicochemical descriptors correctly classified only 54% of the compounds.

Age relationships beteen low level rock platforms and the high coastal slopes in Jersey and the surrounding area.

Recent research along the coastal cliffs and embayments of Jersey has revealed new aspects of the geomorphology of the rocky shore platform and its relationship with the steep slopes that link it to the island plateau above. Specifically, a rockhead platform meets a 10-30 m high, near vertical cliff at approximately 8-10 m above Jersey Datum (J.D.= ±0 m Ordnance Datum; likewise Guernsey Datum: G.D.), slopes down-towards mid-tide levels becoming ever more deeply dissected. Generalised contours of this platform show it to be distinct from a lower tidal rockhead platform which is comparatively smooth over large areas as it undergoes continuing contemporary abrasion. This lower platform is generally separated from the higher one by low cliffs, less than a metre high at mid-tidal levels, but two to three metres at the base of the backing cliffs. Both of these platforms are shown to antedate the Last Cold Stage (Devensian) head at a number of localities and this relationship is taken to represent the general situation, not only in Jersey, but throughout the other Channel Islands and adjacent coasts of Armorica. Whether either, or both, of these two platforms are older than Marine Oxygen Isotope Substage (MOIS) 5e (Ipswichian) as well is not known. However the considerable age of the numerous and wide intertidal shore platforms of the Channel Islands and adjacent coasts of Amorica makes a greater age quite possible.

Relationships between gluten rheological properties and hearth loaf characteristics

The rheological properties of fresh gluten in small amplitude oscillation in shear (SAOS) and creep recovery after short application of stress was related to the hearth breadbaking performance of wheat flours using the multivariate statistics partial least squares (PLS) regression. The picture was completed by dough mixing and extensional properties, flour protein size distribution determined by SE-HPLC, and high molecular weight glutenin subunit (HMW-GS) composition. The sample set comprised 20 wheat cultivars grown at two different levels of nitrogen fertilizer in one location. Flours yielding stiffer and more elastic glutens, with higher elastic and viscous moduli (G' and G") and lower tan 8 values in SAOS, gave doughs that were better able to retain their shape during proving and baking, resulting in breads of high form ratios. Creep recovery measurements after short application of stress showed that glutens from flours of good breadmaking quality had high relative elastic recovery. The nitrogen fertilizer level affected the protein size distribution by an increase in monomeric proteins (gliadins), which gave glutens of higher tan delta and flatter bread loaves (lower form ratio).

The utility of leaf flavonoids as taxonomic markers for some Malaysian species of the tribe Shoreae (Dipterocarpaceae)

A flavonoid survey was carried out on 45 taxa from the genera Shorea, Hopea, Parashorea, Neobalanocarpus, and Dryobalanops of the tribe Shoreae in the Dipterocarpaceae. The study showed significant chemotaxonomic differences in leaf flavonoid aglycone patterns and the presence of tannins in these taxa. The flavonoid patterns are useful in the delimitation of some taxa. For example, the genus Parashorea is distinguished by the universal presence of kaempferol 3-methyl ether, and the monotypic genus Neobalanocarpus is unique in not producing ellagic and gallo tannins. The presence of chalcones and flavone C-glycosides supports the separation of the genus Hopea into two sections, section Dryobalanoides and section Hopea in Ashton's classification, which is based on the type of venation. The flavonoid distributions in this study show that they can be very useful for differentiating between the Balau group in the genus Shorea, and some scaly barked Hopea species, particularly H. helferi (lintah bukit), H. nutans (giam), and H. ferrea (malut). (C) 2008 The Linnean Society of London.