Unweighted Pair-group Arithmetic Average Clustering Research Articles

Screening for Eruca genotypes tolerant to polyethylene glycol-simulated drought stress based on the principal component and cluster analyses of seed germination and early seedling growth

Water deficit is an environmental factor that constrains crops to express their ecophysiological potential and causes crop yield reduction. Eruca vesicaria has been reported to be one of the most drought-tolerant species in Cruciferae. In this study, polyethylene glycol-simulated drought tolerance was evaluated in one line of Brassica carinata, one line of Brassica napus and 249 Eruca lines based on the principal component analysis (PCA) and unweighted pair-group arithmetic average (UPGMA) cluster analysis. The PCA based on eight drought tolerance indices indicated that the first three components accounted for 85.46% of the total variation, with principal component (PC) 1 accounting for 43.89%, PC2 for 27.85% and PC3 for 13.73% of the total variation. The UPGMA cluster analysis indicated that B. napus cultivar Zhongshuang 9 and Eruca lines could be clustered into five major groups, with group 1 being, in general, drought sensitive, group 2 being slightly–medium drought tolerant, group 3 being drought tolerant, group 4 being highly drought sensitive and group 5 being highly drought tolerant. B. carinata cultivar XB1, as an outstander, showed high drought sensitivity. The UPGMA cluster dendrogram provides a good representation of the similarity matrix (r= 0.68). The drought-tolerant Eruca materials obtained in this study will be valuable for genetic improvement not only in Eruca itself, but also in Brassica crops since they are drought-tolerant lines from a drought-tolerant species.

Fungal Diversity, Dominance, and Community Structure in the Rhizosphere of Clonal Picea mariana Plants Throughout Nursery Production Chronosequences

Fungal diversity in the rhizosphere of healthy and diseased clonal black spruce (Picea mariana) plants was analyzed with regard to nursery production chronosequences. The four key production stages were sampled: mother plants (MP), 8-week-old cuttings (B + 0), second-year cuttings (B + 1), and third-year cuttings (B + 2). A total of 45 fungal taxa were isolated and identified based on cultural, phenotypic, and molecular characters. Members of phylum Ascomycota dominated, followed by Basidiomycota and Zygomycota. Diagnosis characters and distance analysis of the internal transcribed spacer rDNA sequences allowed the identification of 39 ascomycetous taxa. Many belong to the order Hypocreales, families Hypocreaceae and Nectriaceae, which contain many clusters of potentially pathogenic taxa (Cylindrocladium, Fusarium, and Neonectria) and are also ecologically associated with antagonistic taxa (Chaetomium, Hypocrea, Microsphaeropsis, Penicillium, Paecilomyces, Verticillium, Trichoderma, and Sporothrix). This is also the first report of a Cylindrocladium canadense association with disease symptoms and relation with Pestalotiopsis, Fusarium, Exserochilum, Rhizoctonia, and Xenochalara fungal consortia. Both production chronosequence and plant health considerably influenced fungal taxa assemblages. Unweighted pair-group arithmetic average clustering showed that isolates from MP, B + 0, and B + 1 plant rhizospheres clustered together within healthy or diseased health classes, whereas isolates from healthy and diseased B + 2 plants clustered together. Canonical correspondence analysis revealed substantial alteration in community assemblages with regard to plant health and yielded a principal axis direction that regrouped taxa associated with diseased plant rhizosphere soil, whereas the opposite axis direction was associated with healthy plants. Two diversity indices were defined and applied to assess the fungal taxa contribution (Tc) and persistence (Pi) throughout the production.

The use of RAPD genomic fingerprinting to study relatedness in strains of Acidithiobacillus ferrooxidans

Twelve strains of Acidithiobacillus ferrooxidans were recovered from acid mine drainage (AMD) sites from three different geographical locations: Copper Cliff, Ontario, Canada; Mineral City, OH, USA; and Cornwall, England. The spread-plate technique and various culture media were used to isolate and purify all strains. DNA was extracted from each purified culture and amplified using PCR and twenty, 10-mer primers. Amplification products were separated by gel electrophoresis and photographed under UV light. The RAPD (Randomly Amplified Polymorphic DNA) profiles were compared on the basis of the presence or absence of each DNA band and a data matrix was constructed. Strain diversity was calculated using the Jaccard's coefficient and UPGMA (Unweighted Pair-Group Arithmetic Average Clustering) cluster analysis. The variations in the banding patterns indicated genomic variability among the twelve A. ferrooxidans strains tested. The primers used in this study grouped the twelve strains into five major groups. Similarities between the strains ranged from 5.49% to 85.14%. These results show that the strains have a high degree of genomic diversity and that the RAPD procedure is a powerful technique to assess strain variability in this bacterium.

Taxonomy of the New World species of Lotus (Leguminosae: Loteae)

The aims of the present study were to elucidate the relationships of the New World Lotus species groups, subgenera Acmispon Raf. (sections Microlotus Benth. and Simpeteria Ottley), Hosackia Benth. and Syrmatium Vog., and to compare these results with previous classifications and recent morphological and molecular phylogenetic hypotheses. A numerical taxonomic study using unweighted pair-group arithmetic average clustering was performed. The phenogram was generated from 34 operational taxonomic units (OTUs) × 41 characters (four vegetative characters and the basic chromosome numbers, 16 epidermal traits and 20 reproductive characters). The epidermal microcharacters (epidermal cells, stomata, stomatal index and trichomes) are described and summarised for 18 species of Hosackia and Syrmatium, and the remaining characters were derived from the literature. Phenetic results resolved four groups of species which coincide with the new genera Acmispon, Hosackia Douglas ex Benth., Ottleya D.D.Sokoloff and Syrmatium proposed, having taken into consideration the most recent morphological and phylogenetic hypotheses.

Leaf epidermal characteristics of Lotus subgenus Acmispon (Fabaceae: Loteae) and a numerical taxonomic evaluation

This paper describes the leaf epidermal characteristics of the New World species of Lotus L. subgenus Acmispon Raf. (Fabaceae: Loteae), computes their phenetic relationships based on morphological and anatomical characters, and compares these results with previous classifications and a recent phylogenetic hypothesis for the group based on morphological data. Leaves of 16 species of Acmispon were cleared and examined using light microscopy. Data on epidermal cells, stomata, stomatal index, and trichomes were described and summarized. To test the taxonomic value of epidermal characters and to ascertain phenetic relationships, we performed two numerical analyses using unweighted pair-group arithmetic average clustering. Results of the numerical analysis (16 operational taxonomic units (OTUs) × 13 epidermal characters) suggested that epidermal characteristics are insufficient to resolve sections Simpeteria and Microlotus. An additional analysis (16 OTUs × 23 characters) demonstrated that epidermal micro morphological features, together with other characters, are useful and informative for distinguishing these two sections. Results generated by the latter analysis accord well with earlier classifications and a previous phylogenetic hypothesis by showing that the sections Simpeteria and Microlotus are coincident with the two monophyletic subgroups Grandiflorus and Salsuginosus, respectively, inferred using cladistic analysis.Key words: Acmispon, epidermis, Fabaceae, Loteae, Lotus, Microlotus, Simpeteria.

Exotic and native vegetation establishment following channelization of a western Iberian river

Channelization is often a major cause of human impacts on river systems. It affects both hydrogeomorphic features and habitat characteristics and potentially impacts riverine flora and fauna. Human-disturbed fluvial ecosystems also appear to be particularly vulnerable to exotic plant establishment. Following a 12-year recovery period, the distribution, composition and cover of both exotic and native plant species were studied along a Portuguese lowland river segment, which had been subjected to resectioning, straightening and two-stage bank reinforcement, and were compared with those of a nearby, less impacted segment. The species distribution was also related to environmental data. Species richness and floristic composition in the channelized river segment were found to be similar to those at the more ‘natural’ river sites. Floral differences were primarily consistent with the dominance of cover by certain species. However, there were significant differences in exotic and native species richness and cover between the ‘natural’ corridor and the channelized segment, which was more susceptible to invasion by exotic perennial taxa, such as Eryngium pandanifolium, Paspalum paspalodes, Tradescantia fluminensis and Acacia dealbata. Factorial and canonical correspondence analyses revealed considerable patchiness in the distribution of species assemblages. The latter were associated with small differences in substrate composition and their own relative position across the banks and along the river segments in question. Data was also subjected to an unweighted pair-group arithmetic average clustering, and the Indicator Value methodology was applied to selected cluster noda in order to obtain significant indicator species. Copyright © 2001 John Wiley & Sons, Ltd.

Integration of five Southeast Asian accessions into the world-wide phenetic relationships of Hydrilla verticillata as elucidated by random amplified polymorphic DNA analysis

Random amplified polymorphic DNA (RAPD) markers were analyzed for five new accessions of Hydrilla verticillata (L.f.) Royle collected from southeast Asia (Vietnam and Thailand). These were compared to 12 accessions that had been analyzed in a previous study. Five primers produced 91 loci which were used to calculate the Dice similarity metric which was in turn used to compare the accessions phenetically using both the neighbor-joining algorithm and the unweighted pair-group arithmetic average clustering (UPGMA) method. The US dioecious accessions, as previously, clustered closest to a plant from Bangalore, India. The US monoecious accessions again clustered with a Seoul, Korean accession. The five Southeast Asian accessions clustered loosely near accessions from Pinang Island, Malaysia, Rawa Pening, Indonesia and Tainan, Taiwan, but showed less phenetic similarity to the Asian accessions.

Random amplified polymorphic DNA analysis of the phenetic relationships among world-wide accessions of Hydrilla verticillata

The phenetic relationships among forty-four accessions of Hydrilla verticillata from various regions of the world were determined using random amplified polymorphic DNA (RAPD) analysis of bulked genomic samples. Five primers were used producing a total of 85 resolvable, polymorphic bands. The accessions were compared using Gower and Dice metrics, clustered using unweighted pair-group arithmetic average clustering (UPGMA) and consensus algorithms, and factored using principal coordinate analysis. Four major clusters (Asian, Australian, Indonesian, monoecious U.S.) and one minor outlier cluster (Japan/Poland) were identified. The U.S. dioecious accessions formed a group closest to an accession from Bangalore, India, possibly lending credence to historical reports that it was imported from Sri Lanka. The U.S. monoecious plants cluster with an accession from Seoul, Korea. Accessions from Taiwan, Burundi, and Panama join the Asian cluster late. The New Zealand accessions cluster loosely with those from Australia. The use of band intensity in combination with the Gower similarity coefficient generated a cophenetic correlation coefficient (similarity matrix vs. UPGMA matrix) of r = 0.92, superior to that for the corresponding Dice metric ( r = 0.85).

Assessment of inter- and intra-inbred line variability in sunflower (Helianthus annuus) by RFLPs

The restriction fragment length polymorphism (RFLP) between 26 sunflower inbred lines was evaluated with 81 probe-enzyme combinations involving 51 cDNA clones and 4 restriction enzymes (HindIII, EcoRI, EcoRV, and BglII). An average of 4.6 fragments and 4.9 profiles was detected per probe-enzyme combination, across all inbred lines. The RFLPs revealed were characterized by a high percentage (>70%) of multifragment profiles. Nei's average gene diversity was calculated to measure the genetic variability within cultivated sunflower; the average gene diversity computed with 81 probe-enzyme combinations was 0.59. The relationships between the 26 sunflower inbred lines were analysed by estimates of Nei's F index, which ranged from 0.50 to 0.91, as well as Nei's genetic distance, d, which varied from 0.05 to 0.41. A UPGMA (unweighted pair-group arithmetic average clustering) dendrogram was constructed using the genetic distance matrix; likewise, a principal component analysis was performed using the F matrix. The results obtained from the two clustering analyses allowed the separation of maintainer lines (females) from restorer lines (males). After partitioning the 26 lines into a pool of maintainer lines and a pool of restorer lines, the estimation of gene differentiations showed that the absolute difference (Dm) between females and males was only about 5%. Intraline variability was also examined in 4 sunflower inbred lines, using 30 probe-enzyme combinations. Heterogeneity at varying levels was detected in 3 of the 4 lines studied. The RFLPs detected by this set of selected clones in the 26 inbred lines suggests that RFLPs could be very useful descriptors for sunflower inbred line and variety studies.

Statistical properties of molecular tree construction methods under the neutral mutation model.

The statistical properties of three molecular tree construction methods--the unweighted pair-group arithmetic average clustering (UPG), Farris, and modified Farris methods--are examined under the neutral mutation model of evolution. The methods are compared for accuracy in construction of the topology and estimation of the branch lengths, using statistics of these two aspects. The distribution of the statistic concerning topological construction is shown to be as important as its mean and variance for the comparison. Of the three methods, the UPG method constructs the tree topology with the least variation. The modified Farris method, however, gives the best performance when the two aspects are considered simultaneously. It is also shown that a topology based on two genes is much more accurate than that based on one gene. There is a tendency to accept published molecular trees, but uncritical acceptance may lead one to spurious conclusions. It should always be kept in mind that a tree is a statistical result that is affected strongly by the stochastic error of nucleotide substitution and the error intrinsic to the tree construction method itself.