Restriction data from chloroplast DNA for phylogenetic reconstruction: Is there only one accurate way of scoring?

Information from the same restriction analysis of chloroplast DNA of 33 taxa ofRubiaceae was scored in four different ways, two of which were based on fragments, and two on restriction sites, and they were subsequently analysed with Wagner parsimony. The methods resulted in different phylogenetic trees. The inherent differences between the methods relate to the amount of non-homologous characters and dependent characters, but none of the methods will systematically bias the resulting cladograms. The fragment analyses are much less time-consuming, but probably less accurate, than the site analyses. The choice of method is dependent on a trade-off between accuracy and resources (time). One important recommendation is made: all phylogenetic analyses of chloroplast DNA data should be accompanied by a data matrix and contain information on how the matrix was compiled.     

Radioimmunoassays for androsterone, 5alpha-androstane-3alpha, 17beta-diol and 5alpha-androstane-3beta, 17beta-diol

Androsterone (3alpha-hydroxy-5alpha-androstan-17-one), 5alpha-androstane-3alpha, 17beta-diol and 5alpha-androstane-3beta, 17beta-diol were conjugated at C-16 through sulfur to bovine and human serum albumin. Rabbits injected with these conjugates produced antibodies suitable for radioimmunoassays of these hormone metabolites. Samples were purified on Sephadex LH-20 columns. Levels of these steroids were measured in a rat blood serum pool and in ovarian tissue extract pools.     

Construction of phylogenetic trees for proteins and nucleic acids: Empirical evaluation of alternative matrix methods

Summary The methods of Fitch and Margoliash and of Farris for the construction of phylogenetic trees were compared. A phenetic clustering technique - the UPGMA method — was also considered.The three methods were applied to difference matrices obtained from comparison of macromolecules by immunological, DNA hybridization, electrophoretic, and amino acid sequencing techniques. To evaluate the results, we used the goodness-of-fit criterion. In some instances, the F-M and Farris methods gave a comparably good fit of the output to the input data, though in most cases the F-M procedure gave a much better fit. By the fit criterion, the UPGMA procedure was on the average better than the Farris method but not as good as the F-M procedure.On the basis of the results given in this report and the goodness-of-fit criterion, it is suggested that where input data are likely to include overestimates as well as true estimates and underestimates of the actual distances between taxonomic units, the F-M method is the most reasonable to use for constructing phylogenies from distance matrices. Immunological, DNA hybridization, and electrophoretic data fall into this category. By contrast, where it is known that each input datum is indeed either a true estimate or an underestimate of the actual distance between 2 taxonomic units, the Farris procedure appears, on theoretical grounds, to be the matrix method of choice. Amino acid and nucleotide sequence data are in this category.The following abbreviations are used in this work F-M Fitch-Margoliash - UPGMA unweighted pair-group method using arithmetic averages - SD percent standard deviation     

Rain forest composition and patterns of secondary succession in the Vava'u Island Group,Tonga

Abstract. The Vava'u island group, Tonga, comprises ca. 60 limestone islands on a single submarine platform overlain with rich soils derived from tephra deposits from nearby volcanic islands. The island group has moderate topographic relief (215 m) and is characterized by plateaus and steep cliffs. Humans settled in Tonga ca. 3000 yr ago and have exploited the flatter terrain for agriculture since that time. We conducted the first survey of forest composition in Vava'u, sampling remnant patches of late-successional forest as well as stands in various stages of secondary succession following agricultural abandonment. Plant species composition did not vary greatly with elevation over this short gradient, in contrast with patterns found on‘Eua, a higher island in Tonga. The most significant environmental gradient affecting species composition was coastal or maritime influence. However, the greatest variation in species composition and structure appeared to be related to species turnover during secondary succession, and we hypothesize a sequence of species replacements. Secondary forest begins to resemble late-successional forest in 30–50 yr in terms of structure and native species richness and therefore is of significant conservation value.     

Influence of ethanol on the high frequency electric polarizability of E. coli

The interface electric polarizability of bacteria (charge dependent (ChD) and Maxwell-Wagner (MW) polarizabilities) gives information about their electric charge, determined by the structure and functional state. It is well known that the polarizability could be changed significantly by adding some substances to the suspension, and can be measured using an electro-optical (EO) method. There are some literature data, according to which the adding of ethanol decreases the electric polarizability of the cells. However the reason for the change in this parameter is not clear, as well as which component (ChD and/or MW) of polarizability has the main contribution. Generally the present work shows that the effect of ethanol is connected to the change of the internal (cytoplasm) MW polarizability and is mainly caused by increasing the cell membrane permeability. This results in an ionic flow through the membrane, which velocity and direction depends on the relative values of the inner (cytoplasm) and the outer medium ionic strength.     

Relationships among the seed rain,seed bank and vegetation of a Hawaiian forest

Abstract. Hawaiian ecosystems are prone to invasion by alien plant species. I compared the seed rain, seed bank, and vegetation of a native Hawaiian forest to examine the potential role that seed ecology plays in allowing alien species to invade native forest. Absolute cover of seed plants in the forest was 126 %, annual seed rain was 5 713 seeds m^-2 yr^-1, and the mean density of seedlings emerging from the seed bank averaged across four seasons was 1 020/m². The endemic tree Metrosideros polymorpha was the most abundant species in the vegetation, seed rain and winter seed bank. Overall, native seed plants comprised 95 % of the relative cover in the vegetation and 99 % of the seeds in the seed rain, but alien species comprised 67 % of the seeds in the seed bank. Alien species tended to form persistent seed banks while native species formed transient or pseudo-persistent seed banks. Dominance of the seed bank by alien species with persistent seed banks suggests that aliens are favorably placed to increase in abundance in the vegetation if the forest is disturbed.     

Biological invasion on an oceanic island mountain: Do alien plant species have wider ecological ranges than native species?

Abstract. Spatial distribution patterns of alien plant species were compared with those of native species on a windward slope of Mt. Haleakala (3055 m). Oceanic islands are considered susceptible to biological invasion, and this study numerically tested this circumstantial evidence with the following questions: Are all habitats equally susceptible; and, do successful invaders have wider realized niches than natives? The mountain slope consists of three distinct altitudinal bioclimatic zones (hot moist lowland, wet montane cloud, and cool arid high-altitude zones). Ordination indicated that alien species' ranges and population expansions were clustered in the lowland and high-altitude zones. The lowland zone had been subjected to natural canopy dieback, and the high-altitude zone to grazing by domestic and feral ungulates. By contrast, the montane cloud forest was relatively intact in terms of number and cover of native species. Thus, susceptibility to alien invasion clearly differed among zones, and the primary causes seemed to be the obvious disturbance factors. The mean ecological range along the altitude-rainfall gradient was significantly (P < 0.05) greater for native than for alien species in most life-form groups. The reasons for the greater number of climate generalists among the natives vs. the range-restricted aliens appear to be related to: (1) the pre-alien condition with a depauperate flora which allowed for ‘ecological release’ of successful native colonizers, and (2) the climatic pre-adaptation of alien invaders which restricts them from penetrating over a broader spectrum of climatic zones in a floristic matrix subjected to increasing interspecific competition.     

Structure and molecular evolutionary analysis of a plant cytochrome c gene: Surprising implications forArabidopsis thaliana

Summary We have isolated a cytochrome c gene fromArabidopsis thaliana (cv. Columbia), which is the first cytochrome c gene to be cloned from a higher plant. Genomic DNA blot analysis indicates that there is only one copy of cytochrome c inArabidopsis. The gene consists of three exons separated by two introns. Gene features such as regulatory regions, codon usage, and conserved splicing-specific sequences are all present and typical of dicotyledonous plant nuclear genes. We have constructed phenograms and cladograms for cytochrome c amino acid sequences and histone H3, alcohol dehydrogenase, and actin DNA sequences. For both cytochrome c and histone H3,Arabidopsis clusters poorly with other higher plants. Instead, it clusters withNeurospora and/or the yeasts. We suggest that perhaps this observation should be considered when usingArabidopsis as a model system for higher plants.     

Phylogenetic analysis of chloroplast restriction enzyme site mutations in the Saccharinae Griseb. subtribe of the Andropogoneae Dumort. tribe

Chloroplast (cp) DNA from 32 genotypes representing eight genera and 19 species from the Andropogoneae tribe was analyzed using 15 restriction enzymes and Southern hybridization with 12 cpDNA probes that span the complete rice chloroplast genome. Six of the genera, Saccharum, Miscanthus, Erianthus, Narenga, Eccoilopus, and Sclerostachya, are part of the Saccharinae subtribe, whereas the other two, Zea and Sorghum, were used as outgroups. Narenga, Miscanthus, Erianthus, and Sclerostachya are presumed to have been involved in the evolution of Saccharum officinarum (noble or high sucrose sugarcane) via S. spontaneum and S. robustum. Southern hybridization with the rice cpDNA probes surveyed approximately 3% of the S. officinarum Black Cheribon genome and yielded 62 restriction site mutations (18 informative) that were analyzed using cladistic parsimony and maximum likelihood. These site mutations placed the 32 genotypes into nine different chloroplast groups; seven from within the Saccharinae subtribe and the two outgroups (maize and Sorghum). Phylogenetic inferrence under various assumptions showed that the maternal lineages of Narenga, Miscanthus, Sclerostachya, and Saccharum formed a monophyletic group. This group displayed little variation. On the other hand, 5 of 6 Erianthus species and Eccoilopus longisetosus formed a separate group. The Old World Erianthus/Eccoilopus chloroplast was very different from that of the rest of the Saccharum complex members and was slightly more related to that of Sorghum bicolor. Placement of these Erianthus/Eccoilopus genotypes was, therefore, in conflict with analyses based on morphology. Surprisingly, Erianthus trinii, a New World species, had the same restriction sites as did one Miscanthus sinensis. One Miscanthus sp. from New Guinea that has a very high chromosome number (2n=192) had the same restriction sites as the majority of the Saccharum genus, suggesting that introgression between these genera occurs in the wild. The Saccharum genus was separated into two clades by single site mutation: one containing S. spontaneum, and the other containing all of the remaining Saccharum species and all 8 commerical hybrids (from various regions of the world). A physical map of the chloroplast of Saccharum officinarum Black Cheribon was constructed using 5 restriction enzymes.     

Phylogenetic analysis of the aquatic Oligochaeta under the principle of parsimony

Phylogenetic relationships between five subfamilies of Tubificidae and ten other families of microdrile oligochaetes were estimated by a Wanger parsimony analysis using PAUP (Phylogenetic Analysis Using Parsimony, by D. L. Swofford). As the apomorph character state is ambiguous for some characters, different assumptions of directionality as well as deletions of some characters are tested in a number of analyses. A general pattern is evident from the study; (1) the majority of the aquatic families are members of a large monophyletic group (the order Tubificida in a somewhat restricted sense) defined by the shared possession of atria (generally with well developed external prostate glands), but the family Tubificidae is paraphyletic within this group; (2) the Enchytraeidae appear to form a second group (the Enchytraeida) together with the exclusively marine Capilloventridae and Randiellidae, all three families characterized by the anterior location of the spermathecae; (3) the Haplotaxidae are a plesiomorph family, which stands out as a branch of its own and constitutes the ancestral part of a group comprising also all the megadriles (the Haplotaxida). However, monophyly of the Haplotaxida is likely only if the haplotaxid octogonadial condition is assumed to be derived from the tetragonadial condition characterizing most microdriles, a situation not envisaged by previous authors. The implications of the parsimony method are briefly discussed.