A graph theoretic approach to the development of minimal phylogenetic trees

Summary The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the length of any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.     

The role of retinol in the initiation of sporangiophores of Phycomyces blakesleeanus

The initiation of sporangiophores of Phycomyces was analyzed under oxygen-limiting conditions. Mutants lacking -carotene have a higher oxygen threshold than the wild type depending on the residual amount of -carotene. The supersensitivity to low oxygen tension is specific for sporangiophore initiation and can be suppressed by addition of either retinal, retinol or retinol acetate to the medium. It is suggested that retinol is a natural regulator of differentiation in Phycomyces.     

Distributional patterns and an additional species of thePassiflora vitifolia complex: Amazonian species diversity due to edaphically differentiated communities

Field studies in Amazonian Peru show that thePassiflora vitifolia complex, a microcosm of many larger taxa, is concentrated in Amazonia with 4 ecologically separated species. One species is restricted to seasonally inundated forests, a second to non-inundated white sand soils, a third to non-inundated lateritic soils, and the fourth mostly to non-inundated alluvial soils. A new combination is formally proposed to recognize the white sand taxon, previously regarded as a variety, as a distinct species:P. involucrata. The importance of -diversity in maintaining high Amazonian species diversity is emphasized.     

Kinetics of rapid RNA evolution in vitro

Summary A rapidly acquired partial resistance to the replicase antagonist, ethidium bromide (EB), seen by Spiegelman and coresearchers in Q RNA variants competitively replicating under defined conditions in vitro, reflected existence of a pool of mutant RNA molecules, preadapted to EB, and their cross-propagation from the pre-EB optimum species, MDV-1, and from other kindred variants, some of which remained undetected, according to this quantitative analysis of midivariant RNA replication kinetics. DNAlike features of their evolution, such as the cloning of variants from an MDV-1 subtype and a complicance with the fundamental theorem of natural selection, resulted from the suppression, both real and apparent, of intrinsic RNA heterogeneity through sampling and detection methods, and also by the ascendency of self-propagation over cross-propagation with advancement of a superior variant. The deficit in mean polymer fitness, compared with optimum levels, determines the lower limit of this heterogeneity. Stability conditions for frequency equilibrium and strategies for counteracting viral drug resistance have been considered.     

Variation in the genetic structure and reproductive biology of holm oak populations

Five polymorphic enzymatic loci were studied in 30 populations of Quercus ilex distributed from Crete to North Africa. A high within-population genetic diversity was found for each locus studied. Most of the alleles were common to all the populations, indicating that the holm oak corresponds to a single genetic entity. Observation of breeding system characteristics showed that the holm oak is monoecious, wind-pollinated, and likely to possess genetic autoincompatibility. Furthermore, studies of flowering phenology in a single population showed that the period of flowering varied notably among trees. An average of 29% of the trees showed inter-annual variation in flowering time. The male, female or vegetative investment also varied widely among trees from one year to another. This results in a diversification of pollen source received by a given tree each year, and also from one year to another.     

Site Variation in Littoral Periphyton Populations: Correlation and Regression with Environmental Factors

Over a six month period, littoral periphyton communities on vertically oriented glass slides were quantitatively sampled from four stations in Elk Lake, British Columbia. Correlation and multiple regression analyses were employed to assess the temporal interrelationships between 15 environmental variables, concurrently measured, and the periphyton populations, expressed as total cell counts and species diversity, for the complete data set of each station. At all stations there was a statistically significant increase in total cell populations with increasing length of slide exposure; positive correlations also occurred with pH, temperature, nitrite, nitrate and copper, while negative ones occurred with oxygen, orthophosphate and hardness (magnesium and total). At all but one station there was a significant decrease in species diversity with increasing slide exposure duration, a decrease attributed to the simultaneous increase in standing crop resulting in intensified competition for diminishing substrate area suitable for cell colonization. Multiple stepwise regression analyses demonstrated that greater than 80% of the variation in periphyton total cells at all four stations could be reliably predicted or described in terms of length of slide exposure, phosphate (ortho and total), and hardness (calcium and total). On the other hand, exposure duration and total cell populations were the most important variables associated with changes in species diversity at three of the four stations. In general, correlations and regressions between standing crop and environmental variables were more statistically reliable and consistent between stations than comparable analyses with species diversity. Use of multiple regression and correlation disclosed the importance of small, non statistically significant variation in ecologically relevant variables and permitted objective comparison of stations.     

兰州滨河公园自生植物物种组成及多样性分析

调查研究兰州4处滨河公园自生植物的物种组成和多样性特征,为低成本、低养护和野趣自然的园林景观规划提供参考。在黄河兰州主城区段自西向东选取银滩湿地公园、马滩湿地公园、马拉松主题公园、雁滩公园,通过网格系统取样法共设置344个样方,调查研究滨河公园自生植物物种组成和分布特征。结果表明,4处滨河公园共有44科118属163种;在物种来源中,乡土物种79种（48.46%）、国内外来物种53种（32.51%）、国外外来物种14种（8.58%）、入侵植物有17种（10.42%）;4处滨河公园间α多样性存在显著差异（P<0.05）;银滩湿地公园、马滩湿地公园、马拉松主题公园、雁滩公园的多样性指数H''分别为4.76、4.36、4.064、3.99;均匀度指数J''分别为0.53、0.586、0.56、0.54;丰富度指数R''分别为30.68、29.47、22.80、20.27;平均多度分别为55.43、44.82、50.16、39.40。兰州滨河公园自生植物资源较为丰富,在未来的城市园林绿地建设中可合理规划,提高自生植物的应用比例,并根据不同环境营造具有地域特色的自生植物景观。     

Microbiota within the perennial ice cover of Lake Vida, Antarctica

Lake Vida, located in the McMurdo Dry Valleys, Antarctica, is an 'ice-sealed' lake with approximately 19 m of ice covering a highly saline water column (approximately 245 ppt). The lower portions of the ice cover and the lake beneath have been isolated from the atmosphere and land for circa 2800 years. Analysis of microbial assemblages within the perennial ice cover of the lake revealed a diverse array of bacteria and eukarya. Bacterial and eukaryal denaturing gradient gel electrophoresis phylotype profile similarities were low (<59%) between all of the depths compared (five depths spanning 11 m of the ice cover), with the greatest differences occurring between surface and deep ice. The majority of bacterial 16S rRNA gene sequences in the surface ice were related to Actinobacteria (42%) while Gammaproteobacteria (52%) dominated the deep ice community. Comparisons of assemblage composition suggest differences in ice habitability and organismal origin in the upper and lower portions of ice cover. Specifically, the upper ice cover microbiota likely reflect the modern day transport and colonization of biota from the terrestrial landscape, whereas assemblages in the deeper ice are more likely to be persistent remnant biota that originated from the ancient liquid water column of the lake that froze.     

Diversity of halophilic microorganisms: Environments,phylogeny, physiology,and applications

The phylogenetic diversity of microorganisms living at high salt concentrations is surprising. Halophiles are found in each of the three domains: Archaea, Bacteria, and Eucarya. The metabolic diversity of halophiles is great as well: they include oxygenic and anoxygenic phototrophs, aerobic heterotrophs, fermenters, denitrifiers, sulfate reducers, and methanogens. The diversity of metabolic types encountered decreases with salinity. The upper salinity limit at which each dissimilatory process takes place is correlated with the amount of energy generated and the energetic cost of osmotic adaptation. Our understanding of the biodiversity in salt-saturated environments has increased greatly in recent years. Using a combination of culture techniques, molecular biological methods, and chemotaxonomic studies, we have obtained information on the nature of the halophilic Archaea as well as the halophilic Bacteria that inhabit saltern crystallizer ponds. Several halophilic microorganisms are being exploited in biotechnology. In some cases, such as the production of ectoine, the product is directly related to the halophilic behavior of the producing microorganism. In other cases, such as the extraction of β-carotene from Dunaliella or the potential use of Haloferax species for the production of poly-β-hydroxyalkanoate or extracellular polysaccharides, similar products can be obtained from non-halophiles, but halophilic microorganisms may present advantages over the use of non-halophilic counterparts. Journal of Industrial Microbiology & Biotechnology (2002) 28, 56–63 DOI: 10.1038/sj/jim/7000176 Received 20 May 2001/ Accepted in revised form 20 June 2001     

重庆市爬行动物物种多样性研究及保护

1996～2004年对重庆市35个县(区、市)进行野外调查采集,结合有关资料记载,重庆市共有爬行动物2目12科38属58种,其中龟鳖目4种,有鳞目蜥蜴亚目12种、蛇亚目42种(含重庆市蛇类新记录3属4种)。建议加强对该市爬行动物物种多样性及其生境的保护,合理利用爬行动物资源。