Selection and proliferation of rapid growing cell lines from embryo derived cell cultures of yew tree (Taxus cuspidata Sieb. et Zucc)

Calli were induced from 300,000 embryos isolated from immature to mature stage of seeds collected on late September from 14 elite trees. When the embryos were cultured onto plastic Petri-dish containing 20 mL of modified B5 basal medium supplemented with 3% (w/v) sucrose, 500 mg/L casein hydrolysate, 250 mg/L myo-inositol, 0.5% (w/v) polyvinyl polypyrrolidon (PVPP), 2×MS vitamins, 0.5 mg/L gibberellic acid, and 10 mg/L 2,4-D after 2 weeks of culture, yellowish-white calli were immediately formed on the surfaces of embryos, and subcultured for 4 weeks in same culture medium. Because most of calli maintained for more than 3 months were revealed differences in their colors, surface texture, and growth rate, visual selection was made for first round screening. When the size of visually selected calli larger than 19 mm in their diameter were inoculated, persistent proliferation was observed. Among the plating methods tested for the selection of rapid growing cell lines at single cell and/or small cell aggregate level, 2-layer spread plating revealed as the best for single cell cloning. To enhance cell growth and maintain high rate of viability for long-term culture of yew cells in bioreactor, final cell volume less than 50% in SCV seemed to be the best. Time course study revealed that 30% of inoculum density was suitable for fed batch culture. Among the tested conditional media, the rate of 1∶2 (old medium: fresh medium) was recorded at the best for cell growth.     

Diversity of cultivable rhizobacteria across tomato growing regions of Karnataka

Seven hundred and fifty-two rhizobacteria were isolated from 186 rhizosphere soil samples collected across tomato growing regions of Karnataka. Among them, 26% strains were Gram positive and other 74% were Gram negative and dominant being Bacillus and Pseudomonas. Sampling of different locations showed variation in species richness and diversity indices. Similarity matrix computed with Jaccard’s coefficient and principle coordinate analysis to correlate bacterial diversity revealed that rhizobacterial genera of Mysore, Mandya and Kolar soil samples were very closely related and rarefaction curve analysis indicated that these soil samples also harbored higher number of rhizobacteria which included all the genera studied. PGPR trait analysis revealed that most of the rhizobacteria were endowed with more than one beneficial trait which may act individually or simultaneously, and indole acetic acid production and phosphate solubilization are the two predominant traits exhibited by these rhizobacteria. Rhizobacterial isolates also showed a varied level of plant growth promotion traits and offered protection against fungal origin foliar and root pathogens. Among the nine regions studied, Mysore, Mandya and Kolar regions recorded higher percentage of promising PGPRs in comparison with other regions studied of Karnataka.     

Leveraging whole genome sequencing data for demographic inference with approximate Bayesian computation

Accounting for historical demographic features, such as the strength and timing of gene flow and divergence times between closely related lineages, is vital for many inferences in evolutionary biology. Approximate Bayesian computation (ABC) is one method commonly used to estimate demographic parameters. However, the DNA sequences used as input for this method, often microsatellites or RADseq loci, usually represent a small fraction of the genome. Whole genome sequencing (WGS) data, on the other hand, have been used less often with ABC, and questions remain about the potential benefit of, and how to best implement, this type of data; we used pseudo‐observed data sets to explore such questions. Specifically, we addressed the potential improvements in parameter estimation accuracy that could be associated with WGS data in multiple contexts; namely, we quantified the effects of (a) more data, (b) haplotype‐based summary statistics, and (c) locus length. Compared with a hypothetical RADseq data set with 2.5 Mbp of data, using a 1 Gbp data set consisting of 100 Kbp sequences led to substantial gains in the accuracy of parameter estimates, which was mostly due to haplotype statistics and increased data. We also quantified the effects of including (a) locus‐specific recombination rates, and (b) background selection information in ABC analyses. Importantly, assuming uniform recombination or ignoring background selection had a negative effect on accuracy in many cases. Software and results from this method validation study should be useful for future demographic history analyses.     

EVOLUTION AND EXTINCTION IN A CHANGING ENVIRONMENT: A QUANTITATIVE-GENETIC ANALYSIS

Because of the ubiquity of genetic variation for quantitative traits, virtually all populations have some capacity to respond evolutionarily to selective challenges. However, natural selection imposes demographic costs on a population, and if these costs are sufficiently large, the likelihood of extinction will be high. We consider how the mean time to extinction depends on selective pressures (rate and stochasticity of environmental change, and strength of selection), population parameters (carrying capacity, and reproductive capacity), and genetics (rate of polygenic mutation). We assume that in a randomly mating, finite population subject to density-dependent population growth, individual fitness is determined by a single quantitative-genetic character under Gaussian stabilizing selection with the optimum phenotype exhibiting directional change, or random fluctuations, or both. The quantitative trait is determined by a finite number of freely recombining, mutationally equivalent, additive loci. The dynamics of evolution and extinction are investigated, assuming that the population is initially under mutation-selection-drift balance. Under this model, in a directionally changing environment, the mean phenotype lags behind the optimum, but on the average evolves parallel to it. The magnitude of the lag determines the vulnerability to extinction. In finite populations, stochastic variation in the genetic variance can be quite pronounced, and bottlenecks in the genetic variance temporarily can impair the population's adaptive capacity enough to cause extinction when it would otherwise be unlikely in an effectively infinite population. We find that maximum sustainable rates of evolution or, equivalently, critical rates of environmental change, may be considerably less than 10% of a phenotypic standard deviation per generation.     

Morphological and histological changes of dermal scales during the fish‐to‐tetrapod transition

Witzmann F. (2011). Morphological and histological changes of dermal scales during the fish‐to‐tetrapod transition. —Acta Zoologica (Stockholm) 92 : 281–302. The gastral scales of limbed tetrapodomorphs evolved from the ‘elpistostegid’‐type of scale by an enlargement and differentiation of the articulation facets and a shortening and broadening of the keel. These changes caused a tighter connection between gastral scales within a scale row and a greater overlap between the rows. Dorsal round scales of limbed tetrapodomorphs developed from a gastral scale‐type by an alteration of the ontogenetic pathway. The posterolateral direction of scale rows in ‘elpistostegids’ was retained in the gastral scalation of most limbed tetrapodomorphs, whereas the arrangement of round dorsal scales is modified to a transverse orientation. Both gastral and dorsal scales of limbed tetrapodomorphs consist solely of parallel‐fibred bone with circumferential growth marks. The proportionally larger overlap surfaces of gastral scales and their mode of articulation in the ventral midline indicate that the body of limbed tetrapodomorphs might have been more flexible than that of their finned relatives. The alteration of dermal scales was one of the most rapid morphological changes during the fish‐to‐tetrapod transition. Once established, gastral and dorsal scales were retained as a conservative character in different lineages of basal tetrapods, in both the amphibian and the amniote lineages.     

Assessment of Optimal Selected Prognostic Factors

The identification and assessment of prognostic factors is one of the major tasks in clinical research. The assessment of one single prognostic factor can be done by recently established methods for using optimal cutpoints. Here, we suggest a method to consider an optimal selected prognostic factor from a set of prognostic factors of interest. This can be viewed as a variable selection method and is the underlying decision problem at each node of various tree building algorithms. We propose to use maximally selected statistics where the selection is defined over the set of prognostic factors and over all cutpoints in each prognostic factor. We demonstrate that it is feasible to compute the approximate null distribution. We illustrate the new variable selection test with data of the German Breast Cancer Study Group and of a small study on patients with diffuse large B‐cell lymphoma. Using the null distribution for a p‐value adjusted regression trees algorithm, we adjust for the number of variables analysed at each node as well. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Heterosis in Cepaea

A test has been made of the association of heterozygosity with shell breadth in the polymorphic snail Cepaea nemoralis. The material was collected by C. B. Goodhart from a series of paired sites at which individuals reached different adult breadths. Dominant phenotypes, in which a large fraction was heterozygous, had a greater breadth and lower variance than recessive phenotypes regardless of whether the measurement was of shell ground colour, banding or the double recessive vs. the rest. Most of the difference was contributed by samples from the habitat where animals reached the largest size. The result is consistent with existence of heterotic sections of chromosome that include the colour and banding loci, and may help to explain the persistence of the polymorphism.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 49–53.     

Stable isotopic niche predicts fitness of prey in a wolf–deer system

Interindividual variation in niche presents a potentially central object on which natural selection can act. This may have important evolutionary implications because habitat use governs a suite of selective forces encountered by foragers. In a free-living native black-tailed deer, Odocoileus hemionus , population from coastal British Columbia, we used stable isotope analysis to identify individual variation in foraging niche and investigated its relationship to fitness. Using an intragenerational comparison of surviving and nonsurviving O. hemionus over 2 years of predation by wolves, Canis lupus, we detected resource-specific fitness. Individuals with isotopic signatures that suggested they foraged primarily in cedar ( Thuja plicata )-dominated and low-elevation hemlock ( Tsuga heterophylla )-dominated forest stands were more likely to be killed by C. lupus . High-quality forage in T. plicata stands, as indexed by protein content, may be involved in maintaining this foraging phenotype. Moreover, nonsurvivors diverged more than survivors from median isotopic signatures, suggesting selection against foraging specialization. Stable isotope analysis provides a novel opportunity to integrate ecological and selective landscapes in order to identify underlying ecological mechanisms of selection and provide insight into the maintenance of variability.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 125–137.