Comparison of ordinations and classifications of vegetation data

The methodology of comparing the results of multivariate community studies (resemblance matrices, ordinations, hierarchical and nonhierarchical classifications) is reviewed from two viewpoints: basic strategy and measure employed. The basic strategy is determined by 7 choices concerning the type of results, consensus methods or resemblance measures, hypothesis testing or exploratory analysis, lack or presence of reference basis, data set congruence or algorithmic effects, number of factors responsible for differences among results, and the number of properties considered in the comparison. Included is a brief summary of methods applicable to vegetation studies. Examples from a grassland survey demonstrate the utility of comparisons in evaluating the effects of plot size, data type, standardization, taxonomic level and number of species on classifications and ordinations.Abbreviations OUC = Operational Unit of Comparison - PCA = Principal Components Analysis - PCoA = Principal Coordinates Analysis - SSA = Incremental Sum of Squares Agglomeration     

The use of a CCD imaging luminometer in the quantitation of luminogenic immunoassays

We describe the application of a CCD Imaging Luminometer (CCDIL) for the detection and quantitation of rapid, simultaneous, peroxidase-linked chemiluminescent immunoassays of multiple samples of human serum alphafetoprotein (AFP). Results from some analogous immunoassays (total IgE, and thyroid stimulating hormone (TSH)) are included for comparison. Values for precision and antigen concentration obtained using the CCDIL and colorimetric versions of the immunoassays, on human serum samples, were in good agreement. The flexibility of the CCDIL is demonstrated; its ability to detect and quantitate antigen (particularly AFP) on a variety of solid phases is indicated. The work on the AFP immunoassays illustrates not only the flexibility of the CCDIL for sample presentation on a variety of solid phase systems, but also some relative merits of such systems.     

Principles and applications of luminescence spectrometry coupled to liquid chromatographic techniques

An overview is presented of the physicochemical basis of luminescence, and its application to the detection of chemicals (drugs, biomedically important compounds, environmentally active substances) in liquid chromatographic systems.     

Stereological analysis of mitochondria from brains of temperature acclimated goldfish, Carassius auratus L. (5 and 30°C)

1. 1.|The mitochondrial population in hypothalamic and hypophysial brain tissue from warm (30°C) and cold (5°C) acclimated goldfish (Carassius auralus L.) was analyzed using sterological techniques.

2. 2.|It was revealed that there is a significantly larger volume density (Vv) in the cold acclimated tissue, with no significant difference in either of the surface densities (Svext and Svint) from either of the brain areas.

3. 3.|The hypothalamic brain tissue has a significantly lower specific surface (S/V) in the cold acclimated tissue but there is not a significant difference in this parameter for the hypophysial brain tissue.

4. 4.|The values for these three parameters (Vv, Svext and SVint, and S/V) indicate that mitochondria from acclimated brain tissue undergo shape changes in response to thermal stress.

5. 5.|We suggest that the shape changes may be related to the change in the phospholipid composition of the inner mitochondrial membrane with acclimation temperature.

EPISTASIS AS A SOURCE OF INCREASED ADDITIVE GENETIC VARIANCE AT POPULATION BOTTLENECKS

The role of epistasis in evolution and speciation has remained controversial. We use a new parameterization of physiological epistasis to examine the effects of epistasis on levels of additive genetic variance during a population bottleneck. We found that all forms of epistasis increase average additive genetic variance in finite populations derived from initial populations with intermediate allele frequencies. Average additive variance continues to increase over many generations, especially at larger population sizes (N = 32 to 64). Additive-by-additive epistasis is the most potent source of additive genetic variance in this situation, whereas dominance-by-dominance epistasis contributes smaller amounts of additive genetic variance. With additive-by-dominance epistasis, additive genetic variance decreases at a relatively high rate immediately after a population bottleneck, rebounding to higher levels after several generations. Empirical examples of epistasis for murine adult body weight based on measured genotypes are provided illustrating the varying effects of epistasis on additive genetic variance during population bottlenecks.     

A MARKER-BASED METHOD FOR INFERENCES ABOUT QUANTITATIVE INHERITANCE IN NATURAL POPULATIONS

A marker-based method for studying quantitative genetic characters in natural populations is presented and evaluated. The method involves regressing quantitative trait similarity on marker-estimated relatedness between individuals. A procedure is first given for estimating the narrow sense heritability and additive genetic correlations among traits, incorporating shared environments. Estimation of the actual variance of relatedness is required for heritability, but not for genetic correlations. The approach is then extended to include isolation by distance of environments, dominance, and shared levels of inbreeding. Investigations of statistical properties show that good estimates do not require great marker polymorphism, but rather require significant variation of actual relatedness; optimal allocation generally favors sampling many individuals at the expense of assaying fewer marker loci; when relatedness declines with physical distance, it is optimal to restrict comparisons to within a certain distance; the power to estimate shared environments and inbreeding effects is reasonable, but estimates of dominance variance may be difficult under certain patterns of relationship; and any linkage of markers to quantitative trait loci does not cause significant problems. This marker-based method makes possible studies with long-lived organisms or with organisms difficult to culture, and opens the possibility that quantitative trait expression in natural environments can be analyzed in an unmanipulative way.     

INFERENCES ABOUT QUANTITATIVE INHERITANCE BASED ON NATURAL POPULATION STRUCTURE IN THE YELLOW MONKEYFLOWER,MIMULUS GUTTATUS

We used a nonmanipulative, marker-based method to study quantitative genetic inheritance in two habitats of a common monkeyflower population. The method involved regressing quantitative trait similarity on marker-estimated relatedness between individuals sampled in the field. We sampled 300 adult plants from each of two transects, one along a stream habitat and another through a meadow habitat. For each plant we measured 10 quantitative characters and assayed 10 polymorphic isozyme loci. In the meadow habitat, relatedness of plants within 1 m was moderate (r = 0.125, corresponding to half-sibs) as was actual variance of relatedness (V_r = 0.044). Significant heritabilities of 50–70% were found for corolla width and the fitness characters of flower number and plant weight. Genetic correlations were strongly positive, but sharing of environmental effects within 1 m was weak. In the stream habitat, levels of relatedness were lower and similar heritabilities were indicated. To detect dominance variance and the correlation of phenotypes due to shared inbreeding, we also estimated higher-order coefficients of relationship and inbreeding, but these did not significantly differ from zero. Laboratory-based estimates of heritability in the field were lower than the marker-based estimates, indicating that natural heritabilities and genetic correlations may be stronger than indicated by controlled studies.     

Hemoglobin in Chironomus ramosus (Insecta, Diptera): an electrophoretic study of polymorphism, developmental sequence and interspecific relationship

The larvae of the dipteran insect, Chironomus ramosus, found in Shillong, India, contain eleven (11) hemoglobin (Hb) components of which three are monomers (CI, CIV and CVI) and seven are dimers (CIII, CV, CVII, CVIII, CIX, CX and CXI), while one (CII) exists in both monomeric and dimeric states.Four monomeric components were isolated, purified and partially characterized. The N-terminal amino acids were determined and showed glycine for CI and leucine for the other components (CII, CIV and CVI).Three hemoglobin components were found to be present in all stages of larval development, except the first instar larvae. Some Hb components were synthesized in a particular instar, as revealed by electrophoretic appearance.Electrophoretic mobilities of seven components and N-terminal amino acid residues of two components of Hb were similar in both Chironomus ramosus and Chironomus thummi thummi.     

Genomic organization of mouse Dishevelled genes

We report the isolation and characterization of two new genomic loci corresponding to the mouse Dishevelled (Dvl) genes Dvl2 and Dvl3. The Dvl genes are homologs of the Drosophila dsh segment polarity gene, and are involved in the Wnt/wingless signal transduction pathway. Dvl2 and Dvl3 genomic clones were isolated from a mouse 129 strain λFIXII genomic library and have identical exon/intron organization to Dvll. All three Dishevelled genes span 15 exons and 14 introns and have a number of conserved splice junction sites.     

Genetic analysis of agronomic traits in a cross between sugarcane (Saccharum officinarum L.) and its presumed progenitor (S. robustum Brandes & Jesw. ex Grassl)

Saccharum robustum Brandes & Jesw. ex Grassl has been suggested as the immediate progenitor species of cultivated sugarcane (S. officinarum L.) [4]. Chromosome pairing and assortment in these two species were previously studied by genetic analysis of single-dose DNA markers in parents in and 44 F₁ progeny of a cross between euploid, meiotically regular 2n=80S. officinarum LA Purple andS. robustum Mol 5829 [2]. This same population was subsequently clonally propagated and evaluated in replicated trials for quantitative traits important to sugarcane breeders. Numbers of stalks, tasseled stalks, and stalks with smut, and the average diameter of two stalks were determined one day prior to harvest. At harvest, plant material from each plot was weighed and evaluated for pol (sucrose content) and fiber percentages. Clones were significantly different (P<0.01) for all traits analyzed. Associations of 83 single-dose arbitrarily primed PCR genetic markers with quantitative trait loci (QTL) of recorded traits was determined by single-factor ANOVA, and multiple regression. QTL analysis revealed markers significantly (P<0.05) associated with the expression of each trait analyzed. Markers associated with QTL after multiple regression were tested for digenic linear × linear epistatic interactions. The various multilocus models explained between 23% and 58% of the total phenotypic variation and 32% and 76% of the genotypic variation for the various traits. Digenic interactions were uncommon. Implications for marker-assisted selection in sugarcane and sugarcane domestication are discussed.