An application of ordination to the identification of forest types

Summary The problems of allocating new vegetation stands to an existing classification are outlined. As one solution, the vegetation samples from an area may be ordinated by reciprocal averaging and classified by dividing the ordination into community-types. The ordination scores for a short list of species present in a new sample may then be averaged to locate that sample on the ordination axes and in one of the community-types. The method is tested by comparing estimates from incomplete species lists with that from a complete list of species in an forest stand in southern Ghana.We gratefully acknowledge the assistance of Mr. M.O. Hill in the correct formulation of the coordinate estimation procedure.     

On non-linear species response models in ordination

Ordination techniques are plagued by the non-linearity of vegetation data. The purpose of ordination is discussed and considered to be the process of arranging samples (or species) in relation to one or more environmental gradients or abstract axes that may represent such gradients, the arrangement to be ecologically significant. The appropriateness of various models of vegetation to current ordination techniques is considered, particularly the gaussian species response curve. Two alternatives are suggested based on -functions and an ecological response curve model incorporating competition between species.     

Large-scale causes of variation in the serpentine vegetation of California

Serpentine vegetation in California ranges from forest to shrubland and grassland, harbors many rare and endemic species, and is only moderately altered by invasive exotic species at the present time. To better understand the factors regulating the distribution of common/representative species, endemic/rare species, and the threat of exotics in this important flora, we analyzed broad-scale community patterns and environmental conditions in a geographically stratified set of samples from across the state. We considered three major classes of environmental influences: climate (especially precipitation), soils (especially the Mg²⁺/Ca²⁺ ratio), and the indirect influences of climate on soils. We used ordination to identify the major axes of variation in common species abundances, structural equation models to analyze the relationship of community axes and endemic and exotic species richness to the environment, and group analysis techniques to identify consistent groupings of species and characterize their properties. We found that community variation could be explained by a two-axis ordination. One axis ranged from conifer forest to grassland and was strongly related to precipitation. The second axis ranged from chaparral to grassland and had little relationship to current environmental conditions, suggesting a possible role for successional history. Precipitation and elevation were respectively the largest influences on endemic and exotic richness, followed by Mg²⁺/Ca²⁺. The results also support the idea that long-term precipitation patterns have altered the Mg²⁺/Ca²⁺ ratio via selective leaching, resulting in indirect influences on endemics (positive) and exotics (negative) but not affecting the abundances of common species. We discuss implications of these findings for the conservation of the California serpentine flora.     

Structure,diversity, and regeneration of tropical dry deciduous forest of northern India

This study examined the impact of disturbance on the pattern of diversity, forest structure and regeneration of tree species in the Vindhyan dry tropical forest of India. A total of 1500 quadrats distributed over five, 3-ha permanent plots in five sites, differing in degree of disturbance, were used to enumerate and measure the tree species. A total of 65 species with 136,983 individuals were enumerated in the total 15-ha area for stems 30 cm height. The number of species and number of stems ranged from 12 to 50 and 8063–65331 per 3-ha area. The number of species and stems for trees 10 cm dbh ranged from 3 to 28 species, with a mean value of 16 species ha^–1, and from 16 to 477 stems, with a mean value of 256 stems ha^–1, respectively. The adult based PCA ordination indicated uniqueness of sites in terms of species composition and habitat characteristics. PCA ordination also showed uniqueness of sites in terms of seedling composition, but the seedling and adult distributions were not spatially associated. The distinct species composition at the different sites and at the two life-cycle stages on the same site is indicative of marked spatio-temporal dynamics of the dry tropical forest. The density–diameter semi-logarithmic curves ranged from a near linear to an overall concave appearance with a limited plateau in the mid-diameter ranges. The -diversity and its components decreased with increasing disturbance intensity, reflecting enhanced utilization pressure with increasing disturbance. The site-wise and species-wise regression analyses of the number of individuals in different stages of the species revealed that both the level of disturbance and the nature of species strongly affect the regeneration. In conclusion, although the forest is relatively species-poor, the differential species composition on different sites and the temporal dynamics lend a unique level of diversity to the tropical dry deciduous forest.     

On the integrated interpretation of indirect site ordinations: a case study using semi-arid vegetation in southeastern Spain

The need for rigorous methods of interpreting indirect site ordinations is discussed and the problem of oblique habitat and phytosociological trends is emphasized. A sequential approach, termed integrated interpretation, is introduced to overcome this problem. It first involves a technique termed rotational correlation a linear form of trend surface analysis, which locates the best fit between a habitat variable and the coordinates of a pluridimensional ordination. The coordinates at positions of best fit are then used to produce two-way site-species tables (seriation arrays) which summarize floristic variation in relation to each major habitat trend. The seriation arrays can also be used to identify groups of differential species. Integrated interpretation is demonstrated using semi-arid vegetation from Murcia Province, SE Spain. A two-axis site ordination of vegetation data by non-metric multidimensional scaling is shown to have two oblique trends related to aspect-induced topoclimates and types of past anthropogenic disturbance. Rotation of the configuration to maximum linear correlation achieves very high levels of explanation for each factor. Rotated ordination coordinates from the correlation analysis are used to obtain two seriation arrays and floristic noda which relate directly to the two underlying habitat trends. A floristic discontinuity is revealed on the topoclimate continuum and it is hypothesized that temperature conditions are a major determinant of floristic composition, but that moisture partly determines vegetational cover and phytomass. Several patterns of past cultivation are detected and associated with five main kinds of geomorphological unit, together with some evidence that the rate of succession is partly determined by topoclimate. The integrated approach to interpretation is compared with visual methods and other multivariate techniques. A case is made for increased interpretational rigour in site coordinate studies, especially the discontinuation of trend-seeking using individual unrotated ordination axes.Nomenclature of vascular plants follows Tutin et al. (1964–1980) Flora Europaea 5 Vols. Cambridge University Press, Cambridge. Nomenclature of syntaxa follows Rivas-Goday & Rivas-Martinez (1967).I am indebted to J. A. Michel, Dr M. A. Abdelrahman and Monica M. Dargie for field assistance. Field discussion with Dr R. L. Wright, Dr M. P. Austin and Professor F. Esteve Chueca was most helpful; the latter assisted with confirmation of vascular plant voucher specimens. Non-vascular taxonomy was determined by Dr C. Humphries (mosses and one alga) and Dr O. L. Gilbert (lichens). An anonymous referee suggested an approximation of the analytical solution to rotational correlation, and Dr N. R. J. Fieller assisted with its confirmation. The project was assisted by a grant from the University of Sheffield Research Fund.     

The Unusual Amino Acid Triplet Asn–Ile–Cys Is a Glycosylation Consensus Site in Human α-Lactalbumin

Human -lactalbumin has not been described as a glycoprotein, despite the fact that several -lactalbumins of both ruminant and nonruminant species are known to be glycosylated. In all these species the glycosylation site is the ⁴⁵Asn in the usual triplet ⁴⁵Asn–Gly/Gln–⁴⁷Ser. We have found that human -lactalbumin is glycosylated and the glycosylation site has been determined by protein sequencing and mass spectrometry. We report an unusual glycosylation site at ⁷¹Asn in the triplet ⁷¹Asn–Ile–⁷³Cys, which is conserved in all known -lactalbumins except red-necked wallaby. That a relatively small proportion of the protien is glycosylated (about 1%) may reflect the importance of this region of the protein sequence to the molten globule state of -lactalbumin.     

Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores

We describe a repetitive DNA region at the 3 end of the mitochondrial DNA (mtDNA) control region and compare it in 21 carnivore species representing eight carnivore families. The sequence and organization of the repetitive motifs can differ extensively between arrays; however, all motifs appear to be derived from the core motif ACGT. Sequence data and Southern blot analysis demonstrate extensive heteroplasmy. The general form of the array is similar between heteroplasmic variants within an individual and between individuals within a species (varying primarily in the length of the array, though two clones from the northern elephant seal are exceptional). Within certain families, notably ursids, the array structure is also similar between species. Similarity between species was not apparent in other carnivore families, such as the mustelids, suggesting rapid changes in the organization and sequence of some arrays. The pattern of change seen within and between species suggests that a dominant mechanism involved in the evolution of these arrays is DNA slippage. A comparative analysis shows that the motifs that are being reiterated or deleted vary within and between arrays, suggesting a varying rate of DNA turnover. We discuss the evolutionary implications of the observed patterns of variation and extreme levels of heteroplasmy.By acceptance of this article, the publisher acknowledges the right of the US Government to retain non-exclusive, royalty-free license in and to any copyright covering the article. Correspondence to: A.R. Hoetzel     

Submerged plant survival strategies in relation to management and environmental pressures in drainage channel habitats

The abundance of submerged weeds, in relation to management regime and environmental factors, was surveyed during 1992 and 1993 in drainage channels located in four geographically-distinct areas of Britain. The aim of the study was to ascertain, using a multivariate approach, the degree to which species survival strategy and vegetation could be related to disturbance and stress pressures on plant survival. Indices of disturbance and stress were constructed from combined environmental data for each site. A species ordination using Canonical Correspondence Analysis showed that the combined disturbance variable explained more of the variability that did stress. Two main groups of species could be distinguished. The larger group scored low on the disturbance gradient and these species, with different tolerances to stress (especially light-limitation), appeared to be those better-adapted to habitats with low disturbance (e.g. Potamogeton pectinatus and Potamogeton lucens). The smaller group comprised species which tended to occur in sites with higher disturbance (e.g. regular cutting) such as Callitriche stagnalis. Using the terminology of strategy theory, most of the dominant species could be classed as competitive/disturbance tolerators (CD) or variants of this established-phase strategy. The limitations are discussed of applying the strategy approach at species level in a defined habitat-type which shows a high degree of uniformity between sites, such as artificial drainage channels.     

Activation of Lyt-2 associated with distant upstream insertion of an SL3-3 provirus

Two Lyt-2⁺ mutants of the T-cell lymphoma SL12.4.10 were selected by fluorescence activated cell sorting. Both mutants expressed Lyt-2 (CD8 -chain) but not Lyt-3 (CD8 -chain). Derivatives of one Lyt-2⁺ mutant that expressed Lyt-3 could be isolated by sorting for Lyt-3⁺ cells. Southern blotting analysis indicated that both mutants had structural rearrangements within or immediately 3 of the Lyt-3 gene, accompanied by demethylation of at least one Hpa II site within the Lyt-2 gene. Gene cloning analysis of one mutant demonstrated that the structural rearrangement was due to insertion of an SL3-3 provirus 35 kb 5 to the Lyt-2 gene. It is likely that Lyt-2 gene activation is a direct or indirect consequence of proviral insertion at this site. Address correspondence and offprint requests to: R. Hyman.     

P141-T A New Array Format for Protein Kinase Substrate Determination

Peptide arrays are useful tools to characterize antibodies, enzyme substrates or sequence specificities of interaction partners with given peptide sequences (e.g., SH2, SH3, MH2 and other domains). Here we present a new method¹ that allows production of hundreds of identical peptide arrays from a single synthesis run on modified, individual cellulose-disks. The disks are dissolved in the acid cleavage-mixture after synthesis and the resulting solutions of peptide-cellulose-conjugates are then spotted onto multiple slides by conventional spotting techniques. As application example we show results obtained with arrays of kinase substrate libraries and various consensus sequences of known kinase targets. These arrays can be used with different detection methods to profile known and unknown kinases for their substrate specificity.The new arrays are derived from the the well known SPOT method² but offer several major improvements: A smaller volume of sample (only 100 μL) is needed for incubation, and a high number of identical copies of the arrays enables large scale, parallel screening experiments. The cost of an individual array is considerably lower than that of a SPOT membrane. Unlike DNA hybridization, protein-protein interactions frequently suffer from low binding affinities. The new cellulose substrate with peptides linked to it generates a three dimensional scaffold on the array support with a peptide loading exceeding that of a monolayer by a factor of 100. The high peptide density of the spots should be advantageous to identify protein-interaction sites, even if their binding constants are low.

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Detrended correspondence analysis: An improved ordination technique

Summary Detrended correspondence analysis (DCA) is an improvement upon the reciprocal averaging (RA) ordination technique. RA has two main faults: the second axis is often an arch or horseshoe distortion of the first axis, and distances in the ordination space do not have a consistent meaning in terms of compositional change (in particular, distances at the ends of the first RA axis are compressed relative to the middle). DCA corrects these two faults. Tests with simulated and field data show DCA superior to RA and to nonmetric multidimensional sealing in giving clear, interpretable results. DCA has several advantages. (a) Its performance is the best of the ordination techniques tested, and both species and sample ordinations are produced simultaneously. (b) The axes are scaled in standard deviation units with a definite meaning, (c) As implemented in a FORTRAN program called DECORANA, computing time rises only linearly with the amount of data analyzed, and only positive entries in the data matrix are stored in memory, so very large data sets present no difficulty. However, DCA has limitations, making it best to remove extreme outliers and discontinuities prior to analysis. DCA consistently gives the most interpretable ordination results, but as always the interpretation of results remains a matter of ecological insight and is improved by field experience and by integration of supplementary environmental data for the vegetation sample sites.This research was supported by the Institute of Terrestrial Ecology, Bangor, Wales, and by a grant from the National Science Foundation to R.H. Whittaker. We thank R.H. Whittaker for encouragement and comments, S.B. Singer for assistance with the Cornell computer, and H.J.B. Birks, S.R. Sabo, T.C.E. Wells, and R.H. Whittaker for data sets used for ordination tests.     

Pattern of species dominance and factors affecting community composition in areas deforested due to air pollution

Vegetation of mountain areas affected by SO₂ pollution (Kruné hory Mts., Czech Republic) was analysed using multivariate methods. Communities with prevailing species Calamagrostis villosa, a rhizomatous grass expanding into deforested sites, were sampled by Braun-Blanquet relevé method. Canonical correspondence analysis was used to assess the effect of environmental variables (soil removal, deforestation, and shading). To test the effects of light, moisture, soil acidity and nitrogen, mean sample indicator values were correlated a posteriori with sample axes on ordination scores. Light, soil acidity, moisture, and site history (in terms of past deforestation and soil removal applied in reclamation procedures) were found to be the main factors responsible for the community composition. Nitrogen level had not a significant effect on the community composition. When analyzing the whole data set, i.e. including also remnants of natural spruce forests, light was the factor affecting at most the composition of communities. Within the bare spot vegetation, if treated separately, the highest variation was found along the soil acidity/moisture gradient. The effect of soil removal was only obvious at early successional stages. Species diversity increased with moisture and decreased with soil acidity. Species exhibiting S- and/or R-strategy are successful on extremely acid soils whereas forbs present in bare spots appear to be supported by disturbances.     

Carbohydrate metabolism and transport in Bacillus subtilis. A study of ctr mutations

Summary Indirect ultraviolet induction of prophage occurs when lysogenic E. coli K12 cells are mated with ultraviolet-irradiated donor strains carrying a transmissible episome such as F lac ⁺. Indirect induction occurs in wild type, uvrA, or recB recipient lysogens, but not in recA lysogens. When nonpermissive lysogens carrying prophages susO or susP are similarly mated, the defective prophages are induced and indirect curing takes place.Although indirect induction is independent of the capacity of the lysogen for repair by pyrimidine dimer excision, indirect curing (and hence indirect induction) is subject to photoreactivation when the recipient lysogen is exposed to visible light after mating. This confirms that the structure initiating indirect ultraviolet induction is a damaged transferred episome consisting of one DNA strand containing ultraviolet photoproducts and a newly synthesized discontinuous DNA strand such that pyrimidine dimers remain in single-stranded regions.F^- lac ⁺ recombinants are formed in either nonlysogenic or lysogenic Lac^- cells receiving damaged F lac ⁺ episomes from ultraviolet irradiated F lac ⁺ donors. prophage induction occurs more frequently in zygotes that form Lac⁺ recombinants than in zygotes that remain Lac^-. In contrast, cells receiving intact (undamaged) episomes are converted to F lac ⁺ secondary donors, but are rarely induced or cured.     

Composition and species diversity of pine-wiregrass savannas of the Green Swamp,North Carolina

Fire-maintained, species-rich pine-wiregrass savannas in the Green Swamp, North Carolina were sampled over their natural range of environmental conditions and fire frequencies. Species composition, species richness, diversity (Exp H′, 1/C), and aboveground production were documented and fertilization experiments conducted to assess possible mechanisms for the maintenance of high species diversity in these communities. Although savanna composition varies continuously, DECORANA ordination and TWINSPAN classification of 21 sites facilitated recognition of 3 community types: dry, mesic, and wet savannas. These savannas are remarkably species-rich with up to 42 species/0.25 m² and 84 species/625 m². Maximum richness occurred on mesic, annually burned sites. Aboveground production, reported as peak standing crop, was only 293 g · m^?2 on a frequently burned mesic savanna but was significantly higher (375 g · m^?2) on an infrequently burned mesic site. Production values from fertilized high and low fire frequency sites were equivalent. Monthly harvest samples showed that savanna biomass composition by species groups did not vary seasonally, but within groups the relative importance of species showed clear phenological progressions. The variation in species richness with fire frequency is consistent with non-equilibrium theories of species diversity, while phenological variation in production among similar species and the changing species composition across the moisture gradient suggest the importance of equilibrium processes for maintenance of savanna diversity.     

A new triple-resonance experiment for the sequential assignment of backbone resonances in proteins

Summary A new protocol is described for obtaining intraresidual and sequential correlations between carbonyl carbons and amide ¹H and ¹⁵N resonances of amino acids. Frequency labeling of ¹³CO spins occurs during a period required for the ¹³C-¹⁵N polarization transfer, leading to an optimized transfer efficiency. In a four-dimensional version of the experiment, ¹³C chemical shifts are used to improve the dispersion of signals. The resonance frequencies of all backbone nuclei can be detected in a 3D variant in which cross peaks are split along two frequency axes. This pulse scheme is the equivalent of a five-dimensional experiment. The novel pulse sequences are applied to flavodoxin from Desulfovibrio vulgaris.     

Maturation and germination of Phaseolus vulgaris embryonic axes in culture

In this study of embryo development in Phaseolus vulgaris L., we found that immature embryonic axes placed in culture show a growth lag before germinating. The length of this lag phase varies according to axis age at excision, but is not affected by transfer to fresh medium, alteration of sucrose concentration between 0.5 and 2%, or whether the culture medium is liquid or agar-solidified. The lag phase was shortened by both actinomycin D and cordycepin treatment, and by treatment with 10^-5 to 10^-6 M benzyladenine. The effect of abscisic acid (ABA) varied with concentration: below a certain level, it had no effect on the lag phase, but above that level it inhibited, germination. This threshold concentration was 10^-7 M for 20-d-old axes but increased to 10^-5 M by the time the axes were 32 to 34 d old. To determine whether the axes were continuing their embryonic development during the lag phase, we tested them for desiccation-tolerance and for synthesis of phaseolin, a seed storage protein which is specific for embryos of P. vulgaris. The ability to germinate after rapid desiccation was acquired by axes at 26 d past anthesis; when axes younger than this were placed in culture, they developed desiccation-tolerance during the lag phase of growth, indicating that they were continuing embryonic maturation. Phaseolin was present in isolated axes, although at lower levels than in cotyledons. It accumulated during axis development in parallel with total protein, staying at about 1% of total protein content. When isolated immature axes were pulsed with ³H-or ¹⁴C-amino acids, they incorporated label into phaseolin, shown by precipitation with anti-phaseolin antibody. Isolated axes from mature seeds, however, did not synthesize detectable amounts of phaseolin. Immature axes cultured in vitro for a period of one to several days continued synthesizing phaseolin until the day prior to visible germination. Treatment of cultured axes with ABA increased the amount of precursor amino acids incorporated into protein, but had a small or no effect on the relative proportion of phaseolin synthesized. We conclude that P. vulgaris axes in culture continue to develop embryonically for a period of time which seems to be under intrinisc control by the axis. This contrasts with precocious germanation, a pattern of embryo behavior seen in many other species. When such embryos are excised from seeds while immature and placed in culture, they switch promptly from embryo development into germination. If ABA or water stress is responsible for preventing precocious germination, it may be that a high level of ABA is maintained or synthesized internally by embryonic axes of Phaseolus, while in other embryos the maternal environment supplies ABA and/or causes water stress.Abbreviations ABA Abscisic acid - BA benzyladenine     

Factors controlling the distribution of vascular and non-vascular epiphytes in the northern Andes

The epiphytic vegetation on host trees along an altitudinal transect on the west slope of the Central Cordillera in Colombia was sampled. Bark-type restricted sampling comprised four full-grown forest trees, not necessarily four species, at altitudinal intervals of c. 200 meters from 1000 to 4130 m a.s.l. and included the canopy. Both vascular and non-vascular epiphytes, the latter often more abundant in the montane rain forest, were included in the analyses. Using a method of direct gradient analysis, canonical correspondence analysis, the variation explained by various environmental variables could be discriminated from a great amount of variation that seemed not related to any ecological factor. To a large extent, the randomness in propagule supply appears to determine the floristic composition on branch/trunk segments. The grouping of relevés in a phytosociological analysis concurred with a clustering of samples in an ordination diagram of the first two extracted constrained axes. The sample scores on these two axes were strongly correlated with the complex variables altitude and height within the host tree. Specialists and generalists with respect to the two variables were defined based on tolerances provided by the canonical correspondence analysis as was the position of species on the gradients involved. Independently from any of the other variables entered, a relation between the epiphytic vegetation and host species was detected, particularly in the case of Brunellia occidentalis, a fast growing tree species of higher altitude. No relation between chemical characteristics of suspended soil in the Upper Montane Rain forest and its supporting species could be demonstrated.     

Insect food preferences analysed using 13C/12C ratios

Summary Stable carbon isotope ratio analysis is a powerful technique in tracing ecosystem carbon flows, especially those between primary and secondary producers. The distinctive ¹³C/¹²C ratios of plant species tend to pass along the food chain with little further fractionation, hence the stable carbon isotope composition of an animal is an important clue to what it has eaten. We compared the stable carbon isotope composition of plants and insects in an old field in Georgia. Of the dominant plants in the old field, 6 were C₄ species and had ¹³C¹ values of-10.9 to 12.9, and 7 were C₃ species with values of-27.3 to-29.1. Insects known to be feeding on only one plant species had ¹³C values within 1 of the isotopic composition of the plant. Wasp larvae parasitizing two insect species had ¹³C values 1.3 and 1.7 higher than that of the food plant. A variety of insects of unknown food habits collected on monospecific and mixed species plant stands in the old field had ¹³C values ranging from-10.1 to-30.0. Two species of leafhopper and a grasshopper had isotopic compositions within the range of C₄ plant values; a tortoise beetle and a lace bug had isotopic compositions within C₃ plant values. Other insects had intermediate ¹³C values, suggesting a mixed diet composed of both C₃ and C₄ plants. The carbon isotopic ratios of field collected insects appears to be a useful qualitative indicator of their feeding preference.     

Beetles (Coleoptera) on brownfield sites in England: An important conservation resource?

A total of 78 brownfield (post-industrial and urban) sites were surveyed for beetles between 1991 and 2001 throughout England using pitfall traps. The distribution of ground, rove and phytophagous beetle assemblages was investigated using ordination and classification analyses. Site drainage and vegetation cover had a profound effect on the distribution of ground and rove beetle assemblages but site location was also important for phytophagous beetle assemblages. A total of 182 records of 46 nationally rare and scarce species (16 ground, 10 rove and 20 phytophagous species) were generated. A number of these species are more usually associated with other, more natural habitats such as riverine sediments, sandy heaths and chalk grassland. Brownfield sites provide habitat conditions similar to more natural habitats and they may help maintain populations of some rare and scarce species. The results indicate that brownfield sites are important habitats for beetles and there is evidence that the situation is similar for other invertebrate groups. There should be no further assumptions that post-industrial and urban sites have no conservation interest.