A Technique to Analyse Succession Data from Permanent Plots

IIntroductionSuccessionstudyIsaspeclalfleldInvegetationecology（Greig—Smith1983）．ItreferstocummulatlvechangeInvegetationovertime．Florl幻IcgradientsIndicativeofsuccessionaltrendsmayemergefromconventionalordinationIfextrinsic！nformatlonallowsthemtobel－dentlfledassuch．Inthespedalcaseofforestvegetation,forInstance,Informationonthesize—classesoftreespedespresentmaypermitsuccessionalgradientslobeldentlfleddirectly（Goff1968,Carleton＆Maycock1978）．Fewauthors,however,haveattempted…     

Models for relating pH measurements in water and calcium chloride for a wide range of pH,soil types and depths

Soil pH is commonly measured in water (pHw) or 0.01 M CaCl₂ (pH_Ca). The need to convert between these methods has led to the publication of linear, quadratic and cubic polynomial relationships for limited suites of soils. Concerns over the applicability of such relationships when mapping a wide range of soils and pH led to the establishment of a database of pH_W and pH_Ca values on each of 7894 samples from soil survey and field experimental sites in Queensland. The relationship between pH_W and pH_Ca across all soils was investigated and preliminary results examining the effect of soil depth and soil type on the relationship are presented.For all soils and depths, a linear regression accounted for 93.2% of the variation but did not predict pH_Ca well at very high or low pH_W values. The inclusion of second and third powers of pH_W accounted for significantly more of the variation (R²=0.94) in pH_Ca and the resultant curve matched the data better at high and low pH.Analysis of surface, sub-surface and subsoil groupings did not reveal any appreciable differences in the relationship between pH_W and pH_Ca attributable to depth. In contrast, differences in the relationship were evident between soil types. Generally, the mildly leached soils had linear relationships, while the weathered soils were distinctly curvilinear at low pH.     

A method for estimating the numbers of synonymous and nonsynonymous substitutions per site

A method for estimating the numbers of synonymous (Ks) and nonsynonymous (Ka) substitutions per site is proposed. The method is based on the Li's (J Mol. Evol. 36:96–99, 1993) and Pamilo and Bianchi's (Mol. Biol. Evol. 10:271–281, 1993) method, but a putative source of bias is solved. It is proposed that the number of synonymous substitutions that are actually transitions or transversions should be computed by separating the twofold degenerate sites into two types of sites, 2S-fold and 2V-fold, where only transitional and transversional substitutions are synonymous, respectively. Kimura's (J. Mol. Evol. 16:111–120, 1980) two-parameter correcting method for multiple substitutions at a site is then applied using the overall observed synonymous transversion frequency to estimate both the numbers of synonymous transversional (Bs) and transitional (As) substitutions per site. This approach, therefore, also minimizes stochastic errors. Computer simulations indicate that the method presented gives more accurate Ks and Ka estimates than the aforementioned methods. Furthermore, the obtention of confidence intervals for divergence estimates by computer simulation is proposed.     

Identification of two Drosophila TGF-β family members in the grasshopper Schistocerca americana

Intercellular signaling molecules of the transforming growth factor- (TGF-) superfamily are required for pattern formation in many multicellular organisms. The decapentaplegic (dpp) gene of Drosophila melanogaster has several developmental roles. To improve our understanding of the evolutionary diversification of this large family we identified dpp in the grasshopper Schistocerca americana. S. americana diverged from D. melanogaster approximately 350 million years ago, utilizes a distinct developmental program, and has a 60-fold-larger genome than D. melanogaster. Our analyses indicate a single dpp locus in D. melanogaster and S. americana, suggesting that dpp copy number does not correlate with increasing genome size. Another TGF- superfamily member, the D. melanogaster gene 60A, is also present in only one copy in each species. Comparison of homologous sequences from D. melanogaster, S. americana, and H. sapiens, representing roughly 900 million years of evolutionary distance, reveals significant constraint on sequence divergence for both dpp and 60A. In the signaling portion of the dpp protein, the amino acid identity between these species exceeds 74%. Our results for the TGF- superfamily are consistent with current hypotheses describing gene duplication and diversification as a frequent response to high levels of selective pressure on individual family members.     

A scanning electron microscope study of Craspedella sp. from the branchial chamber of redclaw crayfish,Cherax quadricarinatus,from Queensland,Australia

Epidermal topography was examined, including papillate ridges, grooves and ciliated sensory papillae of Craspedella sp. from the branchial chamber of redclaw crayfish, Cherax quadricarinatus, from Queensland, Australia. Rhandites were observed to discharge from ducts opening mainly in a small distal region of the ventral epidermis of the three central (of five) tentacles. These regions, devoid of ciliated sensory papillae, serve to adhere the anterior end of the worms during locomotion. Secretions from glands associated with the posterior attachment organ were observed to discharge from pores on the outside region of the ventral surface of the disc.A comparison of various scanning electron microscopy (SEM) fixation techniques showed that (1) hot fixatives at 90 °C provide most information on the largest number of epidermal structures and (2) different fixation regimes highlight different epidermal features.     

Responses of benthic macroinvertebrates in small intermittent streams to silvicultural practices

We examined macroinvertebrate communities in small(0.1-1.0 m²) pools of intermittent streams (alwayscontainingsome water but without perennial flow) with small watersheds(2-6 ha) subjected to five types of forest harvest to assesspotential impacts of the different harvest methods. Bufferstrips10 m wide were left on each side of the streams. Each harvesttreatment was coupled with a similar unharvested referencestand.An incomplete block design included three 0.05 m² vacuumsamples from each treatment paired with three from theadjacentreferences. There was a high degree of similarity amongreferencesfor parameters other than taxonomic composition (e.g.macroinvertebrate density, number of species, Shannondiversity,functional groups, etc.). Statistically significantdifferenceswere found between references and treatments and among harvestmethods but the responses varied among response variables(density,Shannon-Weiner diversity, species composition), differentspeciesassemblages (all invertebrates, chironomids,Ephemeroptera-Plecoptera-Trichoptera [EPT], isopods), andfunctional group categories (shredders, collector-gatherers).Wecollected 56 taxa, 7–16 per site, with low communitysimilarity(mean Jaccards=0.18, mean Bray-Curtis percentdissimilarity=81). The most severe harvest treatmentsresultedin the highest diversities of total invertebrates in thesesmallspring pool communities.     

Elemental composition of seston and nutrient dynamics in the Sea of Marmara

The Sea of Marmara, an intercontinental basin with shallow and narrowstraits, connects the Black and Mediterranean Seas. Data obtained during1991–1996 have permitted the determination of the elementalcomposition of seston in the euphotic zone and the N:P ratio of thesubhalocline waters of the Marmara Sea. Since primary production is alwayslimited to the less saline upper layer (15–20 m), of the Marmara Sea,the subhalocline waters of Mediteranean origin are always rich in nutrients(NO₃ + NO₂ = 8–10 μm, PO₄ = 0.8–1.2 μm) but depleted in dissolvedoxygen (30–50 μm) throughout the basin, yielding an -O_{_2} : N : P ratio of 178 : 9 : 1. Pollution of the surfacewaters since the 60s has modified the subhalocline nutrient chemistryslightly. In the euphotic zone, the N : P ratio of the seston changes from5.9 to 9.5 between the less and more productive periods. Though the biologyof the Marmara has changed significantly during the previous two decades,the close relationship observed between the elemental composition of thesurface seston and the NO₃ : PO₄ ratio of thesubhalocline waters strongly suggests that during the whole year primaryproduction throughout the basin and POM export to the lower layer remainnitrogen-limited. This suggestion needs to be confirmed by bio-assays,biological studies and sediment trap data from the upper subhaloclinedepths. Nonetheless, the counterflows in the Marmara basin possessrelatively low N : P ratios in both dissolved and particulate nutrients andextend as far as the adjacent seas. This revised version was published online in July 2006 with corrections to the Cover Date.     

Uncertain branch lengths, taxonomic sampling error, and the egg to body size allometry in temperate butterflies (Lepidoptera)

The allometry of egg to body size in temperate butterflies, and the relationships between egg size and larval host structure, taxonomy, voltinism, and duration of the egg stage, are investigated using cross-species analysis and the comparative analysis of independent contrasts. In addition, the effect of two sources of uncertainty that may affect continuous data when treated under a statistical, comparative, framework, is assessed: (1) unknown evolutionary distances, and (2) taxonomic representativity (proportion of species of a given taxon, from which data are available). It is suggested that the effects of taxonomic under-representation could be important in comparative, quantitative studies, but this problem may be tempered by means of weighted regression. Under the assumption that taxonomy represents butterfly phylogeny, egg and adult body size are related by negative allometry (i.e. the slope of the line fitted to the logarithmically transformed data is lower than 1.0). However, the precise slope (0.2-0.9) depends on the method used, branch lengths, and taxonomic sampling. There is evidence for a relationship between a species' voltinism and the number of days it spends in the egg stage, as well as between adult butterfly size and the gross structure of the plants used as larval hosts (woody plants or herbs). Egg size proves to be related to foodplant taxonomy, voltinism, and duration of the egg stage when the data are analysed using species means, but these relationships become non-significant when the comparative method is employed.