CENTRAL MOMENTS AND PROBABILITY DISTRIBUTION OF COLLESS'S COEFFICIENT OF TREE IMBALANCE

The great increase in the number of phylogenetic studies of a wide variety of organisms in recent decades has focused considerable attention on the balance of phylogenetic trees—the degree to which sister clades within a tree tend to be of equal size—for at least two reasons: (1) the degree of balance of a tree may affect the accuracy of estimates of it; (2) the degree of balance, or imbalance, of a tree may reveal something about the macroevolutionary processes that produced it. In particular, variation among lineages in rates of speciation or extinction is expected to produce trees that are less balanced than those that result from phylogenetic evolution in which each extant species of a group has the same probability of speciation or extinction. Several coefficients for measuring the balance or imbalance of phylogenetic trees have been proposed. I focused on Colless's coefficient of imbalance (7) for its mathematical tractability and ease of interpretation. Earlier work on this statistic produced exact methods only for calculating the expected value. In those studies, the variance and confidence limits, which are necessary for testing the departure of observed values of I from the expected, were estimated by Monte Carlo simulation. I developed recursion equations that allow exact calculation of the mean, variance, skewness, and complete probability distribution of I for two different probability-generating models for bifurcating tree shapes. The Equal-Rates Markov (ERM) model assumes that trees grow by the random speciation and extinction of extant species, with all species that are extant at a given time having the same probability of speciation or extinction. The Equal Probability (EP) model assumes that all possible labeled trees for a given number of terminal taxa have the same probability of occurring. Examples illustrate how these theoretically derived probabilities and parameters may be used to test whether the evolution of a monophyletic group or set of monophyletic groups has proceeded according to a Markov model with equal rates of speciation and extinction among species, that is, whether there has been significant variation among lineages in expected rates of speciation or extinction.     

Phylogenetic analysis of the stress-70 protein family

The eukaryotic cyto-/nucleoplasmatic 70-kDa heat-shock protein (HSP70) has homologues in the endoplasmic reticulum as well as in bacteria, mitochondria, and plastids. We selected a representative subset from the large number of sequenced stress-70 family members which covers all known branches of the protein family and calculated and manually improved an alignment. Here we present the consensus sequence of the aligned proteins and putative nuclear localization signals (NLS) in the eukaryotic HSP70 homologues. The phylogenetic relationships of the stress-70 group family members were estimated by use of different computation methods. We present a phylogenetic tree containing all known stress-70 subfamilies and demonstrate the usefulness of stress-70 protein sequences for the estimation of intertaxonic phylogeny. Correspondence to: S.A. Reusing     

P-type ATPases of eukaryotes and bacteria: Sequence analyses and construction of phylogenetic trees

The amino acid sequences of 47 P-type ATPases from several eukaryotic and bacterial kingdoms were divided into three structural segments based on individual hydropathy profiles. Each homologous segment was (1) multiply aligned and functionally evaluated, (2) statistically analyzed to determine the degrees of sequence similarity, and (3) used for the construction of parsimonious phylogenetic trees. The results show that all of the P-type ATPases analyzed comprise a single family with four major clusters correlating with their cation specificities and biological sources as follows: cluster 1: Ca²⁺-transporting ATPases; cluster 2: Na⁺- and gastric H⁺-ATPases; cluster 3: plasma membrane H⁺-translocating ATPases of plants, fungi, and lower eukaryotes; and cluster 4: all but one of the bacterial P-type ATPases (specific for K⁺, Cd²⁺, Cu²⁺ and an unknown cation). The one bacterial exception to this general pattern was the Mg²⁺-ATPase of Salmonella typhimurium, which clustered with the eukaryotic sequences. Although exceptions were noted, the similarities of the phylogenetic trees derived from the three segments analyzed led to the probability that the N-terminal segments 1 and the centrally localized segments 2 evolved from a single primordial ATPase which existed prior to the divergence of eukaryotes from prokaryotes. By contrast, the C-terminal segments 3 appear to be eukaryotic specific, are not found in similar form in any of the prokaryotic enzymes, and are not all demonstrably homologous among the eukaryotic enzymes. These C-terminal domains may therefore have either arisen after the divergence of eukaryotes from prokaryotes or exhibited more rapid sequence divergence than either segment 1 or 2, thus masking their common origin. The relative rates of evolutionary divergence for the three segments were determined to be segment 2 < segment 1 < segment 3. Correlative functional analyses of the most conserved regions of these ATPases, based on published site-specific mutagenesis data, provided preliminary evidence for their functional roles in the transport mechanism. Our studies define the structural and evolutionary relationships among the P-type ATPases. They should provide a guide for the design of future studies of structure-function relationships employing molecular genetic, biochemical, and biophysical techniques. Correspondence to: M.H. Saier, Jr.     

Strong synergistic effects of gibberellins with the synthetic cytokinin N-(2-chloro-4-pyridyl)-N-phenylurea on parthenocarpic fruit set and some other fruit characteristics of apple

The induction of parthenocarpic fruit set was investigated using the apple cvs. Golden Delicious and Jonagold. The gibberellins GA₃, GA₄, GA₅ and GA₇ and the synthetic phenylurea-type cytokinin CPPU (N-(2-chloro-4-pyridyl)-N-phenylurea), were applied alone and in combination to unpollinated flowers at the end of petal fall. Gibberellins induced only a marginal final set of parthenocarpic fruits. CPPU sprays were more effective, particularly in the first year. When applied in combination, CPPU and gibberellins had a positive synergistic effect on parthenocarpic fruit set and fruit size, but a negative effect on flower induction the next year. After CPPU + GA sprays, percent fruit set was similar, or greater, compared to natural pollinated trees. The parthenocarpic fruits induced by CPPU + GA had an increased length to diameter ratio. CPPU stimulated, and GA₄ and GA₇ reduced, the russeting of the parthenocarpic fruits. The internal quality of the fruits was hardly affected, but Ca-deficiency symptoms occurred more frequently in parthenocarpic fruits.     

Phylogenetic relationships of the garter snakes based on DNA sequence and allozyme variation

We estimated phylogenetic relationships among 26 species of garter snakes (genus Thamnophis ) using allozyme and mitochondrial cytochrome b gene nucleotide sequence variation. Parsimony analyses of the two data sets give substantially different estimates of phylogeny. Several lines of evidence indicate that much of this conflict is due to error associated with the restricted number of characters in each data set. Such sampling error may be reduced by combining all the characters; we therefore present an estimate of phylogeny based on parsimony analysis of all the data combined. All our analyses support several conclusions in conflict with previous views: a very distant relationship between T.errans and T. elegans , non-monophyly of the elegans group (even excluding T: errans ), and nesting of the form validus (previously considered a member of the genus Nerodia ) within Thamnophis.
The combined analysis gives an almost fully resolved tree. However, bootstrapping indicates only weak support for many clades in this tree. Furthermore, paraphyly of the assemblages of cytochrome b gene lineages within T. elegans and T. radix indicate the potential for discordance between the mitochondrial DNA (mtDNA) and species phylogenies through the sorting of ancestral mtDNA polymorphisms. These problems suggest the need for assaying additional characters, especially ones likely to be independent of those used in the present study.     

Water relations,gas exchange,and growth of resprouts and mature plant shoots of Arbutus unedo L. and Quercus ilex L.

Resprout and mature plant shoot growth, leaf water status and gas exchange behavior, tissue nutrient content, flowering, and production were studied for co-occurring shallow-rooted (Arbutus unedo L.) and deeprooted (Quercus ilex L.) Mediterranean tree species at the Collserola Natural Park in Northeast Spain Resprouts showed higher growth rates than mature plant shoots. During fall, no differences in eco-physiological performance of leaves were found, but mobilization of carbohydrates from burls strongly stimulated growth of fall resprouts compared to spring resprouts, despite low exposed leaf area of the fall shoots. During summer drought, resprouts exhibited improved water status and carbon fixation compared to mature plant shoots. Shoot growth of Q. ilex was apparently extended due to deep rooting so that initial slower growth during spring and early summer as compared to A. unedo was compensated. Tissue nutrient contents varied only slightly and are postulated to be of minor importance in controlling rate of shoot growth, perhaps due to the relatively fertile soil of the site. Fall flowering appeared to inhibit fall shoot growth in A. unedo, but did not occur in Q. ilex. The results demonstrate that comparative examinations utilizing vegetation elements with differing morphological and physiological adaptations can be used to analyze relatively complex phenomena related to resprouting behavior. The studies provide an important multi-dimensional background framework for further studies of resprouting in the European Mediterranean region.     

Woody-tissue respiration for Simarouba amara and Minquartia guianensis,two tropical wet forest trees with different growth habits

We measured CO₂ efflux from stems of two tropical wet forest trees, both found in the canopy, but with very different growth habits. The species were Simarouba amara, a fast-growing species associated with gaps in old-growth forest and abundant in secondary forest, and Minquartia guianensis, a slow-growing species tolerant of low-light conditions in old-growth forest. Per unit of bole surface, CO₂ efflux averaged 1.24 mol m^–2 s^–1 for Simarouba and 0.83 mol m^–2s^–1 for Minquartia. CO₂ efflux was highly correlated with annual wood production (r ²=0.65), but only weakly correlated with stem diameter (r ²=0.22). We also partitioned the CO₂ efflux into the functional components of construction and maintenance respiration. Construction respiration was estimated from annual stem dry matter production and maintenance respiration by subtracting construction respiration from the instantaneous CO₂ flux. Estimated maintenance respiration was linearly related to sapwood volume (39.6 mol m^–3s^–1 at 24.6° C, r ²=0.58), with no difference in the rate for the two species. Maintenance respiration per unit of sapwood volume for these tropical wet forest trees was roughly twice that of temperate conifers. A model combining construction and maintenance respiration estimated CO₂ very well for these species (r ²=0.85). For our sample, maintenance respiration was 54% of the total CO₂ efflux for Simarouba and 82% for Minquartia. For our sample, sapwood volume averaged 23% of stem volume when weighted by tree size, or 40% with no size weighting. Using these fractions, and a published estimate of aboveground dry-matter production, we estimate the annual cost of woody tissue respiration for primary forest at La Selva to be 220 or 350 g C m^–2 year^–1, depending on the assumed sapwood volume. These costs are estimated to be less than 13% of the gross production for the forest.     

Transpiration measurements on apple trees with an improved stem heat balance method

Since the late eighties a handy and user-friendly sap flow meter (Dynagage®) is on the market which can quantify 0205 the sap flow through intact plant stems, based on the stem heat balance method. The documentation about its accuracy and reliability, however, is still too limited to use it as a standard method in field experiments with apple trees. We therefore tested this commercial system on potted apple trees (Malus domestica L.; cv. Red Elstar and Jonagold; on rootstock M9 vf) with stem diameters of 1.8 to 4 cm. The measured sap flow was compared with mass loss measured by an automated balance, supposing the total mass loss of the trees was equal to the water loss by transpiration. The results revealed three major problems:

Distribution of soil invertase in relation to the root systems ofPicea sitchensis (Bong.) Carr. andAcer pseudoplatanus L. during development of young plants

A method is described for sampling rhizosphere soil under newly establishedPicea sitchensis andAcer pseudoplatanus. The technique involves taking soil samples to a depth of 150 mm at 100 mm intervals along transects, each 45° from its neighbour, radiating from the base of the stem. Invertase activities were measured in the soil samples and compared to their activities in fallow and rhizosphere soils. When the field soil was dry, the tree root systems were carefully excavated to retain as many fine roots as possible. The distribution of the soil invertase was matched to the spatial distribution of the roots showing the precise position of the rhizosphere relative to the initial blind soil sampling. Statistics were applied to derive equations for calculating the percentage enzyme activity relative to that found in rhizosphere soil at various locations radiating from the base of the stem. This information was subsequently applied to soil sampled under trees of the same age as those excavated to give a non-destructive method for sampling rhizosphere soil routinely from under a large number of trees.     

Recovery of transgenic trees after electroporation of poplar protoplasts

Protoplasts from leaflets ofin vitro cuttings were electroporated in osmotically adjusted and buffered solutions containing plasmid DNA: pABD1, carrying thenptII gene for resistance to neomycin; pGH1, carrying a mutant acetolactate synthase gene,als, for resistance to sulfonylurea; and pGSFR781A, carrying a synthetic phosphinothricin acetyltransferase (pat) for resistance to phosphinothricin (Basta). Gene transfer was repeatedly efficient, without use of carrier DNA, in the range of one transformant for 10⁵ to 10⁴ protoplast-derived cell colonies. This was probably due to the high plating efficiency (30%) of protoplasts in our culture process. Selection for expression of foreign genes was applied in liquid medium and repeatedly achieved with 30 M paromomycin for NPTII, 200 nM chlorsulfuron for the mutant ALS ofArabidopsis and 25 M phosphinothricin for PAT expression. Integration of foreign genes into genomic DNA of resistant poplar trees was demonstrated by Southern blot hybridizations, which revealed that for some transformants practically no other part of the vector plasmid than the selected gene was integrated.Effective processes for protoplast culture, efficient selection at the cell colony stage and gene transfer will provide new possibilities in poplar breeding.