The redistribution of soil water by tree root systems

Plant roots transfer water between soil layers of different water potential thereby significantly affecting the distribution and availability of water in the soil profile. We used a modification of the heat pulse method to measure sap flow in roots of Grevillea robusta and Eucalyptus camaldulensis and demonstrated a redistribution of soil water from deeper in the profile to dry surface horizons by the root system. This phenomenon, termed “hydraulic lift” has been reported previously. However, we also demonstrated that after the surface soils were rewetted at the break of season, water was transported by roots from the surface to deeper soil horizons – the reverse of the “hydraulic lift” behaviour described for other woody species. We suggest that “hydraulic redistribution” of water in tree roots is significant in maintaining root viability, facilitating root growth in dry soils and modifying resource availability. Received: 26 January 1998 / Accepted: 15 April 1998     

Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: An avian case study

Whole mitochondrial genome sequences have been used in studies of animal phylogeny for two decades, and current technologies make them ever more available, but methods for their analysis are lagging and best practices have not been established. Most studies ignore variation in base composition and evolutionary rate within the mitogenome that can bias phylogenetic inference, or attempt to avoid it by excluding parts of the mitogenome from analysis. In contrast, partitioned analyses accommodate heterogeneity, without discarding data, by applying separate evolutionary models to differing portions of the mitogenome. To facilitate use of complete mitogenomic sequences in phylogenetics, we (1) suggest a set of categories for dividing mitogenomic datasets into subsets, (2) explore differences in evolutionary dynamics among those subsets, and (3) apply a method for combining data subsets with similar properties to produce effective and efficient partitioning schemes. We demonstrate these procedures with a case study, using the mitogenomes of species in the grackles and allies clade of New World blackbirds (Icteridae). We found that the most useful categories for partitioning were codon position, RNA secondary structure pairing, and the coding/noncoding distinction, and that a scheme with nine data groups outperformed all of the more complex alternatives (up to 44 data groups) that we tested. As hoped, we found that analyses using whole mitogenomic sequences yielded much better-resolved and more strongly-supported hypotheses of the phylogenetic history of that locus than did a conventional 2-kilobase sample (i.e. sequences of the cytochrome b and ND2 genes). Mitogenomes have much untapped potential for phylogenetics, especially of birds, a taxon for which they have been little exploited except in investigations of ordinal-level relationships.     

Inferring the root of a phylogenetic tree

Phylogenetic trees can be rooted by a number of criteria. Here, we introduce a Bayesian method for inferring the root of a phylogenetic tree by using one of several criteria: the outgroup, molecular clock, and nonreversible model of DNA substitution. We perform simulation analyses to examine the relative ability of these three criteria to correctly identify the root of the tree. The outgroup and molecular clock criteria were best able to identify the root of the tree, whereas the nonreversible model was able to identify the root only when the substitution process was highly nonreversible. We also examined the performance of the criteria for a tree of four species for which the topology and root position are well supported. Results of the analyses of these data are consistent with the simulation results.     

Stereotyped pruning of long hippocampal axon branches triggered by retraction inducers of the semaphorin family

Like naturally occurring neuronal cell death, stereotyped pruning of long axon branches to temporary targets is a widespread regressive phenomenon in the developing mammalian brain that helps sculpt the pattern of neuronal connections. The mechanisms controlling stereotyped pruning are, however, poorly understood. Here, we provide evidence that semaphorins, activating the Plexin-A3 receptor, function as retraction inducers to trigger-stereotyped pruning of specific hippocampal mossy fiber and pyramidal axon branches. Both pruning events are defective in Plexin-A3 mutants, reflecting a cell-autonomous requirement for Plexin-A3. The distribution of mRNAs for Sema3F and Sema3A makes them candidates for triggering the pruning. In vitro, hippocampal neurons respond to semaphorins by retracting axon branches. These results implicate semaphorins as retraction inducers controlling stereotyped pruning in the mammalian brain.     

Relation between diameter and flow in branches of the bronchial tree

Two methods are described for calculating the value of the exponentx in the equation flow =k×diameter ^x , as pertaining to a branch of the bronchial tree. In the lungs from three humans, two dogs, one hamster, and one rat mean values ofx between 2.419 and 2.903 were found. They lie within the range of 2.333 to 3.0 predicted by the analysis of Uylings (Bull. Math. Biol. 39, 501–519, 1977).     

Angles of branching and diameters of branches in the human bronchial tree

The principle of minimal work requires that the conducting airways of the human lung should have a maximum radius for minimal resistance to gas flow. At the same time there is a requirement that the airways should have a minimal volume for economy of space. These two opposing requirements have been investigated mathematically, and a method for calculating the angle of branching which produces minimal volume has been derived. The relationship of the radii of the parent and daughter branches to produce minimal resistance has been similarly defined. By measurement of a bronchial cast from a human lung the extent to which the predicted optimum structure is realized in practice has been shown. The change in structure associated with change of function at the transition from conducting airway to diffusion zone has been demonstrated.     

Routing of transported materials in the dorsal root and nerve fiber branches of the dorsal root ganglion

After injection of the L7 dorsal root ganglion with ³H-leucine, fast axoplasmic transport carries some 3–5 × more labeled materials down the sensory fibers branches entering the sciatic nerve as compared to the dorsal root fiber branches of the neurons. Freeze-substitution preparations taken from the two sides of the lumbar seventh dorsal root ganglia of cats and monkeys showed little difference in the histograms of nerve fiber diameters of the sensory nerve fiber branch of these neurons as compared to the dorsal root fiber branches. A similar density of microtubules and of neurofilaments in the dorsal root and sensory nerve fiber branches over a wide range of fiber diameters was found in electron micrograph preparations. In the absence of an anatomical difference in the fibers to account for the asymmetrical outflow, a functional explanation based on the transport filament model was advanced.     

Diameters, generations, and orders of branches in the bronchial tree

Studies of bronchial tree data by West et al. (J. Appl. Physiol. 60: 1089-1097, 1986) have shown that plots of mean diameter against generation, using log-log scales, can be represented by a power function with harmonic modulations. Other studies have shown that the mean diameter of the airways is exponentially related to order of branching. This paper demonstrates that both observations are compatible with a fractal model of branching, and because airway branching is fractal, this may explain why both are also true of the bronchial tree. Furthermore, the exponential relationship of mean diameter with generation in the larger airways, demonstrated by Weibel, is shown to result from the exponential relation of diameter with order in the fractal model.     

Routing of transported materials in the dorsal root and nerve fiber branches of the dorsal root ganglion.

After injection of the L7 dorsal root ganglion with 3H-leucine, fast axoplasmic transport carries some 3--5 x more labeled materials down the sensory fibers branches entering the sciatic nerve as compared to the dorsal root fiber branches of the neurons. Freeze-substitution preparations taken from the two sides of the lumbar seventh dorsal root ganglia of cats and monkeys showed little difference in the histograms of nerve fiber diameters of the sensory nerve fiber branch of these neurons as compared to the dorsal root fiber branches. A similar density of microtubules and of neurofilaments in the dorsal root and sensory nerve fiber branches over a wide range of fiber diameters was found in electron micrograph preparations. In the absence of an anatomical difference in the fibers to account for the asymmetrical outflow, a functional explanation based on the transport filament model was advanced.     

The root of the phylogenetic tree of human populations

Although African populations have been shown to be most divergent from any other human populations, it has been difficult to establish the root of the phylogenetic tree of human populations since the rate of evolutionary change may vary from population to population owing to the fluctuation of population size and other factors. However, the root can be determined by using the chimpanzee as an outgroup and by employing proper statistical methods. Using this strategy, we constructed phylogenetic trees of human populations for five different sets of gene frequency data. The data sets used were two sets of microsatellite loci data (25 and 8 loci, respectively), restriction fragment length polymorphism (RFLP) data (79 loci), protein polymorphism data (15 loci), and Alu insertion frequency data (4 loci). All these data sets showed that the root is located in the branch connecting African and non-African populations, and in the four data sets the root was established at a significant level. These results indicate that Africans are the first group of people that split from the rest of the human populations.      

The use of tree root suckers to estimate root water potential

Abstract. This paper describes a simple method to estimate the root water potential of trees using the root suckers as xylemic probes. On the day before the water potentials were measured in pressure chamber, all the sucker shoots were enclosed in plastic bags to prevent transpiration. Under the premise that the potential at two points in a flow system would be equal if there were no flux between these points, the sucker shoot water potential estimates the root water potential. The results are not dependent on the sucker architecture, are consistent with the soil-plant-atmosphere continuum concept, and are supported by psychrometric measurements.     

Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features

We report complete mitochondrial (mt) genomes for a penguin (little blue, Eudyptula minor) and a goose (greater white-fronted, Anser albifrons). A revised annotation of avian and reptile mt genomes has been carried out, which improves consistency of labeling gene start and stop positions. In conjunction with this, a summary of mt gene features is presented and a number of conserved patterns and interesting differences identified. The protein-coding genes from the two new genomes were analysed together with those from 17 other birds plus outgroup (reptile) taxa. The unrooted amino acid tree from 19 avian genomes was locally stable with many high bootstrap values using several maximum likelihood methods. In particular, Anseriformes (goose and duck) grouped strongly with Galliformes (chicken) to form Gallianseres, while the penguin paired firmly with the stork. The position where the outgroup joined the avian tree varied with the combination of outgroup taxa used. The three best supported positions of the root were passerine, but the traditional rooting position between paleognaths and neognaths could not be excluded.     

Modeling of Cs-137 vertical soil transfer by a tree root system

A model of 137Cs vertical soil transport by a tree root system is presented. As distinct from other models the radionuclide root uptake is described as a reversible process and depth distribution of roots is given as a function of time. The model was used for prediction of 137Cs release from a surface disposal site located in a territory with conditions similar to that in the Chernobyl NPP exclusion zone. Prediction indicates that during several decades 137Cs transport from the waste layer by the root system of pine can lead to significant contamination of the soil surface due to needles fallout and, probably, ionic leakage from roots.