Year class coexistence or competitive exclusion for strict biennials?

 We consider a discrete time model of semelparous biennial population dynamics. Interactions between individuals are modelled with the aid of an ``environmental' variable I. The impact on and the sensitivity to the environmental condition is age specific. The main result is that competitive exclusion between the year classes is possible as is their coexistence. For moderate values of the basic reproduction ratio R ₀ there is a strict dichotomy: depending on the other parameters we either find competitive exclusion or coexistence. We characterize rather precisely the patterns of age specific impact and sensitivity that lead to either of these outcomes. Received: 13 July 2001 / Revised version: 26 June 2002 / Published online: 19 November 2002 Key words or phrases: Competitive exclusion – Semelparous species – Periodical insects     

Competitive reversals inside ecological reserves: the role of external habitat degradation

 Habitat degradation is the slow – and often subtle – deterioration in habitat quality that accompanies human activities through increases in road density, pesticide use, hunting pressure, etc. Such degradation is of particular concern in fragmented habitats where economic or jurisdictional boundaries rather than ecological ones determine the level of exploitation adjoining habitat patches endure. To examine the consequences habitat degradation might have on species interactions, we posited a patch of pristine habitat surrounded by “matrix” habitat whose degradation level was variable. Using a coupled pair of diffusive Lotka–Volterra competition equations with Robin (mixed) boundary conditions, we modeled the dynamics of two competing species inhabiting the pristine patch and incorporated matrix degradation through a tunable “hostility” parameter representing species’ mortality rates in the matrix. We found that the numerical range of competition coefficients over which one species is the competitive dominant and the other inferior may grow or shrink as matrix quality deteriorates. In some cases, degradation of the exterior habitat would bring about a complete competitive reversal inside the preserve. This result, wherein a formerly inferior species supplants a formerly dominant one – even inside the “protected” remnant patch itself – has policy implications for both nature reserve design and management of human activities outside park boundaries. Received: 30 April 1997     

Morphology and ecology of two new species of Polypleurum (Podostemaceae) from Kerala, India

 Two new species of the Asiatic genus Polypleurum (Podostemaceae – Podostemoideae), Polypleurum prostratum and Polypleurum disciforme from Kerala, India are described. They differ in the shape of the thalloid plant body from the other species of Polypleurum. A key to the species occurring in India is provided. Though sharing the habitat with some other species of the Podostemaceae, the new species inhabit special niches in the rocky riverbed. – The chemical components of the (hard) water in which they grow differ considerably from what is known from black water rivers of the New World. The results thus widen considerably our knowledge of the ecological needs of Podostemaceae. Received December 10, 2002; accepted January 10, 2003 Published online: March 31, 2003     

Bifurcation analysis of an orientational aggregation model

 We consider an integro-differential equation for the evolution of a function f on the circle, describing an orientational aggregation process. In the first part we analyze generic bifurcations of steady-state solutions when a single eigenvalue changes sign. Lyapunov-Schmidt reduction leads to the bifurcation equation which is solved explicitly by formal power series. We prove that these series have positive radius of convergence. Two examples exhibit forward and backward bifurcations, respectively. In the second part we assume that the first and second eigenvalues become positive. Again we use Lyapunov-Schmidt reduction to arrive at the reduced bifurcation system from which we get the bifurcating branches as power series. We calculate the two most important parameters of the reduced system for two examples; one of them has interesting mode interactions which lead to various kinds of time-periodic solutions. Received: 23 April 2001 / Revised version: 29 October 2002 / Published online: 28 February 2003 Key words or phrases: Actin – Cytoskeleton – Orientational Aggregation – Bifurcation Analysis – Mode Interaction – Power Series Expansion     

Words in DNA sequences: some case studies based on their frequency statistics

 One of the critical requirements of data analysis involving large DNA sequences is an effective statistical summarization of those sequences. In this article DNA sequences have been analyzed based on word frequencies. Our analysis focuses on the detection of structural signature of a genome reflected in word frequencies and identification of phylogenetic relationships among different species reflected in the variation of word distributions in their DNA sequences. We have carried out a statistical study of the complete genome of baker's yeast, of various ribosomal RNA sequences from different prokaryotic and eukaryotic organisms and of the full genomes of some bacteriophages. Our exploratory analysis amply demonstrates the usefulness of DNA word frequencies in reducing the dimensionality of large sequences while retaining some of the structural information there that can have biological significance. Some conceptual issues that arise in course of our investigation have been addressed. A few interesting problems related to the statistics of DNA words have been pointed out with some indication of their possible solutions. The work has been partially motivated by the fact that sequence alignment and homology techniques that are quite popular for comparing and analyzing relatively smaller DNA sequences of nearly equal sizes are not applicable to data consisting of large sequences with widely varying sizes, which may contain segments with unknown or no biological functions, and consequently their comparison through functional homology is either impossible or extremely difficult. Received: 15 October 2000 / Revised version: 8 October 2002 Published online: 28 February 2003 Current address: CF186, Salt lake, Calcutta 700064, India Research presented here was supported in part by a grant from Indian Statistical Institute. Key words or phrases: Average linkage clustering – Chernoff's faces – Dendrograms – DNA words – F-ranks of words – F-ratios of words – l ₁-distance – Phylogenetic relationships – Rank correlation – Single linkage clustering     

Ecology meets molecular genetics in Arabidopsis

 Arabidopsis thaliana has been used as a model plant for molecular genetics studies. Recently, Arabidopsis has been utilized in an increasing number of ecological and evolutionary studies. These studies are beginning to explain three “black boxes” of ecology: the nature of the mutations responsible for phenotypic variation, female–male interactions in the pistil, and the genetic basis of speciation. Among the advances are the inclusive fitness of haploid gametophytes, the testing of the arms-race model, morphological diversity, and reproductive isolation. Important methods include quantitative trait locus (QTL) mapping and molecular population genetics. Most significantly, natural variations of various aspects are now available via the taxonomic revision of its closely related species, and by the worldwide collection of accessions. Some conspicuous works using maize, Drosophila, and other species will be also discussed. Received: June 1, 2002 / Accepted: October 15, 2002 Acknowledgments I would like to express my deepest gratitude to Prof. K. Okada for supporting this research. I thank the organizers of the symposium for fruitful discussion, T. Yahara and M. Kanaoka for critical reading, T. Araki and T. Kenta for valuable discussions, and members of the Okada laboratory for technical assistance and discussion. The work was supported by JSPS Research Fellowships for Young Scientists.     

Numerical and exact solutions for continuum of alleles models

 Two results are presented for problems involving alleles with a continuous range of effects. The first result is a simple yet highly accurate numerical method that determines the equilibrium distribution of allelic effects, moments of this distribution, and the mutational load. The numerical method is explicitly applied to the mutation-selection balance problem of stabilising selection. The second result is an exact solution for the distribution of allelic effects under weak stabilising selection for a particular distribution of mutant effects. The exact solution is shown to yield a distribution of allelic effects that, depending on the mutation rate, interpolates between the ``House of Cards' approximation and the Gaussian approximation. The exact solution is also used to test the accuracy of the numerical method. Received: 7 November 2001 / Revised version: 5 September 2002 / Published online: 18 December 2002 Key words or phrases: Continuum of alleles – Numerical solution – Exact solution – Mutation selection balance – Stabilising selection     

Why some tits store food and others do not: evaluation of ecological factors

Paridae are among the bird families benefiting from food storing. However, not all its members hoard food. Our objective was to clarify the role of ecological factors in occurrence of food storing. We reviewed the data on major ecological characteristics of the Paridae species and analysed their association with the presence/absence of food storing. Our statistical model revealed that geography (distribution in North America) and taxonomy (genus Poecile) are better predictors of food storing than any of the studied ecological traits. Nevertheless, food-storing Poecile species inhabit mixed or coniferous woodlands with seasonal richness of food, while non-storing species tend to prefer edge and open habitats, where alternative food sources are available. Sociality and territoriality outside breeding season coincides with food storing. The analysis performed within the Baeolophus–Lophophanes–Periparus–Poecile clade with ancestral food storing revealed no factor except continental climate that would explain the persistence of food storing. The phylogenetic analysis of ancestral states of the studied characters allowed us to propose a possible scenario for the emergence of food storing in Paridae. (1) Food storing is not ancestral in Paridae and appeared only once in the common ancestor of the Baeolophus–Lophophanes–Periparus–Poecile group. (2) According to estimation of molecular clock in Paridae, food storing appeared before their radiation in North America.     

Monotone travelling fronts in an age-structured reaction-diffusion model of a single species

 We consider a partially coupled diffusive population model in which the state variables represent the densities of the immature and mature population of a single species. The equation for the mature population can be considered on its own, and is a delay differential equation with a delay-dependent coefficient. For the case when the immatures are immobile, we prove that travelling wavefront solutions exist connecting the zero solution of the equation for the matures with the delay-dependent positive equilibrium state. As a perturbation of this case we then consider the case of low immature diffusivity showing that the travelling front solutions continue to persist. Our findings are contrasted with recent studies of the delayed Fisher equation. Travelling fronts of the latter are known to lose monotonicity for sufficiently large delays. In contrast, travelling fronts of our equation appear to remain monotone for all values of the delay. Received: 1 November 2001 / Revised version: 10 May 2002 / Published online: 23 August 2002 Mathematics Subject Classification (2000): 35K57, 92D25 Key words or phrases: Age-structure – Time-delay – Travelling Fronts – Reaction-diffusion     

Extrinsic control of species replacement on a Holocene reef in Belize: the role of coral disease

 Well-preserved, Holocene coral reefs provide the opportunity to discriminate between models of intrinsically driven succession and extrinsically driven species replacement, especially when paleontological patterns can be combined with ecological observations of the underlying mechanisms. Rhomboid shoals in the central shelf lagoon of the Belizean Barrier Reef experienced a recent and dramatic change in community composition. Agaricia tenuifolia replaced Acropora cervicornis as the dominant coral species at 3–15 m depth along the flanks of the reefs. We tested the hypothesis that shallowing upward caused this shift in dominance. A core extracted from 0.5 m water depth on one of the shoals, Channel Cay, revealed a shallowing-upward shift in dominance from Acropora to Porites divaricata. This successional sequence was quite different from the Acropora-to-Agaricia transition observed in four cores from 6–11 m water depth. Ecological observations showed that Agaricia became the dominant at ≥3 m depth after Acropora populations were decimated by a regional outbreak of white-band disease. The Acropora-to-Agaricia transition was clearly a case of extrinsically driven species replacement rather than an intrinsically driven, successional, shallowing-upward sequence. Accepted: 14 May 1998     

Parasitism <Emphasis Type="Italic">versus</Emphasis> mutualism in the ant-garden parabiosis between <Emphasis Type="Italic">Camponotus femoratus</Emphasis> and <Emphasis Type="Italic">Crematogaster levior</Emphasis>

Ant-gardens represent a special type of association between ants and epiphytes. Frequently, two ant species can share the same nest in a phenomenon known as ‘parabiosis’, but the exact nature (i.e., mutualistic or parasitic) of this interaction is the subject of debate. We thus attempted to clarify the mutual costs and benefits for each partner (ants and plants) in the Crematogaster levior/Camponotus femoratus ant-garden parabiosis. The ants’ response to experimental foliar damage to the epiphytes and to the host tree as well as their behavior and interactions during prey capture were investigated to see if the purported parasitic status of Cr. levior could be demonstrated in either the ant-ant or in the ant-plant interactions. The results show that both species take part in protecting the epiphytes, refuting the role of Cr. levior as a parasite of the ant-garden mutualism. During capture of large prey Ca. femoratus took advantage from the ability of Cr. levior to discover prey; by following Cr. levior trails Ca. femoratus workers discover the prey in turn and usurp them during agonistic interactions. Nevertheless, the trade-off between the costs and benefits of this association seems then to be favorable to both species because it is known that Cr. levior benefits from Ca. femoratus building the common carton nests and furnishing protection from vertebrates. Consequently, parabiosis can then be defined as the only mutualistic association existing between ant species, at least in ant-gardens. Received 31 August 2006 ; revised 8 December 2006 ; accepted 12 December 2006     

Utilization of mutants to analyze the interaction between Arabidopsis thaliana and its naturally root-associated Pseudomonas

 A model system based on the Arabidopsis thaliana (L.) Heynh. Ws ecotype and its naturally colonizing Pseudomonas thivervalensis rhizobacteria was defined. Pseudomonas strains colonizing A. thaliana were found to modify the root architecture either in vivo or in vitro. A gnotobiotic system using bacteria labelled with green fluorescent protein revealed that P. thivervalensis exhibited a colonization profile similar to that of other rhizobacterial species. Mutants of A.thaliana affected in root hair development and possible hormone perception were used to analyze the plant genetic determinants of bacterial colonization. A screen for mutants insensitive to P. thivervalensis colonization yielded two mutants found to be auxin resistant. This further supports a proposed role for bacterial auxin in inducing morphological modifications of roots. This work paves the way for studying the interaction between plants and non-pathogenic rhizobacteria in a gnotobiotic system, derived from a natural association, where interactions between both partners can be genetically dissected. Received: 6 January 2000 / Accepted: 20 May 2000     

Habitat association and depth distribution of two sympatric groupers of the genus Cephalopholis (Serranidae: Epinephelinae)

 Habitat association and depth distribution of two sympatric coral reef groupers of the genus Cephalopholis were examined at Rota, Mariana Islands. The two species are similar in body size, morphology, and social organization. In this study, they differed in their association with habitat and microhabitat and in depth distribution. Cephalopholis spiloparaea occurred on the reef slope between the reef terrace and deep sand flats at depths between 15 and 26 m. This species was associated mainly with Porites rus corals. Cephalopholis urodeta occurred largely on the upper reef terrace at 1–12 m. This species was associated mainly with coral pavement. The observed pattern of segregation might be the result of competitive or noncompetitive interactions or of phylogenetic constraints, but the exact mechanism or combination thereof remains unknown. Received: May 30, 2000 / Revised: September 5, 2001 / Accepted: October 25, 2001     

Exact sampling formulas for multi-type Galton-Watson processes

 Exact formulas for the mean and variance of the proportion of different types in a fixed generation of a multi-type Galton-Watson process are derived. The formulas are given in terms of iterates of the probability generating function of the offspring distribution. It is also shown that the sequence of types backwards from a randomly sampled particle in a fixed generation is a non-homogeneous Markov chain where the transition probabilities can be given explicitly, again in terms of probability generating functions. Two biological applications are considered: mutations in mitochondrial DNA and the polymerase chain reaction. Received: 10 June 2001 / Revised version: 21 November 2001 / Published online: 23 August 2002 Mathematics Subject Classification (2000): Primary 60J80, Secondary 92D10, 92D25 Key words or phrases: Multi-type Galton-Watson process – sampling formula – PCR – mitochondrial DNA     

Species composition and correlation of understory woody plants in Chinese fir plantation in the lower subtropical area

There are 71 species in the shrub layer of the Cunninghamia lanceolata plantation after natural succession. The species richness and diversity have increased with slight anthropogenic disturbance. The status and function of understory woody species were judged by the analysis of the important value (IV). x ² statistics and r test were used for testing the significance of interspecific association and correlation among 25 main understory woody plants selected from the woody population. The results clearly showed their interspecific relationships and their differences in resource utilization. Species-pairs of positive association were in the majority. Most species were accommodated in the shady habitat. There was a positive correlation between the IV of the species and the interspecific association. The higher the IV of the species, the closer and more significant was the interspecific association. Based on analytical results of interspecific association and correlation, 25 woody plants in the shrub layer could be divided into four ecological species groups: I. Ficus hispida + Antidesma bunius + Mallotus barbatus + Ficus cunia + Saurauia tristyla + Mallotus philippinensis + Maesa japonica + Ficus hirta + Alchornea rugosa + Ficus fulva + Mallotus apelta; II. Cudrania tricuspidata + Schefflera octophylla; III. Cunninghamia lanceolata + Clerodendron cytophyllum + Millettia semicastrata + Randia spinosa + Litsea cubeba + Litsea pungens; IV. Ardisia japonica + Psychotria rubra + Vitex quinata + Cephalanthus occidentalis + Pithecellobium lucidum + Mycetia sinensis. If species group III or II is the advantaged species in the shrub layer, the community would change from a coniferous forest to a sparse evergreen broad-leaved forest. For group IV, the community would be relatively stable. For group I, the coniferous forest would be mixed with coniferous-broad leaved forest. The classification of ecological species groups would provide a theoretical basis on judging its ecological function, adjusting the stand structure of the plantation and directing the suitable natural vegetation type through the close-natural restoration process. __________ Translated from Acta Ecologica Sinica, 2005, 25(9): 2173–2179 [译自: 生态学报, 2005, 25(9): 2173–2179]     

On the dynamics of discrete food chains: low- and high-frequency behavior and optimality of chaos

 In this paper we derive and analyze a discrete version of Rosenzweig's (Am. Nat. 1973) food-chain model. We provide substantial analytical and numerical evidence for the general dynamical patterns of food chains predicted by De Feo and Rinaldi (Am. Nat. 1997) remaining largely unaffected by this discretization. Our theoretical analysis gives rise to a classification of the parameter space into various regions describing distinct governing dynamical behaviors. Predator abundance has a local optimum at the edge of chaos. Received: 13 August 1999 / Revised version: 12 March 2002 / Published online: 17 October 2002 Mathematics Subject Classification (1991): 92D40 Keywords or phrases: Discrete food-chain – Discrete Hopf (Neimark-Sacker) bifurcation – Pulsewise birth processes – Mean yield maximization – Nicholson-Bailey model     

A discrete,size-structured model of phytoplankton growth in the chemostat: introduction of inhomogeneous cell division size

 We introduce inhomogeneous, substrate dependent cell division in a time discrete, nonlinear matrix model of size-structured population growth in the chemostat, first introduced by Gage et al. [8] and later analysed by Smith [13]. We show that mass conservation is verified, and conclude that our system admits one non zero globally stable equilibrium, which we express explicitly. Then we run numerical simulations of the system, and compare the predictions of the model to data related to phytoplankton growth, whose obtention we discuss. We end with the identification of several parameters of the system. Received: 9 February 2000 / Revised version: 10 October 2001 / Published online: 23 August 2002 RID="*" ID="*" Present address: Department of Mathematics and Statistics, University of Victoria, B.C., Canada. e-mail: jarino@math.uvic.ca Key words or phrases: Chemostat – Structured population models – Discrete model – Inhomogeneous division size     

Photosynthesis rates of selected tree species in lowland dipterocarp rainforest of Sabah, Malaysia

 Diurnal courses of net photosynthesis, transpiration and water potential of leaves of ten woody species from the natural lowland dipterocarp forests in Sabah (North Borneo, Malaysia) and one exotic tree species were studied in the field. The indigenous species represent different ecological niches and successional stages in the various layers of the dipterocarp forest, such as pioneers, trees of the understorey or main canopy and emergents. Diurnal changes in CO₂ exchange and transpiration reflected primarily differences in irradiance. The diurnal courses of water potential mainly tracked the rate of transpiratory water loss. Light-dependency describes most of the diurnal variations of leaves’ gas exchange. Light response curves of net photosynthesis of the investigated species of the Dipterocapaceae were almost equal (light saturated assimilation rate, A_max: 5.0–7.2 μmol CO₂ m^–2 s^–1), while those of the other species exhibited remarkable differences (A_max: 5.5–14.2 μmol CO₂ m^–2 s^–1). Leaf area, chlorophyll content and specific leaf dry weight as the reference parameters for assimilation gave a general ranking of the A_max, which is highest for the pioneering species, less for the understorey trees and lowest for emergents. Light compensation points and light saturation of net photosynthesis were attained mainly between 6 and 9 μmol photons m^–2 s^–1 and between 230 and 534 μmol photons m^–2 s^–1, respectively, but were higher for pioneering species. Photosynthetic performance may be a diagnostic feature of the successional and ecological status of species, i.e. to characterize pioneering species from understorey species or from emergents of the dipterocarp forest. Received: 3 March 1997 / Accepted: 15 December 1997     

A temperature-sensitive DNA adenine methyltransferase mutant of Salmonella typhimurium

A temperature-sensitive mutant of Salmonella typhimurium was isolated earlier after transposon mutagenesis with Tn10d Tet. The mutant D220 grows well at 28 °C but has a lower growth rate and forms filaments at 37 °C. Transposon-flanking fragments of mutant D220 DNA were cloned and sequenced. The transposon was inserted in the dam gene between positions 803 and 804 (assigned allele number: dam-231 : : Tn10d Tet) and resulted in a predicted ten-amino-acid-shorter Dam protein. The insertion created a stop codon that led to a truncated Dam protein with a temperature-sensitive phenotype. The insertion dam-231 : : Tn10d Tet resulted in a dam“leaky” phenotype since methylated and unmethylated adenines in GATC sequences were present. In addition, the dam-231 : : Tn10d Tet insertion rendered dam mutants temperature-sensitive for growth depending upon the genetic background of the S. typhimurium strain. The wild-type dam gene of S. typhimurium exhibited 82% identity with the Escherichia coli dam gene.