Non-random Structure Research Articles

Helminth communities of yellow perch (Perca flavescens (Mitchill)): determinants of pattern

Twenty-eight parasite species were recorded from 504 yellow perch (Perca flavescens) collected from Dauphin Lake and Beaufort Lake, Manitoba, and Lake Winnebago, Green Bay, and Lake Michigan, Wisconsin. Four parasite species, Diplostomum spp., Urocleidus adspectus, Proteocephalus pearsei, and Raphidascaris acus, occurred in perch from all localities. Infracommunities and component communities were low in richness. The Dauphin Lake and Beaufort Lake samples had the richest parasite communities, while those in the Green Bay and Lake Michigan samples were the least rich. The effect of host size and age on parasite community structure was equivocal. A positive association between P. pearsei and Bothriocephalus cuspidatus and more multispecies infracommunities than expected provide evidence of nonrandom associations in the Manitoba samples, while the Wisconsin infracommunities were random associations. Significant infracommunity nestedness in all samples indicated nonrandom community organization and structure. Parasite faunas were richer in samples with complex invertebrate communities than in samples with complex fish communities. The trophic status of the aquatic system indirectly affected the parasite communities by limiting the variety of potential intermediate hosts. Predictions regarding relationships between parasite community structure and lake trophic status were not supported. We show that predictable patterns at the fine-scale local level of the parasite infracommunity and component communities of perch are best explained by a rich invertebrate community upon which the host feeds.

Helminth communities of yellow perch (<i>Perca flavescens</i> (Mitchill)): determinants of pattern

Twenty-eight parasite species were recorded from 504 yellow perch (Perca flavescens) collected from Dauphin Lake and Beaufort Lake, Manitoba, and Lake Winnebago, Green Bay, and Lake Michigan, Wisconsin. Four parasite species, Diplostomum spp., Urocleidus adspectus, Proteocephalus pearsei, and Raphidascaris acus, occurred in perch from all localities. Infracommunities and component communities were low in richness. The Dauphin Lake and Beaufort Lake samples had the richest parasite communities, while those in the Green Bay and Lake Michigan samples were the least rich. The effect of host size and age on parasite community structure was equivocal. A positive association between P. pearsei and Bothriocephalus cuspidatus and more multispecies infracommunities than expected provide evidence of nonrandom associations in the Manitoba samples, while the Wisconsin infracommunities were random associations. Significant infracommunity nestedness in all samples indicated nonrandom community organization and structure...

Synthesis and structure characterization of 2,3‐ O‐ carboxymethylcellulose

2,3-O-Carboxymethylcellulose (CMC) samples of different degree of substitution (DS) were synthesized via 6-O-(4-monomethoxytriphenylmethyl)cellulose under a variety of conditions and with different carboxymethylating agents. The highest DS of carboxymethyl groups of 1.7 was reached with sodium monochloroacetate in dimethyl sulfoxide containing 1% of water as reaction medium. The CMC's dissolve in water starting from a DS of 0.6. In any case, the carboxymethylation is more effective at 0-2 compared to 0-3. While samples up to a DS of I possess a random distribution of the different repeating units, samples of higher DS show a non-random structure. Consequently, a control of the distribution of carboxymethyl groups within both the repeating units and the polymer chain was possible for the first time.

Solution structure and dynamics of a serpin reactive site loop using interleukin 1beta as a presentation scaffold.

Human interleukin-1beta (IL1beta) was used as a presentation scaffold for the characterization of the reactive site loop (RSL) of the serpin alpha1-antitrypsin (A1AT), the physiological inhibitor of leukocyte elastase. A chimeric protein was generated by replacement of residues 50-53 of IL1beta, corresponding to an exposed reverse turn in IL1beta, with the 10-residue P5-P5' sequence EAIPMSIPPE from A1AT. The chimera (antitrypsin-interleukin, AT-IL) inhibits elastase specifically and also binds the IL1beta receptor. Multinuclear NMR characterization of AT-IL established that, with the exception of the inserted sequence, the structure of the IL1beta scaffold is preserved in the chimera. The structure of the inserted RSL was analyzed relative to that of the isolated 10-residue RSL peptide, which was shown to be essentially disordered in solution. The chimeric RSL was also found to be solvent exposed and conformationally mobile in comparison with the IL1beta scaffold, and there was no evidence of persisting interactions with the scaffold outside of the N- and C-terminal linkages. However, AT-IL exhibits sigificant differences in chemical shift and NOE patterns relative to the isolated RSL that are consistent with local features of non-random structure. The proximity of these features to the P1-P1' residues suggests that they may be responsible for the inhibitory activity of the chimera.

Conformational analysis of peptide fragments derived from the peripheral subunit-binding domain from the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus: Evidence for nonrandom structure in the unfolded state

There is currently a great deal of interest in the early events in protein folding. Two issues that have generated particular interest are the nature of the unfolded state under native conditions and the role of local interactions in folding. Here, we report the results of a study of a set of peptides derived from a small two-helix protein, the peripheral subunit-binding domain of the pyruvate dehydrogenase multienzyme complex. Five peptides of overlapping sequence were prepared, including sequences corresponding to each of the helices and to the region connecting them. The peptides were characterized by CD and, where possible, nmr. A peptide corresponding to the second helix is between 12 and 17% helical at neutral pH. CD also indicates a lower percentage of helical structure in the peptide corresponding to the first α-helix, although the values of the α-proton chemical shifts suggest some preference for nonrandom structure. Peptides corresponding to the interhelical loop, which in the full domain contains two overlapping β-turns and a 5-residue 310-helix, are less structured. There is no significant change in the helicity of any of these peptides with pH. To test for fragment complementation, CD spectra of the two peptides derived from each helix and the long connecting peptide were compared to the spectra of each possible pair, as well as to a mixture containing all three. No increase in structure was observed. We complement our peptide studies by characterizing a point mutant, D34V, which disrupts a critical hydrogen bonding network. This mutant is unable to fold and provides a useful model of the denatured state. The mutant is between 9 and 16 % helical as judged by CD. The modest amount of helical structure formed in some of the peptide fragments and in the point mutant suggests that the denatured state of the peripheral subunit binding domain is not completely unstructured. This may contribute to the very rapid folding observed for the intact protein. © 1999 John Wiley & Sons, Inc. Biopoly 49: 29–40, 1999

Conformational analysis of peptide fragments derived from the peripheral subunit-binding domain from the pyruvate dehydrogenase multienzyme complex ofBacillus stearothermophilus: Evidence for nonrandom structure in the unfolded state

There is currently a great deal of interest in the early events in protein folding. Two issues that have generated particular interest are the nature of the unfolded state under native conditions and the role of local interactions in folding. Here, we report the results of a study of a set of peptides derived from a small two-helix protein, the peripheral subunit-binding domain of the pyruvate dehydrogenase multienzyme complex. Five peptides of overlapping sequence were prepared, including sequences corresponding to each of the helices and to the region connecting them. The peptides were characterized by CD and, where possible, nmr. A peptide corresponding to the second helix is between 12 and 17% helical at neutral pH. CD also indicates a lower percentage of helical structure in the peptide corresponding to the first alpha-helix, although the values of the alpha-proton chemical shifts suggest some preference for nonrandom structure. Peptides corresponding to the interhelical loop, which in the full domain contains two overlapping beta-turns and a 5-residue 3(10)-helix, are less structured. There is no significant change in the helicity of any of these peptides with pH. To test for fragment complementation, CD spectra of the two peptides derived from each helix and the long connecting peptide were compared to the spectra of each possible pair, as well as to a mixture containing all three. No increase in structure was observed. We complement our peptide studies by characterizing a point mutant, D34V, which disrupts a critical hydrogen bonding network. This mutant is unable to fold and provides a useful model of the denatured state. The mutant is between 9 and 16% helical as judged by CD. The modest amount of helical structure formed in some of the peptide fragments and in the point mutant suggests that the denatured state of the peripheral subunit binding domain is not completely unstructured. This may contribute to the very rapid folding observed for the intact protein.

Responses of auditory-cortex neurons to structural features of natural sounds.

Sound-processing strategies that use the highly non-random structure of natural sounds may confer evolutionary advantage to many species. Auditory processing of natural sounds has been studied almost exclusively in the context of species-specific vocalizations, although these form only a small part of the acoustic biotope. To study the relationships between properties of natural soundscapes and neuronal processing mechanisms in the auditory system, we analysed sound from a range of different environments. Here we show that for many non-animal sounds and background mixtures of animal sounds, energy in different frequency bands is coherently modulated. Co-modulation of different frequency bands in background noise facilitates the detection of tones in noise by humans, a phenomenon known as co-modulation masking release (CMR). We show that co-modulation also improves the ability of auditory-cortex neurons to detect tones in noise, and we propose that this property of auditory neurons may underlie behavioural CMR. This correspondence may represent an adaptation of the auditory system for the use of an attribute of natural sounds to facilitate real-world processing tasks.

Conformational analysis of the endogenous μ-opioid agonist endomorphin-1 using NMR spectroscopy and molecular modeling

Endomorphin-1 (Tyr-Pro-Trp-Phe-NH 2) is a highly selective and potent agonist of the μ-opioid receptor. To identify structural attributes unique to this opioid peptide and potential sites of recognition, a conformational analysis has been performed using multidimensional NMR and molecular modeling techniques. The spectroscopic results, derived from experiments in both DMSO and water, indicate that endomorphin-1 exists in the cis- and trans-configuration with respect to the Pro-omega bond in approximately 25% and 75% populations, respectively. In DMSO, the cis-configuration adopts a compact sandwich conformation in which the Tyr and Trp aromatic rings pack against the proline ring, whereas the trans-configuration adopts an extended conformation. Although non-random structure was not observed in water, condensed phase molecular dynamics calculations indicate that trans-isomers dominate the population in this higher dielectric medium. Structural comparison of the cis- and trans-configurations with morphine and selective μ-peptide ligands PL-017 and d-TIPP, as well as the δ-selective peptide ligands TIPP (δ-antagonist, μ-agonist) and DPDPE were also performed and suggest the trans-isomer is likely the bioactive form. A hypothesis is proposed to explain μ- and δ-selectivity based on the presence of spatially distinct selectivity pockets among these ligands.

Peptide models of local and long-range interactions in the molten globule state of human α-lactalbumin

α-Lactalbumin, a small calcium-binding protein, forms an equilibrium molten globule state under a variety of conditions. A set of four peptides designed to probe the role of local interactions and the role of potential long-range interactions in stabilizing the molten globule of α-lactalbumin has been prepared. The first peptide consists of residues 20 through 36 of human α-lactalbumin and includes the entire B-helix. This peptide is unstructured in solution as judged by CD. The second peptide is derived from residues 101 through 120 and contains both the D and 3 10helices. When this peptide is crosslinked via the native 28 to 111 disulfide to the B-helix peptide, a dramatic increase in helicity is observed. The crosslinked peptide is monomeric, as judged by analytical ultracentrifugation. The peptide binds 1-anilinonaphthalene-8-sulphonate (ANS) and the fluorescence emission maximum of the construct is consistent with partial solvent exposure of the tryptophan residues. The peptide corresponding to residues 101 to 120 adopts significant non-random structure in aqueous solution at low pH. Two hydrophobic clusters, one involving residues 101 through 104 and the other residues 115 through 119 have been identified and characterized by NMR. The hydrophobic cluster formed by residues 101 through 104 is still present in a smaller peptide containing only residues 101 to 111 of α-lactalbumin. The cluster also persists in 6 M urea. A non-native, pH-dependent interaction between the Y103 and H107 side-chains that was previously identified in the acid-denatured molten globule state was examined. This interaction was found to be more prevalent at low pH and may therefore be an example of a local interaction that stabilizes preferentially the acid-induced molten globule state.

Statistical methodology for assessing homology of intronic regions of genes

AbstractWe consider the problem of statistically evaluating the similarity of DNA intronic regions of genes. Present algorithms are based on matching a sequence of interest with known DNA sequences in a gene bank and are designed primarily to assess homology among exonic regions of genes. Most research focuses on exonic regions because they have a clear biological significance, coding for proteins, and therefore tend to be more conserved in evolution than intronic regions. To investigate whether the intronic features of genes whose expression is highly sensitive to environmental perturbations differ from genes that have a more constant expression, a collection of oncogenes, tumor suppressor genes, and nonregulatory genes involved in energy metabolism are compared. An analysis of the features of these genes' intronic regions result in clustering by regulatory group. In addition, Billingsley's test for Markov structure (1961) suggests that 67% of the intronic regions in this collection of genes show evidence of nonrandom structure, indicating the possibility of a biological function for these regions. The result of Billingsley's test for homology is used as input to a clustering algorithm. The biological significance of this methodology lies in the identification of groups based on the intronic regions from genes of unknown function. With the advent of rapid sequencing techniques, there is a great need for statistical techniques to help identify the purpose of poorly understood portions of genes. These methods can be utilized to assess the functional group to which such a gene might possibly belong.

Feature-based classification of myoelectric signals using artificial neural networks.

A pattern classification system, designed to separate myoelectric signal records based on contraction tasks, is described. The amplitude of the myoelectric signal during the first 200 ms following the onset of a contraction has a non-random structure that is specific to the task performed. This permits the application of advanced pattern recognition techniques to separate these signals. The pattern classification system described consists of a spectrographic preprocessor, a feature extraction stage and a classifier stage. The preprocessor creates a spectrogram by generating a series of power spectral densities over adjacent time segments of the input signal. The feature extraction stage reduces the dimensionality of the spectrogram by identifying features that correspond to subtle underlying structures in the input signal data. This is realised by a self-organising artificial neural network (ANN) that performs an advanced statistical analysis procedure known as exploratory projection pursuit. The extracted features are then classified by a supervised-learning ANN. An evaluation of the system, in terms of system performance and the complexity of the ANNs, is presented.

Simulations of the structural and dynamical properties of denatured proteins: the “molten coil” state of bovine pancreatic trypsin inhibitor

The dynamic nature of denatured, unfolded proteins makes it difficult to characterize their structures experimentally. To complement experiment and to obtain more detailed information about the structure and dynamic behavior of the denatured state, we have performed eleven 2.5 ns molecular dynamics simulations of reduced bovine pancreatic trypsin inhibitor (BPTI) at high temperature in water and a control simulation at 298 K, for a total of 30 ns of simulation time. In a neutral pH environment (acidic residues ionized), the unfolded protein structures were compact with an average radius of gyration 9% greater than the native state. The compact conformations resulted from the transient formation of non-native hydrophobic clusters, turns and salt bridges. However, when the acidic residues were protonated, the protein periodically expanded to a radius of gyration of 18 to 20 Å. The early steps in unfolding were similar in the different simulations until passing through the major transition state of unfolding. Afterwards, unfolding proceeded through one of two general pathways with respect to secondary structure: loss of the C-terminal helix followed by loss of β-structure or the opposite. To determine whether the protein preferentially sampled particular conformational substates in the denatured state, pairwise C α root-mean-square deviations were measured between all structures, but similar structures were found between only two trajectories. Yet, similar composite properties (secondary structure content, side-chain and water contacts, solvent accessible surface area, etc.) were observed for the structures that unfolded through different pathways. Somewhat surprisingly, the unfolded structures are in agreement with both past experiments suggesting that reduced BPTI is a random coil and more recent experiments providing evidence for non-random structure, demonstrating how ensembles of fluctuating structures can give rise to experimental observables that are seemingly at odds.

Structure of the inactivating gate from the Shaker voltage gated K+ channel analyzed by NMR spectroscopy.

Rapid inactivation of voltage-gated K+ (Kv) channels is mediated by an N-terminal domain (inactivating ball domain) which blocks the open channel from the cytoplasmic side. Inactivating ball domains of various Kv channels are also biologically active when synthesized separately and added as a peptide to the solution. Synthetic inactivating ball domains from different Kv channels with hardly any sequence homology mediate quite similar effects even on unrelated Kv channel subtypes whose inactivation domain has been deleted. The solution structure of the inactivating ball peptide from Shaker (Sh-P22) was analyzed with NMR spectroscopy. The NMR data indicate a non-random structure in an aqueous environment. However, while other inactivating ball peptides showed well-defined three-dimensional structures under these conditions, Sh-P22 does not have a unique, compactly folded structure in solution.

EXAFS studies of the effect of glass composition on the coordination of trivalent chromium in glasses in the system Na 2OAl 2O 3SiO 2

A recent study of the epr and optical characteristics of Cr 3+ [Hollis et al., submitted to Phys. Chem. Glasses; Hollis and Harris, submitted to Phys. Chem. Glasses] has shown the importance of nearest neighbour and second nearest neighbour coordination of the Cr 3+ in determining optical absorption and fluorescence parameters. In this study, station 8.1 of the Daresbury S.R.S., UK was used to determine the near neighbour environment of these glasses. The results show clear evidence that the next nearest neighbours to the chromium are affected by the phasefield of the system Na 2OAl 2O 3SiO 2 to which any particular glass belongs. This systematic behaviour follows that of the optical and epr parameters observed in the previous study [Hollis et al., submitted to Phys. Chem. Glasses; Hollis and Harris, submitted to Phys. Chem. Glasses]. This result implies that a non-random structure of the glass exists in the nearest and next nearest neighbour coordination spheres of the chromium. A significant effect on the optical properties of trivalent chromium is produced by the site distortions at the chromium ion [Hollis et al., submitted to Phys. Chem. Glasses; Hollis and Harris, submitted to Phys. Chem. Glasses]. These distortions in turn result from the packing of the next nearest neighbours, which are studied here.

Organisation of basement membrane components in the human adult and fetal pituitary gland and in pituitary adenomas.

Cell-matrix interactions undoubtedly have a role in the development and maintenance of the complex nonrandom structure of the human pituitary gland. We have extended previous studies by documenting the patterns of immunoreactivity for type IV collagen, laminin and fibronectin in the fetal gland, comparing these with the adult patterns. In both we have examined the differences between the anterior lobe and intermediate zone in an attempt to elucidate the apparent differences in functional response between corticotrophs in the two areas. We have also examined expression of these proteins in a series of pituitary adenomas. Finally, we have immunolocalised beta 4 integrin, a component of the alpha 6 beta 4 laminin receptor, in the adult gland and in adenomas. In the anterior lobe of the adult gland, type IV collagen and laminin were present in both epithelial and vascular basement membrane. Fibronectin was related to the basement membrane but showed a less continuous distribution. beta 4 Integrin was expressed on the basal aspects of pituitary cells, in association with laminin, suggesting that this did identify the alpha 6 beta 4 laminin receptor. In addition, immunoreactivity was present on the lateral margins of some pituitary cells, which might indicate a role in cell-cell adhesion. None of the proteins showed specific association with any particular cell type, suggesting that these specific interactions do not regulate differentiation. This pattern of expression had developed in the fetal gland by the second trimester, with expression relating to vessels preceding that in epithelial basement membrane. Type IV collagen, laminin and fibronectin were also expressed in epithelial and vascular basement membrane in the intermediate zone of the adult gland, and around Rathke's cleft in the fetal gland. However, the organisation differed, with larger groups of cells enclosed within a single basement membrane. Possible vascular connections demonstrated between the posterior lobe and the intermediate zone would permit access of posterior lobe hormones to this zone. Our data confirmed disruption of expression in pituitary adenomas, type IV collagen, laminin and beta 4 integrin having a mainly perivascular distribution, with more variable immunoreactivity for fibronectin.

Stability, ephemerality and dispersal ability: microarthropod assemblages on fungal sporophores

Abstract A comprehensive analysis of the microarthropod fauna from fungal sporophores revealed a series of recurrent patterns demonstrating the non-random structure of these assemblages. Despite the existence of a strong species-area relationship from sporophores of certain fungi, particularly among perennial species, several small sporophores always maintained a more diverse microarthropod fauna than fewer large sporophores of equivalent total area. A consistently high degree of overlap in microarthropod species occurrence between larger and smaller sporophores was indicated by the presence of highly significant nested subset structure. The fauna from Heterobasidion annosum sporophores was the most nested, followed by Hypholoma fasciculare and a collection of pooled agarics, respectively. When the fauna was split into functional groups, microphytophages were always significantly nested in their distributions but, when significant, macrophytophages and panphytophages had stronger nested hierarchies. Non-random organization was least evident among predatory species. Microarthropods had significantly ordered distributions on sporophores of various fungi. Many species occurred on perennial H. annosum sporophores of all sizes while others had more restricted distributions. Most species from very ephemeral agarics, including those which were widely distributed on H. annosum , were restricted to a small number of larger sporophores. The pattern from H. fasciculare was intermediate; most species had narrow distributions and were present only on larger sporophores, except a small number of more widely distributed species.

Stability, ephemerality and dispersal ability: microarthropod assemblages on fungal sporophores

A comprehensive analysis of the microarthropod fauna from fungal sporophores revealed a series of recurrent patterns demonstrating the non-random structure of these assemblages. Despite the existence of a strong species-area relationship from sporophores of certain fungi, particularly among perennial species, several small sporophores always maintained a more diverse microarthropod fauna than fewer large sporophores of equivalent total area. A consistently high degree of overlap in microarthropod species occurrence between larger and smaller sporophores was indicated by the presence of highly significant nested subset structure. The fauna fromHeterobasidion annosumsporophores was the most nested, followed byHypholoma fasciculareand a collection of pooled agarics, respectively. When the fauna was split into functional groups, microphytophages were always significantly nested in their distributions but, when significant, macrophytophages and panphytophages had stronger nested hierarchies. Non-random organization was least evident among predatory species. Microarthropods had significantly ordered distributions on sporophores of various fungi. Many species occurred on perennialH. annosumsporophores of all sizes while others had more restricted distributions. Most species from very ephemeral agarics, including those which were widely distributed onH. annosum, were restricted to a small number of larger sporophores. The pattern fromH. fascicularewas intermediate; most species had narrow distributions and were present only on larger sporophores, except a small number of more widely distributed species.

Reduced BPTI is collapsed. A pulsed field gradient NMR study of unfolded and partially folded bovine pancreatic trypsin inhibitor.

Pulsed field gradient NMR was used to measure the hydrodynamic behavior of unfolded variants of bovine pancreatic trypsin inhibitor (BPTI). The unfolded BPTI species studied were [R]Abu, at pH 4.5 and pH 2.5, and unfolded [14-38]Abu, at pH 2.5. These were prepared by chemical synthesis. [R]Abu is a model for reduced BPTI; all cysteine residues are replaced by alpha-amino-n-butyric acid (Abu). [14-38]Abu retains cysteines 14 and 38, which form a disulfide bond, while the other cysteine residues are replaced by Abu. In the PFG experiments, the diffusion coefficient is measured as a function of protein concentration, and the value of D degree -the diffusion coefficient extrapolated to infinite dilution-is determined. From D degree, a value of the hydrodynamic radius. Rh, is computed from the Stokes-Einstein relationship. At pH 4.5, [R]Abu has an Rh value significantly less than the value calculated for a random coil, while at pH 2.5 the experimental Rh value is the same as for a random coil. In view of the changes in NMR detected structure of [R]Abu at pH 4.5 versus pH 2.5 (Pan H, Barbar E, Barany G, Woodward C. 1995. Extensive non-random structure in reduced and unfolded bovine pancreatic trypsin inhibitor. Biochemistry 34:13974-13981), the collapse of reduced BPTI at pH 4.5 may be associated with the formation of non-native hydrophobic clusters of pairs of side chains one to three amino acids apart in sequence. The diffusion constant of [14-38]Abu was also measured at pH 4.5, where the protein is partially folded. An increase in hydrodynamic radius of partially folded [14-38]Abu, relative to native BPTI, is similar to the increase in radius of gyration measured for other proteins under "molten globule" conditions.

Solid-solution structure and the weakly first-order displacive transformation in Fe-Pd alloys

The solid-solution structure of an Fe-31 at. pct Pd single crystal quenched from 1173 K was measured by combined X-ray diffraction (XRD) and atom-probe microanalysis, with analysis of diffuse X-ray scattering supplemented by computer simulation. Detailed comparison of composition-fluctuation amplitudes on the size scale of 50 atoms shows good agreement between diffraction and atom-probe results, revealing a nonrandom solution structure with a broadened composition distribution, consistent with the existence of a miscibility gap in the system. Also consistent with the L10-FePd ordering present in the Fe-Pd system, the diffuse scattering indicates some short-range order in the higher Pd regions. Computer simulation of the diffuse scattering indicates Fe atom displacements in 〈100〉 directions in Fe-rich regions forming microdomains oriented along {110} planes, consistent with previous electron microscopy observations of fine structures above the nominal transformation temperature. Combining the measured composition distribution with a magnetics-based model of the composition dependence of the parent-phase instability temperature predicts a spreading of the weakly first-order cubic-tetragonal phase transformation, whereby tetragonal domains are locally stabilized at temperatures 300 K above the temperature where macroscopic plate products first appear. Composition fluctuations can thus introduce a significant component of continuous character to a weakly first-order displacive transformation.

Analyses of spatial patterns and population processes of clonal plants

AbstractThe nonrandom spatial structure of terrestrial plants is formed by ecological interactions and reproduction with a limited dispersal range, and in turn this may strongly affect population dynamics and population genetics. The traditional method of modelling in population ecology is either to neglect spatial pattern (e.g. in transition matrix models) or to do straightforward computer simulation. We review here three analytical mothods to deal with plant populations in a lattice‐structured habitat, which propagate both by seeds that scatter over the whole habitat and by vegetative reproduction (producing runners, rhizomes, etc.) to neighboring vacant sites. [1]Dynamics of global and local densities: Dynamical equations of population density considering nearest‐neighbor correlation (spatial clumping) are developed as the joint dynamics of global average density and local density (comparable to mean crowding) based on pair approximation. If there is a linear trade‐off between seed production and vegetative reproduction, the equilibrium abundance of the population may be maximized by engaging both means of reproduction. This result is accurately predicted by the pair approximation method, but not by mean‐field approximation (neglect of spatial structure). [2]Cluster size distributions: Using global and local densities obtained by pair approximation, we predicted cluster size distribution, i.e. the number of clusters of occupied sites of various sizes. [3]Clonal identity probability decreasing with distance: Multi‐locus measurement of allozymes or other neutral molecular markers tells us whether or not a given pair of individuals belong to the same clone. From the pattern of clonal identity probability decreasing with the distance between ramets, we can estimate the relative importance of two modes of reproduction: vegetative propagation and sexual seed production.