A simulation test of the resource‐averaging hypothesis of ecotone formation

Abstract. The pattern at an ecotone may indicate the processes that created that ecotone. Such patterns may in turn affect the responses of ecotones to environmental change. The resource averaging hypothesis suggests a process for the development of tree lines that should produce patterns that are modifications of patterns in soil resources. A computer simulation model that embodies the resource averaging hypothesis is used to generate tree‐line patterns. Different spatial patterns in the variation of soil resources are represented in the model. The patterns of tree line computed by the simulation closely correspond to the patterns of soil resources that were input. These patterns are compared to patterns recorded in the field and by aerial photography. For the patterns of soil resources observed at some alpine tree lines, the model cannot produce the kinds of patterns of vegetation observed. Resource averaging alone cannot be an explanation of such tree lines.     

Ecogeographical rules: elements of a synthesis

The development of a more synthetic approach to understanding spatial patterns in biogeography, particularly of the way in which these patterns interact, constitutes a major challenge for the field. Here we propose some key elements of such a synthesis for what can broadly be termed 'ecogeographical rules', that is spatial patterns in biological traits. These include understanding: (1) the different kinds of patterns (intraspecific, interspecific and assemblage), and the distinctions between them; (2) the unifying role that geographical ranges play in linking the patterns together; (3) that this unification can be obscured by the methodological assumptions made in documenting some patterns (e.g. assuming that intraspecific variation does not significantly influence interspecific and assemblage patterns in traits); (4) the implications of other methodological issues for the nature of observed patterns (e.g. how ranges are located on positional or environmental axes for interspecific patterns); (5) the need for further development of models linking different types of traits; (6) the nature of the generality of documented patterns at all levels, and particularly the difference between the frequency with which patterns are documented in the literature and the variety of extant species; and (7) the constraints that the form of intraspecific patterns place on interspecific and assemblage patterns, and that interspecific patterns place on assemblage patterns.     

The evolution of pattern camouflage strategies in waterfowl and game birds

Visual patterns are common in animals. A broad survey of the literature has revealed that different patterns have distinct functions. Irregular patterns (e.g., stipples) typically function in static camouflage, whereas regular patterns (e.g., stripes) have a dual function in both motion camouflage and communication. Moreover, irregular and regular patterns located on different body regions (“bimodal” patterning) can provide an effective compromise between camouflage and communication and/or enhanced concealment via both static and motion camouflage. Here, we compared the frequency of these three pattern types and traced their evolutionary history using Bayesian comparative modeling in aquatic waterfowl (Anseriformes: 118 spp.), which typically escape predators by flight, and terrestrial game birds (Galliformes: 170 spp.), which mainly use a “sit and hide” strategy to avoid predation. Given these life histories, we predicted that selection would favor regular patterning in Anseriformes and irregular or bimodal patterning in Galliformes and that pattern function complexity should increase over the course of evolution. Regular patterns were predominant in Anseriformes whereas regular and bimodal patterns were most frequent in Galliformes, suggesting that patterns with multiple functions are broadly favored by selection over patterns with a single function in static camouflage. We found that the first patterns to evolve were either regular or bimodal in Anseriformes and either irregular or regular in Galliformes. In both orders, irregular patterns could evolve into regular patterns but not the reverse. Our hypothesis of increasing complexity in pattern camouflage function was supported in Galliformes but not in Anseriformes. These results reveal a trajectory of pattern evolution linked to increasing function complexity in Galliformes although not in Anseriformes, suggesting that both ecology and function complexity can have a profound influence on pattern evolution.     

Representations of specific acoustic patterns in the auditory cortex and hippocampus

Previous behavioural studies have shown that repeated presentation of a randomly chosen acoustic pattern leads to the unsupervised learning of some of its specific acoustic features. The objective of our study was to determine the neural substrate for the representation of freshly learnt acoustic patterns. Subjects first performed a behavioural task that resulted in the incidental learning of three different noise-like acoustic patterns. During subsequent high-resolution functional magnetic resonance imaging scanning, subjects were then exposed again to these three learnt patterns and to others that had not been learned. Multi-voxel pattern analysis was used to test if the learnt acoustic patterns could be ‘decoded’ from the patterns of activity in the auditory cortex and medial temporal lobe. We found that activity in planum temporale and the hippocampus reliably distinguished between the learnt acoustic patterns. Our results demonstrate that these structures are involved in the neural representation of specific acoustic patterns after they have been learnt.     

Finding composite regulatory patterns in DNA sequences

Pattern discovery in unaligned DNA sequences is a fundamental problem in computational biology with important applications in finding regulatory signals. Current approaches to pattern discovery focus on monad patterns that correspond to relatively short contiguous strings. However, many of the actual regulatory signals are composite patterns that are groups of monad patterns that occur near each other. A difficulty in discovering composite patterns is that one or both of the component monad patterns in the group may be 'too weak'. Since the traditional monad-based motif finding algorithms usually output one (or a few) high scoring patterns, they often fail to find composite regulatory signals consisting of weak monad parts. In this paper, we present a MITRA (MIsmatch TRee Algorithm) approach for discovering composite signals. We demonstrate that MITRA performs well for both monad and composite patterns by presenting experiments over biological and synthetic data.     

哈尔滨市绿脓杆菌质粒图谱分析

本文对近年来从哈尔滨市五所临床医院分离的109株绿脓杆菌作了质粒图谱分析,结果发现在哈尔滨市流行的绿脓杆菌呈六种质粒图谱型别,其中77.1％的菌株呈两种相似的质粒图谱型别,且均含有一个共同的75Kb质粒。另外,还证实绿脓杆菌质粒图谱型别与血清型无明显相关性,而与耐药谱有一定的对应关系。     

Trait-based species richness: ecology and macroevolution

Understanding the origins of species richness patterns is a fundamental goal in ecology and evolutionary biology. Much research has focused on explaining two kinds of species richness patterns: (i) spatial species richness patterns (e.g. the latitudinal diversity gradient), and (ii) clade-based species richness patterns (e.g. the predominance of angiosperm species among plants). Here, I highlight a third kind of richness pattern: trait-based species richness (e.g. the number of species with each state of a character, such as diet or body size). Trait-based richness patterns are relevant to many topics in ecology and evolution, from ecosystem function to adaptive radiation to the paradox of sex. Although many studies have described particular trait-based richness patterns, the origins of these patterns remain far less understood, and trait-based richness has not been emphasised as a general category of richness patterns. Here, I describe a conceptual framework for how trait-based richness patterns arise compared to other richness patterns. A systematic review suggests that trait-based richness patterns are most often explained by when each state originates within a group (i.e. older states generally have higher richness), and not by differences in transition rates among states or faster diversification of species with certain states. This latter result contrasts with the widespread emphasis on diversification rates in species-richness research. I show that many recent studies of spatial richness patterns are actually studies of trait-based richness patterns, potentially confounding the causes of these patterns. Finally, I describe a plethora of unanswered questions related to trait-based richness patterns.     

THE INCIDENCE AND ORIGIN OF SPOTTED PATTERNS IN THE ESTRILDIDAE

The plumage of the Estrildidae was examined in order to determine the incidence and origin of the spotted patterns.
In the Australian grassfinches a series of feathers showing the derivation of spotted patterns from transverse barring was found in two species. In most species such patterns consisted of single broad spots, but in two species paired spots were present.
The mannikins show three types of spotted pattern. One is derived from transverse barring, another from a rachial streak, and the third from a combination of both bars and streaks. The last one is not a true spotted pattern, the effect being due to overlapping feathers.
The waxbills show spotted patterns derived from transverse barring, the development of which exactly parallels that shown by the grassfinches, but differs in that almost all patterns show paired spots.
The spotted patterns appear to have been derived from a basic barred pattern in most cases, and to represent an increasing complexity of pattern rather than a gradual loss.
It is considered that similar patterns in widely separated species are due to parallel evolution of patterns and not to phylogenetically close relationship.
Where various species show different successive stages in the evolution of a pattern, this does not indicate that one is ancestral to another. Since the species concerned have a common family relationship, the potential for such a pattern may be present throughout the family.
Since the patterns have a function in specific recognition, it is suggested that similar patterns are likely to recur in widely separated localities and that the patterns of sympatric species are likely to differ. If similar patterns are present in one area they will probably indicate close relationship.
The inference of this in relation to plumage pattern problems in some other orders is briefly discussed.     

A single structural type in the regular surface layer of Aeromonas salmonicida

The surface protein array of Aeromonas salmonicida (or A-layer) appears, in negatively stained preparations, as two distinct patterns, type I and type II. Type I patterns were restricted to, and predominated in, darkly stained areas, whereas lighter staining regions exclusively displayed type II patterns. The type I morphology was faithfully reproduced in computer-simulated superimpositions of type II patterns, as was the intermediate transition zone frequently seen between the two patterns. Variations in the lattice constant of both patterns, presumably due to artifactual flattening, demonstrated that these patterns could not be distinguished on this basis. The conceptual model presented points to the type II pattern as the only single A-layer structural type. We propose the use of the terms type 1/type II to exclusively describe the morphological patterns that appear upon negative staining and the open/closed nomenclature to describe the conformations that a single structural type can adopt.     

Travelling wave dynamics and self-organization in a spatio-temporally structured population

We analyse spatial population dynamics showing that periodic or period-like chaotic dynamics produce self-organization structures, such as travelling waves. We suggest that self-organized patterns are associated with spatial synchrony patterns that often depend on geographical distance between subpopulations. The population dynamics also show statistical spatial autocorrelation patterns. We contrast our theoretical simulations with empirical data on annual damages in young sapling stands caused by voles. We conclude, on the basis of the periodicity, synchrony, and spatial autocorrelation patterns, and our simulation results, that vole dynamics represent travelling waves in population dynamics. We suggest that because such synchrony patterns are frequently observed in natural populations, spatial self-organization may be more common in population dynamics than reported in the literature.     

Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis

Recent experiments with combinatorial libraries of de novo proteins have demonstrated that sequences designed to contain polar and non-polar amino acid residues arranged in an alternating pattern form fibrillar structures resembling beta-amyloid. This finding prompted us to probe the distribution of alternating patterns in the sequences of natural proteins. Analysis of a database of 250,514 protein sequences (79,708,024 residues) for all possible binary patterns of polar and non-polar amino acid residues revealed that alternating patterns occur significantly less often than other patterns with similar compositions. The under-representation of alternating binary patterns in natural protein sequences, coupled with the observation that such patterns promote amyloid-like structures in de novo proteins, suggests that sequences of alternating polar and non-polar amino acids are inherently amyloidogenic and consequently have been disfavored by evolutionary selection.     

On the significance of alternating patterns of polar and non-polar residues in beta-strands

A common assumption about protein sequences in beta-strands is that they have alternating patterns of polar and non-polar residues. It is thought that such patterns reflect the interior/exterior geometry of amino acid residue side-chains on a beta-sheet. Here we study the prevalence of simple hydrophobicity patterns in parallel and antiparallel beta-sheets in proteins of known structure and in the sequences of amyloidogenic proteins. The occurrence of 32 possible pentapeptide binary patterns (polar (P)/non-polar (N)) is computed in 1911 non-homologous protein structures. Despite their tendency to aggregate in experimentally designed proteins, the purely alternating hydrophobic/polar patterns (PNPNP and NPNPN) are most frequent in beta-sheets, typically occurring in antiparallel strands. The overall distribution of the pentapeptide binary patterns is significantly different in strands within parallel and antiparallel sheets. In both types of sheets, complementary patterns (where the hydrophobic and polar residues pair with one another) associate preferentially. We do not find alternating patterns to be common in amyloidogenic proteins or in short fragments involved directly in amyloid formation. However, we do note some similarities between patterns present in amyloidogenic sequences and those in parallel strands.     

Selective adhesion and mineral deposition by osteoblasts on carbon nanofiber patterns

In an effort to develop better orthopedic implants, osteoblast (bone-forming cells) adhesion was determined on microscale patterns (30 microm lines) of carbon nanofibers placed on polymer substrates. Patterns of carbon nanofibers (CNFs) on a model polymer (polycarbonate urethane [PCU]) were developed using an imprinting method that placed CNFs in selected regions. Results showed the selective adhesion and alignment of osteoblasts on CNF patterns placed on PCU. Results also showed greater attraction forces between fibronectin and CNF (compared with PCU) patterns using atomic force microscope force-displacement curves. Because fibronectin is a protein that mediates osteoblast adhesion, these results provide a mechanism of why osteoblast adhesion was directed towards CNF patterns. Lastly, this study showed that the directed osteoblast adhesion on CNF patterns translated to enhanced calcium phosphate mineral deposition along linear patterns of CNFs on PCU. Since CNFs are conductive materials, this study formulated substrates that through electrical stimulation could be used in future investigations to further promote osteoblasts to deposit anisotropic patterns of calcium-containing mineral similar to that observed in long bones.     

Labyrinthine versus straight-striped patterns generated by two-dimensional Turing systems

Striped patterns are often observed on fish skin. Such patterns have been accounted for by reaction-diffusion (RD) Turing-type models, in which two substances can spontaneously form a spatially heterogeneous pattern in a homogeneous field. Among the striped patterns generated by Turing-type models, some are "straight-striped patterns," with many stripes running in parallel, while others are "labyrinthine patterns," in which the stripes often change direction, merge with each other, and frequently branch out. RD models differ in terms of their tendency to generate either labyrinthine or straight-striped patterns. Here, we studied the conditions under which either a labyrinthine or straight-striped pattern would emerge. First, we defined an index for stripe clearness, Sh. Straight-striped patterns (large Sh) are formed if only a narrow range of spatial periods corresponds to an unstable mode. Labyrinthine patterns (small Sh) are formed when a wide range of spatial periods is unstable. More specifically, labyrinthine patterns are formed when the maximum spatial period of unstable modes is more than twice that of the minimum spatial period of unstable modes; otherwise, straight-striped patterns are formed. We then examined RD models with nonlinear reaction terms, including both activator-inhibitor and substrate-depletion models, and we demonstrated that the same conclusions hold with respect to the conditions required for labyrinthine versus straight-striped patterns.     

Comparison of microridges in juvenile and adult sunfish,Lepomis gibbosus

Microridges are F-actin-based surface protrusions of the superficial layer cells of fish epidermis. Microridge patterns progress in complexity during fish embryogenesis, often transitioning from abundant surface microvilli to the classical fingerprint arrangement. This progression suggests pattern changes may also occur during later stages of fish development. Fluorescent labelling of F-actin and morphometric analysis were therefore used to assess changes in epidermal microridge patterns in juvenile and adult sunfish (Lepomis gibbosus). The microridge patterns found in adult pumpkinseed were similar to that described for many fishes, consisting of whorls or complex multi-branched ridges. The microridge patterns of the scales from three different-sized groups of juvenile pumpkinseed were distinctly different from that of adult, however, and were present mainly as unbranched concentric or nearly concentric rings in the two larger juvenile groups. In the smallest juveniles, microridges were often apparent as fragmented ridges with abundant actin puncta. Larger juveniles sometimes displayed mixed patterns, with some microridges similar to that of both adult and juvenile patterns. The results show a transition from simple microridge patterns in juvenile pumpkinseeds to distinctly different, diverse and more complex patterns in adults. The different pattern types may reflect particular microridge functions relevant to fish size and age.     

The roles of shifting and filtering in generating community‐level flowering phenology

Plant phenologies are key components of community assembly and ecosystem function, yet we know little about how phenological patterns differ among ecosystems. Community‐level phenological patterns may be driven by the filtering of species into communities based on their phenology or by intraspecific responses to local conditions that shift when species flower. To understand the relative roles of filtering and shifting on community‐level phenological patterns we compared patterns of first flowering dates (FFD) for herbaceous species at Konza Prairie, KS, USA with those from the colder Fargo, ND, USA area and from Chinnor, England, which has a less continental climate. Comparing patterns of FFD supports that Konza's flowering patterns are potentially influenced both by filtering species that flower early in the growing season and by phenological shifting. Konza species flowering dates were earlier in the spring and later in the fall compared to Fargo, but were not shifted compared to Chinnor, which had a unique suite of early‐flowering species. In all, comparing flowering phenology among three sites reveals that intraspecific responses to climate can generate phenological shifts that compress or stretch community‐level phenological patterns, while novel niches in phenological space can also alter community‐level patterns. Community flowering patterns related to climate suggest that climatic warming has the potential to further distribute flowering of the Konza flora over a longer period, but also could further open it to introductions of non‐native species that have evolved to flower early in the season.     

Modern European cranial variables and blood polymorphisms show comparable spatial patterns

Spatial patterns in cranial traits for modern European populations are compared with patterns described by Sokal et al. (1989) for blood polymorphisms. Spatial patterns in these variables are described from both one-dimensional and directional autocorrelation correlograms. Manhattan distances computed among one-dimensional correlograms are used (1) to cluster variables with similar patterns and (2) to test the hypothesis that these clusters are to some extent accounted for by the type of variable. The one-dimensional correlograms for cranial traits do not show a significant contrast with either red cell antigens or the set of blood polymorphisms that excludes HLA. The only contrast that accounts for any of the cluster structure among one-dimensional correlograms is that between HLA and non-HLA variables. A cluster analysis of the directional correlograms demonstrates that cranial traits reflect patterns comparable to those for blood polymorphisms. This finding implies that patterns in cranial variables can be accounted for by the same, or similar, population processes as those inferred from patterns in blood polymorphisms. The implications of this finding for the likely origin of the northwest-southeast cline seen in some modern blood polymorphisms and modern cranial variables, but not in Neolithic cranial variables, are discussed.     

Phyllotactic Pattern Generation: A Conceptual Model

A conceptual model is proposed here that shows how all typesof whorled and peculiar patterns in phyllotaxis derive straightforwardlyfrom normal and anomalous spiral patterns. This is a completemodel of phyllotaxis, integrating the author's interpretativemodel for generating spiral patterns. The paper underlines thata better understanding of the variety of phyllotactic patterns,and of the transitions between them, involves a phylogeneticperspective. It stresses the working hypothesis that spiralpatterns are primitive and that all other patterns, such aswhorled systems, are by-products of evolution from spirality.An important epistemological consequence on mathematical modellingis drawn out of this hypothesis, namely that models of knowledgeor interpretative models, able to take care of the spiral patterns,must be formulated and then followed by simulation, mechanisticor conceptual models that are able to reproduce the transitionsto all other types of patterns. Phyllotaxis, parastichy pair, shoot apex, multijugy, spirality, whorl, modelling, phylogeny, telome theory, Hofmeister's rule     

Changing clothes easily: connexin41.8 regulates skin pattern variation

The skin patterns of animals are very important for their survival, yet the mechanisms involved in skin pattern formation remain unresolved. Turing's reaction-diffusion model presents a well-known mathematical explanation of how animal skin patterns are formed, and this model can predict various animal patterns that are observed in nature. In this study, we used transgenic zebrafish to generate various artificial skin patterns including a narrow stripe with a wide interstripe, a narrow stripe with a narrow interstripe, a labyrinth, and a 'leopard' pattern (or donut-like ring pattern). In this process, connexin41.8 (or its mutant form) was ectopically expressed using the mitfa promoter. Specifically, the leopard pattern was generated as predicted by Turing's model. Our results demonstrate that the pigment cells in animal skin have the potential and plasticity to establish various patterns and that the reaction-diffusion principle can predict skin patterns of animals.     

成都平原不同土地利用方式对土壤剖面钾素分布的影响

为探索快速城市化背景下土地利用方式变化对土壤剖面钾素变化的影响,本研究选取成都平原4种典型土地利用方式(稻-麦、稻-蔬、稻-油和园林),基于187个土壤剖面数据,分析了不同土地利用方式下土壤剖面速效钾、缓效钾、矿物钾和全钾4种不同形态钾的含量特征及相互关系.结果表明: 从表层土壤来看,相较传统轮作(稻-麦、稻-油)而言,土地利用方式显著影响了土壤速效钾和缓效钾含量变化,稻-蔬轮作提高了表层土壤速效钾和缓效钾含量,园林用地则加剧了土壤速效钾和缓效钾的消耗.对于较为稳定的土壤矿物钾和全钾而言,其含量在不同土地利用方式间均无显著差异.从深层土壤来看,稻-蔬轮作方式下速效钾含量随土层加深下降最为明显,传统轮作土壤速效钾含量显著高于园林用地,缓效钾变化趋势与速效钾相反.不同土地利用方式土壤矿物钾和全钾含量差异较小.在4种土地利用方式中,稻-蔬轮作方式下表层土壤速效钾和缓效钾占全钾比例相对其他3种土地利用方式较高,20～40 cm土层,不同土地利用方式下速效钾占全钾比例均显著下降,缓效钾随土层向下比例变化与速效钾变化趋势恰好相反.矿物钾占全钾比例在不同土地利用方式下无显著差异.可见,不同土地利用方式对成都平原土壤速效钾和缓效钾在剖面中的分布具有显著影响.