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.     

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.     

How much have we learned about seasonality in tropical insect abundance since Wolda (1988)?

Seasonal patterns in climatic conditions affect the life cycles and temporal patterns in the abundance of most temperate insect species. In tropical regions where there is no winter season, the situation may be different. For a better understanding of the evolution of seasonal life cycles, and the dynamics affecting temporal patterns in abundance of tropical insect populations and assemblages, it is important to study the life cycles of tropical insects and the presence or absence of seasonality in relation to climatic conditions. By reviewing studies on temporal patterns of abundance, this article examines the patterns of seasonality in adult tropical forest insects and discusses the variation in such patterns in various forest types. Seasonal and aseasonal patterns were found to be common in tropical dry and wet regions, respectively. In wet regions, which lack a distinctive dry season, there exists a wide variety of temporal patterns in addition to aseasonal patterns: distinctively seasonal and supra‐annual fluctuations in some insect species. Some of the problems of hidden ecological mechanisms underlying seasonal patterns in abundance are discussed, and the definition of seasonality in temporal patterns of insect abundance at a particular stage in the life cycle is considered. Methodological problems are also discussed.     

The Concept of Taxon Invariance in Ecology: Do Diversity Patterns Vary with Changes in Taxonomic Resolution?

Diversity patterns cannot be properly interpreted without a theory providing criteria for their evaluation. We propose a concept to prevent artifictions caused by improper consideration of changes in observed patterns due to variation in taxon delimitation. Most biodiversity patterns concern assemblages of species of given higher taxon (e.g. class). Some patterns seem to be universal, e.g., body size distribution, species-abundance distribution, species-area relationship, or the relationship between diversity and energy availability. However, truly universal patterns should not change when we change taxonomic scope by focusing on subtaxa or when we merge several sister taxa together and analyze patterns in resulting higher taxon. Similarly, some patterns may not change when changing the basic unit of the study e.g., when replacing species by genera or families (or any monophyletic clades), although other patterns may not be invariant against the variation of the basic unit. In fact, there are only two possibilities: biodiversity patterns are either taxon-invariant or they vary systematically with taxonomic resolution, which would indicate some fundamental taxonomic level with interesting implications for biological processes behind those patterns. Here we develop the concept of taxon invariance of diversity patterns and apply it on the abovementioned patterns. We show that simple theoretical considerations markedly constrain the set of possible patterns, as some of them cannot be simultaneously valid for both a taxon and its subtaxa – frequency distributions of abundances cannot be simultaneously lognormal for a given taxon and all its subtaxa, the taxa-area relationship cannot follow a power-law for all levels of taxonomic resolution, and energy availability cannot affect diversity of all taxonomic units in the same way. Analyses of the variation in the form of biodiversity patterns with changing taxonomic resolution thus provide an extremely useful tool for revealing properties of respective patterns, their universality and logical consistency.     

The colour patterns of cypraeid gastropods

Colour patterns on mollusc shells are usually controlled by one-dimensional morphogenetic programmes. In adult cypraeids, by comparison, colour patterns are two-dimensional in morphogenesis and three-dimensional in structure. Visible patterns usually result from the uneven thickness of a pigmented layer, rather than from a spatially uneven concentration of pigment. Specialized sculptures in a few cypraeids may be regarded as extreme examples of three-dimensional colour patterns. Morphogenesis of some patterns is controlled by three-dimensional relief of the underlying shell surface. Computer models successfully reproduce key characteristics of cypraeid colour patterns. Since most cypraeids possess colour patterns, while few of the combinations of factors controlling these programmes yield a pattern, these patterns can be expected to have a yet undemonstrated adaptive value.     

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.     

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.     

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.     

An equilibrium-point model of electromyographic patterns during single-joint movements based on experimentally reconstructed control signals

The purpose of this work has been to develop a model of electromyographic (EMG) patterns during single-joint movements based on a version of the equilibrium-point hypothesis, a method for experimental reconstruction of the joint compliant characteristics, the dual-strategy hypothesis, and a kinematic model of movement trajectory. EMG patterns are considered emergent properties of hypothetical control patterns that are equally affected by the control signals and peripheral feedback reflecting actual movement trajectory. A computer model generated the EMG patterns based on simulated movement kinematics and hypothetical control signals derived from the reconstructed joint compliant characteristics. The model predictions have been compared to published recordings of movement kinematics and EMG patterns in a variety of movement conditions, including movements over different distances, at different speeds, against different-known inertial loads, and in conditions of possible unexpected decrease in the inertial load. Changes in task parameters within the model led to simulated EMG patterns qualitatively similar to the experimentally recorded EMG patterns. The model's predictive power compares it favourably to the existing models of the EMG patterns.     

Elephants in space and time

Autocorrelation in animal movements can be both a serious nuisance to analysis and a source of valuable information about the scale and patterns of animal behavior, depending on the question and the techniques employed. In this paper we present an approach to analyzing the patterns of autocorrelation in animal movements that provides a detailed picture of seasonal variability in the scale and patterns of movement. We used a combination of moving window Mantel correlograms, surface correlation and crosscorrelation analysis to investigate the scales and patterns of autocorrelation in the movements of three herds of elephants in northern Botswana. Patterns of autocorrelation of elephant movements were long‐range, temporally complicated, seasonally variable, and closely linked with the onset of rainfall events. Specifically, for the three elephant herds monitored there was often significant autocorrelation among locations up to lags of 30 days or more. During many seasonal periods there was no indication of decreasing autocorrelation with increasing time between locations. Over the course of the year, herds showed highly variable and complex patterns of autocorrelation, ranging from random use of temporary home ranges, periodic use of focal areas, and directional migration. Even though the patterns of autocorrelation were variable in time and quite complex, there were highly significant correlations among the autocorrelation patterns of the different herds, indicating that they exhibited similar patterns of movement through the year. These major patterns of autocorrelation seem to be related to patterns of rainfall. The strength of correlation in movement patterns of the different herds decreased markedly at the cessation of major rain events. Also, there was a strong crosscorrelation between strength of autocorrelation of movement and rainfall, peaking at time lags of between three and four weeks. Overall, these approaches provide a powerful way to explore the scales and patterns of autocorrelation of animal movements, and to explicitly link those patterns to temporally variable environmental attributes, such as rainfall or vegetation phenology.     

Parameterization and classification of the protein universe via geometric techniques

We present a scheme for the classification of 3487 non-redundant protein structures into 1207 non-hierarchical clusters by using recurring structural patterns of three to six amino acids as keys of classification. This results in several signature patterns, which seem to decide membership of a protein in a functional category. The patterns provide clues to the key residues involved in functional sites as well as in protein-protein interaction. The discovered patterns include a "glutamate double bridge" of superoxide dismutase, the functional interface of the serine protease and inhibitor, interface of homo/hetero dimers, and functional sites of several enzyme families. We use geometric invariants to decide superimposability of structural patterns. This allows the parameterization of patterns and discovery of recurring patterns via clustering. The geometric invariant-based approach eliminates the computationally explosive step of pair-wise comparison of structures. The results provide a vast resource for the biologists for experimental validation of the proposed functional sites, and for the design of synthetic enzymes, inhibitors and drugs.     

Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity

The exact extent of microbial diversity remains unknowable. Nevertheless, fingerprinting patterns [denaturing gradient electrophoresis (DGE), single-strand conformation polymorphism (SSCP)] provide an image of a microbial ecosystem and contain diversity data. We generated numerical simulation fingerprinting patterns based on three types of distribution (uniform, geometric and lognormal) with a range of units from 10 to 500,000. First, simulated patterns containing a diversity of around 1000 units or more gave patterns similar to those obtained in experiments. Second, the number of bands or peaks saturated quickly to about 35 and were unrelated to the degree of diversity. Finally, assuming lognormal distribution, we used an estimator of diversity on in silico and experimental fingerprinting patterns. Results on in silico patterns corresponded to the simulation inputs. Diversity results in experimental patterns were in the same range as those obtained from the same DNA sample in molecular inventories. Thus, fingerprinting patterns contain extractable data about diversity although not on the basis of a number of bands or peaks, as is generally assumed to be the case.     

Discover 1: a new program to search for unusually represented DNA motifs.

DISCOVER1 (DIStribution COunter VERsion 1) is a new program that can identify DNA motifs occurring with a high deviation from the expected frequency. The program generates families of patterns, each family having a common set of defined bases. Undefined bases are inserted amongst the defined bases in different ways, thus generating the diverse patterns of each family. The occurrences of the different patterns are then compared and analysed within each family, assuming that all patterns should have the same probability of occurrence. An extensive use of computer memory, combined with the immediate sorting of counts by address calculation allow a complete counting of all DNA motifs on a single pass on the DNA sequence. This approach offers a very fast way to search for unusually distributed patterns and can identify inexact patterns as well as exact patterns.     

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.     

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.     

Characterization of Staphylococcus species by ribosomal RNA gene restriction patterns

The rRNA gene restriction pattern sof 110 strains belonging to 12 staphylococcal species have been determined. The strains, isolated from various sources, were epidemiologically unrelated. Total DNA was cleaved with restriction enzymes HindIII and EcoRI, electrophoretically separated and probed with radiolabelled 16S rDNA from Bacillus subtilis inserted in a plasmid vector, pBR322. Fourty-four distinct HindIII patterns and 44 distinct EcoRI patterns were observed. Strains belonging to different species had different patterns. Although distinct patterns were also observed with some species, a core of common bands could be discerned within each species or subspecies. Analysis of the patterns revealed two taxa in Staphylococcus xylosus which were not evident using phenotypic characteristics. Of 18 strains which were difficult to identify using phenotypic schemes, 15 showed patterns typical of known species. The three remaining atypical strains showed unusual patterns and may belong either to a known species, not included in the study, or to a new species. Since various patterns were observed within some species (e.g.S.aureus and S. epidermidis), rRNA gene restriction patterns may have epidemiological, as well as taxonomic interest.     

Inferring a District-Based Hierarchical Structure of Social Contacts from Census Data

Researchers have recently paid attention to social contact patterns among individuals due to their useful applications in such areas as epidemic evaluation and control, public health decisions, chronic disease research and social network research. Although some studies have estimated social contact patterns from social networks and surveys, few have considered how to infer the hierarchical structure of social contacts directly from census data. In this paper, we focus on inferring an individual’s social contact patterns from detailed census data, and generate various types of social contact patterns such as hierarchical-district-structure-based, cross-district and age-district-based patterns. We evaluate newly generated contact patterns derived from detailed 2011 Hong Kong census data by incorporating them into a model and simulation of the 2009 Hong Kong H1N1 epidemic. We then compare the newly generated social contact patterns with the mixing patterns that are often used in the literature, and draw the following conclusions. First, the generation of social contact patterns based on a hierarchical district structure allows for simulations at different district levels. Second, the newly generated social contact patterns reflect individuals social contacts. Third, the newly generated social contact patterns improve the accuracy of the SEIR-based epidemic model.     

Wheel-Running Activity Patterns of Five Species of Desert Rodents

In contrast to the extensive laboratory data on activity patterns in rodent species inhabiting temperate zones, much less is known about the activity patterns of desert rodents. In order to address this issue, we measured wheel-running activity patterns in males and females of five species of wild-trapped desert rodents (Dipodillus dasyurus, Gerbillus andersoni, Gerbillus pyramidum, Meriones shawi, and Acomys cahirinus) in long 'summer-like' and short, 'winter-like' day lengths. The specific goals of the present study were to characterize activity patterns in several desert rodent species in the laboratory and to determine if activity patterns are expressed in a seasonal or sexually dimorphic manner. Specifically, wheel-running was measured for 11 weeks in long days followed by 11 weeks in short days to test for photoperiodic entrainment as well as responsiveness to changes in the light-dark cycle. All animals exhibited rhythmic patterns of wheel-running with consistent onsets and offsets that had well-defined relations with the light-dark cycle. All individuals of G. andersoni showed nocturnal activity patterns. Most individuals of G. pyramidum had nocturnal activity patterns, but some individuals showed a short bout of activity at the beginning of the light period. Most individuals of D. dasyurus and M. shawi showed bimodal (i.e., nocturnal and diurnal) activity patterns, although some showed markedly nocturnal activity patterns. There was no sexual dimorphism in wheel running activity rhythms in any of the species examined. As expected, decreases in day length resulted in an overall increase in the duration of activity in all species. Collectively, these data provide an initial characterization of activity patterns within desert rodents in a controlled laboratory setting.     

Detection of irregular spatial structures

Wilson et al.'s (1997) study on Glass patterns suggested that the integration of stimulus features into a linear shape occurs quite locally, whereas curved structures--such as circular--require global summation. Their conclusion was based on experiments in which they varied the size of the signal area containing a spatial structure. In the present study, we tested the integration of constant-sized linear and curved Glass patterns by varying their global irregularity. If the mechanisms underlying the detection of a Glass pattern pool features globally throughout the stimulus, the irregularity should have a strong effect on detection performance. The irregular Glass patterns were composed of a variable number of sub-areas, each of which contained its own linear or curved structure. The structural irregularity impaired the detection of the curved patterns, whereas the thresholds for the linear patterns were not affected. Thus, our results are in line with the notion that the integration of curved Glass patterns occurs more globally than the integration of linear patterns.     

Evolutionary origins of novel conchologic growth patterns in tropical American corbulid bivalves

We conducted a combined sclerochronologic and phylogenetic analysis to document patterns and rates of shell accretion in several subclades of related corbulids, and to explore the evolutionary origins of novel conchologic developmental patterns. We found three disparate patterns of valve development in Neogene tropical American corbulid genera. These patterns include growth through primarily radial accretion along the sagittal plane, and two derivative patterns: one characterized by initial deposition of a thin shell followed by valve thickening with little increase in valve height, and another producing a well-defined nepioconch through a marked change in the primary growth direction. We conducted a species-level phylogenetic analysis of the taxa surveyed for growth patterns, focusing on the ([Bothrocorbula+Hexacorbula]+Caryocorbula) clade. The phylogenetic distribution of shell growth patterns suggests that this clade is characterized by derivative patterns of growth. Oxygen-isotope calibrated ontogenetic age estimates of species in the derived Bothrocorbula subclade further suggest that transitions from the ancestral radial (sagittal) growth pattern to a derived pattern of growth are a function of heterochrony (peramorphosis by acceleration). These findings are significant because they link previously observed patterns of morphological constraint with a specific evolutionary process, demonstrate how morphologic constraint and innovation can be interrelated, and serve as a model for understanding the evolution of morphologic diversity in the clade as a whole. Furthermore, this study highlights the utility of sclerochronologic records as an important component of evolutionary developmental research on organisms with accretionary skeletal growth.