A Constant of temporal structure in the human hierarchy and other systems

The levels that compose biological hierarchies each have their own energetic, spatial and temporal structure. Indeed, it is the discontinuity in energy relationships between levels, as well as the similarity of sub-systems that support them, that permits levels to be defined. In this paper, the temporal structure of living hierarchies, in particular that pertaining to Human society, is examined. Consideration is given to the period defining the lifespan of entities at each level and to a periodic event considered fundamental to the maintenance of that level. The ratio between the duration of these two periods is found to be approximately 2.5 × 10⁴. A similar relationship is found when lower, non-living levels of molecules and atoms are considered. This suggests that there is a constant factor of amplification between analogous periodic events at successive levels of the Human hierarchy.     

A unified model of dominance hierarchy formation and maintenance

In many different species it is common for animals to spend large portions of their lives in groups. Such groups need to divide available resources amongst the individuals they contain and this is often achieved by means of a dominance hierarchy. Sometimes hierarchies are stable over a long period of time and new individuals slot into pre-determined positions, but there are many situations where this is not so and a hierarchy is formed out of a group of individuals meeting for the first time. There are several different models both of the formation of such dominance hierarchies and of already existing hierarchies. These models often treat the two phases as entirely separate, whereas in reality, if there is a genuine formation phase to the hierarchy, behaviour in this phase will be governed by the rewards available, which in turn depends upon how the hierarchy operates once it has been formed. This paper describes a method of unifying models of these two distinct phases, assuming that the hierarchy formed is stable. In particular a framework is introduced which allows a variety of different models of each of the two parts to be used in conjunction with each other, thus enabling a wide range of situations to be modelled. Some examples are given to show how this works in practice.     

The role of individual differences and patterns of resolution in the formation of dominance orders in domestic hen triads

This research compares the role of initial individual characteristics to that of patterns of resolution in which successive dominance relationships are established during the formation of triads in the domestic hen. Combining weight and comb size with prior victory or defeat in the site of encounter, we created three levels of asymmetries of characteristics for triads of hens. The effects of these asymmetries were then examined on the resultant hierarchies and on the order of conflict resolution within triads under two different conditions of assembly. In one condition (simultaneous triad), the three hens were simultaneously introduced to each other and could thus freely choose their opponent. In the other condition (step-assembled triad), the hen predicted to occupy the highest rank was left on standby and introduced once the other two hens had settled dominance. This condition disrupts the normal process of hierarchy formation by imposing the first sequence of dominance settlement. We found that the structure of triadic hierarchies can be predicted from individual characteristics existing prior to hierarchy formation. No difference in the resultant structures were found between conditions of introduction, though different paths of conflict resolution were followed indicating that individual differences had a more determining role on the resultant hierarchies than patterns of resolution. In addition to demonstrating that individual differences determine resultant triadic structures, the present results also show that the same end structures can be reached by following resolution paths that are not necessarily of the Double Dominance and Double Subordinance types as prescribed by Chase's model. It is also found that in the simultaneous condition hens select each other to form pairs. Therefore, individuals do not meet at random but choose each other as opponents. The two hens predicted from individual differences to occupy the highest ranks first settle dominance, followed by settlement between the winner of the previous encounter and the bystander.     

ETE: a python Environment for Tree Exploration

Background  

Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale.     

Consequences of hierarchical allocation for the evolution of life-history traits

Resource allocation within individuals may often be hierarchical, and this may have important effects on genetic correlations and on trait evolution. For example, organisms may divide energy between reproduction and somatic growth and then subdivide reproductive resources. Genetic variation in allocation to pathways early in such hierarchies (e.g., reproduction) can cause positive genetic correlations between traits that trade off (e.g., offspring size and number) because some individuals invest more resources in reproduction than others. We used quantitative-genetic models to explore the evolutionary implications of allocation hierarchies. Our results showed that when variation in allocation early in the hierarchy exceeds subsequent variation in allocation, genetic covariances and initial responses to selection do not reflect trade-offs occurring at later levels in the hierarchy. This general pattern was evident for many starting allocations and optima and for whether traits contributed multiplicatively or additively to fitness. Finally, artificial selection on a single trait revealed masked trade-offs when variation in early allocation was comparable to subsequent variation in allocation. This result confirms artificial selection as a powerful, but not foolproof, method of detecting trade-offs. Thus, allocation hierarchies can profoundly affect life-history evolution by causing traits to evolve in the opposite direction to that predicted by trade-offs.     

Functional morphology and phylogenetic testing within the framework of symecomorphosis

On the basis of the contrasting evolutionary patterns of the Teleostei and the "Chondrostei" the merit of phylogenetic testing is summarized as a non-arbitrary method for assessing the possible role of various designs in producing differential morphological diversity in different lineages. Arguments are presented for the recognition of a genealogical (reproductive, informational) and an ecological hierarchy. Various levels are proposed within hierarchies, because there are processes intrinsic to each level that are not reducible to those of lower levels or subsumed by higher levels. Mutual influences exist between successive levels within a hierarchy and possible interhierarchical mutual influences are hypothesized between organisms, demes, and avatars, and from the germ line to functional units. The term symecomorphosis is proposed to denote the balanced symmetry of the co-existing and mutually interdependent ecological and genealogical hierarchies. Symecomorphosis predicts that a disturbance in environmental systems can destroy this balance with profound effects on the genealogical hierarchy. Using the evolutionary differentiation of four lineages of air breathing teleosts as an example, it is demonstrated how the principle of symecomorphosis can be included in tests establishing a causal relationship between design and differential diversity among lineages.     

A new perspective on size hierarchies in nature: patterns, causes, and consequences

Many plant and animal aggregations have size hierarchies within which a variety of sizes of individuals, from large to small, can be found. Size hierarchies are thought to indicate the existence of competition amongst individuals within the aggregation, but determining their exact cause is difficult. The key to understanding size hierarchies lies in first quantifying the pattern of size and growth of individuals. We conducted a quantitative investigation of pattern in the size hierarchy of the clown anemonefish Amphiprion percula, in Madang Lagoon, Papua New Guinea. Here, groups of A. percula occupy sea anemones (Heteractis magnifica) that provide protection from predators. Within each anemone there is a single group composed of a breeding pair and zero to four non-breeders. Within each group there is a single size hierarchy; the female is largest (rank 1), the male is second largest (rank 2), and the non-breeders get progressively smaller (ranks 3–6). We demonstrate that individuals adjacent in rank are separated by body size ratios whose distribution is significantly different from the distribution expected under a null model—the growth of individuals is regulated such that each dominant ends up being about 1.26 times the size of its immediate subordinate. We show that it is decisions about growth at the individual level that generate the size hierarchy at the group level, and thereby determine maximum group size and population size. This study provides a new perspective on the pattern, causes and consequences of size hierarchies.     

The smell of success and failure: the role of intrinsic and extrinsic chemical signals on the social behavior of crayfish

Animals commonly modify their behavior in the presence of aconspecific or in response to signals. This is particularlytrue in the context of aggressive exchanges, which animals useto form networks of social relationships and to communicatesocial status associated with those relationships. Althoughhierarchical structures are a widespread phenomenon that hasbeen studied extensively, the dynamic communication processes,specifically chemical communication in this review, is relativelyoverlooked. In particular, it is the exchange of informationduring agonistic interactions that mediates hierarchies and/oralters the outcomes of agonistic interactions. Given the theoreticalappeal of these interactions, and the evolutionary importanceand taxonomic diversity associated with social hierarchies,it is not surprising that the sensory mechanisms involved inthe formation and maintenance of hierarchical structures havereceived recent attention. In crayfish, dominance is thoughtto be largely determined by physical superiority, where encountersare largely dyadic and fighting behavior is highly stereotyped.However, recent evidence has shown that the outcome of dyadicencounters are dependent upon a number of factors other thanphysical size, that include the exchange of chemical informationduring encounters, previous social history, and the intrinsicneurochemical state of opponents. We have attempted to providea comprehensive analysis of the extrinsic chemical processes(previous history, sensory communication, etc.) and intrinsicchemical processes (neurochemical state) that produce and maintaindominance relations and social hierarchies in crayfish. We hopethat this review will bring together a global picture of theprocesses that determine a crayfish's social standing and howintrinsic and extrinsic chemicals have substantial effects onaggressive states and agonistic bouts.     

Sex and rank in competitive brood hierarchies influence stress levels in nestlings of a sexually dimorphic bird

Studies of sibling competition within brood hierarchies have rarely assessed simultaneously the effects of sex and rank in the brood hierarchy on traits other than offspring mortality and differential growth. We studied the expression of heat-shock proteins (Hsps) to assess the physiological stress response to different combinations of sex and position within competitive brood hierarchies in the black kite Milvus migrans (Bodd.), a sexually dimorphic raptor showing facultative siblicide. Senior males showed higher stress levels than did senior females and younger siblings of each sex as revealed by Hsp60 values. The analysis of Hsp70 levels indicated that nestlings from broods in which the senior chick was a male showed higher stress levels than did nestlings from broods in which the senior chick was a female. In addition, levels of Hsp60 were related negatively to nutritional condition expressed as levels of plasmatic albumin. This suggests that the sex of senior chicks may be key in determining their stress level and that of their siblings, which is probably associated with sibling competition by fighting within brood hierarchies. The comparatively higher stress levels of senior males (and their siblings) may be a consequence of their ability to exploit their potential advantage from being the head start while avoiding a possible competitive disadvantage from being the smaller sex, independent of environmental conditions determining the probability of brood reduction. Differential stress levels depending on sex and rank in the brood hierarchy may be a consequence of parental control of offspring behaviour through differential resource allocation (e.g. yolk androgens) or it may reflect adaptations of particular chicks (senior males) to enhance their competitive ability within brood hierarchies.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 383–390.     

Introduction: Who's at the bottom? Examining claims about racial hierarchy

Why do claims about racial hierarchy matter? The question whether some groups are worse off than others is highly pertinent at a time when there is growing recognition of multiple forms of racisms and racial oppression. It is widely accepted that racial hierarchies are still with us today, and this concept is peppered throughout writings on “race” and racisms, but, what, exactly, are racial hierarchies, how do racial hierarchies continue to matter, and in what ways do they operate? This special issue, which focuses on the USA and Britain, also addresses the following questions: Does the concept of racial hierarchy aid us in illuminating racial inequalities and the differential experiences of groups in Western multi-ethnic societies such as the USA and Britain? What sorts of criteria are used in arguments about the place of groups along racial hierarchies? What are the political implications of claims made about racial hierarchies?     

Optimal Behavioral Hierarchy

Human behavior has long been recognized to display hierarchical structure: actions fit together into subtasks, which cohere into extended goal-directed activities. Arranging actions hierarchically has well established benefits, allowing behaviors to be represented efficiently by the brain, and allowing solutions to new tasks to be discovered easily. However, these payoffs depend on the particular way in which actions are organized into a hierarchy, the specific way in which tasks are carved up into subtasks. We provide a mathematical account for what makes some hierarchies better than others, an account that allows an optimal hierarchy to be identified for any set of tasks. We then present results from four behavioral experiments, suggesting that human learners spontaneously discover optimal action hierarchies.     

Relative roles of primary sequence and (G + C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species

To an approximation Chargaff's rule (%A = %T; %G = %C) applies to single-stranded DNA. In long sequences, not only complementary bases but also complementary oligonucleotides are present in approximately equal frequencies. This applies to all species studied. However, species usually differ in base composition. With the goal of understanding the evolutionary forces involved, I have compared the frequencies of trinucleotides in long sequences and their shuffled counterparts. Among the 32 complementary trinucleotide pairs there is a hierarchy of frequencies which is influenced both by base composition (not affected by shuffling the order of the bases) and by base order (affected by shuffling). The influence of base order is greatest in DNA of 50% G + C and seems to reflects a more fundamental hierarchy of dinucleotide frequencies. Thus if TpA is at low frequency, all eight TpA-containing trinucleotides are at low frequency. Mammals and their viruses share similar hierarchies, with intra- and intergenomic differences being mainly associated with differences in base composition (percentage G + C). E. coli and, to a lesser extent, Drosophila melanogaster hierarchies differ from mammalian hierarchies; this is associated with differences both in base composition and in base order. It is proposed that Chargaff's rule applies to single-stranded DNA because there has been an evolutionary selection pressure favoring mutations that generate complementary oligonucleotides in close proximity, thus creating a potential to form stem-loops. These are dispersed throughout genomes and are rate-limiting in recombination. Differences in (G + C)% between species would impair interspecies recombination by interfering with stem-loop interactions.     

Entity grammar systems: A grammatical tool for studying the hierarchal structures of biological systems

The hierarchal structures of biological systems are the typical complex hierarchal dynamical structures in the physical world, the effective investigations on which could not be performed with the existing formal grammar systems. To meet the needs of the investigation on these kinds of systems, especially the emerging field of system biology, a grammatical tool was proposed in the present article. Because the grammatical toolmainly deals with the systems composed of structured entities, they are called entity grammar systems (EGSs). The structure of entities in EGSs have the general form of the objects in the physical world, which means EGSs could be used as a tool to study the complex system composed of many objects with different structures, just like the biological systems. The article contains the formal definition of EGSs and the hierarchy of EGSs, which is congruent with the Chomsky hierarchy. The relationship between EGSs and array grammar systems, graph grammar systems, tree grammar systems, multi-set grammar systems are discussed to show the generative power of EGSs. At the end of the present article, the steps to define new grammar systems with the form of EGS are provided and the possible applicable fields of EGSs are discussed.     

A model of apical bifurcation applicable to trees and other organisms

An elementary model to describe the branching process in tree-like structures is proposed. It is assumed that when the apex reaches a certain size, it divides into two apices. The relative sizes of the two apices depends upon a branching parameter λ, which is the critical parameter of the model. With this constraint, and with some supplementary assumptions about growth, a computer is used to generate branched structures, and these are analyzed using Strahler's method of ordering. Diverse tree-like structures can be obtained by simply varying the parameter λ, and these resemble natural structures when compared on the basis of Strahler's technique.     

Modes of Interaction between Individuals Dominate the Topologies of Real World Networks

We find that the topologies of real world networks, such as those formed within human societies, by the Internet, or among cellular proteins, are dominated by the mode of the interactions considered among the individuals. Specifically, a major dichotomy in previously studied networks arises from modeling networks in terms of pairwise versus group tasks. The former often intrinsically give rise to scale-free, disassortative, hierarchical networks, whereas the latter often give rise to single- or broad-scale, assortative, nonhierarchical networks. These dependencies explain contrasting observations among previous topological analyses of real world complex systems. We also observe this trend in systems with natural hierarchies, in which alternate representations of the same networks, but which capture different levels of the hierarchy, manifest these signature topological differences. For example, in both the Internet and cellular proteomes, networks of lower-level system components (routers within domains or proteins within biological processes) are assortative and nonhierarchical, whereas networks of upper-level system components (internet domains or biological processes) are disassortative and hierarchical. Our results demonstrate that network topologies of complex systems must be interpreted in light of their hierarchical natures and interaction types.     

Epigenetic regulation of germ cell differentiation

Germ cells and somatic cells have the identical genome. However, unlike the mortal fate of somatic cells, germ cells have the unique ability to differentiate into gametes that retain totipotency and produce an entire organism upon fertilization. The processes by which germ cells differentiate into gametes, and those by which gametes become embryos, involve dramatic cellular differentiation accompanied by drastic changes in gene expression, which are tightly regulated by genetic circuitries as well as epigenetic mechanisms. Epigenetic regulation refers to heritable changes in gene expression that are not due to changes in primary DNA sequence. The past decade has witnessed an ever-increasing understanding of epigenetic regulation in many different cell types/tissues during embryonic development and adult homeostasis. In this review, we focus on recent discoveries of epigenetic regulation of germ cell differentiation in various metazoan model organisms, including worms, flies, and mammals.     

Modelling the ecological-functional diversification of marine Metazoa on geological time scales

The ecological traits and functional capabilities of marine animals have changed significantly since their origin in the late Precambrian. These changes can be analysed quantitatively using multi-dimensional parameter spaces in which the ecological lifestyles of species are represented by particular combinations of parameter values. Here, we present models that describe the filling of this multi-dimensional 'ecospace' by ecological lifestyles during metazoan diversification. These models reflect varying assumptions about the processes that drove ecological diversification; they contrast diffusive expansion with driven expansion and niche conservatism with niche partitioning. Some models highlight the importance of interactions among organisms (ecosystem engineering and predator-prey escalation) in promoting new lifestyles or eliminating existing ones. These models reflect processes that were not mutually exclusive; rigorous analyses will continue to reveal their applicability to episodes in metazoan history.