Effect of unknown relationships on linearity, steepness and rank ordering of dominance hierarchies: simulation studies based on data from wild monkeys

The presence of unknown dyadic relationships is a common problem in constructing dominance hierarchies for groups of social animals. Although previously acknowledged, the influence of unknown relationships on hierarchy measures like linearity and steepness has not been studied in detail. Using real data-sets from four groups of wild monkeys, we illustrate how unknown relationships affect linearity and steepness of hierarchies and the consistency of rank ordering based on de Vries’ I&SI method. Monte Carlo simulations revealed significant negative linear relationships between the proportion of unknown relationships and both linearity and steepness. These simulations over-estimated steepness and linearity indices relative to additional real-data input matrices. Rank orders became inconsistent at 26–38% unknown relationships, depending on the group. Group size and the specific input matrix substantially affected how much unknown relationships influenced steepness and linearity, the values of these indices and the point at which rank order became inconsistent. We recommend caution in characterizing the dominance structure of a group with many unknown relationships, and in drawing conclusions about hierarchy linearity and steepness based on few input matrices, especially if they contain many unknown relationships. Quantitative characterizations of hierarchies are perhaps best viewed as a somewhat fluid range rather than fixed values.     

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.     

A Novel Method of Assessing Dominance Hierarchies Shows Nuance,Linearity and Stability in the Dinosaur Ant Dinoponera quadriceps

Many social species with relatively simple societies have dominance hierarchies of individuals, with dominant individuals achieving fitness and subordinate individuals either queuing to obtain fitness or achieving only indirect fitness by helping relatives. Assessing the dominance hierarchy in a social group is generally based upon observing dyadic interactions as and when they occur spontaneously within the whole‐group setting. However, this method can be very time‐consuming because many dyads interact only very rarely, necessitating either extremely long observation periods or many dyadic relationships being unresolved. Here, we report an alternative method using the queenless dinosaur ant Dinoponera quadriceps, which lives in colonies containing tens of individuals. We removed all individuals from their nest and observed the dominance behaviours expressed in isolated dyadic interactions for every pairwise combination of individuals. Individuals showed a classic dominance behaviour in this setting, and the rapid nature of the assay allowed us to observe every dyadic relationship on a weekly basis over 4 weeks. The dominance hierarchies based on these isolated dyadic interactions correlated well with those produced by the conventional method of colony observations. They showed the hierarchies to be highly linear and stable, and also revealed that dominance relationships may extend further down the hierarchy than previously thought. Although highly manipulative, the isolated dyadic interaction method works well and will likely make more feasible the study of other social species in which pairs of individuals can be isolated together.     

Architectures of biological complexity

Three features contribute to the complexity of an entity: numberof parts, their order, and their iteration. Many functionalbiological entities are complex when measured by those attributes,and although they are produced in tree-like architectures, theorganizational structures that permit them to function are inthe form of hierarchies. Natural hierarchies can be thoughtof as organizing structures that are emergent properties ofcomplex functional entities, and which are transformed fromtrees by process networks. For example, hierarchies are observedin the architecture of metazoan bodies (the somatic hierarchy)and in the biotic structure of ecogeographic units (the ecologicalhierarchy). As the metazoan developmental genome is quite complexand has been evolved through tree-like processes, it must harborat least one hierarchy, which is most clearly indicated in thedevelopmental processes that create the somatic hierarchy. Formulticellular organisms, the processes that serve to transformtrees of gene expression events into a somatic hierarchy haveproduced complicated signaling networks whose histories canprobably be recovered in general outline.     

Inferring dominance interactions from automatically recorded temporal data

Understanding dominance hierarchies is an important aspect of many studies of animal groups. Collecting the necessary data requires a large amount of time and effort to detect only a small number of interactions. Here, we assess the viability of extracting interactions from a temporal data stream of arrival and departures to a feeder equipped with a radio‐frequency identifier antenna. We show that the interactions extracted from this type of data can create similar dominance hierarchies to those produced by analysing video data of interactions. Additionally, we assessed the amount of temporal data required to obtain a dominance hierarchy and discuss the advantages and disadvantages of utilising temporal data streams to generate dominance hierarchies of animal groups. The code to extract the dominance interactions and test the correlation between different dominance hierarchies is included in the Supporting Information .     

Comparing the Hierarchy of Keywords in On-Line News Portals

Hierarchical organization is prevalent in networks representing a wide range of systems in nature and society. An important example is given by the tag hierarchies extracted from large on-line data repositories such as scientific publication archives, file sharing portals, blogs, on-line news portals, etc. The tagging of the stored objects with informative keywords in such repositories has become very common, and in most cases the tags on a given item are free words chosen by the authors independently. Therefore, the relations among keywords appearing in an on-line data repository are unknown in general. However, in most cases the topics and concepts described by these keywords are forming a latent hierarchy, with the more general topics and categories at the top, and more specialized ones at the bottom. There are several algorithms available for deducing this hierarchy from the statistical features of the keywords. In the present work we apply a recent, co-occurrence-based tag hierarchy extraction method to sets of keywords obtained from four different on-line news portals. The resulting hierarchies show substantial differences not just in the topics rendered as important (being at the top of the hierarchy) or of less interest (categorized low in the hierarchy), but also in the underlying network structure. This reveals discrepancies between the plausible keyword association frameworks in the studied news portals.     

Nested effects models for high-dimensional phenotyping screens

MOTIVATION: In high-dimensional phenotyping screens, a large number of cellular features is observed after perturbing genes by knockouts or RNA interference. Comprehensive analysis of perturbation effects is one of the most powerful techniques for attributing functions to genes, but not much work has been done so far to adapt statistical and computational methodology to the specific needs of large-scale and high-dimensional phenotyping screens. RESULTS: We introduce and compare probabilistic methods to efficiently infer a genetic hierarchy from the nested structure of observed perturbation effects. These hierarchies elucidate the structures of signaling pathways and regulatory networks. Our methods achieve two goals: (1) they reveal clusters of genes with highly similar phenotypic profiles, and (2) they order (clusters of) genes according to subset relationships between phenotypes. We evaluate our algorithms in the controlled setting of simulation studies and show their practical use in two experimental scenarios: (1) a data set investigating the response to microbial challenge in Drosophila melanogaster, and (2) a compendium of expression profiles of Saccharomyces cerevisiae knockout strains. We show that our methods identify biologically justified genetic hierarchies of perturbation effects. AVAILABILITY: The software used in our analysis is freely available in the R package 'nem' from www.bioconductor.org.     

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.     

Queen Succession in the Social Wasp,Polistes annularis

Outcomes of conflicts among social animals can strongly affect individual fitness and therefore partly determine how sociality evolves. In the social wasp, Polistes annularis, conflicts over egg laying result in a linear dominance hierarchy discernible from which wasps attack which others. We investigated the structure and maintenance of dominance hierarchies in colonies containing both nest foundresses and workers. We also investigated the outcome of a potential conflict between foundresses and workers over the identity of the female which becomes queen after the original queen disappears. To investigate queen replacement we recorded individuals' behavior before and after removal of the queen from 13 nests. This experiment simulated natural queen disappearance which occurs frequently. All foundresses were ranked over workers; high ranking females were most aggressive and directed most of their attacks to the female directly beneath them in the hierarchy. This hierarchy determined succession to queenship; the beta female became queen within 3 h. Therefore a foundress became the new queen whenever one was present. There was no evidence of conflict between workers and foundresses when a foundress became queen. This chance of becoming queen contributes to the expected fitness of a female that accepts a subordinate role in spring.     

Dominance hierarchies reduce the number of hopeful reproductives in polygynous queenless ants

Summary. In many animal societies aggressive interactions regulate essential features such as feeding order and reproductive rights. Because aggressive interactions are costly the number of individuals competing for direct reproduction (hopeful reproductives) affects colony productivity. Using mathematical models, based on the costs/benefits trade-off for a worker to attempt to become a reproductive, we determine the number of hopeful reproductives expected to occur in insect societies with totipotent workers and several reproductives. The model is based on the biology of the polygynous queenless ant Rhytidoponera confusa (Formicidae: Ectatomminae), where every worker can potentially reproduce but only a few actually do, but is valid for all societies with totipotent individuals. We compare the number of hopeful reproductives predicted in the absence of a dominance hierarchy and with a linear dominance hierarchy, and we investigate the effects of colony size, relatedness, and mortality. The models show that a linear dominance hierarchy reduces the number of hopeful reproductives, and additional unpublished models show that this reduction is lower in non-linear hierarchies. Dominance hierarchies are thus favoured by natural selection. Larger colony size and higher mortalities result in longer hierarchy, whereas higher relatedness shortens hierarchy length. These predictions were successfully tested with eight colonies of R. confusa.Received 2 August 2004; revised 10 January 2005; accepted 12 January 2005.     

Self-organizing dominance hierarchies in a wild primate population

Linear dominance hierarchies, which are common in social animals, can profoundly influence access to limited resources, reproductive opportunities and health. In spite of their importance, the mechanisms that govern the dynamics of such hierarchies remain unclear. Two hypotheses explain how linear hierarchies might emerge and change over time. The ‘prior attributes hypothesis’ posits that individual differences in fighting ability directly determine dominance ranks. By contrast, the ‘social dynamics hypothesis’ posits that dominance ranks emerge from social self-organization dynamics such as winner and loser effects. While the prior attributes hypothesis is well supported in the literature, current support for the social dynamics hypothesis is limited to experimental studies that artificially eliminate or minimize individual differences in fighting abilities. Here, we present the first evidence supporting the social dynamics hypothesis in a wild population. Specifically, we test for winner and loser effects on male hierarchy dynamics in wild baboons, using a novel statistical approach based on the Elo rating method for cardinal rank assignment, which enables the detection of winner and loser effects in uncontrolled group settings. Our results demonstrate (i) the presence of winner and loser effects, and (ii) that individual susceptibility to such effects may have a genetic basis. Taken together, our results show that both social self-organization dynamics and prior attributes can combine to influence hierarchy dynamics even when agonistic interactions are strongly influenced by differences in individual attributes. We hypothesize that, despite variation in individual attributes, winner and loser effects exist (i) because these effects could be particularly beneficial when fighting abilities in other group members change over time, and (ii) because the coevolution of prior attributes and winner and loser effects maintains a balance of both effects.     

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.     

Some consequences of the hierarchical approach to phyllotaxis

This paper presents some of the consequences of the introduction of a concept of information and of a principle of optimal design in a representation of phyllotaxis by means of hierarchies. Our approach, which we call phylogenetic, has experimental supports and is based on the concept of an algorithm: growth matrices generate rhythms and vortices of growth among which is the hierarchy of Fibonacci representing the phyllotaxis of Fibonacci. It gives a necessary and sufficient condition which produces this type of phyllotaxis, and in the light of the propositions obtained, it can explain why Fibonacci's phyllotaxis is the most omnipresent in Nature.     

Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures

ABSTRACT: BACKGROUND: The NCBI Conserved Domain Database (CDD) consists of a collection of multiple sequence alignments of protein domains that are at various stages of being manually curated into evolutionary hierarchies based on conserved and divergent sequence and structural features. These domain models are annotated to provide insights into the relationships between sequence, structure and function via web-based BLAST searches. RESULTS: Here we automate the generation of conserved domain (CD) hierarchies using a combination of heuristic and Markov chain Monte Carlo sampling procedures and starting from a (typically very large) multiple sequence alignment. This procedure relies on statistical criteria to define each hierarchy based on the conserved and divergent sequence patterns associated with protein functional-specialization. At the same time this facilitates the sequence and structural annotation of residues that are functionally important. These statistical criteria also provide a means to objectively assess the quality of CD hierarchies, a non-trivial task considering that the protein subgroups are often very distantly related--a situation in which standard phylogenetic methods can be unreliable. Our aim here is to automatically generate (typically sub-optimal) hierarchies that, based on statistical criteria and visual comparisons, are comparable to manually curated hierarchies; this serves as the first step toward the ultimate goal of obtaining optimal hierarchical classifications. A plot of runtimes for the most time-intensive (non-parallelizable) part of the algorithm indicates a nearly linear time complexity so that, even for the extremely large Rossmann fold protein class, results are obtained in about a day. CONCLUSIONS: This approach automates the rapid creation of protein domain hierarchies and thus will eliminate one of the most time consuming aspects of conserved domain database curation. At the same time, it also facilitates protein domain annotation by identifying those pattern residues that most distinguish each protein domain subgroup from other related subgroups.     

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.     

Distributing and searching concept hierarchies: an adaptive DHT-based system

Concept hierarchies greatly help in the organization and reuse of information and are widely used in a variety of information systems applications. In this paper, we describe a method for efficiently storing and querying data organized into concept hierarchies and dispersed over a DHT. In our method, peers individually decide on the level of indexing according to the granularity of the incoming queries. Roll-up and drill-down operations are performed on a per-node basis in order to minimize the required bandwidth for answering queries on variable aggregation levels. We motivate our approach by applying it on a large-scale Grid system: Specifically, we apply our fully decentralized scheme that creates, queries and updates large volumes of hierarchical data on-line and replace the traditional centralized and strictly indexed information systems. Our extensive experimental results support this argument on many diverse configurations: Our system proves very efficient in skewed workloads, both over single and multiple hierarchy levels at the same time. It adapts to sudden changes in popularity and effectively stores and updates large amounts of data at very low cost.     

雄性大仓鼠体重对其斗殴行为及社会等级的作用

在实验室条件下测定雄性大仓鼠体重对社会等级和斗殴行为的作用模式,检验体重对雄性大仓鼠社会等级及斗殴行为序列具有重要影响的假设。本实验以16只成年雄性大仓鼠为目标个体,采用等级内部的线性概率、组内循环三元组数量（d）和优势等级的线性度（K）,排列个体的社会等级序位。研究结果表明,雄性大仓鼠可形成近似线性的优势等级,体重与个体的优势等级,攻击行为和胁腺标记行为均呈显著的正相关关系,与防御行为和攻击潜伏期存在显著的负相关关系。说明独居性物种大仓鼠雄体间可形成优势等级关系,体重对此关系具有重要的作用。     

Female dominance over males in primates: self-organisation and sexual dimorphism

The processes that underlie the formation of the dominance hierarchy in a group are since long under debate. Models of self-organisation suggest that dominance hierarchies develop by the self-reinforcing effects of winning and losing fights (the so-called winner-loser effect), but according to 'the prior attribute hypothesis', dominance hierarchies develop from pre-existing individual differences, such as in body mass. In the present paper, we investigate the relevance of each of these two theories for the degree of female dominance over males. We investigate this in a correlative study in which we compare female dominance between groups of 22 species throughout the primate order. In our study female dominance may range from 0 (no female dominance) to 1 (complete female dominance). As regards 'the prior attribute hypothesis', we expected a negative correlation between female dominance over males and species-specific sexual dimorphism in body mass. However, to our surprise we found none (we use the method of independent contrasts). Instead, we confirm the self-organisation hypothesis: our model based on the winner-loser effect predicts that female dominance over males increases with the percentage of males in the group. We confirm this pattern at several levels in empirical data (among groups of a single species and between species of the same genus and of different ones). Since the winner-loser effect has been shown to work in many taxa including humans, these results may have broad implications.     

Intratumoral heterogeneity: Clonal cooperation in epithelial-to-mesenchymal transition and metastasis

Although phenotypic intratumoral heterogeneity was first described many decades ago, the advent of next-generation sequencing has provided conclusive evidence that in addition to phenotypic diversity, significant genotypic diversity exists within tumors. Tumor heterogeneity likely arises both from clonal expansions, as well as from differentiation hierarchies existent in the tumor, such as that established by cancer stem cells (CSCs) and non-CSCs. These differentiation hierarchies may arise due to genetic mutations, epigenetic alterations, or microenvironmental influences. An additional differentiation hierarchy within epithelial tumors may arise when only a few tumor cells trans-differentiate into mesenchymal-like cells, a process known as epithelial-to-mesenchymal transition (EMT). Again, this process can be influenced by both genetic and non-genetic factors. In this review we discuss the evidence for clonal interaction and cooperation for tumor maintenance and progression, particularly with respect to EMT, and further address the far-reaching effects that tumor heterogeneity may have on cancer therapy.     

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.