Contextual organismality: Beyond pattern to process in the emergence of organisms

Biologists have taken the concept of organism largely for granted. However, advances in the study of chimerism, symbiosis, bacterial‐eukaryote associations, and microbial behavior have prompted a redefinition of organisms as biological entities exhibiting low conflict and high cooperation among their parts. This expanded view identifies organisms in evolutionary time. However, the ecological processes, mechanisms, and traits that drive the formation of organisms remain poorly understood. Recognizing that organismality can be context dependent, we advocate elucidating the ecological contexts under which entities do or do not act as organisms. Here we develop a “contextual organismality” framework and provide examples of entities, such as honey bee colonies, tumors, and bacterial swarms, that can act as organisms under specific life history, resource, or other ecological circumstances. We suggest that context dependence may be a stepping stone to the development of increased organismal unification, as the most integrated biological entities generally show little context dependence. Recognizing that organismality is contextual can identify common patterns and testable hypotheses across different entities. The contextual organismality framework can illuminate timeless as well as pressing issues in biology, including topics as disparate as cancer emergence, genomic conflict, evolution of symbiosis, and the role of the microbiota in impacting host phenotype.     

Beyond society: the evolution of organismality

The evolution of organismality is a social process. All organisms originated from groups of simpler units that now show high cooperation among the parts and are nearly free of conflicts. We suggest that this near-unanimous cooperation be taken as the defining trait of organisms. Consistency then requires that we accept some unconventional organisms, including some social insect colonies, some microbial groups and viruses, a few sexual partnerships and a number of mutualistic associations. Whether we call these organisms or not, a major task is to explain such cooperative entities, and our survey suggests that many of the traits commonly used to define organisms are not essential. These non-essential traits include physical contiguity, indivisibility, clonality or high relatedness, development from a single cell, short-term and long-term genetic cotransmission, germ–soma separation and membership in the same species.     

Does Biology Need an Organism Concept?

Among biologists, there is no general agreement on exactly what entities qualify as ‘organisms’. Instead, there are multiple competing organism concepts and definitions. While some authors think this is a problem that should be corrected, others have suggested that biology does not actually need an organism concept. We argue that the organism concept is central to biology and should not be abandoned. Both organism concepts and operational definitions are useful. We review criteria used for recognizing organisms and conclude that they are not categorical but rather continuously variable. Different organism concepts are useful for addressing different questions, and it is important to be explicit about which is being used. Finally, we examine the origins of the derived state of organismality, and suggest that it may result from positive feedback between natural selection and functional integration in biological entities.     

Evolution of the individual

This article studies the transition in evolution from single cells to multicellular organisms as a case study in the origin of individuality. The issues considered are applicable to all major transitions in the units of selection that involve the emergence of cooperation and the regulation of conflict. Explicit genetic models of mutation and selection both within and between organisms are studied. Cooperation among cells increases when the fitness covariance at the level of the organism overcomes within-organism change toward defection. Selection and mutation during development generate significant levels of within-organism variation and lead to variation in organism fitness at equilibrium. This variation selects for gem-line modifiers and other mediators of within-organism conflict, increasing the heritability of fitness at the organism level. The evolution of these modifiers is the first new function at the emerging organism level and a necessary component of the evolution of individuality.     

Transitions in individuality.

The evolution of multicellular organisms is the premier example of the integration of lower levels into a single, higher-level individual. Explaining the evolutionary transition from single cells to multicellular organisms is a major challenge for evolutionary theory. We provide an explicit two locus genetic framework for understanding this transition in terms of the increase of cooperation among cells and the regulation of conflict within the emerging organism. Heritability of fitness and individuality at the new level emerge as a result of the evolution of organismal functions that restrict the opportunity for conflict within and ensure cooperation among cells. Conflict leads, through the evolution of adaptations that reduce it, to greater individuality and harmony for the organism.     

Adaptation in the face of internal conflict: the paradox of the organism revisited

The paradox of the organism refers to the observation that organisms appear to function as coherent purposeful entities, despite the potential for within-organismal components like selfish genetic elements and cancer cells to erode them from within. While it is commonly accepted that organisms may pursue fitness maximisation and can be thought to hold particular agendas, there is a growing recognition that genes and cells do so as well. This can lead to evolutionary conflicts between an organism and the parts that reside within it. Here, we revisit the paradox of the organism. We first outline its conception and relationship to debates about adaptation in evolutionary biology. Second, we review the ways selfish elements may exploit organisms, and the extent to which this threatens organismal integrity. To this end, we introduce a novel classification scheme that distinguishes between selfish elements that seek to distort transmission versus those that seek to distort phenotypic traits. Our classification scheme also highlights how some selfish elements elude a multi-level selection decomposition using the Price equation. Third, we discuss how the organism can retain its status as the primary fitness-maximising agent in the face of selfish elements. The success of selfish elements is often constrained by their strategy and further limited by a combination of fitness alignment and enforcement mechanisms controlled by the organism. Finally, we argue for the need for quantitative measures of both internal conflicts and organismality.     

Cooperation and conflict in the evolution of individuality. IV. Conflict mediation and evolvability in Volvox carteri

The continued well being of evolutionary individuals (units of selection and evolution) depends upon their evolvability, that is their capacity to generate and evolve adaptations at their level of organization, as well as their longer term capacity for diversifying into more complex evolutionary forms. During a transition from a lower- to higher-level individual, such as the transition between unicellular and multicellular organisms, the evolvability of the lower-level (cells) must be restricted, while the evolvability of the new higher-level unit (multicellular organism) must be enhanced. For these reasons, understanding the factors leading to an evolutionary transition should help us to understand the factors underlying the emergence of evolvability of a new evolutionary unit. Cooperation among lower-level units is fundamental to the origin of new functions in the higher-level unit. Cooperation can produce a new more complex evolutionary unit, with the requisite properties of heritable fitness variations, because cooperation trades fitness from a lower-level (the costs of cooperation) to the higher-level (the benefits for the group). For this reason, the evolution of cooperative interactions helps us to understand the origin of new and higher-levels of fitness and organization. As cooperation creates a new level of fitness, it also creates the opportunity for conflict between levels of selection, as deleterious mutants with differing effects at the two levels arise and spread. This conflict can interfere with the evolvability of the higher-level unit, since the lower and higher-levels of selection will often "disagree" on what adaptations are most beneficial to their respective interests. Mediation of this conflict is essential to the emergence of the new evolutionary unit and to its continued evolvability. As an example, we consider the transition from unicellular to multicellular organisms and study the evolution of an early-sequestered germ-line in terms of its role in mediating conflict between the two levels of selection, the cell and the cell group. We apply our theoretical framework to the evolution of germ/soma differentiation in the green algal group Volvocales. In the most complex member of the group, Volvox carteri, the potential conflicts among lower-level cells as to the "right" to reproduce the higher-level individual (i.e. the colony) have been mediated by restricting immortality and totipotency to the germ-line. However, this mediation, and the evolution of an early segregated germ-line, was achieved by suppressing mitotic and differentiation capabilities in all post-embryonic cells. By handicapping the soma in this way, individuality is ensured, but the solution has affected the long-term evolvability of this lineage. We think that although conflict mediation is pivotal to the emergence of individuality at the higher-level, the way in which the mediation is achieved can greatly affect the longer-term evolvability of the lineage.     

A mathematical approach to defining clade names, with potential applications to computer storage and processing

Clade names may be objectively defined based on conditions of phylogeny. Definitions usually take one of three forms — node-, branch- or apomorphy-based — but other forms and complex permutations of these forms are also possible. Some database projects have attempted to store definitions of clade names in a manner accessible to computer applications, but, so far, they have only provided ways of storing the most common types of definition. To create a more extensible system, I have taken a mathematical approach to defining clade names. To render definitions accessible to computer storage and analysis, I propose using Mathematical Markup Language (M ath ML) with extensions. Since the mathematical approach is granular to the level of the organism, not to fuzzy higher levels such as population or species, it sheds light on some theoretical difficulties with defining clade names. For example, some definitions do not resolve to a single organism as the ancestor, but to sets of organisms which are not ancestral to each other and share common descendants. I term such sets 'cladogenetic sets'.     

Evolutionary maintenance of genomic diversity within arbuscular mycorrhizal fungi

Most organisms are built from a single genome. In striking contrast, arbuscular mycorrhizal fungi appear to maintain genomic variation within an individual fungal network. Arbuscular mycorrhizal fungi dwell in the soil, form mutualistic networks with plants, and bear multiple, potentially genetically diverse nuclei within a network. We explore, from a theoretical perspective, why such genetic diversity might be maintained within individuals. We consider selection acting within and between individual fungal networks. We show that genetic diversity could provide a benefit at the level of the individual, by improving growth in variable environments, and that this can stabilize genetic diversity even in the presence of nuclear conflict. Arbuscular mycorrhizal fungi complicate our understanding of organismality, but our findings offer a way of understanding such biological anomalies.     

Hierarchical selection in modular organisms

Modular organisms, such as colonial marine invertebrates and most seed plants, develop by a repetition of physically interrelated subunits colloquially called modules. Modules may include some or all features of single organisms. Modular organisms have no separate germ line; instead, several cell lineages can remain totipotent throughout the life span of the organism or the clone. Due to this somatic embryogenesis, the basic reproductive units are found at the level of the module. The products of modular repetition, i.e. physically coherent organisms, colonies and clones consisting of modules, mainly function as interactive units that modify survival and reproduction at the level of the module. Together these levels of interaction and reproduction make up a hierarchical causal system, which we frequently tend to encapsulate into a single functional unit of selection.     

Learning to get along despite struggling to get by

How cooperation can evolve by natural selection is important for understanding the evolutionary transition from unicellular to multicellular life. Here we review the evolutionary theories for cooperation, with emphasis on the mechanisms that can favor cooperation and reduce conflict in multicellular organisms.     

On the reorganization of fitness during evolutionary transitions in individuality

The basic problem in an evolutionary transition is to understandhow a group of individuals becomes a new kind of individual,possessing the property of heritable variation in fitness atthe new level of organization. During an evolutionary transition,for example, from single cells to multicellular organisms, thenew higher-level evolutionary unit (multicellular organism)gains its emergent properties by virtue of the interactionsamong lower-level units (cells). We see the formation of cooperativeinteractions among lower-level units as a necessary step inevolutionary transitions; only cooperation transfers fitnessfrom lower levels (costs to group members) to higher levels(benefits to the group). As cooperation creates new levels offitness, it creates the opportunity for conflict between levelsas deleterious mutants arise and spread within the group. Fundamentalto the emergence of a new higher-level unit is the mediationof conflict among lower-level units in favor of the higher-levelunit. The acquisition of heritable variation in fitness at thenew level, via conflict mediation, requires the reorganizationof the basic components of fitness (survival and reproduction)and life-properties (such as immortality and totipotency) aswell as the co-option of lower-level processes for new functionsat the higher level. The way in which the conflicts associatedwith the transition in individuality have been mediated, andfitness and general life-traits have been re-organized, caninfluence the potential for further evolution (i.e., evolvability)of the newly emerged evolutionary individual. We use the volvocaleangreen algal group as a model-system to understand evolutionarytransitions in individuality and to apply and test the theoreticalprinciples presented above. Lastly, we discuss how the differentnotions of individuality stem from the basic properties of fitnessin a multilevel selection context.     

Evolution,epigenetics and cooperation

Explanations for biological evolution in terms of changes in gene frequencies refer to outcomes rather than process. Integrating epigenetic studies with older evolutionary theories has drawn attention to the ways in which evolution occurs. Adaptation at the level of the gene is giving way to adaptation at the level of the organism and higher-order assemblages of organisms. These ideas impact on the theories of how cooperation might have evolved. Two of the theories, i.e. that cooperating individuals are genetically related or that they cooperate for self-interested reasons, have been accepted for a long time. The idea that adaptation takes place at the level of groups is much more controversial. However, bringing together studies of development with those of evolution is taking away much of the heat in the debate about the evolution of group behaviour.     

Co-occurrence in nature of different clones of the social amoeba,Dictyostelium discoideum

The social amoeba, Dictyostelium discoideum, produces a multicellular fruiting body and has become a model system for cell-cell interactions such as signalling, adhesion and development. However, unlike most multicellular organisms, it forms by aggregation of cells and, in the laboratory, forms genetic chimeras where there may be competition among clones. Here we show that chimera formation is also likely in nature, because different clones commonly co-occur on a very small scale. This suggests that D. discoideum will likely have evolved strategies for competing in chimeras, and that the function of some developmental genes will be competitive. Natural chimerism also makes D. discoideum a good model organism for the investigation of issues relating to coexistence and conflict between cells.     

Problems of multi-species organisms: endosymbionts to holobionts

The organism is one of the fundamental concepts of biology and has been at the center of many discussions about biological individuality, yet what exactly it is can be confusing. The definition that we find generally useful is that an organism is a unit in which all the subunits have evolved to be highly cooperative, with very little conflict. We focus on how often organisms evolve from two or more formerly independent organisms. Two canonical transitions of this type—replicators clustered in cells and endosymbiotic organelles within host cells—demonstrate the reality of this kind of evolutionary transition and suggest conditions that can favor it. These conditions include co-transmission of the partners across generations and rules that strongly regulate and limit conflict, such as a fair meiosis. Recently, much attention has been given to associations of animals with microbes involved in their nutrition. These range from tight endosymbiotic associations like those between aphids and Buchnera bacteria, to the complex communities in animal intestines. Here, starting with a reflection about identity through time (which we call “Theseus’s fish”), we consider the distinctions between these kinds of animal–bacteria interactions and describe the criteria by which a few can be considered jointly organismal but most cannot.     

Species delimitation in downy mildews: the case of Hyaloperonospora in the light of nuclear ribosomal ITS and LSU sequences

Species definitions for plant pathogens have considerable practical impact for measures such as plant protection or biological control, and are also important for comparative studies involving model organisms. However, in many groups, the delimitation of species is a notoriously difficult taxonomic problem. This is particularly evident in the obligate biotrophic downy mildew genera (Peronosporaceae, Peronosporales, Oomycetes), which display a considerable diversity with respect to genetic distances and host plants, but are, for the most part, morphologically rather uniform. The recently established genus Hyaloperonospora is of particular biological interest because it shows an impressive radiation on virtually a single host family, Brassicaceae, and it contains the downy mildew parasite, Arabidopsis thaliana, of importance as a model organism. Based on the most comprehensive molecular sampling of specimens from a downy mildew genus to date, including various collections from different host species and geographic locations, we investigate the phylogenetic relationships of Hyaloperonospora by molecular analysis of the nuclear ribosomal ITS and LSU sequences. Phylogenetic trees were inferred with ML and MP from the combined dataset; partitioned Bremer support (PBrS) was used to assess potential conflict between data partitions. As in other downy mildew groups, the molecular data clearly corroborate earlier results that supported the use of narrow species delimitations and host ranges as taxonomic markers. With few exceptions, suggested species boundaries are supported without conflict between different data partitions. The results indicate that a combination of molecular and host features is a reliable means to discriminate downy mildew species for which morphological differences are unknown.     

Comparative genomics: the key to understanding the Human Genome Project

The sequencing of the human genome is well underway. Technology has advanced, such that the total genomic sequence is possible, along with an extensive catalogue of genes via comprehensive cDNA libraries. With the recent completion of the Saccharomyces cerevisiae sequencing project and the imminent completion of that of Caenorhabditis elegans, the most frequently asked question is how much can sequence data alone tell us? The answer is that that a DNA sequence taken in isolation from a single organism reveals very little. The vast majority of DNA in most organisms is noncoding. Protein coding sequences or genes cannot function as isolated units without interaction with noncoding DNA and neighboring genes. This genomic environment is specific to each organism. In order to understand this we need to look at similar genes in different organisms, to determine how function and position has changed over the course of evolution. By understanding evolutionary processes we can gain a greater insight into what makes a gene and the wider processes of genetics and inheritance. Comparative genomics (with model organisms), once the poor relation of the human genome project, is starting to provide the key to unlock the DNA code.     

Reply to Lawler: feeding competition, cooperation, and the causes of primate sociality

This is a reply to Richard Lawler's commentary on our previous work [Lawler, 2011; this issue] in which he develops a set of operational models to test socioecological theories of the evolutionary importance of feeding competition. We strongly agree that we need to critically re-evaluate the basic assumptions of all models of primate sociality, and to verify the explanatory power of alternative models. We also feel Lawler's commentary provides an important opportunity to broaden the debate concerning the fundamental roles of cooperation, competition, and aggression in understanding primate social systems. Lawler provides a number of suggestions as to how models developed in primate socioecology might be tested. We agree with these suggestions, make further suggestions, and call for specific operational definitions so that researchers might begin to develop and test various methodologies. However, we also call for testing alternative theories. Current socioecological theory is based on the assumption that competition and positive selection is always in operation and has driven the evolution of living organisms. We believe that this "explanation of choice" often is treated as an assumed truth to which data are forced to fit, rather than being seen as a theory to be tested. Furthermore, we agree with Weiss and Buchanan [2009. The Mermaid's Tale: Four Billion Years of Cooperation in the Making of Living Things] that on ecological and developmental scales, where organisms actually live out their lives, cooperation may play a more fundamental role than competition.     

Thermodynamic perspectives on genetic instructions, the laws of biology and diseased states

This article examines in a broad perspective entropy and some examples of its relationship to evolution, genetic instructions and how we view diseases. Living organisms are programmed by functional genetic instructions (FGI), through cellular communication pathways, to grow and reproduce by maintaining a variety of hemistable, ordered structures (low entropy). Living organisms are far from equilibrium with their surrounding environmental systems, which tends towards increasing disorder (increasing entropy). Organisms free themselves from high entropy (high disorder) to maintain their cellular structures for a period of time sufficient to allow reproduction and the resultant offspring to reach reproductive ages. This time interval varies for different species. Bacteria, for example need no sexual parents; dividing cells are nearly identical to the previous generation of cells, and can begin a new cell cycle without delay under appropriate conditions. By contrast, human infants require years of care before they can reproduce. Living organisms maintain order in spite of their changing surrounding environment that decreases order according to the second law of thermodynamics. These events actually work together since living organisms create ordered biological structures by increasing local entropy. From a disease perspective, viruses and other disease agents interrupt the normal functioning of cells. The pressure for survival may result in mechanisms that allow organisms to resist attacks by viruses, other pathogens, destructive chemicals and physical agents such as radiation. However, when the attack is successful, the organism can be damaged until the cell, tissue, organ or entire organism is no longer functional and entropy increases.     

Defining Life: The Virus Viewpoint

Are viruses alive? Until very recently, answering this question was often negative and viruses were not considered in discussions on the origin and definition of life. This situation is rapidly changing, following several discoveries that have modified our vision of viruses. It has been recognized that viruses have played (and still play) a major innovative role in the evolution of cellular organisms. New definitions of viruses have been proposed and their position in the universal tree of life is actively discussed. Viruses are no more confused with their virions, but can be viewed as complex living entities that transform the infected cell into a novel organism—the virus—producing virions. I suggest here to define life (an historical process) as the mode of existence of ribosome encoding organisms (cells) and capsid encoding organisms (viruses) and their ancestors. I propose to define an organism as an ensemble of integrated organs (molecular or cellular) producing individuals evolving through natural selection. The origin of life on our planet would correspond to the establishment of the first organism corresponding to this definition.