Levels of diversity in endomycorrhizal fungi (Glomales,Zygomycetes) and their role in defining taxonomic and non-taxonomic groups

Diversity in glomalean fungi is manifested at the molecular, morphological, and ecological levels. Characters at any of these levels can be ordered into hierarchical patterns defining taxonomic groups if they are conserved enough to be heritable through geologic time in all descendants of a common ancestor. At present, only morphological characters associated with mode of spore formation and in subcellular structure of spores are sufficiently stable and diverse to recognize at least 150 species. Ontogenetic comparisons indicate that species integrity, despite asexual reproduction, is the result of rigid internal constraints imposed on variation during the process of spore subcellular differentiation. Epigenetic factors dominate because the differentiation sequence is linear and each new stage is causally linked to preceding stages. Some morphological characters of the fungal mycelium also exist, but they define more inclusive groups at the family level and above. Most diversity in the mycorrhizae consists of life-history traits associated with abundance and architecture of fungal components, their rate of formation and longevity, and their cost in the symbiosis. These characters participate in processes at the molecular and ecological levels, so they are autonomous from morphological determinants. They often are labile or affected by external environmental conditions, so fewer stable taxonomic characters are likely to be discovered. Instead, molecular and ecological diversity has greater potential to define; (a) niche specificity of organisms/populations and (b) causal processes linked to host-fungus compatibility and mycorrhizal efficiency. Any taxonomic characters that relate to mycorrhizal functions will come only from comparative studies involving organisms from shared habitats rather than those having shared spore morphologies.     

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.     

SCALE AND HIERARCHY IN MACROEVOLUTION

Abstract: Scale and hierarchy must be incorporated into any conceptual framework for the study of macroevolution, i.e. evolution above the species level. Expansion of temporal and spatial scales reveals evolutionary patterns and processes that are virtually inaccessible to, and unpredictable from, short‐term, localized observations. These larger‐scale phenomena range from evolutionary stasis at the species level and the mosaic assembly of complex morphologies in ancestral forms to the non‐random distribution in time and space of the origin of major evolutionary novelties, as exemplified by the Cambrian explosion and post‐extinction recoveries of metazoans, and the preferential origin of major marine groups in onshore environments and tropical waters. Virtually all of these phenomena probably involve both ecological and developmental factors, but the integration of these components with macroevolutionary theory has only just begun. Differential survival and reproduction of units can occur at several levels within a biological hierarchy that includes DNA sequences, organisms, species and clades. Evolution by natural selection can occur at any level where there is heritable variation that affects birth and death of units by virtue of interaction with the environment. This dynamic can occur when selfish DNA sequences replicate disproportionately within genomes, when organisms enjoy fitness advantages within populations (classical Darwinian selection), when differential speciation or extinction occurs within clades owing to organismic properties (effect macroevolution), and when differential speciation or extinction occurs within clades owing to emergent, species‐level properties (in the strict sense species selection). Operationally, emergent species‐level properties such as geographical range can be recognized by testing whether their macroevolutionary effects are similar regardless of the different lower‐level factors that produce them. Large‐scale evolutionary trends can be driven by transformation of species, preferential production of species in a given direction, differential origination or extinction, or any combination of these; the potential for organismic traits to hitch‐hike on other factors that promote speciation or damp extinction is high. Additional key attributes of macroevolutionary dynamics within biological hierarchies are that (1) hierarchical levels are linked by upward and downward causation, so that emergent properties at a focal level do not impart complete independence; (2) hierarchical effects are asymmetrical, so that dynamics at a given focal level need not propagate upwards, but will always cascade downwards; and (3) rates are generally, although not always, faster at lower hierarchical levels. Temporal and spatial patterns in the origin of major novelties and higher taxa are significantly discordant from those at the species and genus levels, suggesting complex hierarchical effects that remain poorly understood. Not only are many of the features promoting survivorship during background times ineffective during mass extinctions, but also they are replaced in at least some cases by higher‐level, irreducible attributes such as clade‐level geographical range. The incorporation of processes that operate across hierarchical levels and a range of temporal and spatial scales has expanded and enriched our understanding of evolution.     

Macroecology and the hierarchical expansion of evolutionary theory

The constraint envelope describing the relationship between geographical range size and body size has usually been explained by a minimum viable population size model, furnishing a strong argument for species selection if geographical range size turns out to be ‘heritable’. Recent papers have questioned this assumption of nonzero geographical range heritability at a phylogenetic level, meaning that the logic that constraint envelopes provide support for higher‐level selection fails. However, I believe that analysis of constraint envelopes can still furnish insights for the hierarchical expansion of evolutionary theory because the fitness furnished by variation in body size, which is frequently measured as a highly ‘heritable’ trait at the species level, can be partitioned into anagenetic and cladogenetic components. The constraint envelope furnishes an explicit mechanism for large‐body biased extinction rates influencing the distribution of body size. More importantly, it is possible to envisage a scenario in which anagenetic trends driving an increase in body size in higher latitudes within species (Bergmann's rule) are counteracted by available habitat area or continental edges constraining overall species distribution in these higher latitudes, increasing the probability of extinction. Under this combined model, faunas at higher latitudes and under habitat constraints may reach equilibrium points between these opposing hierarchical adaptive forces at smaller body size than faunas with less intense higher‐level constraints and will tend to be more right‐skewed.     

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.     

Can't see the colony for the bees: behavioural perspectives of biological individuality

The question ‘what is an individual’ does not often arise in studies within the field of behavioural ecology. Generally behavioural ecologists do not think about what makes an individual because they tend to use intuitive working concepts of individuality. Rarely do they explicitly mention how individuality affects their experimental design and interpretation of results. By contrast, the concept of individuality continues to intrigue philosophers of biology. It is interesting that while philosophers of biology debate definitions of individuality, biologists generally use the concept of individuality every day without much thought. Here we review the philosophical approaches to defining biological individuality, and illustrate how the biological individuality concepts used by biologists are affected by their study question and choice of organism. We clarify the behavioural perspective of biological individuality by introducing the concept of the behavioural individual. The notion of the behavioural individual is particularly interesting when explored in less‐conventional study organisms. By including less‐conventional organisms, it becomes clear why the concept of biological individuality is usually intuitive in behavioural ecology.     

Analyzing nested variation in the body form of Lepomid sunfishes

Phylogenetic hierarchies are often composed of younger diverging lineages nested within older diverging lineages. Comparing phenotypic variation among several hierarchical levels can be used to test hypotheses about selection, phenotypic evolution and speciation. Such hierarchical comparisons have only been performed in threespine stickleback, and so here we use a hierarchical pattern of divergences between near-shore littoral and off-shore pelagic habitats to test for selection on the evolution of body form in Lepomis sunfish in lakes. We compare variation in external body form between fish from littoral and pelagic habitats at three levels: among ecomorphs within individual lake populations (intrapopulation), among populations of the same species in different lakes (interpopulation), and between bluegill and pumpkinseed sunfish species (interspecifically). Using geometric morphometric methods, we first demonstrate that interpopulation variation in mean body form of pumpkinseed sunfish varies with the presence of pelagic habitat. We then incorporate these results with existing data in order to test the similarity of phenotypic divergence between littoral and pelagic habitats at different hierarchical levels. Parallel relationships between certain body form traits (head length, caudal length and pectoral length) and habitat occur at all three levels suggesting that selection persistently acts at all levels to diversify these traits and so may contribute to species formation. For other traits (caudal depth and pectoral altitude), divergence between habitats is inconsistent at different hierarchical levels. Thus, nested biological variation in Lepomid body form reflects a history of deterministic selection and historical contingency, and also identifies traits that likely have likely influenced fitness and so serve important functions.     

A complexity drain on cells in the evolution of multicellularity

A hypothesis has been advanced recently predicting that, in evolution, as higher-level entities arise from associations of lower-level organisms, and as these entities acquire the ability to feed, reproduce, defend themselves, and so on, the lower-level organisms will tend to lose much of their internal complexity (McShea 2001a). In other words, in hierarchical transitions, there is a drain on numbers of part types at the lower level. One possible rationale is that the transfer of functional demands to the higher level renders many part types at the lower level useless, and thus their loss in evolution is favored by selection for economy. Here, a test is conducted at the cell level, comparing numbers of part types in free-living eukaryotic cells (protists) and the cells of metazoans and land plants. Differences are significant and consistent with the hypothesis, suggesting that tests at other hierarchical levels may be worthwhile.     

The minor transitions in hierarchical evolution and the question of a directional bias

The history of life shows a clear trend in hierarchical organization, revealed by the successive emergence of organisms with ever greater numbers of levels of nestedness and greater development, or ‘individuation’, of the highest level. Various arguments have been offered which suggest that the trend is the result of a directional bias, or tendency, meaning that hierarchical increases are more probable than decreases among lineages, perhaps because hierarchical increases are favoured, on average, by natural selection. Further, what little evidence exists seems to point to a bias: some major increases are known – including the origin of the eukaryotic cell from prokaryotic cells and of animals, fungi and land plants from solitary eukaryotic cells – but no major decreases (except in parasitic and commensal organisms), at least at the cellular and multicellular levels. The fact of a trend, combined with the arguments and evidence, might make a bias seem beyond doubt, but here I argue that its existence is an open empirical question. Further, I show how testing is possible.     

Cellular differentiation and individuality in the ‘minor’ multicellular taxa

Biology needs a concept of individuality in order to distinguish organisms from parts of organisms and from groups of organisms, to count individuals and compare traits across taxa, and to distinguish growth from reproduction. Most of the proposed criteria for individuality were designed for ‘unitary’ or ‘paradigm’ organisms: contiguous, functionally and physiologically integrated, obligately sexually reproducing multicellular organisms with a germ line sequestered early in development. However, the vast majority of the diversity of life on Earth does not conform to all of these criteria. We consider the issue of individuality in the ‘minor’ multicellular taxa, which collectively span a large portion of the eukaryotic tree of life, reviewing their general features and focusing on a model species for each group. When the criteria designed for unitary organisms are applied to other groups, they often give conflicting answers or no answer at all to the question of whether or not a given unit is an individual. Complex life cycles, intimate bacterial symbioses, aggregative development, and strange genetic features complicate the picture. The great age of some of the groups considered shows that ‘intermediate’ forms, those with some but not all of the traits traditionally associated with individuality, cannot reasonably be considered ephemeral or assumed transitional. We discuss a handful of recent attempts to reconcile the many proposed criteria for individuality and to provide criteria that can be applied across all the domains of life. Finally, we argue that individuality should be defined without reference to any particular taxon and that understanding the emergence of new kinds of individuals requires recognizing individuality as a matter of degree.     

Role of Utility and Inference in the Evolution of Functional Information

Functional information means an encoded network of functions in living organisms from molecular signaling pathways to an organism’s behavior. It is represented by two components: code and an interpretation system, which together form a self-sustaining semantic closure. Semantic closure allows some freedom between components because small variations of the code are still interpretable. The interpretation system consists of inference rules that control the correspondence between the code and the function (phenotype) and determines the shape of the fitness landscape. The utility factor operates at multiple time scales: short-term selection drives evolution towards higher survival and reproduction rate within a given fitness landscape, and long-term selection favors those fitness landscapes that support adaptability and lead to evolutionary expansion of certain lineages. Inference rules make short-term selection possible by shaping the fitness landscape and defining possible directions of evolution, but they are under control of the long-term selection of lineages. Communication normally occurs within a set of agents with compatible interpretation systems, which I call communication system. Functional information cannot be directly transferred between communication systems with incompatible inference rules. Each biological species is a genetic communication system that carries unique functional information together with inference rules that determine evolutionary directions and constraints. This view of the relation between utility and inference can resolve the conflict between realism/positivism and pragmatism. Realism overemphasizes the role of inference in evolution of human knowledge because it assumes that logic is embedded in reality. Pragmatism substitutes usefulness for truth and therefore ignores the advantage of inference. The proposed concept of evolutionary pragmatism rejects the idea that logic is embedded in reality; instead, inference rules are constructed within each communication system to represent reality, and they evolve towards higher adaptability on a long time scale.     

Hierarchical pre-dispersal fitness assessment in a Mediterranean shrub plant

Under the concept of modularity, it is possible to recognise how seed production, as well as any other process affecting it, are hierarchically structured within fruits, within individual plants and within populations. In this work, we analysed the effects of pre-dispersal seed predation by insects upon a set of hierarchical levels in a population of the Mediterranean shrub plant Cistus ladanifer (“rock rose”) throughout a complete fruit-producing season (which takes place during the summer months). Almost all individual plants were predated, which implies that the effects of predation at the population level (regardless of the extent of predation within each individual) were virtually uniform. Within the individuals, however, the predation rate was close to a proportion of 0.5 (half of the fruits of each individual were predated), which indicates that this hierarchical level is likely to be subjected to a differential action of selection. Predation rates within the fruits showed an intermediate value (lower than that observed at the population level but higher than that at the individual level). According to these results, the pressure of phenotypic selection may therefore give rise to greater variation among fruits of the same individual than among seeds of the same fruit. In terms of the temporal patterns observed there was a large variation in the increments of predation along the fruiting season, which implies a high degree of heterogeneity in the temporal distribution of the effects of predation pressure on fitness. Besides its use in the specific example of the plant species studied in this work, the methodological procedure presented in this paper (integration of the temporal changes of different hierarchical levels) might be foreseen, in fact, as a useful tool for analysing the hierarchical structuring of fitness in modular organisms in general. This procedure allows to discriminate and integrate selection pressures and their effects across different phenotypic levels, from the infra-individual ones up to the population level.     

克隆植物的表型可塑性与等级选择

表型可塑性是指生物个体生长发育过程中遭受不同环境条件作用时产生不同表型的能力。进化的发生有赖于自然选择对种群遗传可变性产生的效力以及各基因型的表型可塑性。有足够的证据说明表型可塑性的可遗传性,它实际上是进化改变的一个成分。一般通过优化模型、数量遗传模型和配子模型来研究表型可塑性的进化。植物的构型是相对固定的,并未完全抑制表型可塑性。克隆植物因其双构件性而具有更广泛的、具有重要生态适应意义的表型可塑性。构件性使克隆植物具有以分株为基本单位的等级结构,从而使克隆植物的表型选择也具有等级性。构件等级一般包含基株、克隆片段或分株系统以及分株3个典型水平。目前认为克隆植物的自然选择有两种模式,分别以等级选择模型和基因型选择模型表征。等级选择模型认为:不同的等级水平同时也是表型选择水平,环境对各水平具有作用,各水平之间也有相互作用,多重表型选择水平的净效应最终通过繁殖水平——分株传递到随后的世代中。基因型选择模型指出:克隆生长引起分株的遗传变异,并通过基株内分株间以及基株间的非随机交配引起种子库等位基因频率的改变,产生微进化。这两种选择模式均突出强调了分株水平在自然选择过程中的变异性以及在进化中的重要性,强调了克隆生长和种子繁殖对基株适合度的贡献。基因型选择模型包含等级选择模型的观点,是对等级选择模型的重要补充。克隆植物的表型可塑性表现在3个典型等级层次上,由于各层次对自然选择压力具有不同的反应,其表型变异程度一般表现出“分株层次>分株片段层次>基株层次”的等级性反应模式。很多证据表明,在构件有机体中构件具有最大的表型可塑性,植物的表型可塑性实际上是构件而非整个遗传个体的反应。这说明克隆植物的等级反应模式可能具有普适性。如果该反应模式同时还是构件等级中不同“个体”适应性可塑性反应的模式,那么可以预测:1)在克隆植物中,分株层次受到的自然选择强度也最大,并首先发生适应性可塑性变化,最终引起克隆植物微进化;2)由于较弱的有性繁殖能力,克隆植物在进化过程中的保守性可能大于非克隆植物。克隆植物等级反应模式的普适性亟待验证。     

Individuality and the existence of species through time

The individuality of species provides the basis for linking practical taxonomy with evolutionary and ecological theory. An individual is here defined as a collection of parts (lower-level entities) that are mutually connected. Different types of species individual exist, based on different types of connection between organisms. An interbreeding species is a group of organisms connected by the potential to share common descendants, whereas a genealogical species is integrated by the sharing of common ancestors. Such species definitions serve to set the limits of species at a moment of time and these slices connect through time to form time-extended lineages. This perspective on the nature of individuality has implications that conflict with traditional views of species and lineages: (1) Several types of connections among organisms may serve to individuate species in parallel (species pluralism); (2) each kind of species corresponds to a distinct kind of lineage; (3) although lineage branching is the most obvious criterion to break lineages into diachronic species, it cannot be justified simply by reference to species individuality; (4) species (like other individuals) have fuzzy boundaries; (5) if we wish to retain a species rank, we should focus on either the most- or least-inclusive individual in a nested series; (6) not all organisms will be in any species; and (7) named species taxa are best interpreted as hypotheses of real species. Although species individuality requires significant changes to systematic practice and challenges some preconceptions we may have about the ontology of species, it provides the only sound basis for asserting that species exist independently of human perception.     

The hologenome concept: we need to incorporate function

Are we in the midst of a paradigm change in biology and have animals and plants lost their individuality, i.e., are even so-called ‘typical’ organisms no longer organisms in their own right? Is the study of the holobiont—host plus its symbiotic microorganisms—no longer optional, but rather an obligatory path that must be taken for a comprehensive understanding of the ecology and evolution of the individual components that make up a holobiont? Or are associated microbes merely a component of their host’s environment, and the holobiont concept is just a beautiful idea that does not add much or anything to our understanding of evolution? This article explores different aspects of the concept of the holobiont. We focus on the aspect of functional integration, a central holobiont property, which is only rarely considered thoroughly. We conclude that the holobiont comes in degrees, i.e., we regard the property of being a holobiont as a continuous trait that we term holobiontness, and that holobiontness is differentiated in several dimensions. Although the holobiont represents yet another level of selection (different from classical individual or group selection because it acts on a system that is composed of multiple species), it depends on the grade of functional integration whether or not the holobiont concept helps to cast light on the various degrees of interactions between symbiotic partners.     

Spatial study of juvenile corals in the Northern region of the Mesoamerican Barrier Reef System (MBRS)

Juvenile coral abundance and community composition depend on the spatial scale studied. To investigate this, an evaluation was made of juvenile coral density with hierarchical spatial analysis in the northern Mesoamerican Barrier Reef System (MBRS) at ~10 m depth. Study scope included semi-protected and unprotected areas located in this region. A total of 19 juvenile coral taxa were found, including 10 scleractinian species, 8 scleractinian coral genera not identified to species, and 1 Millepora species (Hydrozoa-Milleporidae). In terms of relative abundance, Agaricia spp., Siderastrea spp., and Porites spp. were the main juvenile taxa in the coral community at the surveyed sites, reefs, and regions levels. Greater variance was seen at smaller scales, at site level for taxa richness, and at the transect level for juvenile density, and lower variance was seen at larger scales (reefs and regions). The variance component contribution from each scale likely differed from other studies because of the different factors affecting the community and the different extensions of each scale used in each study. Densities (1–6.4 juvenile corals/m²) and dominant taxa found in this study agree with other studies from the Western Atlantic. Detected variability was explained by different causal agents, such as low grazing rates by herbivorous organisms, turbidity, and/or sediment suffocation and some nearby or distant localized disturbance (human settlement and a hurricane).