Although the mathematical principles underpinning population-level evolution are now well studied, the origin and evolution of morphological novelties has received far less attention. Here, a broad but general theory for how this sort of change takes place is outlined, relying on functional continuity, least-constrained components of morphology, redundancy and preadaptation. At least four distinct sorts of redundancy are identified: (i) redundancy arising through duplication (amplification); (ii) redundancy arising through regionalisation (parcellation); (iii) redundancy arising through functional convergence; and (iv) redundancy arising from shared function (functional degeneracy). Although organisms are here recognised to be functionally constrained (“burdened”, in Riedl's terminology), these constraints can be overcome through the combination of the four principles given above. Contrary to its common treatment, functional constraint is neither an ever-increasing restriction on the scope of evolution, nor does it require drastic events to overcome or “break” it. Rather, it is an evolutionary quantity, subject to selection at some level. The rules that govern morphological evolution are the primary controls on what is allowed to happen in the evolution of the overall genotype-phenotype system, suggesting strong controls on the sorts of developmental changes that might be associated with macroevolution. This model, then, sees organism functionality as the primary control on evolvability, with exact genetic make-up being of secondary importance. It should prove possible to recast traditional notions of body-plan evolution into the formulations of complex system analysis, which in the future may prove a unifying discipline for fields as disparate as palaeontology and gene regulatory networks. In particular, understanding how morphology can evolve may provide the critical link between the ecological and morphological networks that are currently the intense focus of evolutionary investigations.

Recent data concerning ultradian (circahoralian) intracellular rhythms are used to assess the biochemical mechanisms of direct cell-cell communication. New results and theoretical considerations suggest a fractal nature of ultradian rhythms and their self-organisation. The fundamental and innate nature of these rhythms relates to their self-similarity at different levels of cell and tissue organisation. They can be detected in cell-free systems as well as in cells and organs in vivo. Such rhythms are a means of finding an optimal state of cell function rather than achieving a state of absolute stability. As a consequence, oscillations, being irregular and numerous by the set of periods, are resilient to functional overload and injury. Recent data on the maintenance of their fractal structure and, especially on the selection of optimal periods are discussed. The positive role of chaotic dynamics is stressed.

The ultradian rhythm of protein synthesis in hepatocytes in vitro was used as a marker of direct cell-cell communication. The system demonstrates cell cooperation and synchronisation throughout the cell population, and suggests that the ultradian rhythms are self-organised. These observations also led to the detection of mechanisms of direct cell-cell communication in which extracellular factors have an essential role. Experimental evidence indicated the involvement of gangliosides and/or catecholamines in this large-scale synchronisation of protein synthesis. The response of all, or a major part, of the cell population is important; after the initial trigger effect, a periodic pattern is retained for some time. The influence of Ca2+-dependent protein kinases on protein phosphorylation can be a final step in the phase modulation of rhythms during cell-cell synchronisation.

The intercellular medium plays an important role in self-synchronisation of ultradian rhythms between individual cells. Low cooperative activity of hepatocytes of old rats resulted from altered composition of the intercellular medium rather than direct effects of animal and cellular ageing. Similarly, in the whole body, changes in levels of gangliosides and catecholamines in the blood serum, a natural intercellular medium, can be critical events in age-dependent changes of the serum and accordingly cell-cell synchronisation. Hepatocytes of old rats exhibit some of the properties of young cells following an increase in blood serum ganglioside level, as well as, in in vitro conditions, after the addition of gangliosides to the culture medium.

Together with data on ultradian functional and metabolic rhythms, all the material reviewed here allows us to propose a mechanism of direct cell-cell cooperation via the medium in which the cells exist, that supplements the nervous and hormonal central regulation of organ functions. Ultradian intracellular rhythms may thus provide a finer framework within which the integrated dynamics of respiration, heart rate, brain activity, and even behavioural patterns, are brought to an optimal functional pattern. Innate and direct cell-cell cooperation may have been employed as a means of intercellular regulation during the course of metazoan evolution, that preceded nervous regulation and is presently retained in mammals.

The Parisian comparative anatomist Claude Perrault, dissecting an Indian giant tortoise in 1676, was the first to observe that the urinary bladder is of an extraordinary size in terrestrial tortoises. In 1799, the English comparative physiologist Robert Townson suggested that the bladder functioned as a water reservoir, as he had shown previously for frogs and toads. However, these observations went unnoticed in subsequent reports on tortoise water economy that were made by travellers and naturalists visiting the Galapagos Archipelago and marvelling over the huge numbers of giant tortoises that inhabited these desert-like islands. The first such report was by an American naval officer, David Porter, who was a privateer in the 1812–15 war with England. In his journal he referred to the constant supply of water which the Galapagos tortoises carried with them. References to the location in the body, as well as the amounts and quality of the water stored, were, however, contradictory.

The confusion concerning the anatomical identity of the water reservoir in the Galapagos tortoise, Geochelone elephantopus, persisted throughout the nineteenth century, and continued when studies of tortoise water economy and drinking behaviour in arid environments were taken up independently in the desert tortoise, Gopherus agassizii, which inhabits the desert regions in the south-western United States. In 1881 Cox found large sacs filled with clear water under the carapace, but it was half a century later that these sacs were identified as the large bilobed bladder; references to specific water sacs continued to appear in the literature until the 1960s.

Since 1970, information on the water economy of desert tortoises has been obtained from extensive field studies. Rates of disappearance of tritiated water injected into the body have shown that during the drought periods of the summer, water turnover (intake) rates do not differ from the rates of metabolic water production. Under these conditions urine is not voided, but is stored in the large bladder. During a drought period the bladder urine increases from initially low osmolality finally to reach isosmolality with the blood plasma. Soluble K+ is the major cation of the urine, but large amounts of K+ are also present as precipitated urates. During a drought period the body is in negative water balance, but despite substantial losses of total body water, the plasma concentrations of Na+ and Cl− can remain constant for many months, indicating regulation of the extracellular fluid and water content of the body tissues by reabsorption of water from the urinary bladder. The bladder thus acts both as a store for nitrogenous waste and K+ and as a water reservoir during droughts. Following rain showers, there is a sharp decline in tritium activity correlated with copious drinking from temporary pools of rain water. The old bladder urine is voided and most of the water drunk is stored as a highly dilute urine.

In 1676 Perrault observed that in a freshwater turtle, Emys orbicularis, but not in the giant tortoise, two other bladders opened into the cloaca. By the mid-twentieth century it had been established that these cloacal bladders typically were restricted to species of chelonians that led a semi-terrestrial or semi-aquatic life. The function of the bladders has been debated since Townson observed in 1799 that dehydrated freshwater turtles took up water by anal drinking, suggesting that anal drinking served in the water economy of semi-terrestrial turtles. Since then, the bladders have been ascribed hydrostatic and respiratory functions, but the recent literature mostly argues for a respiratory function. The possible role of the cloacal bladders as a water reservoir in amphibious turtles is still open.

Terrestrial amphibians and tortoises are unique among vertebrates in possessing large urinary bladders that may function as water reservoirs in dry environments. This function depends upon copious water intake when water becomes available combined with discontinued voiding of urine in the absence of water. Adaptation to terrestrial habitats in ureotelic amphibians is correlated with tolerance of high urea concentrations in the body fluids. In arid-zone tortoises and uricotelic tree frogs, nitrogenous waste products are precipitated in the bladder, which functions as the main sink. Renewed contact with water releases drinking behaviour and voiding of the bladder urine until the accumulated excretory products are eliminated from the body and/or bladder, preparing the organism for re-exposure to arid conditions.

The evolution of dominance by the selection of modifiers of the phenotypes of deleterious mutations was proposed as a hypothesis by R. A. Fisher in 1928. It has been strongly criticized ever since, is regarded by many as having been made irrelevant by metabolic control theory, and most recently has been claimed to have been ‘falsified’ by H. A. Orr. Is it indeed not only obsolete but wrong? Its history is reviewed and its present status evaluated. We conclude (1) that it has a role as the explanation of the dominance found in many cases of selection through visual predation and (2) that the selection mechanism long claimed to be ineffective (the increase in frequency of a single modifier) will be effective under certain special conditions that may be different from those Fisher proposed.

Chemical information, carried by genes, is one of several types of information important for the functioning of cells and organisms. While genes govern the two-dimensional flow of information, the cell walls are at the basis of a structural, three-dimensional framework of plant form and growth. Recent data show the walls to be a cellular ‘organelle’ undergoing dynamic changes in response to a plethora of stimuli. In this review, an integrated approach, rooted in the organismal perspective, is taken to consider the role of cell walls in the biology of plants. First, the complexity of molecular and biochemical events leading to the biosynthesis of wall components is described within the framework of its spatial cellular organisation, and the major regulatory check-points are characterised. Second, cell walls form a structural and functional continuum within the whole plant and thus could be defined in relation to the protoplasts that produce them and in relation to the plant itself. Model systems of suspension-cultured cells are used to reveal the existence of a bidirectional exchange of information between the protoplast and its walls. The ‘plasticity’ of plant cell reactions, seen in defence responses or in changes in wall composition, to e.g. stress, plant growth regulators or chemical agents as well as the role of cell walls and/or wall components in somatic embryogenesis are also discussed. Third, being a continuum within the plant body, the walls fulfil vital functions in plant growth and development. The examples characterised include the determination of cellular polarity and the plane of cell division, cytokinesis, and the role of plasmodesmata in cell-to-cell communication and the formation of functional symplastic domains. Fourth, the exocellular control of morphogenetic processes is described and the potential of cell walls as determinants or reservoirs of positional information is indicated. Particular emphasis is put on the (bio)chemical signals coming through or derived from cell walls as well as the mechanical properties of the walls. Based on those data, the ‘plant body’ concept is formulated. The plant is thus treated as a unit filled with intertwining networks: (1) symplastic, (2) the endomembrane system and (3) cytoskeletal, with cell walls providing an architectural scaffolding and communication ports formed within (4) the cytoskeleton-plasma membrane-cell wall continuum.

The present review examines the developments in the elucidation of the mechanisms of amphibian respiration and olfaction. Research in these two areas has largely proceeded along independent lines, despite the fact that ventilation of the nasobuccopharyngeal cavity is a basic element in both functions. The English naturalist Robert Townson demonstrated, in the 1790s, that amphibians, contrary to general belief, ventilated the lungs by a pressure-pump mechanism. Frogs and other amphibians respire by alternatively dilating and contracting the buccopharyngeal cavity. During dilatation, with the mouth and glottis closed, air is sucked in through the open nostrils to fill the cavity. During contraction of the throat, with nostrils closed and glottis open, the air in the buccopharyngeal cavity is pressed into the lungs. During expiration, the glottis and nostrils open and air is expelled from the lungs ‘by their own contraction from a state of distention’. Herholdt (1801), a Danish army surgeon, independently described the buccal pressure-pump mechanism in frogs, his experiments being confirmed by the commissioners of the Société Philomatique in Paris. Haro (1842) reintroduced a suction mechanism for amphibian respiration, which Panizza (1845) refuted: excision of the tympanic membranes prevented lung inflation, the air in the buccopharyngeal cavity leaving through the tympanum holes. Closure of the holes with the fingers restored lung inflation. The importance of cutaneous respiration in frogs and other amphibians was discovered by Spallanzani (1803), who found that frogs might survive excision of the lungs and that the amounts of exhaled carbon dioxide were small compared with those eliminated through the skin. Edwards (1824) confirmed and extended Spallanzani's findings, and Regnault & Reiset (1849) attempted to establish the relative importance of skin and lungs as respiratory organs in frogs. The problem was solved by Krogh (1904a) who measured respiration through the skin and lungs separately and simultaneously. Krogh (1904a) confirmed that carbon dioxide was chiefly eliminated through the skin, correlated with its high diffusion rate in water and tissue, whereas the pattern of oxygen uptake varied seasonally, the pulmonary uptake being lower than the cutaneous during autumn and winter, but substantially higher during the breeding period. Dolk & Postma (1927) confirmed this respiratory pattern. More recently, Hutchison and coworkers have examined the relative role of pulmonary and cutaneous gas exchange in a large number of amphibians, equipped with head masks for the separate measurement of the lung respiration in normally ventilating animals (Vinegar & Hutchison, 1965; Guimond & Hutchison, 1968; Hutchison, Whitford & Kohl, 1968; Whitford & Hutchison, 1963, 1965, 1966). As early as 1758, Rösel von Rosenhof suggested that the lungs of frogs in water functioned as hydrostatic organs that permitted the animal to float at the surface or rest on the bottom of the pond. The suggestion was inspired by observations made in the second half of the seventeenth century by members of the Royal Academy of Sciences in Paris. The French anatomists demonstrated that a tortoise, presumably the European freshwater turtle Emys orbicularis, could regulate its buoyancy by changing the volume of the lungs, to descend passively or ascend in the water. The hydrostatic function of the lungs has been repeatedly rediscovered, by Emery (1869) in the frog, by Marcacci (1895) in frogs, toads and salamanders, by Whipple (1906b) in a newt, by Willem (1920, 1931) in frogs and Xenopus laevis, by Speer (1942) in several anurans and urodeles, and finally by de Jongh (1972) in Xenopus laevis. In the second half of the nineteenth century a number of important papers appeared which confirmed and extended Townson's (1794) and Panizza's (1845) analysis of the normal respiratory movements in frogs. Lung ventilation cycles, interspaced by oscillatory movements of the throat, might periodically be replaced by a sequence predominated by inspirations, resulting in lung inflation, followed by exhalations that restored normal lung volume. Babák (1912a) established that inflations were reactions to the experimental manipulations, and that in resting, undisturbed frogs, lung ventilations normally occurred singly, interspaced by series of approximately 10–50 buccal oscillations. Extensive comparative studies early in the century showed that the respiratory mechanisms and patterns were basically similar in all anurans and urodeles investigated. The modern era of investigations in amphibian respiration began with the work of de Jongh & Gans (1969). They recorded pressures in the buccal cavity, lungs and visceral cavity and electrical activity of some 15 muscles possibly associated with respiration in the bullfrog Rana catesbeiana. The respiration recorded in the frogs was predominated by cycles of lung inflation and deflation, consistent with substantially but not excessively disturbed frogs. Studies by other investigators on various anuran species showed respiratory patterns that varied strongly with respect to the frequency and degree of lung inflations, presumably reflecting degrees to which the experimental conditions affected the breathing.

The elucidation of the role of the buccopharyngeal ventilation in amphibian olfaction can be traced to the realization in the 1890s that the nasal cavity has a double function in being both the seat of the sense of smell and part of the respiratory passages. The ability of amphibians to smell and to react to air-borne or water-borne chemical cues in the environment thus depends on the oscillatory movements of the buccal floor which ventilate the nasal cavity. Experimental evidence for a sense of smell was, however, lacking, and it was first furnished in urodele feeding early in the present century. Despite the demonstration of the fundamental role of the nasobuccal oscillatory ventilation in olfactory responses to food in newts, the oscillatory throat movements in amphibians continued, however, to be referred to as respiratory. Evidence concerning the role of the buccopharyngeal ventilation in respiration had been circumstantial until Whitford & Hutchison (1963, 1965, 1966) determined the relative importance of cutaneous and pulmonary/buccopharyngeal respiration in lunged and lungless salamanders. In lungless salamanders, the buccopharyngeal mucosa accounted for approximately 25% of the total oxygen consumption, and it was concluded that buccopharyngeal oscillatory ventilation in salamanders is primarily respiratory in function, a possible olfactory function being secondary. During the last decades an extensive literature has accumulated on the role played by olfaction in the life of urodeles, but also in feeding in anurans. Often the descriptions of behaviour elicited by air-borne or water-borne odours also note increased oscillatory movements of the buccal floor, indicating the importance of the ventilation of the nasal cavity. In the elucidation of the functional significance of buccal oscillations in vertebrate evolution, the reptiles are of particular interest because such oscillations are also known in chelonians, crocodiles and some lizards. Olfaction plays a role in the life of chelonians and crocodiles which respire by means of suction mechanisms. The throat movements are thus not concerned with the ventilation of the lungs but presumably with olfaction. It is thus indicated that in lower vertebrates, including the amphibians, the shallow oscillatory movements of the buccal floor primarily serve to establish olfactory contact with the surrounding medium, air or water, whereas a respiratory function is secondary.

Theorists and experimental researchers have long debated whether animals are able to imitate. A variety of definitions of imitation have been proposed to describe this complex form of social learning. Experimental research on imitation has often been hampered by either a too loose ‘anthropomorphic’ approach or by too narrow ‘behaviourist’ definitions. At present neither associative nor cognitive theories are able to offer an exhaustive explanation of imitation in animals. An ethological approach to imitation offers a different perspective. By integrating questions on function, mechanism, development and evolution one can identify possible directions for future research. At present, however, we are still far from developing a comprehensive theory of imitation.

A functional approach to imitation shows that, despite some evidence for imitative learning in food processing in apes, such learning has not been shown to be involved in the social transmission of either tool-use skills or communicative signals. Recently developed procedures offer possible ways of clarifying the role of imitation in tool use and visual communication. The role of imitation in explorative play in apes is also investigated and the available data suggest that copying during play might represent a behavioural homologue of human imitation.

It is proposed that the ability to copy the behaviour of a companion is under a strong genetic influence in many social species. Many important factors have not been examined experimentally, e.g. the effect of the demonstrator, the influence of attention and memory and the ability to generalize. The potential importance of reinforcement raises the possibility that copying abilities serving divergent functions might be partly under the control of different mechanisms.

We shall examine the impact of Charles S. Elton's 1924 article on periodic fluctuations in animal populations on the development of modern population ecology. We argue that his impact has been substantial and that during the past 75 years of research on multi-annual periodic fluctuations in numbers of voles, lemmings, hares, lynx and game animals he has contributed much to the contemporary understanding of the causes and consequences of population regulation. Elton was convinced that the cause of the regular fluctuations was climatic variation. To support this conclusion, he examined long-term population data then available. Despite his firm belief in a climatic cause of the self-repeating periodic dynamics which many species display, Elton was insightful and far-sighted enough to outline many of the other hypotheses since put forward as an explanation for the enigmatic long-term dynamics of some animal populations. An interesting, but largely neglected aspect in Elton's paper is that it ends with speculation regarding the evolutionary consequences of periodic population fluctuations. The modern understanding of these issues will also be scrutinised here. In population ecology, Elton's 1924 paper has spawned a whole industry of research on populations displaying multi-annual periodicity. Despite the efforts of numerous research teams and individuals focusing on the origins of multi-annual population cycles, and despite the early availability of different explanatory hypotheses, we are still lacking rigorous tests of some of these hypotheses and, consequently, a consensus of the causes of periodic fluctuations in animal populations. Although Elton would have been happy to see so much effort spent on cyclic populations, we also argue that it is unfortunate if this focus on a special case of population dynamics should distract our attention from more general problems in population and community dynamics.

Previous phylogenetic analyses of caecilian neuroanatomical data yield results that are difficult to reconcile with those based upon more traditional morphological and molecular data. A review of the literature reveals problems in both the analyses and the data upon which the analyses were based. Revision of the neuroanatomical data resolves some, but not all, of these problems and yields a data set that, based on comparative measures of data quality, appears to represent some improvement over previous treatments. An extended data set of more traditional primarily morphological data is developed to facilitate the evaluation of caecilian relationships and the quality and utility of neuroanatomical and more traditional data. Separate and combined analyses of the neuroanatomical and traditional data produce a variety of results dependent upon character weighting, with little congruence among the results of the separate analyses and little support for relationships among the ‘higher’ caecilians with the combined data. Randomization tests indicate that: (1) there is significantly less incompatibility within each data set than that expected by chance alone; (2) the between-data-set incompatibility is significantly greater than that expected for random partitions of characters so the two data sets are significantly heterogeneous; (3) the neuroanatomical data appear generally of lower quality than the traditional data; (4) the neuroanatomical data are more compatible with the traditional data than are phylogenetically uninformative data. The lower quality of the neuroanatomical data may reflect small sample sizes. In addition, a subset of the neuroanatomical characters supports an unconventional grouping of all those caecilians with the most rudimentary eyes, which may reflect concerted homoplasy. Although the neuroanatomical data may be of lower quality than the traditional data, their compatibility with the traditional data suggests that they cannot be dismissed as phylogenetically meaningless. Conclusions on caecilian relationships are constrained by the conflict between the neuroanatomical and traditional data, the sensitivity of the combined analyses to weighting schemes, and by the limited support for the majority of groups in the majority of the analyses. Those hypotheses that are well supported are uncontroversial, although some have not been tested previously by numerical phylogenetic analyses. However, the data do not justify an hypothesis of ‘higher’ caecilian phylogeny that is both well resolved and well supported.

The various mutualistic and antagonistic symbioses between fig trees (Ficus: Moraceae) and chalcid wasps comprise a community in microcosm. Phylogenetic estimates of figs and fig wasps show general topological correspondence, making the microcosm a model system for cophylogeny. Incongruence between phylogenies from associated organisms can be reconciled through a combination of evolutionary events. Cophylogeny mapping reconciles phylogenies by embedding an associate tree into a host tree, finding the optimal combinations of events capable of explaining incongruence and evaluating the level of codivergence. This review addresses the results of cophylogeny analysis concerning Ficus and discusses the plausibility of different evolutionary events. Five different associations encompassing fig-pollinator, fig-parasite and pollinator-parasitoid interactions are reconciled. The method improves on previous comparisons by employing ‘jungles’ to provide an exhaustive and quantitative analysis of cophylogeny. A jungle is a mechanism for inferring host switches and obtaining all potentially optimal solutions to the reconciliation problem. The results support the consensus that figs codiverge significantly with pollinators but not non-pollinators. However, pollinators still appear to have switched between hosts in contradiction to the traditional model of faithful codivergence. This emphasises the growing realisation that evolutionary transitions in the microcosm are more flexible than previously thought and host specificity is necessary but not sufficient for codivergence. The importance of sampling strategy is emphasised by the influence of taxon set on the fig-pollinator and fig-parasite jungles. Spurious significant results for fig-parasite and fig-parasitoid jungles indicate that the choice of congruence measure influences significance; the total number of events required to reconcile two trees (‘total cost’) is not a good measure of congruence when switches cannot be realistically weighted.

The response of the gill of Aplysia californica Cooper to weak to moderate tactile stimulation of the siphon, the gill-withdrawal response or GWR, has been an important model system for work aimed at understanding the relationship between neural plasticity and simple forms of non-associative and associative learning. Interest in the GWR has been based largely on the hypothesis that the response could be explained adequately by parallel monosynaptic reflex arcs between six parietovisceral ganglion (PVG) gill motor neurons (GMNs) and a cluster of sensory neurons termed the LE cluster. This hypothesis, the Kupfermann–Kandel model, made clear, falsifiable predictions that have stimulated experimental work for many years. Here, we review tests of three predictions of the Kupfermann–Kandel model: (1) that the GWR is a simple, reflexive behaviour graded with stimulus intensity; (2) that central nervous system (CNS) pathways are necessary and sufficient for the GWR; and (3) that activity in six identified GMNs is sufficient to account for the GWR. The available data suggest that (1) a variety of action patterns occur in the context of the GWR; (2) the PVG is not necessary and the diffuse peripheral nervous system (PNS) is sufficient to mediate these action patterns; and (3) the role of any individual GMN in the behaviour varies. Both the control of gill-withdrawal responses, and plasticity in these responses, are broadly distributed across both PNS and CNS pathways. The Kupfermann–Kandel model is inconsistent with the available data and therefore stands rejected. There is, no known causal connection or correlation between the observed plasticity at the identified synapses in this system and behavioural changes during non-associative and associative learning paradigms.

Critical examination of these well-studied central pathways suggests that they represent a ‘wetware’ neural network, architecturally similar to the neural network models of the widely used ‘Perceptron’ and/or ‘Back-propagation’ type. Such models may offer a more biologically realistic representation of nervous system organisation than has been thought. In this model, the six parallel GMNs of the CNS correspond to a hidden layer within one module of the gill-control system. That is, the gill-control system appears to be organised as a distributed system with several parallel modules, some of which are neural networks in their own right. A new model is presented here which predicts that the six GMNs serve as components of a ‘push-pull’ gain control system, along with known but largely unidentified inhibitory motor neurons from the PVG. This ‘push-pull’ gain control system sets the responsiveness of the peripheral gill motor system. Neither causal nor correlational links between specific forms of neural plasticity and behavioural plasticity have been demonstrated in the GWR model system. However, the GWR model system does provide an opportunity to observe and describe directly the physiological and biochemical mechanisms of distributed representation and parallel processing in a largely identifiable ‘wetware’ neural network.

There is no logical or theoretical barrier to the proposition that organismal and cell signaling could transduce environmental signals into specific, beneficial changes in primary structure of noncoding DNA via repetitive element movement or mutation. Repetitive DNA elements, including transposons and microsatellites, are known to influence the structure and expression of protein-coding genes, and to be responsive to environmental signals in some cases. These effects may create fodder for adaptive evolution, at rates exceeding those observed for point mutations. In many cases, the changes are no doubt random, and fitness is increased through simple natural selection. However, some transposons insert at specific sites, and certain regions of the genome exhibit selectively and beneficially high mutation rates in a range of organisms. In multicellular organisms, this could benefit individuals in situations with significant potential for clonal expansion: early life stages or regenerative tissues in animals, and most plant tissues. Transmission of the change to the next generation could occur in plants and, under some circumstances, in animals.

The pattern of the evolutionary radiation of modern birds (Neornithes) has been debated for more than 10 years. However, the early fossil record of birds from the Paleogene, in particular, the Lower Eocene, has only recently begun to be used in a phylogenetic context to address the dynamics of this major vertebrate radiation. The Cretaceous-Paleogene (K-P) extinction event dominates our understanding of early modern bird evolution, but climate change throughout the Eocene is known to have also played a major role. The Paleocene and Lower Eocene was a time of avian diversification as a result of favourable global climatic conditions. Deteriorations in climate beginning in the Middle Eocene appear to be responsible for the demise of previously widespread avian lineages like Lithornithiformes and Gastornithidae. Other groups, such as Galliformes display replacement of some lineages by others, probably related to adaptations to a drier climate. Finally, the combination of slowly deteriorating climatic conditions from the Middle Eocene onwards, appears to have slowed the evolutionary rate in Europe, as avian faunas did not differentiate markedly until the Oligocene. Taking biotic factors in tandem with the known Paleogene fossil record of Neornithes has recently begun to illuminate this evolutionary event. Well-preserved fossil taxa are required in combination with ever-improving phylogenetic hypotheses for the inter-relationships of modern birds founded on morphological characters. One key avifauna of this age, synthesised for the first time herein, is the Lower Eocene Fur Formation of Denmark. The Fur birds represent some of the best preserved (often in three dimensions and with soft tissues) known fossil records for major clades of modern birds. Clear phylogenetic assessment of these fossils will prove critical for future calibration of the neornithine evolutionary timescale. Some early diverging clades were clearly present in the Paleocene as evidenced directly by new fossil material alongside the phylogenetically constrained Lower Eocene taxa. A later Oligocene radiation of clades other than Passeriformes is not supported by available fossil data.

Complexity in the networks of interactions among and between the living and abiotic components forming ecosystems confounds the ability of ecologists to predict the economic consequences of perturbations such as species deletions in nature. Such uncertainty hampers prudent decision making about where and when to invest most intensively in species conservation programmes. Demystifying ecosystem responses to biodiversity alterations may be best achieved through the study of the interactions allowing biotic communities to compensate internally for population changes in terms of contributing to ecosystem function, or their intrinsic functional redundancy. Because individual organisms are the biologically discrete working components of ecosystems and because environmental changes are perceived at the scale of the individual, a mechanistic understanding of functional redundancy will hinge upon understanding how individuals' behaviours influence population dynamics in the complex community setting. Here, I use analytical and graphical modelling to construct a conceptual framework for predicting the conditions under which varying degrees of interspecific functional redundancy can be found in dynamic ecosystems. The framework is founded on principles related to food web successional theory, which provides some evolutionary insights for mechanistically linking functional roles of discrete, interacting organisms with the dynamics of ecosystems because energy is the currency both for ecological fitness and for food web commerce. Net productivity is considered the most contextually relevant ecosystem process variable because of its socioeconomic significance and because it ultimately subsumes all biological processes and interactions. Redundancy relative to productivity is suggested to manifest most directly as compensatory niche shifts among adaptive foragers in exploitation ecosystems, facilitating coexistence and enhancing ecosystem recovery after disturbances which alter species' relative abundances, such as extinctions. The framework further explicates how resource scarcity and environmental stochasticity may constitute ‘ecosystem legacies’ influencing the emergence of redundancy by shaping the background conditions for foraging behaviour evolution and, consequently, the prevalence of compensatory interactions. Because it generates experimentally testable predictions for a priori hypothesis testing about when and where varying degrees of functional redundancy are likely to be found in food webs, the framework may be useful for advancing toward the reliable knowledge of biodiversity and ecosystem function relations necessary for prudent prioritization of conservation programmes. The theory presented here introduces explanation of how increasing diversity can have a negative influence on ecosystem sustainability by altering the environment for biotic interactions – and thereby changing functional compensability among biota – under particular conditions.

The human large intestine is recognised as a physiologically important organ responsible for the conservation of water and salts. Through its resident bacteria, it is also capable of complex, enzyme catalysed, hydrolytic-digestive functions that have a high biological impact on the host. These microorganisms metabolise dietary components, principally complex carbohydrates that are not hydrolysed or absorbed in the upper gastrointestinal tract, and in this way, sequester energy for the host, through fermentation. This process involves a series of anaerobic, energy-yielding, catabolic reactions which complete digestive processes in the gut, resulting in end products that in turn influence the distribution of microbial species present as well as having some systemic effects. Some of the bacteria are thought to possess important health-promoting activities, especially with respect to their influence on mucosal and systemic immune responses to disease. These bioactivities can be modulated by substrates that support and influence microbial development, growth and survival. For these reasons, it is necessary to review dietary factors that may delimit bacterial diversity, to be able to predict responses and sensitivities to various environmental pressures and manipulations that occur in this area of human microbiology.

In the order Lipotyphla (Insectivora), certain reproductive features differ quite distinctly from the eutherian norms, and are of interest with regard to the evolution of mammalian gamete function and perhaps for questions of lipotyphlan phylogeny. As seen in one or more members of five lipotyphlan families (shrews, moles, hedgehogs, golden moles, tenrecs), these features can involve the configuration of the male tract including the penis, the morphology of the sperm head, the anatomy of the oviduct and the patterns of sperm transport within it, the character of the cumulus oophorus, and the way in which fertilising spermatozoa interact with the eggs. However, the picture is by no means uniform within the order. Reproductive idiosyncrasies occur variously in the different lipotyphlan families, and appear consistently and strikingly in shrews – the group studied most extensively. Compared to the patterns in most Eutheria, the most interesting anomalies in soricids include (a) the regulation of sperm transport to the site of fertilisation by oviduct crypts, whose arrangement can vary even according to species, (b) a circumscribed matrix-free cumulus oophorus that appears essential for fertilisation as the inducer of the acrosome reaction, (c) barbs on the acrosome-reacted sperm head by which it may attach to the zona pellucida.

With regard to the bearing such reproductive traits might have on lipotyphlan systematics, the African mouse shrew (Myosorex varius) displays a mix of traits that characterize either crocidurine or soricine shrews, consistent with the proposal that it belongs in a more primitive tribe, Myosoricinae, or subfamily, the Crocidosoricinae, from which the crocidurine and soricine lines probably evolved. Moreover, although elephant shrews are assigned now to a separate order (Macroscelidea), they display several of the unusual reproductive features seen in lipotyphlans, particularly in chrysochlorids and tenrecs. On the other hand, if used as a phylogenetic yardstick, none of the reproductive features described serves to define the Lipotyphla as classically constituted within one order, nor necessarily all the relationships suggested by recent sequencing studies of nuclear and mitochondrial genes.

Ecological science is often organised as a hierarchical series of entities: genes, individuals, populations, species, communities, ecosystems and biosphere. Here, I consider an alternative process-based approach to ecology, and analyse the nature of the fundamental processes in ecology. These fundamental processes are discussed in the context of the following question: ‘for any planet with carbon-based life, which persists over geological time scales, what are the minimum set of ecological processes that must be present?’ I suggest that the following processes would be present on any such planet: energy flow, multiple guilds, ecological trade-offs leading to within-guild biodiversity, ecological hypercycles, merging of organismal and ecological physiology, carbon sequestration and possibly photosynthesis. Nutrient cycling is described as an emergent property of these fundamental processes. I discuss reasons why a biosphere based on a single species with no nutrient cycling is very unlikely to exist. I also describe the concept of ‘Gaian effect’. This suggests that some processes will always tend to extend the lifespan of a biosphere in which they develop (positive Gaian effect) while others could either increase or decrease (negative Gaian effect) such a lifespan. These ideas are discussed in the context of astrobiology, ecosystem services, conservation biology and Gaia theory.

The merging of two independent populations of heterotrophs and autotrophs into a single population of mixotrophs has occurred frequently in evolutionary history. It is an example of a wide class of related phenomena, known as symbiogenesis. The physiological basis is almost always (reciprocal) syntrophy, where each species uses the products of the other species. Symbiogenesis can repeat itself after specialization on particular assimilatory substrates. We discuss quantitative aspects and delineate eight steps from two free-living interacting populations to a single fully integrated endosymbiotic one. The whole process of gradual interlocking of the two populations could be mimicked by incremental changes of particular parameter values. The role of products gradually changes from an ecological to a physiological one. We found conditions where the free-living, epibiotic and endobiotic populations of symbionts can co-exist, as well as conditions where the endobiotic symbionts outcompete other symbionts. Our population dynamical analyses give new insights into the evolution of cellular homeostasis. We show how structural biomass with a constant chemical composition can evolve in a chemically varying environment if the parameters for the formation of products satisfy simple constraints. No additional regulation mechanisms are required for homeostasis within the context of the dynamic energy budget (DEB) theory for the uptake and use of substrates by organisms. The DEB model appears to be closed under endosymbiosis. This means that when each free-living partner follows DEB rules for substrate uptake and use, and they become engaged in an endosymbiotic relationship, a gradual transition to a single fully integrated system is possible that again follows DEB rules for substrate uptake and use.

The relationship between phylogenetic reconstruction and evolutionary theory is reassessed. It is argued here that phylogenies, and evolutionary principles, should be analysed initially as independently from each other as possible. Only then can they be used to test one another. If the phylogenies and evolutionary principles are totally consistent with one another, this consilience of independent lines of evidence increases confidence in both. If, however, there is a conflict, then one should assess the relative support for each hypothesis, and tentatively accept the more strongly supported one. We review examples where the phylogenetic hypothesis is preferred over the evolutionary principle, and vice versa, and instances where the conflict cannot be readily resolved. Because the analyses of pattern and process must initially be kept separate, the temporal order in which they are performed is unimportant. Therefore, the widespread methodology of always proceeding from cladogram to evolutionary ‘scenario’ cannot be justified philosophically. Such an approach means that cladograms cannot be properly tested against evolutionary principles, and that evolutionary ‘scenarios’ have no independent standing. Instead, we propose the ‘consilience’ approach where phylogenetic and evolutionary hypotheses are formulated independently from each other and then examined for agreement.

Current progress on the mechanisms of ethylene signal perception and transduction are reviewed with an emphasis on reconciling data from molecular genetics and from biochemical approaches. It is proposed that there exist two or more interacting transduction pathways.