Recycling to remodel: evolution of dosage-compensation complexes

In diploid species where sex determination involves heteromorphic sex chromosomes, a mechanism has evolved to compensate for gene-dosage differences in sex-linked genes between the sexes. This regulatory mechanism, which is based on chromatin remodeling, is the function of complexes that include components themselves involved in other cellular functions or with homologs that are involved in such functions. Directing these complexes to the correct chromosome in the appropriate sex relies on pioneer or novel components as well as on the presence of sequence-dependent target sites.     

The evolution of immune mechanisms

From early on in evolution, organisms have had to protect themselves from pathogens. Mechanisms for discriminating "self" from "non-self" evolved to accomplish this task, launching a long history of host-pathogen co-evolution. Evolution of mechanisms of immune defense has resulted in a variety of strategies. Even unicellular organisms have rich arsenals of mechanisms for protection, such as restriction endonucleases, antimicrobial peptides, and RNA interference.In multicellular organisms, specialized immune cells have evolved, capable of recognition, phagocytosis, and killing of foreign cells as well as removing their own cells changed by damage, senescence, infection, or cancer. Additional humoral factors, such as the complement cascade, have developed that co-operate with cellular immunity in fighting infection and maintaining homeostasis. Defensive mechanisms based on germline-encoded receptors constitute a system known as innate immunity. In jaw vertebrates, this system is supplemented with a second system, adaptive immunity, which in contrast to innate immunity is based on diversification of immune receptors and on immunological memory in each individual.Usually, each newly evolved defense mechanism did not replace the previous one, but supplemented it, resulting in a layered structure of the immune system. The immune system is not one system but rather a sophisticated network of various defensive mechanisms operating on different levels, ranging from mechanisms common for every cell in the body to specialized immune cells and responses at the level of the whole organism. Adaptive changes in pathogens have shaped the evolution of the immune system at all levels.     

The evolution of developmental mechanisms

Over the past two to three decades, developmental biology has demonstrated that all multicellular organisms in the animal kingdom share many of the same molecular building blocks and many of the same regulatory genetic pathways. Yet we still do not understand how the various organisms use these molecules and pathways to assume all the forms we know today. Evolutionary developmental biology tackles this problem by comparing the development of one organism to another and comparing the genes involved and gene functions to understand what makes one organism different from another. In this review, we revisit a set of seven concepts defined by Lewis Wolpert (fate maps, asymmetric division, induction, competence, positional information, determination, and lateral inhibition) that describe the characters of many developmental systems and supplement them with three additional concepts (developmental genomics, genetic redundancy, and genetic networks). We will discuss examples of comparative developmental studies where these concepts have guided observations on the advent of a developmental novelty. Finally, we identify a set of evolutionary frameworks, such as developmental constraints, cooption, duplication, parallel and convergent evolution, and homoplasy, to adequately describe the evolutionary properties of developmental systems.     

The evolution of arthropodan locomotory mechanisms

The evidence was presented in Part 10 for the conclusions that the Onychophora, Myriapoda and Hexapoda comprise a separate arthropodan phylum, the Uniramia; that the myriapod classes have evolved in parallel from multilegged ancestors and not one from another; that the hexapod classes did not come from any myriapodan stock connected with the modern groups; and that the hexapod classes are independent, parallel evolutions from multilegged ancestors with little trunk sclerotization, descendant neither from each other nor from one sort of ancestral insect. Here in Part 11 are demonstrated the fundamental differences between the morphology and modes of action of a parapodium and a lobopodium. The latter could not have arisen from the former, but could have given rise to all types of uniramian limbs, together with their jointing, which differs in many ways from those of other arthropods. Consideration is given to the diversification of habits which must have occurred in the early terrestrial Uniramia and to those which set in later and led to the evolution of the extant classes. A diversification of feeding, locomotory and other habits must have taken place at a lobopodial stage in which considerable sclerotization first became established on the head. The trunk morphology and leg jointing in the various uniramian taxa could have arisen from animals with lobopodial limbs and little trunk sclerotization. A review is given of the data assembled in Parts 1 to 11 and of the conclusions reached concerning:– the mechanical uses of the haemocoel in evolving Uniramia and the essential features of the locomotory mechanisms, including:– the uses of trunk musculature; speeds of progression; the phase differences between the legs; the loading on the legs; segment numbers; etc. The relationships between the gaits used by the various Uniramia and their probable evolution are considered, together with an outline of the facilitating morphology. Finally the diversification of habits in the Uniramia is considered along with the morphological consequences. The detailed evidences of evolution of the Uniramia derived from the study of functional morphology far exceeds that derived from any other field. A comparison between the locomotory mechanisms and facilitating morphology of the Arachnida and Uniramia shows great differences. The usual fixation of the arachnid coxa on the body has led to a variety of subtle leg rocking mechanisms differing from those of the Uniramia and often secondary arrangements giving a promotor-remotor swing which are quite unlike those of the Uniramia. Arachnid gaits are different from those of Uniramia and show little variability. Stability is gained by arachnids in different manners from those in Uniramia and the parallel evolution of hexapody in the two groups results in marked differences.     

The evolution of sex-change mechanisms in fishes

Synopsis Five distinct sex-change mechanisms are identified among sequentially hermaphroditic fishes based on socio-ecological characteristics. The primary determinants of the sex-change mechanisms appear to be social organization and mating system, which in turn depend on resource distribution in space and time. The ability of a single individual to control all mating in the social unit, which is related to the size of the social unit, differentiates three suppression mechanisms from two induction mechanisms. Sex-change suppression, which is characteristic of species with small group size and rigid dominance hierarchies, refers to inevitable sex change in the absence of group dominance. Ability to migrate between resource patches differentiates protogynous suppression (e.g. inLabroides dimidiatus) from protandrous suppression (e.g. inAmphiprion spp.). Early sex change appears to have evolved from protogynous suppression under special conditions involving the loss of mating control by a single dominant individual in certain species (e.g.Centropyge spp. ). Sex-change induction, which is characteristic of species with large social groups lacking rigid dominance hierarchies, refers to the requirement that sex change must be induced by specific characteristics of (or changes in) the social group, regardless of dominance status. Ability to distinguish sex, or its importance, differentiates sex-ratio induction (e.g.Anthias squamipinnis) from size-ratio induction (e.g.Thalassoma spp.). Alternative models account for the possibility that all cases of sex change require stimulation from smaller conspecifics (universal induction-inhibition model) or that all fish have the genetic capacity to switch mechanisms, depending on changing ecological conditions and resulting changes in mating system (behavioral-scaling model). Neurophysiological models suggest that induction mechanisms, which require at least two categories of environmental stimuli, may have evolved from the simpler suppression mechanisms, which require only one kind of input from the environment.     

The evolution of embryonic patterning mechanisms in animals

Animals exhibit an enormous diversity of life cycles and larval morphologies. The developmental basis for this diversity is not well understood. It is clear, however, that mechanisms of pattern formation in early embryos differ significantly among and within groups of animals. These differences show surprisingly little correlation with phylogenetic relationships; instead, many are correlated with ecological factors, such as changes in life histories.     

The importance of mechanisms for the evolution of cooperation

Studies aimed at explaining the evolution of phenotypic traits have often solely focused on fitness considerations, ignoring underlying mechanisms. In recent years, there has been an increasing call for integrating mechanistic perspectives in evolutionary considerations, but it is not clear whether and how mechanisms affect the course and outcome of evolution. To study this, we compare four mechanistic implementations of two well-studied models for the evolution of cooperation, the Iterated Prisoner''s Dilemma (IPD) game and the Iterated Snowdrift (ISD) game. Behavioural strategies are either implemented by a 1 : 1 genotype–phenotype mapping or by a simple neural network. Moreover, we consider two different scenarios for the effect of mutations. The same set of strategies is feasible in all four implementations, but the probability that a given strategy arises owing to mutation is largely dependent on the behavioural and genetic architecture. Our individual-based simulations show that this has major implications for the evolutionary outcome. In the ISD, different evolutionarily stable strategies are predominant in the four implementations, while in the IPD each implementation creates a characteristic dynamical pattern. As a consequence, the evolved average level of cooperation is also strongly dependent on the underlying mechanism. We argue that our findings are of general relevance for the evolution of social behaviour, pleading for the integration of a mechanistic perspective in models of social evolution.     

The evolution of sperm transfer mechanisms in the Diptera

The known occurrence of spermatophores in the Diptera and some possible modes of transition to other mechanisms of sperm transfer are outlined. The closed systems of transfer, and the significance of modifications of gonopore shape in some species, are discussed.     

The evolution of inorganic carbon concentrating mechanisms in photosynthesis

Inorganic carbon concentrating mechanisms (CCMs) catalyse the accumulation of CO(2) around rubisco in all cyanobacteria, most algae and aquatic plants and in C(4) and crassulacean acid metabolism (CAM) vascular plants. CCMs are polyphyletic (more than one evolutionary origin) and involve active transport of HCO(3)(-), CO(2) and/or H(+), or an energized biochemical mechanism as in C(4) and CAM plants. While the CCM in almost all C(4) plants and many CAM plants is constitutive, many CCMs show acclimatory responses to variations in the supply of not only CO(2) but also photosynthetically active radiation, nitrogen, phosphorus and iron. The evolution of CCMs is generally considered in the context of decreased CO(2) availability, with only a secondary role for increasing O(2). However, the earliest CCMs may have evolved in oxygenic cyanobacteria before the atmosphere became oxygenated in stromatolites with diffusion barriers around the cells related to UV screening. This would decrease CO(2) availability to cells and increase the O(2) concentration within them, inhibiting rubisco and generating reactive oxygen species, including O(3).     

Molecular mechanisms of colicin evolution

This review explores features of the origin and evolution of colicins in Escherichia coli. First, the evolutionary relationships of 16 colicin and colicin-related proteins are inferred from amino acid and DNA sequence comparisons. These comparisons are employed to detail the evolutionary mechanisms involved in the origin and diversification of colicin clusters. Such mechanisms include movement of colicin plasmids between strains of E. coli and subsequent plasmid cointegration, transposition- and recombination-mediated transfer of colicin and related sequences, and rapid diversification of colicin and immunity proteins through the action of positive selection. The wealth of information contained in colicin sequence comparisons makes this an ideal system with which to explore molecular mechanisms of evolutionary change.      

The evolution of resource specialization through frequency-dependent and frequency-independent mechanisms

Levins's fitness set approach has shaped the intuition of many evolutionary ecologists about resource specialization: if the set of possible phenotypes is convex, a generalist is favored, while either of the two specialists is predicted for concave phenotype sets. An important aspect of Levins's approach is that it explicitly excludes frequency-dependent selection. Frequency dependence emerged in a series of models that studied the degree of character displacement of two consumers coexisting on two resources. Surprisingly, the evolutionary dynamics of a single consumer type under frequency dependence has not been studied in detail. We analyze a model of one evolving consumer feeding on two resources and show that, depending on the trait considered to be subject to evolutionary change, selection is either frequency independent or frequency dependent. This difference is explained by the effects different foraging traits have on the consumer-resource interactions. If selection is frequency dependent, then the population can become dimorphic through evolutionary branching at the trait value of the generalist. Those traits with frequency-independent selection, however, do indeed follow the predictions based on Levins's fitness set approach. This dichotomy in the evolutionary dynamics of traits involved in the same foraging process was not previously recognized.     

Phosphorylation mechanisms in chemical evolution

An objective of this work is to elucidate the mechanism of phosphorylation of nucleosides in amide solvents and in urea. A second objective is to assess the importance of phosphorylation and dephosphorylation of nucleotide derivatives in amide environments. Although the most complex amide studied here was N-methylacetamide, inferences are made on the importance of dephosphorylation for nucleotides in oligopeptide environments.Phosphorylations in amide solvents and in urea are suggested to proceed through monomeric metaphosphate, which was first postulated as a reaction intermediate thirty years ago (Butcher and Westheimer, 1955). Phosphorylation of nucleosides and nucleotides and dephosphorylation of nucleotide derivatives have been studied in formamide, N-methylformamide, urea and N-methylacetamide. Hydrated forms of 5-ADP and 5ATP are unstable in hot amide solvents and in urea. They decompose to a mixture of adenosine and its phosphorylated derivatives. The rate of decomposition is much slower in N-methylacetamide than in formamide or urea. Experiments designed to prepare oligonucleotides in the presence of oligopeptides have been reported (White, 1983). According to the present study, it is not unreasonable to expect that nucleotide derivatives can be condensed with nucleosides to form oligonucleotides in a peptide environment. However, nucleotide monomers such as 5-ATP, 5-ADP or 5AMP will suffer isomerization or decomposition during condensation use of activated phosphate derivatives is preferable.Monomeric metaphosphate has not been isolated or characterized in amide solvents. It is proposed here as a reaction intermediate, probably in a complexed form with the amide.     

'Lamarckian' mechanisms in darwinian evolution

Since the Modern Synthesis, evolutionary biologists have assumed that the genetic system is the sole provider of heritable variation, and that the generation of heritable variation is largely independent of environmental changes. However, adaptive mutation, epigenetic inheritance, behavioural inheritance through social learning, and language-based information transmission have properties that allow the inheritance of induced or learnt characters. The role of induced heritable variation in evolution therefore needs to be reconsidered, and the evolution of the systems that produce induced variation needs to be studied.     

The impact of endosymbionts on the evolution of host sex-determination mechanisms

The past years have revealed that inherited bacterial endosymbionts are important sources of evolutionary novelty for their eukaryotic hosts. In this review we discuss a fundamental biological process of eukaryotes influenced by bacterial endosymbionts: the mechanisms of sex determination. Because they are maternally inherited, several endosymbionts of arthropods, known as reproductive parasites, have developed strategies to convert non-transmitting male hosts into transmitting females through feminization of genetic males and parthenogenesis induction. Recent investigations have also highlighted that endosymbionts can impact upon host sex determination more subtly through genetic conflicts, resulting in selection of host nuclear genes resisting endosymbiont effects. Paradoxically, it is because of their selfish nature that reproductive parasites are such powerful agents of evolutionary change in their host sex-determination mechanisms. They might therefore represent excellent models for studying transitions between sex-determining systems and, more generally, the evolution of sex-determination mechanisms in eukaryotes.