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 locomotory behavior in profitable and unprofitable simulated prey

Prey that are unprofitable to attack (for example, those containing noxious chemicals) frequently exhibit slower and more predicable movement than species that lack these defenses. Possible explanations for the phenomenon include a lack of selection pressure on unprofitable prey to avoid predators and active selection on unprofitable prey to advertise their noxiousness. We explicitly tested these and other hypotheses using a novel artificial world in which the locomotory characteristics (step size, waiting time, and angular direction) of artificial profitable and unprofitable computer-generated prey were subject to continued selection by humans over a number of generations. Unprofitable prey evolved significantly slower movement behavior than profitable prey when they were readily recognized as unprofitable, and also when they frequently survived predatory attacks. This difference arose primarily as a consequence of more intense selection on profitable prey to avoid capture. When unprofitable prey were very similar (but not identical) in morphological appearance to profitable prey, unprofitable prey evolved particularly slow movement behavior, presumably because when they were slow-moving they could be more readily recognized as being unprofitable. When unprofitable prey were constrained to move slowly, a morphologically identical profitable prey species evolved locomotor mimicry only when it had no more effective means of avoiding predation. Overall, our results provide some of the first empirical support for a number of earlier hypotheses for differences in movement between unprofitable and profitable prey and demonstrate that locomotor mimicry is not an inevitable outcome of selection even in morphologically similar prey.     

The evolution of dosage-compensation mechanisms

Dosage compensation is the process by which the expression levels of sex-linked genes are altered in one sex to offset a difference in sex-chromosome number between females and males of a heterogametic species. Degeneration of a sex-limited chromosome to produce heterogamety is a common, perhaps unavoidable, feature of sex-chromosome evolution. Selective pressure to equalize sex-linked gene expression in the two sexes accompanies degeneration, thereby driving the evolution of dosage-compensation mechanisms. Studies of model species indicate that what appear to be very different mechanisms have evolved in different lineages: the male X chromosome is hypertranscribed in drosophilid flies, both hermaphrodite X chromosomes are downregulated in the nematode Caenorhabditis elegans, and one X is inactivated in mammalian females. Moreover, comparative genomic studies demonstrate that the trans-acting factors (proteins and non-coding RNAs) that have been shown to mediate dosage compensation are unrelated among the three lineages. Some tantalizing similarities in the fly and mammalian mechanisms, however, remain to be explained.     

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 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 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).     

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.     

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.      

Pseudo 2-fold symmetry in the copper-binding domain of arthropodan haemocyanins. Possible implications for the evolution of oxygen transport proteins

Investigation of the copper-binding centre of Panulirus interruptus haemocyanin led to the discovery of a pseudo 2-fold axis relating two helical pairs surrounding and co-ordinating the two copper ions. The pseudo 2-fold symmetry relating one helical pair, co-ordinating Cu-A, to the second helical pair co-ordinating Cu-B is quite precise with 31 equivalent C alpha atoms having a root-mean-square deviation of only 1.47 A. The 2-fold consists of a rotation of 174.6 degrees and a translation parallel to the rotation axis of 0.7 A. After superposition of the helical pairs, the two copper ions are within 1.1 A and the three C alpha atoms of the histidine ligands of Cu-A are within a root-mean-square deviation of 1.0 A from the C alpha atoms of the histidine residues co-ordinating Cu-B. Of the superimposed residues, 26% are identical in sequence. These data suggest that the current oxygen-binding centre of arthropodan haemocyanins is the result of dimerization, gene duplication and gene fusion of an ancestral mono-copper-binding helical pair. This suggestion is supported by the recent discovery that in the sequence of functional domains of molluscan haemocyanins only amino acid sequence homology with the arthropodan Cu-B helical pair has been found and no evidence for similarity with a Cu-A binding helical pair was observed. This provides strong evidence that a mono-copper-binding helical pair has been the ancestor of both the arthropodan and molluscan haemocyanins. Turning to the Fe-binding helical pairs in haemerythrins, it appears that they are less similar to each other than the two Cu-binding helical pairs in arthropodan haemocyanins. Nevertheless, the Fe-B haemerythrin helical pair superimposes well onto the Cu-A helical pair of Panulirus haemocyanin. A root-mean-square deviation of 1.9 A for 24 equivalent C alpha carbon atoms is obtained, while Fe-B deviates 1.4 A from Cu-A after superposition of the helices. Moreover, the three histidine ligands of the Cu-A helical pair are equivalent with three histidine ligands of the Fe-B pair. The structural similarity and correspondence in metal-binding ligands suggests that both haemocyanins and haemerythrins have originated from an ancestral mono-metal-binding helical pair having two ligands provided by the first helix and one ligand by the second helix.(ABSTRACT TRUNCATED AT 400 WORDS)     

AMiGA: the arthropodan mitochondrial genomes accessible database

SUMMARY: The Arthropodan Mitochondrial Genomes Accessible database (AMiGA) is a relational database developed to help in managing access to the increasing amount of data arising from developments in arthropodan mitochondrial genomics (136 mitochondrial genomes as of September 2005). The strengths of AMiGA include (1) a more accessible and up-to-date database containing a more comprehensive set of mitochondrial genomes for this phylum, (2) the provision of flexible search options for retrieving detailed information such as bibliographical data, genomic graphics, FASTA sequences and taxonomical status, (3) the possibility of enhanced comparative analyses by multiple alignment of single or concatenated sets of genes, (4) more accurate and updated information resulting from a specific curation process called AMiGA Notes and (5) the possibility of including unpublished sequences in a password-restricted area for comparative analysis with the other sequences stored in the database. AVAILABILITY: http://amiga.cbmeg.unicamp.br CONTACT: lessinger@amiga.cbmeg.unicamp.br SUPPLEMENTARY INFORMATION: Detailed information, including an illustrated tutorial, is available from the above URL.     

The dorsal compartment locomotory control system in amphioxus larvae

Amphioxus myotomes consist of separate sets of superficial and deep muscle fibers, each with its own innervation, that are thought to be responsible for slow swimming and escape behavior, respectively. Tracings from serial EM sections of the anterior nerve cord in the larva show that the motoneurons and premotor interneurons controlling the superficial fibers (the dorsal compartment, or DC pathway) are linked by specialized junctions of a previously undescribed type, referred to here as juxta-reticular (JR) junctions for the characteristic presence of a cisterna of endoplasmic reticulum on each side. JR junctions link the DC motoneurons with each other, with the largest of the anterior paired neurons (LPN3s) and with one class of ipsilateral projection neurons (IPNs), but occur nowhere else. Because of the paucity of synaptic input to the DC system, larval behavior can only be explained if the JR junctions act as functional links between cells. An analysis of the pattern of cell contacts also suggests that the LPN3s are probably pacemakers for both slow and fast locomotion, but act through junctions in the former case and conventional synapses in the latter. The only major synaptic input to the DC system identified in somites 1 and 2 was from four neurons located in the cerebral vesicle, referred to here as Type 2 preinfundibular projection neurons (PPN2s). They have unusually large varicosities, arranged in series, that make periodic contacts with the DC motoneurons. More caudally, the DC motoneurons receive additional input via similar large varicosities from the receptor cells of the first dorsal ocellus, located in somite 5. The overall circuitry of the locomotory control system suggests that the PPN2s may be instrumental in sustaining slow swimming, whereas mechanical stimulation, especially of the rostrum, preferentially activates the fast mode.     

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.