Chemical evolution and the evolution of the Earth's crust

It is hypothesized that there is a close relationship between the geologic evolution of the global plates of the Earth's crust and the chemical evolution of life on the Earth. Characteristics of the axes of plate spreading are discussed in relation to postulated environments conducive to the synthesis of chemical compounds thought to be important biological precursors. Likely locations forin situ measurements to test the hypothesis are identified.     

Genome evolution and the evolution of exon-shuffling--a review

Recent studies on the genomes of protists, plants, fungi and animals confirm that the increase in genome size and gene number in different eukaryotic lineages is paralleled by a general decrease in genome compactness and an increase in the number and size of introns. It may thus be predicted that exon-shuffling has become increasingly significant with the evolution of larger, less compact genomes. To test the validity of this prediction, we have analyzed the evolutionary distribution of modular proteins that have clearly evolved by intronic recombination. The results of this analysis indicate that modular multidomain proteins produced by exon-shuffling are restricted in their evolutionary distribution. Although such proteins are present in all major groups of metazoa from sponges to chordates, there is practically no evidence for the presence of related modular proteins in other groups of eukaryotes. The biological significance of this difference in the composition of the proteomes of animals, fungi, plants and protists is best appreciated when these modular proteins are classified with respect to their biological function. The majority of these proteins can be assigned to functional categories that are inextricably linked to multicellularity of animals, and are of absolute importance in permitting animals to function in an integrated fashion: constituents of the extracellular matrix, proteases involved in tissue remodelling processes, various proteins of body fluids, membrane-associated proteins mediating cell-cell and cell-matrix interactions, membrane associated receptor proteins regulating cell cell communications, etc. Although some basic types of modular proteins seem to be shared by all major groups of metazoa, there are also groups of modular proteins that appear to be restricted to certain evolutionary lineages. In summary, the results suggest that exon-shuffling acquired major significance at the time of metazoan radiation. It is interesting to note that the rise of exon-shuffling coincides with a spectacular burst of evolutionary creativity: the Big Bang of metazoan radiation. It seems probable that modular protein evolution by exon-shuffling has contributed significantly to this accelerated evolution of metazoa, since it facilitated the rapid construction of multidomain extracellular and cell surface proteins that are indispensable for multicellularity.     

Cognition and evolution: learning and the evolution of sex traits

The evolution of gender characteristics is an outcome of mate choice, which has been assumed to be genetically mediated. Recent research suggests that learning also has a role to play as an agent of sexual selection.     

Protein evolution drives the evolution of the genetic code and vice versa

A model for the developmental pathway of the genetic code, grounded on group theory and the thermodynamics of codon-anticodon interaction is presented. At variance with previous models, it takes into account not only the optimization with respect to amino acid attributes but, also physicochemical constraints and initial conditions. A 'simple-first' rule is introduced after ranking the amino acids with respect to two current measures of chemical complexity. It is shown that a primeval code of only seven amino acids is enough to build functional proteins. It is assumed that these proteins drive the further expansion of the code. The proposed primeval code is compared with surrogate codes randomly generated and with another proposal for primeval code found in the literature. The departures from the 'universal' code, observed in many organisms and cellular compartments, fit naturally in the proposed evolutionary scheme. A strong correlation is found between, on one side, the two classes of aminoacyl-tRNA synthetases, and on the other, the amino acids grouped by end-atom-type and by codon type. An inverse of Davydov's rules, to associate the amino acid end atoms (O/N and non-O/non-N) of 18 amino acids with codons containing a weak base (A/U), extended to the 20 amino acids, is derived.     

The structure of protein evolution and the evolution of protein structure

The observed distribution of protein structures can give us important clues about the underlying evolutionary process, imposing important constraints on possible models. The availability of results from an increasing number of genome projects has made the development of these models an active area of research. Models explaining the observed distribution of structures have focused on the inherent functional capabilities and structural properties of different folds and on the evolutionary dynamics. Increasingly, these elements are being combined.     

The evolution of the environment and its influence on the evolution of life

Thermodynamic data and known paleogeological data were used to deduce when and what elements (compounds) were readily available during the whole history of the earth. On the basic assumption that available compounds would dictate the type of organisms to emerge, we attempted to derive a kind of evolutionary tree. This was then compared with the existing evolutionary trees derived from the sequences of proteins and polynucleotides.     

Mosaic evolution,preadaptation, and the evolution of evolvability in apes

A major goal in postsynthesis evolutionary biology has been to better understand how complex interactions between traits drive movement along and facilitate the formation of distinct evolutionary pathways. I present analyses of a character matrix sampled across the haplorrhine skeleton that revealed several modules of characters displaying distinct patterns in macroevolutionary disparity. Comparison of these patterns to those in neurological development showed that early ape evolution was characterized by an intense regime of evolutionary and developmental flexibility. Shifting and reduced constraint in apes was met with episodic bursts in phenotypic innovation that built a wide array of functional diversity over a foundation of shared developmental and anatomical structure. Shifts in modularity drove dramatic evolutionary changes across the ape body plan in two distinct ways: (1) an episode of relaxed integration early in hominoid evolution coincided with bursts in evolutionary rate across multiple character suites; (2) the formation of two new trait modules along the branch leading to chimps and humans preceded rapid and dramatic evolutionary shifts in the carpus and pelvis. Changes to the structure of evolutionary mosaicism may correspond to enhanced evolvability that has a “preadaptive” effect by catalyzing later episodes of dramatic morphological remodeling.     

Cooperation and the evolution of intelligence

The high levels of intelligence seen in humans, other primates, certain cetaceans and birds remain a major puzzle for evolutionary biologists, anthropologists and psychologists. It has long been held that social interactions provide the selection pressures necessary for the evolution of advanced cognitive abilities (the 'social intelligence hypothesis'), and in recent years decision-making in the context of cooperative social interactions has been conjectured to be of particular importance. Here we use an artificial neural network model to show that selection for efficient decision-making in cooperative dilemmas can give rise to selection pressures for greater cognitive abilities, and that intelligent strategies can themselves select for greater intelligence, leading to a Machiavellian arms race. Our results provide mechanistic support for the social intelligence hypothesis, highlight the potential importance of cooperative behaviour in the evolution of intelligence and may help us to explain the distribution of cooperation with intelligence across taxa.     

Modularity and the units of evolution

Summary While many developmental processes (e. g., gene networks or signaling pathways) are astonishingly conserved during evolution, they may be employed differently in different metazoan taxa or may be used multiply in different contexts of development. This suggests that these processes belong to building blocks or modules, viz., highly integrated parts of the organism, which develop and/or function relatively independent from other parts. Such modules may be relatively easy to dissociate from other modules and, therefore, could also serve as units of evolution. However, in order to further explore the implications of modularity for evolution, the vague notion of “modularity” as well as its relation to concepts like “unit of evolution” need to be more precisely specified. Here, a module is characterized as a certain type of dynamic pattern of couplings among the constituents of a process. It may or may not form a spatially contiguous unit. A unit of selection is defined as a unit of those constituents of a reproducing process/system, which exists in different variants and acts as a non-decomposable unit of fitness and variant reproduction during a particular selection process. The more general notion of a unit of evolution is characterized as a nondecomposable unit of constituents with reciprocal fitness dependence, be it due to fitness epistasis or due to the lack of independent variability. Because such fitness dependence may only be observed for some combinations of variants, several constituents may act as a unit of evolution only with a certain probability (coevolution probability). It is argued, that under certain conditions modules are likely to act as units of evolution with high coevolution probabilities, because there is likely to be a close tie between the pattern of couplings of the constituents of a reproducing system and their interdependent fitness contributions. Moreover and contrary to the traditional dichotomy of genes versus organisms as units of selection, modules tend to be more important in delimiting actual units of selection than either organisms or genes, because they are less easily disrupted by recombination than organisms, while having less contextsensitive fitness values than genes. Finally, it is suggested that the evolution of modularity is self-reinforcing, because the flexibility of intermodular connections facilitates the recombination among modules and their multiple employment in new contexts.     

Self-fertilization and the evolution of recombination

In this article, we study the effect of self-fertilization on the evolution of a modifier allele that alters the recombination rate between two selected loci. We consider two different life cycles: under gametophytic selfing, a given proportion of fertilizations involves gametes produced by the same haploid individual, while under sporophytic selfing, a proportion of fertilizations involves gametes produced by the same diploid individual. Under both life cycles, we derive approximations for the change in frequency of the recombination modifier when selection is weak relative to recombination, so that the population reaches a state of quasi-linkage equilibrium. We find that gametophytic selfing increases the range of epistasis under which increased recombination is favored; however, this effect is substantial only for high selfing rates. Moreover, gametophytic selfing affects the relative influence of different components of epistasis (additive x additive, additive x dominance, dominance x dominance) on the evolution of the modifier. Sporophytic selfing has much stronger effects: even a small selfing rate greatly increases the parameter range under which recombination is favored, when there is negative dominance x dominance epistasis. This effect is due to the fact that selfing generates a correlation in homozygosity at linked loci, which is reduced by recombination.     

Reputation and the evolution of conflict

The outcomes of conflicts in many human societies generate reputation effects that influence the nature of later conflicts. Those willing to escalate over even trivial offenses are considered honorable whereas those who do not are considered dishonorable (Nisbett & Cohen, 1996). Here I extend Maynard Smith's hawk-dove model of animal conflict to explore the logic of a strategy which uses reputation about its opponents to regulate its behavior. I show that a reputation-based strategy does well when (1) the value of the resource is large relative to the cost of losing a fight, (2) communities are stable, and (3) reputations are well known but subject to some amount of error. Reputation-based strategies may thus result in greater willingness to fight, but less fighting at equilibrium, depending upon the nature of the contests and the local socioecology. Additionally, this strategy is robust in the presence of poor knowledge about reputation.     

Estimating the rate of evolution of the rate of molecular evolution

A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.      

Flavonoids and the evolution of the angiosperms

Data on the distribution of flavonoids in the angiosperms are summarized and patterns of occurence are shown to be related to plant evolution. Different flavonoid types are regarded as primitive or advanced characters on the basis of biosynthetic complexity and on correlated frequencies of occurrence with morphological and anatomical features. The evolutionary significance of distribution patterns of proanthocyanidins, glycosylflavones, biflavonoids, 6- and 8-hydroxyflavonoids and anthocyanins is discussed in turn. The importance of these various distribution patterns is considered in relation to an ecological function for these flavonoids.     

Androdioecy and the evolution of dioecy

The likelihood that dioecy could evolve via androdioecy is examined. It is concluded that female-sterility mutations are unlikely to be able to invade populations of self-compatible hermaphrodite species, even if the resources that an hermaphrodite devotes to seed production can be diverted to yield increased survival and also to increase male fertility. These findings are in agreement with the great rarity of androdioecy. Claimed cases of androdioecy are reviewed. All of the species in question appear to be functionally dioecious, with females retaining substantial anther vestiges. It is argued that this morphological androdioecy is in no way indicative of a previous functionally androdioecious state. The details of the reproductive biology of many of these species seem rather to be consistent with their having evolved dioecy via gynodioecy.
The rarity of androdioecy, as a route to the evolution of dioecy, suggests that re-allocation of reproductive resources is unlikely to be the sole factor of importance, and supports an important role for inbreeding avoidance. The fact that females in some dioecious species retain anthers of substantial size, containing considerable quantities of pollen, gives further support to the view that male-sterility mutations can sometimes be favoured even when little or no resources are re-allocated to male functions. This is impossible without substantial selfing and inbreeding. It is therefore concluded that inbreeding avoidance is generally important in the evolution of dioecy, though reallocation of reproductive resources is also necessary.     

Brooding and the evolution of hermaphroditism

It has been suggested that hermaphroditism may evolve when the resources that females can profitably allocate to ova is limited by factors such as lack of brooding space. Spare resources could then be allocated to produce male gametes in a hermaphrodite. A model is developed to investigate the conditions under which this will occur. Hermaphrodites will displace males (and females) if the hermaphrodites produce at least half as many male gametes as a male. If the hermaphrodite produces less than half the number of gametes produced by a male then a stable equilibrium arises where males and hermaphrodites coexist. In this situation the frequency of males is determined by the ratio of the numbers of male gametes produced by hermaphrodites to the numbers produced by males.     

Morphology and the evolution of cycadeoidales

OneCycadeoidea stem one cycadeoidalean gynoecium and a bisporangiate cone attached to a slender cycadeoidalean trunkCycadeoidella japonica Ogura from the Cretaceous of Japan shows well-preserved internal structure that provides evidence for a better understanding of the morphological architecture of the cycadeoidalean plant. Structural details of the cone were confirmed. The ovule has an intergument enclosing a free nucellus and a thin outer envelope. Both reproductive and vegetative structures support the medullosan affinity of Cycadeoidales. The cone is interpreted as a compressed fertile shoot. Axillary cones characterizing some Cretaceous genera such asCycadeoidea andMonanthesia consist of a lateral shoot subtended by a frond that is the first leaf of the cone shoot itself. The origin of axillary buds in the Cycadeoidales is discussed. Heterochrony may have mediated the morphological changes that resulted in the establishment of the Cycadeoidales.     

Development and evolution of the subpallium

Among vertebrates, the ventral part of the telencephalon called the subpallium presents common basic developmental, hodological, neurochemical and functional features. It is genetically specified by expression of Dlx genes; its progenitor zones contribute a huge variety of neuronal cell types throughout the telencephalon; it is the origin and substrate of multiple and complex migration and navigation pathways during embryogenesis; and its derivatives, i.e. the basal ganglia and the amygdaloid complex, are highly conserved through evolution. Comparative developmental studies point to a largely common basic plan to generate the subpallium in vertebrates, including comparable progenitor domains and similar migratory cellular movements. In the course of telencephalic evolution however, slight variations have occurred, and the subpallium has probably represented a source for significant novelties and diversification in vertebrate forebrain anatomy and physiology.