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.     

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.      

Cooperation and the evolution of anisogamy

In the lights of the concept of cooperation wholes, I discuss why the differentiation of sperm and ova can occur with a mathematical model. Most of Parker's explanations for anisogamy are not completely proper, because it is proved that sperm competition is neither sufficient nor necessary for anisogamy and cooperation to deal with fertilization risks is the real key to understand the evolution of anisogamy. According to the computer simulation results, the transport of gametes between different individuals, risks of the transport, the consequent inequality of sperm and eggs and competition among different individuals were the main causes of gamete differentiation. But these factors have different roles and effects. The transport risk is the main reason for individuals of different mating types to cooperate and differentiate into sperm and egg producers. The transported gametes have an advantage to evolve into sperm to seek for a larger gamete number over the fixed gametes, because they suffer more risks as they can encounter the same fixed gamete and less sibling competition as they can be dispersed better. Gamete competition among different individuals just causes the transported gametes to become as small as possible if they have already become smaller beyond a critical state. In the final discussion, I further put the evolution of anisogamy into a broader background of levels of selection and of the evolution of cooperation, the most important existential mode of matters that makes life as life.     

Cognition and the evolution of camouflage

Camouflage is one of the most widespread forms of anti-predator defence and prevents prey individuals from being detected or correctly recognized by would-be predators. Over the past decade, there has been a resurgence of interest in both the evolution of prey camouflage patterns, and in understanding animal cognition in a more ecological context. However, these fields rarely collide, and the role of cognition in the evolution of camouflage is poorly understood. Here, we review what we currently know about the role of both predator and prey cognition in the evolution of prey camouflage, outline why cognition may be an important selective pressure driving the evolution of camouflage and consider how studying the cognitive processes of animals may prove to be a useful tool to study the evolution of camouflage, and vice versa. In doing so, we highlight that we still have a lot to learn about the role of cognition in the evolution of camouflage and identify a number of avenues for future research.     

Culture and the evolution of obesity

Human predispositions to fatness and obesity are best understood in the context of cultural and biological evolution. Both genes and cultural traits that were adaptive in the context of past food scarcities play a role today in the etiology of maladaptive adult obesity. The etiology of obesity must account for the social distribution of the condition with regard to gender, ethnicity, social class, and economic modernization. This distribution, which has changed throughout history, undoubtedly involves cultural factors. A model of culture is presented that has advantages over an undifferentiated concept of the “environment” for hypothesis generation. Cultural predispositions to obesity are found in the productive economy, the mode of reproduction, social structure, and cultural beliefs about food and ideal body size. Cross-cultural comparison can contribute to an understanding of the prevalence of obesity in some modern affluent societies.     

Development and evolution of the pallium

The neocortex is the most representative and elaborated structure of the mammalian brain and is related to the achievement of complex cognitive capabilities, which are disturbed following malformation or lesion. Searching for the evolutionary origin of this structure continues to be one of the most important and challenging questions in comparative neurobiology. However, this is extremely difficult because of the highly divergent evolution of the pallium in different vertebrates, which has obscured the comparison. Herein, we review developmental neurobiology data for trying to understand the genetic factors that define and underlie the parcellation of homologous pallial subdivisions in different vertebrates. According to these data, the pallium in all tetrapods parcellates during development into four major histogenetic subdivisions, which are homologous as fields across species. The neocortex derives from the dorsal pallium and, as such, is only comparable to the sauropsidian dorsal pallium (avian hyperpallium and lizard/turtle dorsal cortex). We also tried to identify developmental changes in phylogeny that may be responsible of pallial divergent evolution. In particular, we point out to evolutionary differences regarding the cortical hem (an important signaling center for pallial patterning, that also is a source of Cajal–Retzius cells, which are involved in cortical lamination), which may be behind the distinct organization of the pallium in mammals and non-mammals. In addition, we mention recent data suggesting a correlation between the appearance and elaboration of the subventricular zone (a new germinative cell layer of the developing neocortex), and the evolution of novel cell layers (the supragranular layers) and interneuron subtypes. Finally, we comment on epigenetic factors that modulate the developmental programs, leading to changes in the formation of functional areas in the pallium (within some constraints).     

SELEX and the evolution of genomes

The interrupted genome structures of complex multicellular organisms have most likely changed the evolution of the regulation of metabolism and development. Wasted intron sequences make regulation of gene expression in (for example) mammals appear to be unnecessarily complicated. The recent discoveries that globular RNA molecules are very much like the antigen-combining sites of antibodies suggest that intronic RNA may be used to help solve the problems raised by this complexity.     

Hydra and the evolution of apoptosis

Programmed cell death occurs in most, if not all life forms.It is used to sculpt tissue during embryogenesis, to removedamaged cells, to protect against pathogen infection and toregulate cell numbers and tissue homeostasis. In animals celldeath often occurs by a morphologically and biochemically conservedprocess called apoptosis. A novel group of cysteine proteases,referred to as caspases, constitute the central component ofthis process. Caspases are activated following the inductionof apoptosis and cleave a variety of cellular substrates, thusgiving rise to the characteristic morphological events of apoptosis.Apoptosis is rapid and cell corpses are removed by phagocytosis.Recent work has shown that apoptosis also occurs in Cnidariaand Porifera, thus extending the origin of this evolutionaryinnovation down to the first metazoan animal phyla. Here, wereview several examples of the role of apoptosis in cnidariansand then summarize new results on the subcellular localizationof caspases and the control of apoptosis in Hydra. We show byimmuncytochemistry that caspases in Hydra are localized in mitochondria.Following induction of apoptosis caspases are released frommitochondria as proenzymes and then activated by proteolyticcleavage in the cytoplasm. We also present evidence that apoptosisin Hydra is dramatically stimulated by inhibitors of PI3-kinase.Since PI3-kinase is a central component of growth factor signalingcascades in higher metazoans, this result suggests that controlof apoptosis by growth factors is also evolutionarily conserved.We speculate on the role of growth factors in the evolutionof apoptosis.     

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.     

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.