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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.
Embryological studies indicate that the amygdala includes pallial structures, namely the cortical amygdala (olfactory and vomeronasal) and the basolateral complex deep to it. In squamate reptiles, the cortical amygdala includes secondary olfactory (the ventral anterior amygdala) and vomeronasal centres (the nucleus sphericus). In birds, the situation is far less clear, due to the relative underdevelopment of the chemosensory systems. The basolateral amygdala of squamate reptiles includes two ventropallial structures: the posterior dorsal ventricular ridge and the lateral amygdala. Like their mammalian counterparts, these centres give rise to glutamatergic projections to the striatal (centromedial) amygdala and the ventromedial hypothalamus. Using the same criteria, the caudal neostriatum and the ventral intermediate archistriatum may represent the ventral pallial amygdala of birds. The basal nucleus of the mammalian amygdala is a lateropallial territory. In reptiles, the lateral pallium includes the dorsolateral amygdala, which, like the mammalian basal nucleus, projects bilaterally to the striatum/accumbens and receives distinct cholinergic and dopaminergic innervations. In the avian brain, the same embryological, hodological, and histochemical criteria are met by the area temporo-parieto-occipitalis, the caudolateral neostriatum and the dorsal intermediate archistriatum. Therefore, the projections from these structures to the paleostriatum and the lobus paraolfactorius are amygdalostriatal, rather than corticostriatal connections.
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Nervous systems are composed of populations of cells that are synaptically connected in a highly predictable manner, and we have called two interconnected populations a pair of matching populations. Heritable genetic changes that affect a pair of matching populations can be evolutionary only when this matching quality is not disrupted. We distinguish two types of heritable change. Concordant heritable changes autonomously preserve the match and are thus automatically candidates for what we call type I evolutionary change. Nonconcordant heritable changes, on the other hand, are those that do not autonomously preserve the match. Those nonconcordant heritable changes that can use other normally present ontogenetic mechanisms to preserve the match are candidates for what we call type II evolutionary change. One example of such an ontogenetic mechanism consists of the production of excess neuroblasts and the subsequent weeding out (via cell death) of those that do not successfully match. Because normal ontogeny is an integral part of type II evolutionary change, ontogenetic manipulations can give evolutionary insights. Embryonic graft experiments, in particular, can elucidate the nature of ontogenetic mechanisms that participate in type II changes. Thus, some developmental experiments can be considered to be evolutionary experiments.
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The germ theory of disease famously brought a new notion of specificity into concepts of disease. At the same time, the work of Pasteur, Koch and their colleagues was developed during the same decades as Charles Darwin's theories of evolutionary biology challenged traditional notions of the essentialism of biological species. This essay examines some of the ways in which Darwin's work was invoked by British doctors seeking to explain clinical or epidemiological anomalies, in which infectious diseases did not appear to breed true.
The rates of nucleotide substitution at four genes in four orders of eutherian mammals are compared in relative rate tests using marsupial orthologs for reference. There is no evidence of systematic variation in evolutionary rate among the orders. The sequences are used to reconstruct the phylogeny of the orders using maximum likelihood, parsimony and compatibility methods. A branching order of rodent then ungulate then primate and lagomorph is overwhelmingly indicated. The nodes of the nucleotide based cladograms are widely separated in relation to the total lengths of the branches. The assumption of a star phylogeny that underlies Kimura's test for molecular evolutionary rate variation is shown to be invalid for eutherian mammals. Excess variance in nucleotide or amino acid differences between mammalian orders, above that predicted by neutral theory is explained better by variation in divergence time than by variation in evolutionary rate.
Cytochrome c oxidase subunit II (COII), encoded by the mitochondrial genome, exhibits one of the most heterogeneous rates of amino acid replacement among placental mammals. Moreover, it has been demonstrated that cytochrome c oxidase has undergone a structural change in higher primates which has altered its physical interaction with cytochrome c. We collected a large data set of COII sequences from several orders of mammals with emphasis on primates, rodents, and artiodactyls. Using phylogenetic hypotheses based on data independent of the COII gene, we demonstrated that an increased number of amino acid replacements are concentrated among higher primates. Incorporating approximate divergence dates derived from the fossil record, we find that most of the change occurred independently along the New World monkey lineage and in a rapid burst before apes and Old World monkeys diverged. There is some evidence that Old World monkeys have undergone a faster rate of nonsynonymous substitution than have apes. Rates of substitution at four-fold degenerate sites in primates are relatively homogeneous, indicating that the rate heterogeneity is restricted to nondegenerate sites. Excluding the rate acceleration mentioned above, primates, rodents, and artiodactyls have remarkably similar nonsynonymous replacement rates. A different pattern is observed for transversions at four-fold degenerate sites, for which rodents exhibit a higher rate of replacement than do primates and artiodactyls. Finally, we hypothesize specific amino acid replacements which may account for much of the structural difference in cytochrome c oxidase between higher primates and other mammals.
Camarodont sea urchins possess a rapidly evolving actin gene family whose members are expressed in distinct cell lineages in a developmentally regulated fashion. Evolutionary changes in the actin gene family of echinoids include alterations in number of family members, site of expression, and gene linkage, and a dichotomy between rapidly and slowly evolving isoform-specific 3' untranslated regions. We present sequence comparisons and an analysis of the actin gene family in two congeneric sea urchins that develop in radically different modes, Heliocidaris erythrogramma and H. tuberculata. The sequences of several actin genes from the related species Lytechinus variegatus are also presented. We compare the features of the Heliocidaris and Lytechinus actin genes to those of the the actin gene families of other closely related sea urchins and discuss the nature of the evolutionary changes among sea urchin actins and their relationship to developmental mode.
Microsatellites are stretches of repetitive DNA, where individual repeat units comprise one to six bases. These sequences are often highly polymorphic with respect to repeat number and include trinucleotide repeats, which are abnormally expanded in a number of diseases. It has been widely assumed that microsatellite loci are as likely to gain and lose repeats when they mutate. In this review, we present population genetic and empirical data arguing that microsatellites, including normal alleles at trinucleotide-repeat disease loci, are more likely to expand in length when they mutate. In addition, our experiments suggest that the rates of expansion of such sequences differ in related species.
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beta-Lactam antibiotics are produced by prokaryotic and eukaryotic organisms. The genes for beta-lactam biosynthesis are organized in clusters but the location of the different genes is not identical. Biosynthesis genes are clustered with genes for resistance (bla, pbp) and for the efflux of the antibiotic (cmcT) in prokaryotes. Comparison of proteins reveals much larger differences for primary metabolism enzymes than for beta-lactam biosynthesis enzymes in producing organisms. This suggests a horizontal transfer of the beta-lactam antibiotic biosynthesis genes.
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