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PubMed1999

Nuclear ribosomal DNA phylogeny and its implications for evolutionary trends in Mexican Bursera (Burseraceae).

The genus Bursera (Burseraceae) is one of the most diversified and abundant groups of plants of the tropical dry forests of Mexico. In order to provide a basis for better understanding of its evolutionary biology, we reconstructed a phylogeny of 57 species and varieties using the nucleotide sequences of the internal transcribed spacer regions (ITS1 and ITS2) of 18S-26S and the 5.8S coding region of nuclear ribosomal DNA. We used four species of the allied genera Commiphora and Boswellia and one species of Spondias (Anacardiaceae) as outgroups. Our results support the views that Bursera is monophyletic and more closely related to Commiphora than to Boswellia. The division of Bursera into sections Bullockia and Bursera is also strongly supported by our phylogeny. Several other subclades also had high bootstrap values, especially within section Bursera. We use the phylogeny as a basis for discussing evolutionary tendencies in bark, leaves, breeding systems, and fruits.

Journal Article↗
PubMed1999

Development and evolutionary origin of feathers.

Avian feathers are a complex evolutionary novelty characterized by structural diversity and hierarchical development. Here, I propose a functionally neutral model of the origin and evolutionary diversification of bird feathers based on the hierarchical details of feather development. I propose that feathers originated with the evolution of the first feather follicle-a cylindrical epidermal invagination around the base of a dermal papilla. A transition series of follicle and feather morphologies is hypothesized to have evolved through a series of stages of increasing complexity in follicle structure and follicular developmental mechanisms. Follicular evolution proceeded with the origin of the undifferentiated collar (stage I), barb ridges (stage II), helical displacement of barb ridges, barbule plates, and the new barb locus (stage III), differentiation of pennulae of distal and proximal barbules (stage IV), and diversification of barbule structure and the new barb locus position (stage V). The model predicts that the first feather was an undifferentiated cylinder (stage I), which was followed by a tuft of unbranched barbs (stage II). Subsequently, with the origin of the rachis and barbules, the bipinnate feather evolved (stage III), followed then by the pennaceous feather with a closed vane (stage IV) and other structural diversity (stages Va-f). The model is used to evaluate the developmental plausibility of proposed functional theories of the origin of feathers. Early feathers (stages I, II) could have functioned in communication, defense, thermal insulation, or water repellency. Feathers could not have had an aerodynamic function until after bipinnate, closed pennaceous feathers (stage IV) had evolved. The morphology of the integumental structures of the coelurisaurian theropod dinosaurs Sinosauropteryx and Beipiaosaurus are congruent with the model's predictions of the form of early feathers (stage I or II). Additional research is required to examine whether these fossil integumental structures developed from follicles and are homologous with avian feathers. J. Exp. Zool. (Mol. Dev. Evol.) 285:291-306, 1999.

Animals↗
PubMedDate not supplied

[Evolutionary theories of schizophrenia].

The universal distribution of schizophrenia associated with the low fertility of these patients outlines the paradox: why doesn't diminish the prevalence of this dysfunction? A critical revision is made of the main hypotheses that have thought about to solve this question. Some theories have postulated a physiologic or social advantage. Others have analysed this illness from the mark of the Evolutionary Psychology. We stand out the theories that have looked for an association of a Darwinian approach with genetic or neurodevelopmental data. Finally a possibility of integration of the evolutionary and neuropsychological models is proposed.

Biological Evolution↗
PubMed2000

[Evolutionary relationship of Rickettsia and eukaryotic mitochondria].

To clarify the evolutionary relationship of rickettsiae and mitochondria, the conserved flat heat-shock protein Hsp60 was phylogenetically studied in detail by using PHYLIP and PROTML packages. The ample data set (50 species) included as many as possible representatives from the Rickettsiaceae family, mitochondrial-type homologs from Archezoa and mitochondrial homologs from Protozoa. Rickettsia prowazekii (that is the genus Rickettsia) was shown to be the least diverging member within Rickettsia--a sister group to the monophyletic clade of mitochondria. These findings were also evidenced by the phylogenetic analysis of 16S rRNA. Rickettsia-like endosymbionts (the parasites Paramecium caudatum and the etiological agent of hepatopancreatitis in shrimps) included within the order Rickettsiales appear to have diverged prior to the Rickettsiaceae/mitochondria cluster. Thus, the Rickettsiales does not seem to be a monophyletic group. An idea concerning the nature of obligate intracellular parasitism of rickettsiae is proposed in the paper from the suggested profound similarity of Rickettsiae genus bacteria and mitochondria which could have a common evolutionary history.

Animals↗
PubMedDate not supplied

[Evolutionary bioenergetic trap and progressive evolution of animals].

We propose a macroscopic pathway to increase energy metabolism during progressive evolution with reducing size of animal body. If standard metabolism significantly increases in the course of body size reduction through increased coefficient b from the allometric equation (1), two cases are possible: coefficient b remains constant (1) or returns to the normal value (2) at increasing body weight in a given animal group. In the first case, an animal group appears in an evolutionary trap considering possible increase in body size, since the standard metabolism at increasing weight becomes lower starting from a certain point as compared to other animals of the same type. In the second case, increasing body size elevates standard metabolism relative to other animals of the same type, which offers an evolutionary advantage to this group.

Animals↗
PubMed2000

Hybrid fold recognition: combining sequence derived properties with evolutionary information.

Recent assessments of structure prediction have demonstrated that (i) although fold recognition methods can often identify remote similarities when standard sequence search methods fail, the score of the top-ranking fold is not always significant enough to allow a confident prediction; (ii) the use of structural information such as secondary structure increases recognition accuracy; (iii) modern sequence-based methods incorporating evolutionary information from neighboring sequences can often identify very remote similarities; (iv) there is no one single method that is superior to other methods when evaluated over a wide range of targets, and (v) extensive human-expert intervention is usually required for the most difficult prediction targets. Here, I describe a new, hybrid fold recognition method that incorporates structural and evolutionary information into a single fully automated method. This work is a first attempt towards the automation of some of the processes that are often applied by human predictors. The method is tested with two cases that are often applied by human predictors. The method is tested with two fold-recognition benchmarks demonstrating a superior performance. The higher sensitivity and selectivity enable the applicability of this method at genomic scales.

Algorithms↗
PubMed2000

Escaping from an evolutionary prison cell.

To a maternally transmitted parasite, male hosts are evolutionary prison cells. This is because passage into the next host generation is only possible via egg cytoplasm and not sperm. However, these parasites have come up with a neat array of evolutionary tricks to make the best of their custodial sentence.

Animals↗
PubMed2000

The evolutionary dynamics of direct phenotypic overdominance: emergence possible, loss probable.

An evolutionary dynamical system with explicit diploid genetics is used to investigate the likelihood of observing phenotypically overdominant heterozygotes versus heterozygous phenotypes that are intermediate between the homozygotes. In this model, body size evolves in a population with discrete demographic episodes and with competition limiting reproduction. A genotype-phenotype map for body size is used that can generate the two qualitative types of dominance interactions (overdominance versus intermediate dominance). It is written as a single-locus model with one focal locus and parameters summarizing the effects of alleles at other loci. Two types of evolutionarily stable strategy (ESS; continuously stable strategy, CSS) occur. The ESS is generated either (1) by the population ecology; or (2) by a local maximum of the genotype-phenotype map. Overdominant heterozygotes are expected to arise if the population evolves toward the second type of ESS, where nearly maximum body sizes are found. When other loci with partially dominant inheritance also evolve, the location of the maximum in the genotype-phenotype map repeatedly changes. It is unlikely that an evolving population will track these changes; ESSs of the second type now are at best quasi-stationary states of the evolutionary dynamics. Considering the restrictions on its probability, a pattern of phenotypic overdominance is expected to be rare.

Alleles↗
PubMed2000

[Evolutionary theories on schizophrenia].

The universal distribution of schizophrenia associated with the low fertility of these patients outlines the paradox: why doesn't diminish the prevalence of this dysfunction? A critical revision is made of the main hypotheses that have thought about to solve this question. Some theories have postulated a physiologic or social advantage. Others have analysed this illness from the mark of the Evolutionary Psychology. We stand out the theories that have looked for an association of a Darwinian approach with genetic or neurodevelopmental data. Finally a possibility of integration of the evolutionary and neuropsychological models is proposed.

Biological Evolution↗
PubMed2001

Is self-fertilization an evolutionary dead end? Revisiting an old hypothesis with genetic theories and a macroevolutionary approach.

G. Ledyard Stebbins suggested that self-fertilization (selfing) may be an evolutionary dead end because it may result in the loss of genetic diversity and consequently preclude adaptation to changing environments. While the basic premise of selfing as a dead end is widely accepted, there have been few rigorous evaluations of the hypothesis. We examine the foundations of the dead-end hypothesis by considering theoretical advances in the study of mating-system evolution. We discuss theories predicting the irreversibility of self-fertilization and the extinction of selfing lineages through the loss of adaptive potential and genetic degradation. In the second portion of the review, focusing on the irreversibility of selfing, we summarize the contribution of phylogenetic studies of mating-system evolution to determine if evolutionary history supports this well-established hypothesis. Most studies are in accord with the hypothesis; no single study unequivocally demonstrates the transition from highly selfing to outcrossing lineages. Finally, we discuss the problems encountered when phylogenetic studies rely on reconstruction of ancestral mating systems. To avoid some of these problems, we applied likelihood ratio tests of irreversibility of mating-system evolution to several data sets and found that current data sets are probably too small for this test.

Journal Article↗
PubMedDate not supplied

[[Epigenetic theory of evolution as a basis for a new evolutionary synthesis].

There are two evolutionary theories in current biology--"modern synthesis" and "epigenetic theory". The first one is based on the assumption of hard correspondence between phenotypes and genotypes. For this reason the theory of modern synthesis is principally incompatible with developmental biology. In contrast, the epigenetic theory considers evolution as a process of environmentally controlled transformation of ontogeny. It is compatible with observed embryological regularities and used as a basis for wider evolutionary synthesis combining both Darwinian and Lamarckian mechanisms. Individual developmental system can generate only a constrained number of morphologic states. This circumstance is a nomogenetic component of the epigenetic theory: the same morphosis simultaneously appears in a number of individuals in response to environmental influence. Since the initial phenotypic change occurs to be not random, a meeting of a female and a male with the same morphosis is an event of sufficiently high probability. The nomogenetic component allows to get over the famous argument of F. Jenkin--a problem that is still difficult to explain in terms of the theory of modern synthesis.

Animals↗
PubMed2002

Evolutionary computational methods to predict oral bioavailability QSPRs.

This review discusses evolutionary and adaptive methods for predicting oral bioavailability (OB) from chemical structure. Genetic Programming (GP), a specific form of evolutionary computing, is compared with some other advanced computational methods for OB prediction. The results show that classifying drugs into 'high' and 'low' OB classes on the basis of their structure alone is solvable, and initial models are already producing output that would be useful for pharmaceutical research. The results also suggest that quantitative prediction of OB will be tractable. Critical aspects of the solution will involve the use of techniques that can: (i) handle problems with a very large number of variables (high dimensionality); (ii) cope with 'noisy' data; and (iii) implement binary choices to sub-classify molecules with behavior that are qualitatively different. Detailed quantitative predictions will emerge from more refined models that are hybrids derived from mechanistic models of the biology of oral absorption and the power of advanced computing techniques to predict the behavior of the components of those models in silico.

Animals↗
PubMedDate not supplied

[Genetic-evolutionary basis of symbiosis doctrine].

The author presents the current notion of symbiosis as one of the main adaptation of an organism to changeable environment. Symbiosis is considered as a super organism genetic system within which there are different interactions (including mutualism and antagonism). Genetic integration of symbiotic partners can be realized as cross regulation of their genes, exchange of gene products (proteins, RNA), gene amplification and sometimes gene transfer between organisms. On the phenotypic level these processes result in signal interactions, integration of partner metabolic systems and development of symbiotic organs. Co-evolution is considered as an assemblage of micro- and macroevolution processes basing on pre-adaptations and proceeding under influence of different forms of natural selection (individual, frequency-depended and kin selection). Symbiosis can be compared with sexual process since both are the forms of organism integration characterized by different genetic mechanisms and evolutionary consequences. The genome evolution in symbiotic microorganisms can proceed by: 1) simplification of genome in obligate symbiosis (loss of genes that are necessary for independent existence, transfer of some genes to the host organism); 2) complication of genome in facultative symbiosis (increase in genome plasticity, structural and functional differentiation of genome into systems controlling free-living and symbiotic parts of life cycle). Most of symbiotic interactions are correlated to an increase in genetic plasticity of an organism that can lead to evolutionary saltations and origin of new forms of life.

Evolution, Molecular↗
PubMed2001

Adaptive evolutionary conservation: towards a unified concept for defining conservation units.

Recent years have seen a debate over various methods that could objectively prioritize conservation value below the species level. Most prominent among these has been the evolutionarily significant unit (ESU). We reviewed ESU concepts with the aim of proposing a more unified concept that would reconcile opposing views. Like species concepts, conflicting ESU concepts are all essentially aiming to define the same thing: segments of species whose divergence can be measured or evaluated by putting differential emphasis on the role of evolutionary forces at varied temporal scales. Thus, differences between ESU concepts lie more in the criteria used to define the ESUs themselves rather than in their fundamental essence. We provide a context-based framework for delineating ESUs which circumvents much of this situation. Rather than embroil in a befuddled debate over an optimal criterion, the key to a solution is accepting that differing criteria will work more dynamically than others and can be used alone or in combination depending on the situation. These assertions constitute the impetus behind adaptive evolutionary conservation.

Animals↗
PubMed2001

Phylogenetic comparison and artificial selection. Two approaches in evolutionary physiology.

Interspecific comparison has a long and productive history in physiology. Conceptual and statistical advances over the last 15 years have demonstrated several ways in which comparisons can be enhanced by consideration of phylogenetic information, i.e., empirical estimates of the ways in which organisms are related (evolutionary trees). Choice of species to be compared should be informed by phylogenetic information. For example, a comparison of three species that inhabit high altitude with three that live at low altitude would be suspect if each of the two groups were composed of closely-related species (e.g., within single genera). To avoid such "phylogenetic pseudoreplication," one might instead study species from three different genera, each containing one high-altitude and one low-altitude inhabitant. Unfortunately, many studies have not been so carefully designed, sometimes because organisms were not accessible or because the studies incorporated data from the literature. Fortunately, several new statistical methods correct for problems caused by phylogenetic relatedness and descent with modification, the most common being phylogenetically independent contrasts. Another tool that can be used in comparative physiology is selective breeding, which has been practiced for millennia and applied in scientific contexts for over a century. In the last 20 years, ecological and evolutionary physiologists have begun using selection experiments to study processes of genetic adaptation in physiological and behavioral traits. For example, house mice have been maintained in the cold for multiple generations to see what adaptations may occur naturally in response to reduced ambient temperature ("laboratory natural selection"). Our own laboratory has used selective breeding to create four replicate lines of mice that exhibit high levels of voluntary wheel-running behavior, as well as various morphological and physiological characteristics that cause or allow the elevated locomotor activity. Similar experiments could be used to study adaptation to hypoxia.

Animals↗
PubMed2002

[A evolutionary approach to identification of orthologous relationship across proteomes].

How to identify the true orthologous and paralogous relationships among protein families is still a key problem in genome annotation and comparative protemics. Here, a evolutionary approach to ascertainment of the orthologous relationships across the genomes is developed. Forty-four cases of protein families are used in the test for the evolutionary approach. Compared with the method of COG (cluster of orthologous groups of proteins), this approach can generally identify the orthologous relationships and accurately predict the genome function.

Animals↗
PubMed1999

An Evolutionary Trace Method for Functional Prediction of Genomes.

It is essential for functional genomics to develop an accurate and efficient functional prediction method of genomes. Here, a new method is suggested, that is based on the fact that ortholog-specific motif is an evolutionary trace, in which the functional prediction of genomics is carried out. First, orthologous sets in a family were constructed using evolutionary analysis then functional motifs for each orthologous set were found out and a database consisted of these motifs was built. When this database is completed, unknown genes can be predicted accurately and quickly by searching it. The pilot study on five families proves that our method is feasible.

Journal Article↗
PubMed2002

Unifying evolutionary dynamics.

Darwinian evolution is based on three fundamental principles, reproduction, mutation and selection, which describe how populations change over time and how new forms evolve out of old ones. There are numerous mathematical descriptions of the resulting evolutionary dynamics. In this paper, we show that apparently very different formulations are part of a single unified framework. At the center of this framework is the equivalence between the replicator-mutator equation and the Price equation. From these equations, we obtain as special cases adaptive dynamics, evolutionary game dynamics, the Lotka-Volterra equation of ecology and the quasispecies equation of molecular evolution.

Animals↗