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PubMed1996

Evolutionary analyses of hedgehog and Hoxd-10 genes in fish species closely related to the zebrafish.

The study of development has relied primarily on the isolation of mutations in genes with specific functions in development and on the comparison of their expression patterns in normal and mutant phenotypes. Comparative evolutionary analyses can complement these approaches. Phylogenetic analyses of Sonic hedgehog (Shh) and Hoxd-10 genes from 18 cyprinid fish species closely related to the zebrafish provide novel insights into the functional constraints acting on Shh. Our results confirm and extend those gained from expression and crystalline structure analyses of this gene. Unexpectedly, exon 1 of Shh is found to be almost invariant even in third codon positions among these morphologically divergent species suggesting that this exon encodes for a functionally important domain of the hedgehog protein. This is surprising because the main functional domain of Shh had been thought to be that encoded by exon 2. Comparisons of Shh and Hoxd-10 gene sequences and of resulting gene trees document higher evolutionary constraints on the former than on the latter. This might be indicative of more general evolutionary patterns in networks of developmental regulatory genes interacting in a hierarchical fashion. The presence of four members of the hedgehog gene family in cyprinid fishes was documented and their homologies to known hedgehog genes in other vertebrates were established.

Amino Acid Sequence↗
PubMed1998

Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution.

Estimation of evolutionary distances has always been a major issue in the study of molecular evolution because evolutionary distances are required for estimating the rate of evolution in a gene, the divergence dates between genes or organisms, and the relationships among genes or organisms. Other closely related issues are the estimation of the pattern of nucleotide substitution, the estimation of the degree of rate variation among sites in a DNA sequence, and statistical testing of the molecular clock hypothesis. Mathematical treatments of these problems are considerably simplified by the assumption of a stationary process in which the nucleotide compositions of the sequences under study have remained approximately constant over time, and there now exist fairly extensive studies of stationary models of nucleotide substitution, although some problems remain to be solved. Nonstationary models are much more complex, but significant progress has been recently made by the development of the paralinear and LogDet distances. This paper reviews recent studies on the above issues and reports results on correcting the estimation bias of evolutionary distances, the estimation of the pattern of nucleotide substitution, and the estimation of rate variation among the sites in a sequence.

Animals↗
PubMed1998

Peptide design by artificial neural networks and computer-based evolutionary search.

A technique for systematic peptide variation by a combination of rational and evolutionary approaches is presented. The design scheme consists of five consecutive steps: (i) identification of a "seed peptide" with a desired activity, (ii) generation of variants selected from a physicochemical space around the seed peptide, (iii) synthesis and testing of this biased library, (iv) modeling of a quantitative sequence-activity relationship by an artificial neural network, and (v) de novo design by a computer-based evolutionary search in sequence space using the trained neural network as the fitness function. This strategy was successfully applied to the identification of novel peptides that fully prevent the positive chronotropic effect of anti-beta1-adrenoreceptor autoantibodies from the serum of patients with dilated cardiomyopathy. The seed peptide, comprising 10 residues, was derived by epitope mapping from an extracellular loop of human beta1-adrenoreceptor. A set of 90 peptides was synthesized and tested to provide training data for neural network development. De novo design revealed peptides with desired activities that do not match the seed peptide sequence. These results demonstrate that computer-based evolutionary searches can generate novel peptides with substantial biological activity.

Amino Acid Sequence↗
PubMed2000

Evolutionary modification of development in mammalian teeth: quantifying gene expression patterns and topography.

The study of mammalian evolution often relies on detailed analysis of dental morphology. For molecular patterning to play a role in dental evolution, gene expression differences should be linkable to corresponding morphological differences. Because teeth, like many other structures, are complex and evolution of new shapes usually involves subtle changes, we have developed topographic methods by using Geographic Information Systems. We investigated how genetic markers for epithelial signaling centers known as enamel knots are associated with evolutionary divergence of molar teeth in two rodent species, mouse and vole. Our analysis of expression patterns of Fgf4, Lef1, p21, and Shh genes in relation to digital elevation models of developing tooth shapes shows that molecular prepatterns predict the lateral cusp topography more than a day in advance. A heterotopic shift in the molecular prepatterns can be implicated in the evolution of mouse molar, changing locations from which historically homologous cusps form. The subtle but measurable heterotopic shifts may play a large role in the evolution of tooth cusp topographies. However, evolutionary increase in the number of longitudinal cusps in vole molar has involved accelerated longitudinal growth and iterative addition of new cusps without changes in lateral cusp topography. The iterative addition of cusps after the establishment of lateral cusp topography may limit the independence of individual morphological features used in evolutionary studies. The diversity of mammalian molar patterns may largely result from the heterotopic and iterative processes.

Animals↗
PubMed2001

Private and collective interests; conflicts and solutions: the central theme of current thinking in evolutionary biology.

The statement made by the population geneticist Theodosius Dobzhansky (1973): "Nothing in Biology Makes Sense Except in the Light of Evolution", is often quoted as a crucially important generalization on the nature of biology. I am inclined to consider as equally important the statement: "Nothing in Evolutionary Biology Makes Sense Except in the Light of Conflicts between Parts and Systems." This generalization takes account of the dynamic nature of biological phenomena, but also of the fact that the study of transitions from autonomous units to cooperative systems has become one of the most exciting and scientifically rewarding enterprises in all of organismic biology. The problems encountered and the speculations generated in the course of this enterprise will be either of the more unit-centered or of the more system-centered type, most biologists tending to lean towards one or the other. This explains why evolutionary biology is fraught with so many antagonistic attitudes and polarizing points of view. In this essay I want specifically to draw attention to and discuss the following issues which in recent years have polarized biologists: the dual nature of genes; the logic of Hamilton's rule; the relationship between kin selection, signalling networks and systemic manipulation; the semantic problem of progress in evolution; and the evolutionary consequences of the vastly differing time scales over which genotypic and phenotypic information processing occurs in higher animals.

Journal Article↗
PubMed2001

From aardvarks to apples and orchids to ostriches: the simple evolutionary roots of a world of biological complexity and biodiversity.

Most genes arise by gene duplication, a process that has allowed the evolutionary development of new proteins and peptides with diverse functions, based on modifications of pre-existing sequences. Gene duplication creates both new DNA substrate for the encoding of information, and an information substrate for further modification of already evolved information. Because DNA "wants" to copy itself, both vertically from generation to generation and horizontally due to gene duplication, it creates a great deal of nonsense within the genome called "junk" or "selfish" DNA, which has no present function. However, it acts as an inadvertent evolutionary library and as an autocatalytic substrate for the creation of more DNA containing already-preselected sequences. The process, over evolutionary time, has created large families of related hormones, regulatory peptides, and their receptor and signaling systems, for many of which the functions have yet to be described.

Animals↗
PubMed2006

Snakes, spiders, guns, and syringes: how specific are evolutionary constraints on the detection of threatening stimuli?

In three experiments, the efficiency in detecting fear-relevant and fear-irrelevant visual stimuli are compared. A visual search paradigm is used where participants are presented with matrices of different sizes (4 objects/9 objects) and must determine whether all objects are taken from the same category or whether there is a discrepant one. Results from all experiments were consistent with the threat-superiority effect. Participants were quicker when the target was threatening than when it was not. Other indicators confirmed that the detection of threatening targets involves more efficient processes (reduced slopes, absence of position effects). A crucial aspect of these experiments was the comparison of evolutionary-relevant (snakes, spiders, etc.) and modern (guns, syringes, etc.) threats. The threat-superiority effect was repeatedly found for both types of target. Stronger effects were sometimes observed for modern than for evolutionary-relevant threats. The implications for evolutionary explanations of the effect of fear on visual attention are discussed.

Adolescent↗
PubMed2002

Divergence time and evolutionary rate estimation with multilocus data.

Bayesian methods for estimating evolutionary divergence times are extended to multigene data sets, and a technique is described for detecting correlated changes in evolutionary rates among genes. Simulations are employed to explore the effect of multigene data on divergence time estimation, and the methodology is illustrated with a previously published data set representing diverse plant taxa. The fact that evolutionary rates and times are confounded when sequence data are compared is emphasized and the importance of fossil information for disentangling rates and times is stressed.

Algorithms↗
PubMed2006

Reconciling extreme branch length differences: decoupling time and rate through the evolutionary history of filmy ferns.

The rate of molecular evolution is not constant across the Tree of Life. Characterizing rate discrepancies and evaluating the relative roles of time and rate along branches through the past are both critical to a full understanding of evolutionary history. In this study, we explore the interactions of time and rate in filmy ferns (Hymenophyllaceae), a lineage with extreme branch length differences between the two major clades. We test for the presence of significant rate discrepancies within and between these clades, and we separate time and rate across the filmy fern phylogeny to simultaneously yield an evolutionary time scale of filmy fern diversification and reconstructions of ancestral rates of molecular evolution. Our results indicate that the branch length disparity observed between the major lineages of filmy ferns is indeed due to a significant difference in molecular evolutionary rate. The estimation of divergence times reveals that the timing of crown group diversification was not concurrent for the two lineages, and the reconstruction of ancestral rates of molecular evolution points to a substantial rate deceleration in one of the clades. Further analysis suggests that this may be due to a genome-wide deceleration in the rate of nucleotide substitution.

Evolution, Molecular↗
PubMed1998

On the best evolutionary rate for phylogenetic analysis.

The effect of the evolutionary rate of a gene on the accuracy of phylogeny reconstruction was examined by computer stimulation. The evolutionary rate is measured by the tree length, that is, the expected total number of nucleotide substitutions per site on the phylogeny. DNA sequence data were simulated using both fixed trees with specified branch lengths and random trees with branch lengths generated from a model of cladogenesis. The parsimony and likelihood methods were used for phylogeny reconstruction, and the proportion of correctly recovered branch partitions by each method was estimated. Phylogenetic methods including parsimony appear quite tolerant of multiple substitutions at the same site. The optimum levels of sequence divergence were even higher than upper limits previously suggested for saturation of substitutions, indicating that the problem of saturation may have been exaggerated. Instead, the lack of information at low levels of divergence should be seriously considered in evaluation of a gene's phylogenetic utility, especially when the gene sequence is short. The performance of parsimony, relative to that of likelihood, does not necessarily decrease with the increase of the evolutionary rate.

Biological Evolution↗
PubMed2000

Chlamydia pneumoniae and cardiovascular disease: an evolutionary perspective on infectious causation and antibiotic treatment.

Evolutionary considerations implicate infectious causation of atherosclerosis and help to resolve different risk factors as parts of an overall process of disease causation. An evolutionary approach also provides insight for the timing of research efforts to provide better control of pathogen evolution. In particular, evolutionary considerations emphasize the need to understand the transmissibility of Chlamydia pneumoniae from systemic infections in order to control the evolution of antibiotic resistance.

Anti-Bacterial Agents↗
PubMed2002

The evolutionary origin and diversification of feathers.

Progress on the evolutionary origin and diversification of feathers has been hampered by conceptual problems and by the lack of plesiomorphic feather fossils. Recently, both of these limitations have been overcome by the proposal of the developmental theory of the origin of feathers, and the discovery of primitive feather fossils on nonavian theropod dinosaurs. The conceptual problems of previous theories of the origin of feathers are reviewed, and the alternative developmental theory is presented and discussed. The developmental theory proposes that feathers evolved through a series of evolutionary novelties in developmental mechanisms of the follicle and feather germ. The discovery of primitive and derived fossil feathers on a diversity of coelurosaurian theropod dinosaurs documents that feathers evolved and diversified in nonavian theropods before the origin of birds and before the origin of flight. The morphologies of these primitive feathers are congruent with the predictions of the developmental theory. Alternatives to the theropod origin of feathers are critique and rejected. Hypotheses for the initial function of feathers are reviewed. The aerodynamic theory of feather origins is falsified, but many other functions remain developmentally and phylogenetically plausible. Whatever their function, feathers evolved by selection for a follicle that would grow an emergent tubular appendage. Feathers are inherently tubular structures. The homology of feathers and scales is weakly supported. Feathers are composed of a suite of evolutionary novelties that evolved by the duplication, hierarchical organization, interaction, dissociation, and differentiation of morphological modules. The unique capacity for modular subdivision of the tubular feather follicle and germ has fostered the evolution of numerous innovations that characterize feathers. The evolution of feather keratin and the molecular basis of feather development are also discussed.

Adaptation, Physiological↗
PubMed2004

A general theory for the evolutionary dynamics of virulence.

Most theory on the evolution of virulence is based on a game-theoretic approach. One potential shortcoming of this approach is that it does not allow the prediction of the evolutionary dynamics of virulence. Such dynamics are of interest for several reasons: for experimental tests of theory, for the development of useful virulence management protocols, and for understanding virulence evolution in situations where the epidemiological dynamics never reach equilibrium and/or when evolutionary change occurs on a timescale comparable to that of the epidemiological dynamics. Here we present a general theory similar to that of quantitative genetics in evolutionary biology that allows for the easy construction of models that include both within-host mutation as well as superinfection and that is capable of predicting both the short- and long-term evolution of virulence. We illustrate the generality and intuitive appeal of the theory through a series of examples showing how it can lead to transparent interpretations of the selective forces governing virulence evolution. It also leads to novel predictions that are not possible using the game-theoretic approach. The general theory can be used to model the evolution of other pathogen traits as well.

Animals↗
PubMed2001

The hormetic zone: an ecological and evolutionary perspective based upon habitat characteristics and fitness selection.

Fitness varies nonlinearly with environmental variables such as temperature, water availability, and nutrition, with maximum fitness at intermediate levels between more stressful extremes. For environmental agents that are highly toxic at exposures that substantially exceed background levels, fitness is maximized at concentrations near zero--a phenomenon often referred to as hormesis. Two main components are suggested: (1) background hormesis, which derives from the direct adaptation of organisms to their habitats; and (2) stress-derived hormonesis, which derives from metabolic reserves that are maintained as an adaptation to environmental stresses through evolutionary time. These reserves provide protection from lesser correlated stresses. This article discusses illustrative examples, including ethanol and ionizing radiation, aimed at placing hormesis into an ecological and evolutionary context. A unifying approach comes from fitness-stress continua that underlie responses to abiotic variables, whereby selection for maximum metabolic efficiency and hence fitness in adaptation to habitats in nature underlies hormetic zones. Within this reductionist model, more specific metabolic mechanisms to explain hormesis are beginning to emerge, depending upon the agent and the taxon in question. Some limited research possibilities based upon this evolutionary perspective are indicated.

Adaptation, Physiological↗
PubMed2004

Parasites and the evolutionary diversification of primate clades.

Coevolutionary interactions such as those between hosts and parasites have been regarded as an underlying cause of evolutionary diversification, but evidence from natural populations is limited. Among primates and other mammalian groups, measures of host diversification rates vary widely among lineages, but comparative studies have not yet identified a reliable explanation for this variation. In this study, we used a comprehensive data set of disease-causing organisms from free-living primates to illustrate how phylogenetic comparative methods can be used to examine mammalian lineage diversity in relation to parasite species richness. Our results provide evidence that the phylogenetic diversity of primate clades is correlated positively with the number of parasite species harbored by each host and that this pattern is largely independent of other host traits that have been shown to influence diversification rates and parasite species richness in primates. We investigated two possible mechanisms that could explain this association, namely that parasites themselves drive host evolutionary diversification through processes linked with sexual selection and that host shifts or host sharing increases parasite species richness among diverse primate clades. Neither parasite species richness nor host diversification is related to measures of sexual selection in primates. Further, we found only partial evidence that more rapidly diversifying host lineages produced increased opportunities for host sharing or host shifting by parasites through mechanisms involving species' geographic range overlap. Thus, our analyses provide evidence for an important link between the evolutionary diversification of primates and the richness of their parasite communities, but other mechanisms, particularly those related to reciprocal selection or coextinction of hosts and parasites, require further investigation.

Animals↗
PubMed2005

Female polymorphism, frequency dependence, and rapid evolutionary dynamics in natural populations.

Rapid evolutionary change over a few generations has been documented in natural populations. Such changes are observed as organisms invade new environments, and they are often triggered by changed interspecific interactions, such as differences in predation regimes. However, in spite of increased recognition of antagonistic male-female mating interactions, there is very limited evidence that such intraspecific interactions could cause rapid evolutionary dynamics in nature. This is because ecological and longitudinal data from natural populations have been lacking. Here we show that in a color-polymorphic damselfly species, male-female mating interactions lead to rapid evolutionary change in morph frequencies between generations. Field data and computer simulations indicate that these changes are driven by sexual conflict, in which morph fecundities are negatively affected by frequency- and density-dependent male mating harassment. These frequency-dependent processes prevent population divergence by maintaining a female polymorphism in most populations. Although these results contrast with the traditional view of how sexual conflict enhances the rate of population divergence, they are consistent with a recent theoretical model of how females may form discrete genetic clusters in response to male mating harassment.

Animals↗
PubMed2005

Evolutionary conflicts of interest: are female sexual decisions different?

Analyses of reproductive conflicts of interests have yielded important evolutionary insights in many areas of biology. The usefulness of conflict analyses of traits that have been traditionally interpreted as resulting from female choice is controversial, however. This article explores a possible explanation for why conflicts of interest may be ameliorated in female choice situations. In contrast to most other evolutionary contexts in which conflicts of interest are thought to have been important, sexual reproduction usually involves an extensive, irretrievable mixing of the genomes of the participants. Under certain combinations of costs and benefits to females, the genes in the female's genome can benefit, through increased reproduction of her offspring, from the very genes that produce sexually antagonistic traits in the male. In short, females can sometimes gain by "losing." Such Fisherian payoffs are also possible, though probably less important, for males. Gaining by losing is not feasible in most other contexts of evolutionary conflict, except under some conditions in parent-offspring conflict. Some apparent parent-offspring conflicts may instead be parental choice among offspring that is analogous to traditional female choice. Parent-offspring conflict may be relatively common, however, because offspring manipulation of their parents is likely to be damaging to the parents.

Animals↗
PubMed2005

The evolution of phenotypic polymorphism: randomized strategies versus evolutionary branching.

A population is polymorphic when its members fall into two or more categories, referred to as alternative phenotypes. There are many kinds of phenotypic polymorphisms, with specialization in reproduction, feeding, dispersal, or protection from predators. An individual's phenotype might be randomly assigned during development, genetically determined, or set by environmental cues. These three possibilities correspond to a mixed strategy of development, a genetic polymorphism, and a conditional strategy. Using the perspective of adaptive dynamics, I develop a unifying evolutionary theory of systems of determination of alternative phenotypes, focusing on the relative possibilities for random versus genetic determination. The approach is an extension of the analysis of evolutionary branching in adaptive dynamics. It compares the possibility that there will be evolutionary branching, leading to genetic polymorphism, with the possibility that a mixed strategy evolves. The comparison is based on the strength of selection for the different outcomes. An interpretation of the resulting criterion is that genetic polymorphism is favored over random determination of the phenotype if an individual's heritable genotype is an adaptively advantageous cue for development. I argue that it can be helpful to regard genetic polymorphism as a special case of phenotypic plasticity.

Adaptation, Physiological↗