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PubMed2006

The conceptual framework of evolutionary morphology in the studies of Ernst Haeckel and Fritz Müller.

In his Gastraea studies Ernst Haeckel characterized the initial stages of the animal embryo, describing complete and incomplete cleavages in various groups, until the gastrula stage. Thereby, he was able to point out various degrees of developmental diversification in these initial stages of development. As the functional meaning of such cleavages was not clear however, it was difficult to argue about putative functional adaptations. Information about the consequences for tissue formation initiated in this primary phase of development was simply lacking. Haeckel could only provide a vague picture of a highly diversified but systematically inconsistent distribution of various types of early embryogenesis. Thereby he discusses phylogenetically preserved (palingenetic) stages of development and adaptations to certain specific situations of the embryo (cenogenesis). To decide whether such types, in the initial stages of embryogenesis, are ceno- or phaenogenetic is quite difficult. Reference to the highly diversified distribution of certain types within specific groups is an indication that there is no strict adaptive pressure on these early parts of embryonic development. This makes it possible to formulate - as Haeckel did it - the idea, that in these initial phases palingenetic attributes are dominant. Thus, he tried to use these early phases of development for the classification of larger systematic units. The result is a concept of an evolutionary morphology, that was, however, never elaborated in detail by Haeckel. Therefore, it remained without effect for evolutionary biology. On the contrary, following the Darwinian approach towards a comparative analysis of embryogenesis, Fritz Müller presented a series of examples for a comparative developmental biology that allowed one to interpret certain morphological characteristics as the outcome of common evolutionary histories within different species. For various crustacean species, he was able to demonstrate that certain attributes are not to be characterized as functionally relevant adaptations, but are evolutionarily inherited.

Animals↗
PubMed2005

Evolutionary psychology: the emperor's new paradigm.

For some evolutionary psychology is merely a field of inquiry, but for others it is a robust paradigm involving specific theories about the nature and evolution of the human mind. Proponents of this paradigm claim to have made several important discoveries regarding the evolved architecture of the mind. Highly publicized discoveries include a cheater-detection module, a psychological sex difference in jealousy, and motivational mechanisms underlying parental love and its lapses, which purportedly result in child maltreatment. In this article, I argue that the empirical evidence for these "discoveries" is inconclusive, at best. I suggest that, as the reigning paradigm in evolutionary psychology has produced questionable results, the evolutionary study of human psychology is still in need of a guiding paradigm.

Biological Evolution↗
PubMed2026

The genomic alchemist's arsenal: A comprehensive review of gene recruitment, regulatory rewiring, and the evolutionary arms race in snake envenomation.

Snake venom represents a striking example of evolutionary innovation, in which ancestral physiological gene networks have been co-opted into potent biochemical weapons. Advances in multi-omics, single-cell genomics, and structural bioinformatics have catalyzed a conceptual shift from descriptive toxin cataloging to a systems-level understanding of venom evolution, regulation, and function. This Review integrates genomic, cellular, and structural perspectives to delineate the molecular architecture underpinning venom diversification and target-site co-evolution. Emphasis is placed on regulatory mechanisms driving rapid expression plasticity, including super-enhancer activity, transposable element insertion, spatial heterogeneity within the venom gland, and non-coding RNA-mediated modulation. At the protein level, the review examines how hypervariable toxins engage in structural arms races with prey targets, and how multi-toxin complex formation, functional synergy, and molecular dynamics simulations inform models of lethality and resistance. A comparative framework is provided by contrasting high-potency predatory snake venoms with low-potency defensive venoms of hymenopterans such as bees and wasps, revealing how ecological selective pressures shape toxin potency, composition, and target specificity across taxa. Finally, current translational strategies are evaluated, with a focus on the relative merits of recombinant human monoclonal antibodies versus catalytic-site small-molecule inhibitors as deployable interventions for snakebite. By synthesizing evolutionary genomics, structural biology, comparative toxinology, and synthetic antivenomics, this Review outlines a predictive framework for anticipating venom evolutionary trajectories and for designing broad-spectrum, next-generation therapeutics.

Animals↗
PubMed2006

Evolutionary game dynamics with non-uniform interaction rates.

The classical setting of evolutionary game theory, the replicator equation, assumes uniform interaction rates. The rate at which individuals meet and interact is independent of their strategies. Here we extend this framework by allowing the interaction rates to depend on the strategies. This extension leads to non-linear fitness functions. We show that a strict Nash equilibrium remains uninvadable for non-uniform interaction rates, but the conditions for evolutionary stability need to be modified. We analyze all games between two strategies. If the two strategies coexist or exclude each other, then the evolutionary dynamics do not change qualitatively, only the location of the equilibrium point changes. If, however, one strategy dominates the other in the classical setting, then the introduction of non-uniform interaction rates can lead to a pair of interior equilibria. For the Prisoner's Dilemma, non-uniform interaction rates allow the coexistence between cooperators and defectors. For the snowdrift game, non-uniform interaction rates change the equilibrium frequency of cooperators.

Biological Evolution↗
PubMed2004

A major evolutionary transition to more than two sexes?

Two recently discovered cases of genetic caste determination in social insects might provide the first example of a major evolutionary transition from two to more than two sexes. I argue here that the system can be interpreted as comprising primarily individuals requiring gametes from three parental types and having four sexes from the perspective of demographic extinction. Additionally, I show how this mating system can be seen as a major evolutionary transition. For these populations, it is apparent that the mechanism for a three- or four-sex system does not lie within the myriad of possible arrangements of chromosomes within individuals, but at the next level of evolutionary complexity, with the arrangement of chromosomes among individuals within a social system.

Journal Article↗
PubMed2005

Of chicken wings and frog legs: a smorgasbord of evolutionary variation in mechanisms of tetrapod limb development.

The tetrapod limb, which has served as a paradigm for the study of development and morphological evolution, is becoming a paradigm for developmental evolution as well. In its origin and diversification, the tetrapod limb has undergone a great deal of remodeling. These morphological changes and other evolutionary phenomena have produced variation in mechanisms of tetrapod limb development. Here, we review that variation in the four major clades of limbed tetrapods. Comparisons in a phylogenetic context reveal details of development and evolution that otherwise may have been unclear. Such details include apparent differences in the mechanisms of dorsal-ventral patterning and limb identity specification between mouse and chick and mechanistic novelties in amniotes, anurans, and urodeles. As we gain a better understanding of the details of limb development, further differences among taxa will be revealed. The use of appropriate comparative techniques in a phylogenetic context thus sheds light on evolutionary transitions in limb morphology and the generality of developmental models across species and is therefore important to both evolutionary and developmental biologists.

Animals↗
PubMed2003

The general protein secretory pathway: phylogenetic analyses leading to evolutionary conclusions.

We have identified all homologues in the current databases of the ubiquitous protein constituents of the general secretory (Sec) pathway. These prokaryotic/eukaryotic proteins include (1) SecY/Sec61alpha, (2) SecE/Sec61gamma, (3) SecG/Sec61beta, (4) Ffh/SRP54 and (5) FtsY/SRP receptor subunit-alpha. Phylogenetic and sequence analyses lead to major conclusions concerning (1) the ubiquity of these proteins in living organisms, (2) the topological uniformity of some but not other Sec constituents, (3) the orthologous nature of almost all of them, (4) a total lack of paralogues in almost all organisms for which complete genome sequences are available, (5) the occurrence of two or even three paralogues in a few bacteria, plants, and yeast, depending on the Sec constituent, and (6) a tremendous degree of sequence divergence in bacteria compared with that in archaea or eukaryotes. The phylogenetic analyses lead to the conclusion that with a few possible exceptions, the five families of Sec constituents analyzed generally underwent sequence divergence in parallel but at different characteristic rates. The results provide evolutionary insights as well as guides for future functional studies. Because every organism with a fully sequenced genome exhibits at least one orthologue of each of these Sec proteins, we conclude that all living organisms have relied on the Sec system as their primary protein secretory/membrane insertion system. Because most prokaryotes and many eukaryotes encode within their genomes only one of each constituent, we also conclude that strong evolutionary pressure has minimized gene duplication events leading to the establishment of Sec paralogues. Finally, the sequence diversity of bacterial proteins as compared with their archaeal and eukaryotic counterparts is in agreement with the suggestion that bacteria were the evolutionary predecessors of archaea and eukaryotes.

Amino Acid Sequence↗
PubMed1999

Neuropeptide families and their receptors: evolutionary perspectives.

Examination of families of neuropeptides and their receptors can provide information about phyletic relationships and evolutionary processes. Within an individual a given signal molecule may serve many diverse functions, mediated via subtypes of the receptor which may be coupled to their transduction mechanisms in different ways. The rate of evolution of a peptide may reflect or be reflected in the rate of evolution of its receptor. For example, in the neuropeptide Y (NPY) family, pancreatic polypeptide (PP) shows significant structural diversity, while NPY is highly conserved. Molecular forms of a given subtype of NPY receptor that is selectively activated by NPY (Y1 or Y2 or Y5) are also highly conserved, but the subtype that is primarily activated by PP (Y4), shows remarkable diversity. Also, between receptor subtypes there can be remarkable diversity. This is evident in several neuropeptide families, where a neuropeptide sequence is highly conserved across a wide range of species but where the receptor homology of subtypes with species tends to be much lower than homology between species. For example, human and rat vasopressin are identical, but the human V(1)- or V(2)-vasopressin receptors are approximately 80% homologous with rat V(1)- or V(2)-receptors, but within humans or rats the V(1)-receptor is less than 50% homologous with the V(2)-receptor. Furthermore, duplication of an ancestral gene is thought to have led to the co-presence in eutherian mammals of oxytocin and vasopressin, which have maintained a close structural similarity, yet in many species the oxytocin receptor is only 30 to 50% homologous with vasopressin receptors. Thus it appears that there has been greater evolutionary pressure to conserve the signal molecule, than to conserve the structure of the receptor. Evaluation of the evolution of neuropeptides and their receptors may be useful in determining phyletic relationships. Traditional classification places the guinea pig as a hystricomorph rodent within the same order (Rodentia) as the muriform or myomorph rat and mouse. However, molecular analyses of polypeptides have led to the suggestion that guinea pigs belong to a distinct order. Analysis of several neuropeptide sequences and the Y4 receptor supports this view. In general terms for both neuropeptides and receptors, sequence homology reflects phylogeny and taxonomy as based on morphological features. Within the oxytocin/vasopressin family in which peptides and receptors have been characterised in invertebrate representatives as well as fish and amphibia in addition to mammals, the molecular diversity correlates well with evolutionary diversity.

Animals↗
PubMed2003

Modern obstetrical and infertility care may increase the prevalence of disease: an evolutionary concept.

OBJECTIVE: To explore the hypothesis that the increasing prevalence of some polygenetically inherited conditions, may, to a degree, be the consequence of treatment successes of modern health care that have overcome evolutionary blocks to reproductive success. DESIGN: Hypothesis, based on a selective review of the literature. SETTING: University-affiliated private infertility center. Patient(s)None. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Occurrence of polygenetically inherited diseases. RESULT(S): Successfully treated evolutionary blocks to the inheritance of polygenetically inherited diseases result in an increased prevalence of these diseases in subsequent generations. CONCLUSION(S): Evolutionary processes have erected barriers to successful reproduction for many polygenetically inherited diseases, which are now overcome by successful treatment, leading to an increased prevalence, younger age of occurrence, and greater severity of these diseases in next generation offspring.

Biological Evolution↗
PubMed1999

Molecular epidemiology and evolutionary genetics of Leischmania parasites.

In order to illustrate the relevance of the concepts and methods of evolutionary genetics in the understanding of the epidemiology of pathogenic agents, we develop in this paper the case of the Leishmania, a genus of parasitic protozoa. An extensive study of various natural populations of Leishmania in different countries (Old and New World) was carried out by using Multilocus Enzyme Electrophoresis (MLEE) and Random Amplified Polymorphic DNA fingerprinting (RAPD) as genetic markers. The data have been interpreted in evolutionary genetic terms. The main benefit of this approach has been to better define the concept of species in the genus Leishmnania, on rigorous phylogenetic bases. As a matter of fact, a sound taxonomical background is a prerequisite for any epidemiological approach. Since the biological concept of species is difficult or impossible to apply for most pathogenic microorganisms, we recommend relying on criteria of both phylogenetic discreteness and of epidemiological/medical relevance to describe new species of Leishmania. Through this approach, for example, we have shown that the species status of L. ( V.) perzzl.ianza can be supported. On the contrary, we have been unable to clearly distinguish L. (V.) panamensis from L. (V.) guyanensis with genetic tools. Additionally, we have shown that the epidemiological inferences based on a limited set of genetic markers can be misleading. As a matter of fact, we have demonstrated that a collection of L. (L.) infantum stocks identified as zymodeme 'MON 1' by other authors present additional genetic heterogeneity and do not correspond to a distinct 'Discrete Typing Unit' DTU, and are actually polyphyletic. Lastly, in the samples that were conveniently designed, we have confirmed that Leishmania parasites have a basically clonal population structure. As the clonal model specifies it, occasional bouts of genetic exchange remain nevertheless possible. Telling comparisons are drawn with the evolutionary genetics of other pathogens Trypanosoma cruzi and Trypanosoma congolense.

Animals↗
PubMed2002

Co-evolutionary analysis reveals insights into protein-protein interactions.

Protein-protein interactions play crucial roles in biological processes. Experimental methods have been developed to survey the proteome for interacting partners and some computational approaches have been developed to extend the impact of these experimental methods. Computational methods are routinely applied to newly discovered genes to infer protein function and plausible protein-protein interactions. Here, we develop and extend a quantitative method that identifies interacting proteins based upon the correlated behavior of the evolutionary histories of protein ligands and their receptors. We have studied six families of ligand-receptor pairs including: the syntaxin/Unc-18 family, the GPCR/G-alpha's, the TGF-beta/TGF-beta receptor system, the immunity/colicin domain collection from bacteria, the chemokine/chemokine receptors, and the VEGF/VEGF receptor family. For correlation scores above a defined threshold, we were able to find an average of 79% of all known binding partners. We then applied this method to find plausible binding partners for proteins with uncharacterized binding specificities in the syntaxin/Unc-18 protein and TGF-beta/TGF-beta receptor families. Analysis of the results shows that co-evolutionary analysis of interacting protein families can reduce the search space for identifying binding partners by not only finding binding partners for uncharacterized proteins but also recognizing potentially new binding partners for previously characterized proteins. We believe that correlated evolutionary histories provide a route to exploit the wealth of whole genome sequences and recent systematic proteomic results to extend the impact of these studies and focus experimental efforts to categorize physiologically or pathologically relevant protein-protein interactions.

Algorithms↗
PubMed1983

Evolutionary changes in the information content of polypeptides.

Thermal proteins arising from the self-sequencing of amino acids satisfy the necessary conditions required for them to become a candidate of the evolutionary precursors of contemporary proteins. The source matrix of information or, equivalently, the statistical ensemble of polypeptides, in reference to which the information content of each amino acid residue can be defined and determined, changes with time endogenously through the production of and the change in the mechanism of production of polypeptides. The change proceeds in the direction along which the order of autocatalysis, the number of autocatalytic polymers needed for synthesizing one such polymer, increases. The underlying dynamics is material flow equilibration working in any material aggregate open to material flow, saying that any open system changes its interaction with the exterior endogenously and successively so as to maintain the continuity of material flow there. The self-sequencing and the autocatalytic polymerization of amino acids are the forms of producing polypeptides. The change in the mechanism of producing polypeptides results from the incorporation of polynucleotides into the polypeptide synthesis. The earlier polymeric information translation proceeds from polypeptide to polynucleotide. The direction of translation is reversed at a later stage of evolution. All these evolutionary events are consistent with viewing thermal proteins produced by self-sequencing of amino acids as an evolutionary precursor of contemporary proteins.

Amino Acid Sequence↗
PubMed1984

Evolutionary theory and teleology.

The order within and among living systems can be explained rationally by postulating a process of descent with modification, effected by factors which are extrinsic or intrinsic to the organisms. Because at the time Darwin proposed his theory of evolution there was no concept of intrinsic factors which could evolve, he postulated a process of extrinsic effects--natural selection. Biological order was thus seen as an imposed, rather than an emergent, property. Evolutionary change was seen as being determined by the functional efficiency (adaptedness) of the organism in its environment, rather than by spontaneous changes in intrinsically generated organizing factors. The initial incompleteness of Darwin's explanatory model, and the axiomatization of its postulates in neo-Darwinism, has resulted in a theory of functionalism, rather than structuralism. As such, it introduces an unnecessary teleology which confounds evolutionary studies and reduces the usefulness of the theory. This problem cannot be detected from within the neo-Darwinian paradigm because the different levels of end-directed activity--teleomatic, teleonomic, and teleological--are not recognized. They are, in fact, considered to influence one another. The theory of nonequilibrium evolution avoids these problems by returning to the basic principles of biological order and developing a structuralist explanation of intrinsically generated change. Extrinsic factors may affect the resultant evolutionary pattern, but they are neither necessary nor sufficient for evolution to occur.

Adaptation, Biological↗
PubMed1985

Thermodynamics and the conceptual structure of evolutionary theory.

Thermodynamics and evolutionary theory have spent most of their shared history in adversarial relationship to one another. The point of this paper is to consider some qualitative ways in which thermodynamics can enrich both the theory and epistemology of evolution. The "autonomy of biology" posture in evolutionary theory hangs on the supposed uniqueness of why-questions in biology. With this posture, and with the general obstruction of constructive dialogue between evolution and the physical sciences it fosters, come the perennial accusations that Darwinism deals in adaptational teleology but not mechanisms. Thermodynamics provides for a two-tiered hierarchy of causation in nature in which the why-question is rendered not only legitimate materialistically, but essential to understanding the evolutionary process in its totality--from the emergence of life to the branching of lineages in speciation.

Adaptation, Biological↗
PubMed1986

Introns as relict retrotransposons: implications for the evolutionary origin of eukaryotic mRNA splicing mechanisms.

A model is presented for the evolutionary origin of intron sequences within eukaryotic protein-coding genes. We propose that introns are the vestiges of transposable elements and, specifically, that they represent a novel class of retrovirus-like transposons. The attraction of the retrotransposon model is that it gives the RNA splicing mechanism a central role in the evolution of introns. There is a growing body of evidence to suggest that several aspects of splicing are intron-encoded. Consequently, it is reasonable to look for evolutionary explanations of the splicing mechanism in the context of the evolution of the intron sequences themselves. According to this model the ancestral intron genomes were replicated into RNA copies simply because of their insertion within transcriptionally active regions of the host genome. Splicing was necessary not only to minimize their negative effects on host gene expression, but also, and perhaps more importantly, to generate new copies of the intron genome free of flanking exon sequences. These spliced intron copies were then available for reverse transcription and reinsertion elsewhere in the genome. Thus, splicing can be seen as an essential step in the intron replication cycle. Most modern introns have probably lost the majority of their original genetic content and may be considered as degenerate evolutionary relicts. An exception to this degeneracy is the set of splicing signals which must be retained because of its continued importance to host cell survival.(ABSTRACT TRUNCATED AT 250 WORDS)

Biological Evolution↗
PubMed1989

Influenza viruses, comets and the science of evolutionary trees.

The study of phylogeny is becoming increasing scientific in that hypotheses can be tested quantitatively. We report a method of estimating the probabilities of obtaining a tree of a given length from nucleic acid sequence data. The method is applied to the hypothesis of Hoyle & Wickramasinghe that the earth is being continually bombarded by influenza (and other) viruses which originate from comets. A quantitative analysis of sequences from the H1 strain of human influenza viruses contradicts three versions of the Hoyle-Wickramasinghe model. One non-evolutionary version of their model has less than one chance in 10(66) of being correct. A version that allowed extraterrestrial evolution has less than one change in 10(6) of being correct. The sequence data is in agreement with the biological (evolutionary) model. The results are discussed from the aspect of the falsifiability of evolutionary theory.

Base Sequence↗
PubMedDate not supplied

On the evolutionary coexistence of parasite strains.

Classical models of parasite competition show that coexistence is impossible if different strains give complete cross-immunity. However, parasite coexistence is possible if some of the model assumptions are changed. For instance, coexistence is impossible if density-dependence operates only in hosts' fertility, but surprisingly becomes possible if hosts' mortality is density-dependent. Parasite strains can also coexist if a host already infected with one strain may become infected by another strain (superinfection). I examine here if these reasons for coexistence carry over to evolutionary timescales: in other words, suppose that potentially a continuum of parasite strains may arise by mutations; will evolution arrive at a halt? in that case, will only one or several strains persist? The paradigm and methods of adaptive dynamics are used in this study. It is found, under reasonably general assumptions, that a unique evolutionarily stable state for virulence, alpha(*), exist for both models. However, the pattern of the invasibility plots depends on the shape of the trade-off (between virulence and transmissibility, or superinfection rates) functions, and on the host demography. In many cases, the state alpha(*) is evolutionarily stable only with respect to small mutations, not to larger ones; hence, evolutionary dynamics will bring virulence to alpha(*) only if mutations are sufficiently small; for larger mutations, evolutionary dynamics are more complex and still mainly unresolved.

Animals↗
PubMed2000

The homeodomain: an ancient evolutionary motif in animals and plants.

The homeodomain is a DNA-binding motif within transcription factor proteins. These transcription factors may be involved in cell differentiation and control of cell growth, as well as patterning of diverse organisms. Given their strong evolutionary conservation, it has been suggested that homeodomain proteins have been fundamental to the evolution of animal species. We have previously shown that the major classes of animal homeodomains originated early in the evolution of metazoans. Here, I investigate the evolutionary relationships of homeodomain sequences in plants. Using distance matrix approaches with unweighted or weighted character state transitions, the overall results support the same conclusion: in plants, as in animals, multiple independent classes of divergent homeodomains can be distinguished, again suggesting an early evolutionary origin. These studies advance the hypothesis that the homeodomain represents a fundamental motif of gene regulation in multicellular organisms.

Amino Acids↗