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The evolutionary history of crustacean segmentation: a fossil-based perspective.

The evolution of segmentation in Crustacea, that is, the formation of sclerotized and jointed body somites and arrangement of somites into tagmata, is viewed in light of historical traits and functional constraints. The set of Early to Late Cambrian 'Orsten' arthropods have informed our current views of crustacean evolution considerably. These three-dimensionally preserved fossils document ancient morphologies, as opposed to purely hypothetical models and, because of the unusual preservation of larval stages, provide us with unparalleled insight into the morphogenesis of body somites and their structural equipment. The variety of evolutionary levels represented in the 'Orsten' including lobopodians, tardigrades, and pentastomids also allows phylogenetic interpretations far beyond the Crustacea. The 'Orsten' evidence and data from representatives of the Lower Cambrian Chengjiang biota in southwestern China, including phylogenetically earlier forms, form the major source of our morphology-based review of structural and functional developments that led toward the Crustacea. The principal strategy of arthropods is the simultaneous development of head somites, as expressed in a basal "head larva," and a successive addition of postcephalic somites from a preterminal budding zone with progressive maturation of metameric structures. This can be recognized in the developmental patterns of extant and fossil representatives of several euarthropod taxa, particularly crustaceans, trilobites, and chelicerates (at least basally). The development of these taxa points to an early somite-poor and free-living hatching stage. Embryonic development to a late stage within an egg, as occurring in recent onychophorans and certain in-group euarthropods, is regarded as achieved several times convergently.

Animals↗
PubMed2002

Phylogeography of Lake Malawi cichlids of the genus Pseudotropheus: significance of allopatric colour variation.

One of the most compelling features of the cichlid fishes of the African Great Lakes is the seemingly endless diversity of male coloration. Colour diversification has been implicated as an important factor driving cichlid speciation. Colour has also been central to cichlid taxonomy and, thus, to our concept of species diversity. We undertook a phylogeographical examination of several allopatric populations of the Lake Malawi cichlid Pseudotropheus zebra in order to reconstruct the evolutionary history of the populations, which exhibit one of two dorsal fin colours. We present evidence that populations with red dorsal fins (RT) are not monophyletic. The RT population defining the northern limit of the distribution has evidently originated independently of the southern RT populations, which share a common ancestry. This evidence of species-level colour convergence is an important discovery in our understanding of cichlid evolution. It implies that divergence in coloration may accompany speciation, and that allopatric populations with similar coloration cannot be assumed to be conspecific. In addition to this finding, we have observed evidence for introgression, contributing to current evidence that this phenomenon may be extremely widespread. Thus, in species-level phylogenetic reconstructions, including our own, consideration must be given to the potential effects of introgression.

Alleles↗
PubMed1991

Evolved neomycin phosphotransferase from an isolate of Klebsiella pneumoniae.

A new aminoglycoside resistance gene (aphA1-IAB) confers high-level resistance to neomycin. The sequence of aphA1-IAB is closely related to aphA1 found in the transposons Tn4352, Tn903 and Tn602. For example, aphA1-IAB differs from aphA1-903 at five nucleotides that result in four amino acid replacements. The enzyme encoded by aphA1-IAB has a significantly higher turnover number with neomycin, kanamycin and G418 as substrates than does the aphA1-903 enzyme. A parsimonious phylogenetic tree suggests that aphA1-IAB evolved from an ancestral form that is closely related or identical to the aphA1 found in Tn903. The excess of replacement substitutions over silent substitutions in aphA1-IAB, as well as its convergence toward aphA3 from Staphylococcus aureus, is indicative of selective evolution. Our hypothesis to explain these results is that aphA1-IAB evolved under the selective pressure of neomycin use in relatively recent times.

Amino Acid Sequence↗
PubMed2026

Atypical infections caused by pathogenic Neisseria species N. meningitidis and N. gonorrhoeae.

SUMMARYAtypical pathogenic Neisseria infections, including disseminated gonococcal infection, primary meningococcal conjunctivitis, and urogenital meningococcal infection, are clinically important yet under-recognized syndromes that challenge traditional species-disease paradigms. The increasing use of whole-genome sequencing has revealed adaptive convergence within the Neisseria genus, providing new insights into the evolution, pathophysiology, and tissue tropism of these infections. This review aims to outline current epidemiological, clinical, and genomic evidence to define transmission, risk factors, and molecular determinants underpinning disease. Improved understanding of these conditions is essential to optimize diagnosis, treatment, and public health guidance.

Neisseria gonorrhoeae↗
PubMed2003

Evolutionary pace of chromosomal polymorphism in colonizing populations of Drosophila subobscura: an evolutionary time series.

Biologists have long debated the speed, uniformity, and predictability of evolutionary change. However, evaluating such patterns on a geographic scale requires time-series data on replicate sets of natural populations. Drosophila subobscura has proven an ideal model system for such studies. This fly is broadly distributed in the Old World, but was introduced into both North and South America just over two decades ago and then spread rapidly. Rapid, uniform, and predictable evolution would be demonstrated if the invading flies evolved latitudinal clines that progressively converged on those of the native populations. Evolutionary geneticists quickly capitalized on this opportunity to monitor evolutionary dynamics. Just a few years after the introduction, they surveyed chromosomal inversion frequencies in both North and South America. On both continents they detected incipient latitudinal clines in chromosome inversion frequencies that almost always had the same sign with latitude as in the Old World. Thus the initial evolution of chromosomal polymorphisms on a continental scale was remarkably rapid and consistent. Here we report newer samples of inversion frequencies for the colonizing populations: the time series now spans almost one decade for North America and almost two decades for South America. Almost all inversions in the New World continue to show the same sign of frequency with latitude as in the Old World. Nevertheless, inversion clines have not consistently increased in steepness over time; nor have they consistently continued to converge on the Old World baseline. However, five arrangements in South America show directional, continentwide shifts in frequency. Overall, the initial consistency of clinal evolutionary trajectories seen in the first surveys seems not to have been maintained.

Animals↗
PubMed2004

Batesian mimics influence mimicry ring evolution.

Mathematical models of mimicry typically involve artificial prey species with fixed colorations or appearances; this enables a comparison of predation rates to demonstrate the level of protection a mimic might be afforded. Fruitful theoretical results have been produced using this method, but it is also useful to examine the possible evolutionary consequences of mimicry. To that end, we present individual-based evolutionary simulation models where prey colorations are free to evolve. We use the models to examine the effect of Batesian mimics on Müllerian mimics and mimicry rings. Results show that Batesian mimics can potentially incite Müllerian mimicry relationships and encourage mimicry ring convergence.

Animals↗
PubMed2026

Application of emerging technologies in the antiviral field.

Viral diseases pose a serious threat to global public health, agriculture, and biosecurity. Conventional antiviral strategies are often limited by an incomplete understanding of disease mechanisms, poor targeting precision, and slow response times. Emerging technologies are now reshaping the landscape of antiviral research. This review examines the roles of four key frontiers, including organoid models, gene editing, AI-driven molecular design, and synthetic biology. Organoids provide physiologically relevant platforms that model virus-host interactions and disease progression. Viral infections remain a major challenge to human and animal health, agriculture, and biosecurity. Progress in antiviral research is constrained by the complexity of viral pathogenesis, the diversity and rapid evolution of viruses, and the limited translational relevance of some traditional model systems. Recent advances in organoid technology, gene editing, artificial intelligence, and synthetic biology are expanding the toolkit available for antiviral research and development. In this review, we discuss how these four technological frontiers contribute to disease modeling, target discovery, molecular design, and translational innovation. Organoids, in particular, provide physiologically relevant systems for investigating viral infection, tissue tropism, host responses, and pathogenesis. Gene editing tools, such as CRISPR, enable precise manipulation of host and viral genomes, facilitating the development of resistant organisms and next-generation vaccine platforms. AI technologies, including AlphaFold for structure prediction and platforms for de novo protein design, address long-standing bottlenecks in structural biology and offer powerful means to engineer antiviral proteins, antibodies, and vaccine antigens. Synthetic biology, guided by the Design-Build-Test-Learn cycle, integrates computational design, genetic assembly, and functional validation into a cohesive pipeline. Together, these technologies form a synergistic workflow that spans disease modeling, target discovery, molecular design, construction, testing, and iterative optimization. This integrated approach is shifting antiviral development from traditional empirical methods toward more precise, intelligent strategies. The review also highlights ongoing challenges in integration and scalability, stressing that high-quality biological datasets and stronger interdisciplinary collaboration are essential for realizing translational potential. By presenting a cohesive view of these converging methodologies, this review offers a framework to guide the intelligent evolution of antiviral strategies in both human and animal health.

Antiviral↗
PubMed2001

A convergence analysis of unconstrained and bound constrained evolutionary pattern search.

We present and analyze a class of evolutionary algorithms for unconstrained and bound constrained optimization on R(n): evolutionary pattern search algorithms (EPSAs). EPSAs adaptively modify the step size of the mutation operator in response to the success of previous optimization steps. The design of EPSAs is inspired by recent analyses of pattern search methods. We show that EPSAs can be cast as stochastic pattern search methods, and we use this observation to prove that EPSAs have a probabilistic, weak stationary point convergence theory. This convergence theory is distinguished by the fact that the analysis does not approximate the stochastic process of EPSAs, and hence it exactly characterizes their convergence properties.

Algorithms↗
PubMed2006

Genomic convergence toward diploidy in Saccharomyces cerevisiae.

Genome size, a fundamental aspect of any organism, is subject to a variety of mutational and selection pressures. We investigated genome size evolution in haploid, diploid, and tetraploid initially isogenic lines of the yeast Saccharomyces cerevisiae. Over the course of approximately 1,800 generations of mitotic division, we observed convergence toward diploid DNA content in all replicate lines. This convergence was observed in both unstressful and stressful environments, although the rate of convergence was dependent on initial ploidy and evolutionary environment. Comparative genomic hybridization with microarrays revealed nearly euploid DNA content by the end of the experiment. As the vegetative life cycle of S. cerevisiae is predominantly diploid, this experiment provides evidence that genome size evolution is constrained, with selection favouring the genomic content typical of the yeast's evolutionary past.

Chromosomes, Fungal↗
PubMed1980

General theory of evolution.

The biological, neural, cultural and technical evolutions and their phenomena have been explored, and on the basis of our findings the formation of a general theory of evolution has been undertaken. In each of the systems studied, the presence of structural building units, excitable structures and an energy-flow going through the system can be observed. Under the organizing effect of this energy-flow, the spontaneous generation of the replicative information begins and the structures of the system establish functional relations with each other. It can be demonstrated that the evolution of structures has a replicative character. The evolution goes through a phase of non-identical replication, and reaches the phase of identical replication. The parts of the system become separated, that is, compartments develop within it. The replicative information becomes compartmentalized and it converges. As a consequence of the convergence, the compartments compose new structural units which is tantamount to the development of new evolutional levels. The direction of evolution is determined by the growth of replicative information, and this process is concluded when the total system becomes one replicative unit. In the last part of the paper a few of the basic principles of evolution concerning matter, energy and information are drawn up.

Animals↗
PubMed1998

Phylogenetic relations among percid fishes as inferred from mitochondrial cytochrome b DNA sequence data.

Hypotheses of relationship among genera of Percidae have been conflicting. Based on different phylogenetic premises, the evolution of small benthic forms in Percidae has been interpreted as resulting from either convergence or common ancestry. In order to assess various phylogenetic hypotheses of Percidae we collected complete sequences (1140 bp) of mitochondrially encoded cytochrome b for 21 species of percids. Seven species representing four additional families of Perciformes were used as outgroups. Maximum parsimony and minimum evolution analyses both recovered single shortest trees, and the results of these analyses were generally congruent with one another. All analyses consistently recovered three monophyletic groups in Percidae: Etheostomatinae (Ammocrypta, Crystallaria, Etheostoma, and Percina), Percinae (Perca and Gymnocephalus), and Luciopercinae (Stizostedion, Zingel, and Romanichthys). As a result of this analysis we present a revised classification of Percidae and discuss the phylogenetic evidence for the independent evolution of small benthic species within Etheostomatinae and Luciopercinae.

Animals↗
PubMed2000

Developmental regulatory genes and echinoderm evolution.

Modified interactions among developmental regulatory genes and changes in their expression domains are likely to be an important part of the developmental basis for evolutionary changes in morphology. Although developmental regulatory genes are now being studied in an increasing number of taxa, there has been little attempt to analyze the resulting data within an explicit phylogenetic context. Here we present comparative analyses of expression data from regulatory genes in the phylum Echinodermata, considering the implications for understanding both echinoderm evolution as well as the evolution of regulatory genes in general. Reconstructing the independent evolutionary histories of regulatory genes, their expression domains, their developmental roles, and the structures in which they are expressed reveals a number of distinct evolutionary patterns. A few of these patterns correspond to interpretations common in the literature, whereas others have received little prior mention. Together, the analyses indicate that the evolution of echinoderms involved: (1) the appearance of many apomorphic developmental roles and expression domains, some of which have plesiomorphic bilateral symmetry and others of which have apomorphic radial symmetry or left-right asymmetry; (2) the loss of some developmental roles and expression domains thought to be plesiomorphic for Bilateria; and (3) the retention of some developmental roles thought to be plesiomorphic for Bilateria, although with modification in expression domains. Some of the modifications within the Echinodermata concern adult structures; others, transient larval structures. Some changes apparently appeared early in echinoderm evolution (> 450 Ma), whereas others probably happened more recently (< 50 Ma). Cases of likely convergence in expression domains suggest caution when using developmental regulatory genes to make inferences about homology among morphological structures of distantly related taxa.

Animals↗
PubMed2005

Development of the central nervous system in the larvacean Oikopleura dioica and the evolution of the chordate brain.

In non-vertebrate chordates, central nervous system (CNS) development has been studied in only two taxa, the Cephalochordata and a single Class (Ascidiacea) of the morphologically diverse Urochordata. To understand development and molecular regionalization of the brain in a different deeply diverging chordate clade, we isolated and determined the expression patterns of orthologs of vertebrate CNS markers (otxa, otxb, otxc, pax6, pax2/5/8a, pax2/5/8b, engrailed, and hox1) in Oikopleura dioica (Subphylum Urochordata, Class Larvacea). The three Oikopleura otx genes are expressed similarly to vertebrate Otx paralogs, demonstrating that trans-homologs converged on similar evolutionary outcomes by independent neo- or subfunctionalization processes during the evolution of the two taxa. This work revealed that the Oikopleura CNS possesses homologs of the vertebrate forebrain, hindbrain, and spinal cord, but not the midbrain. Comparing larvacean gene expression patterns to published results in ascidians disclosed important developmental differences and similarities that suggest mechanisms of development likely present in their last common ancestor. In contrast to ascidians, the lack of a radical reorganization of the CNS as larvaceans become adults allows us to relate embryonic gene expression patterns to three subdivisions of the adult anterior brain. Our study of the Oikopleura brain provides new insights into chordate CNS evolution: first, the absence of midbrain is a urochordate synapomorphy and not a peculiarity of ascidians, perhaps resulting from their drastic CNS metamorphosis; second, there is no convincing evidence for a homolog of a midbrain-hindbrain boundary (MHB) organizer in urochordates; and third, the expression pattern of "MHB-genes" in the urochordate hindbrain suggests that they function in the development of specific neurons rather than in an MHB organizer.

Animals↗
PubMed2000

Field data do not support a textbook example of convergent character displacement.

Experimental evidence supporting convergent character displacement is rare; only one example exists and it is in the form of orientation and territory competition experiments performed in the laboratory. However, outcomes of laboratory experiments involving behaviour or competition can be artefacts of unnatural conditions and, therefore, the results of the previous experiments supporting convergent character displacement are equivocal. In this study, we re-examine the evolution of melanic nuptial coloration in male three-spined stickleback (Gasterosteus aculeatus) inhabiting the Chehalis River drainage in Washington State. This novel nuptial coloration has been thought to have evolved in response to competition for nesting territories with the co-distributed Olympic mudminnow (Norzumbra hubbsi), which is also melanic and breeds at the same time. I found that melanic stickleback males did not have an advantage over their red counterparts from typical populations when competing for nesting territories with Olympic mudminnows. Additionally competitive interactions between sticklebacks and mudminnows were rare in both cage experiments and naturally breeding sticklebacks. Finally, melanic coloration in the Chehalis populations did not develop until males were parental, well after the hypothesized territory establishment period. These results refute the only experimental support for convergent character displacement and emphasize the importance of conducting behavioural experiments and observations under natural conditions.

Animals↗
PubMed1998

Kinematics of aquatic and terrestrial prey capture in Terrapene carolina, with implications for the evolution of feeding in cryptodire turtles.

Studies of aquatic prey capture in vertebrates have demonstrated remarkable convergence in kinematics between diverse vertebrate taxa. When feeding in water, most vertebrates employ large-amplitude hyoid depression to expand the oral cavity and suck in water along with the prey. In contrast, vertebrates feeding on land exhibit little or no hyoid depression. In this study we compared the kinematics of terrestrial and aquatic prey capture within one species of turtle, Terrapene carolina, in order to determine whether an individual species can modulate the magnitude of hyoid depression between air and water. High-speed video (250 frames per second) showed that hyoid depression was over three times greater in aquatic than in terrestrial feedings, indicating that T. carolina is able to modulate hyoid depression magnitude depending on the medium in which feeding occurs. In addition, we observed medium-dependent modulation of hyoid depression in another turtle, Heosemys grandis, and large-amplitude hyoid depression during aquatic feeding in Kinosternon leucostomum, Platysternon megacephalum, and juvenile Chelydra serpentina. In all of these turtles, hyoid depression produced oral cavity expansion during aquatic feeding, but the earthworm prey were never sucked toward the predators. Prey were captured by neck extension (ram feeding), and we conclude that the function of hyoid depression during aquatic feeding in cryptodire turtles is to prevent the forward motion of the predator from pushing the prey away (compensatory suction). Aquatic feeding is probably the primitive condition for all extant turtles, and thus terrestrial feeding in T. carolina and other turtles is a secondarily derived characteristic. We conclude from this historical pattern that it is not appropriate to use extant turtles in attempts to reconstruct the terrestrial feeding mechanisms of primitive amniotes.

Animals↗
PubMed2001

Nonequilibrium dynamics of random field Ising spin chains: exact results via real space renormalization group.

The nonequilibrium dynamics of classical random Ising spin chains with nonconserved magnetization are studied using an asymptotically exact real space renormalization group (RSRG). We focus on random field Ising model (RFIM) spin chains with and without a uniform applied field, as well as on Ising spin glass chains in an applied field. For the RFIM we consider a universal regime where the random field and the temperature are both much smaller than the exchange coupling. In this regime, the Imry-Ma length that sets the scale of the equilibrium correlations is large and the coarsening of domains from random initial conditions (e.g., a quench from high temperature) occurs over a wide range of length scales. The two types of domain walls that occur diffuse in opposite random potentials, of the form studied by Sinai, and domain walls annihilate when they meet. Using the RSRG we compute many universal asymptotic properties of both the nonequilibrium dynamics and the equilibrium limit. We find that the configurations of the domain walls converge rapidly toward a set of system-specific time-dependent positions that are independent of the initial conditions. Thus the behavior of this nonequilibrium system is pseudodeterministic at long times because of the broad distributions of barriers that occur on the long length scales involved. Specifically, we obtain the time dependence of the energy, the magnetization, and the distribution of domain sizes (found to be statistically independent). The equilibrium limits agree with known exact results. We obtain the exact scaling form of the two-point equal time correlation function and the two-time autocorrelations . We also compute the persistence properties of a single spin, of local magnetization, and of domains. The analogous quantities for the +/-J Ising spin glass in an applied field are obtained from the RFIM via a gauge transformation. In addition to these we compute the two-point two-time correlation function which can in principle be measured by experiments on spin-glass-like systems. The thermal fluctuations are studied and found to be dominated by rare events; in particular all moments of truncated equal time correlations are computed. Physical properties which are typically measured in aging experiments are also studied, focusing on the response to a small magnetic field which is applied after waiting for the system to equilibrate for a time t(w). The nonequilibrium fluctuation-dissipation ratio X(t,t(w)) is computed. We find that for (t-t(w)) approximately t(alpha)(w) with alpha;<1, the ratio equal to its equilibrium value X=1, although time translational invariance does not hold in this regime. For t-t(w) approximately t(w) the ratio exhibits an aging regime with a nontrivial X=X(t/t(w)) not equal to 1, but the behavior is markedly different from mean field theory. Finally the distribution of the total magnetization and of the number of domains is computed for large finite size systems. General issues about convergence toward equilibrium and the possibilities of weakly history-dependent evolution in other random systems are discussed.

Journal Article↗
PubMed1994

Crystal structure of a catalytic antibody with a serine protease active site.

The three-dimensional structure of an unusually active hydrolytic antibody with a phosphonate transition state analog (hapten) bound to the active site has been solved to 2.5 A resolution. The antibody (17E8) catalyzes the hydrolysis of norleucine and methionine phenyl esters and is selective for amino acid esters that have the natural alpha-carbon L configuration. A plot of the pH-dependence of the antibody-catalyzed reaction is bell-shaped with an activity maximum at pH 9.5; experiments on mechanism lend support to the formation of a covalent acyl-antibody intermediate. The structural and kinetic data are complementary and support a hydrolytic mechanism for the antibody that is remarkably similar to that of the serine proteases. The antibody active site contains a Ser-His dyad structure proximal to the phosphorous atom of the bound hapten that resembles two of the three components of the Ser-His-Asp catalytic triad of serine proteases. The antibody active site also contains a Lys residue to stabilize oxyanion formation, and a hydrophobic binding pocket for specific substrate recognition of norleucine and methionine side chains. The structure identifies active site residues that mediate catalysis and suggests specific mutations that may improve the catalytic efficiency of the antibody. This high resolution structure of a catalytic antibody-hapten complex shows that antibodies can converge on active site structures that have arisen through natural enzyme evolution.

Amino Acid Sequence↗
PubMed2001

Reflections: emergency radiology.

In this article, the author compares emergency radiology as it was practiced and taught from the turn of the 20th century to the middle 1970s with the way it is practiced and taught today. Many specific examples are cited. External influences serendipitously converged in the 1960s-1980s, and their effect on the evolution of emergency radiology as it is recognized today are described.

Emergency Medicine↗