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PubMed1995

An evolutionary theory of the family.

An evolutionary framework for viewing the formation, the stability, the organizational structure, and the social dynamics of biological families is developed. This framework is based upon three conceptual pillars: ecological constraints theory, inclusive fitness theory, and reproductive skew theory. I offer a set of 15 predictions pertaining to living within family groups. The logic of each is discussed, and empirical evidence from family-living vertebrates is summarized. I argue that knowledge of four basic parameters, (i) genetic relatedness, (ii) social dominance, (iii) the benefits of group living, and (iv) the probable success of independent reproduction, can explain many aspects of family life in birds and mammals. I suggest that this evolutionary perspective will provide insights into understanding human family systems as well.

Animals↗

PubMed2004

Community assembly through adaptive radiation in Hawaiian spiders.

Communities arising through adaptive radiation are generally regarded as unique, with speciation and adaptation being quite different from immigration and ecological assortment. Here, I use the chronological arrangement of the Hawaiian Islands to visualize snapshots of evolutionary history and stages of community assembly. Analysis of an adaptive radiation of habitat-associated, polychromatic spiders shows that (i) species assembly is not random; (ii) within any community, similar sets of ecomorphs arise through both dispersal and evolution; and (iii) species assembly is dynamic with maximum species numbers in communities of intermediate age. The similar patterns of species accumulation through evolutionary and ecological processes suggest universal principles underlie community assembly.

Adaptation, Physiological↗

PubMed2005

Modelling the evolution of genetic regulatory networks.

An evolutionary model of genetic regulatory networks is developed, based on a model of network encoding and dynamics called the Artificial Genome (AG). This model derives a number of specific genes and their interactions from a string of (initially random) bases in an idealized manner analogous to that employed by natural DNA. The gene expression dynamics are determined by updating the gene network as if it were a simple Boolean network. The generic behaviour of the AG model is investigated in detail. In particular, we explore the characteristic network topologies generated by the model, their dynamical behaviours, and the typical variance of network connectivities and network structures. These properties are demonstrated to agree with a probabilistic analysis of the model, and the typical network structures generated by the model are shown to lie between those of random networks and scale-free networks in terms of their degree distribution. Evolutionary processes are simulated using a genetic algorithm, with selection acting on a range of properties from gene number and degree of connectivity through periodic behaviour to specific patterns of gene expression. The evolvability of increasingly complex patterns of gene expression is examined in detail. When a degree of redundancy is introduced, the average number of generations required to evolve given targets is reduced, but limits on evolution of complex gene expression patterns remain. In addition, cyclic gene expression patterns with periods that are multiples of shorter expression patterns are shown to be inherently easier to evolve than others. Constraints imposed by the template-matching nature of the AG model generate similar biases towards such expression patterns in networks in initial populations, in addition to the somewhat scale-free nature of these networks. The significance of these results on current understanding of biological evolution is discussed.

Algorithms↗

PubMed2003

A complete classification of Darwinian extinction in ecological interactions.

The evolution of a population by individual-level natural selection can result in the population's extinction. Selection causes the spread of phenotypes with higher relative fitness, but at the same time, selection can also indirectly produce changes in the physical, biotic, or genotypical environment through population interactions (e.g., environment modification, interspecific interactions, and genomic conflict). Because fitness is environment dependent, this can cause mean fitness to decrease, resulting in extinction. I call this process "Darwinian extinction." Examples of Darwinian extinction include a variety of dynamics and modes of extinction, but the variation is constrained. I determine the complete classification of possible dynamics and modes of Darwinian extinction due to ecological interactions, using bifurcation theory and models with ecological and evolutionary changes occurring on different timescales. This classification is also extended to extinctions due to interactions within the population. The mode of extinction may be either sudden or gradual (requiring additional stochastic processes), and each mode has specific types of dynamics associated with it. Darwinian extinction is a robust and normal phenomenon, and this reasonably complete classification can help us understand more thoroughly its role in nature.

Animals↗

PubMed2026

Overcoming cancer resistance in pancreatic cancer: toward dynamic precision oncology.

Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal malignancy, largely because of its profound and evolving therapeutic resistance. Resistance is not determined by a single molecular alteration but arises from interconnected mechanisms, including intrinsic resistance, treatment-induced adaptive resistance, acquired resistance, genomic evolution, clonal selection, cancer stemness, phenotypic plasticity, metabolic adaptation, and tumor microenvironment-mediated effects. Emerging therapeutic approaches targeting KRAS/RAS signaling, stromal and immune components, metabolic dependencies, and DNA damage repair pathways offer opportunities to address these mechanisms, although durable efficacy remains limited by biological heterogeneity and adaptive responses. In this review, we examine therapeutic resistance as an evolutionary and multidimensional process and summarize emerging strategies for overcoming resistance. We further propose a Dynamic Precision Oncology (DPO) framework that extends conventional precision oncology beyond baseline molecular profiling by integrating longitudinal assessment of tumor genomics, circulating tumor DNA, CA19-9, imaging, radiomics, and clinical characteristics. This framework emphasizes iterative detection and characterization of emerging resistance, mechanism-informed treatment adaptation, and subsequent reassessment rather than automatic treatment modification based on a single biomarker. DPO may provide a conceptual framework for integrating evolving tumor biology into treatment decision-making, while prospective studies are needed to validate biomarkers, define actionable thresholds, and determine whether longitudinal resistance-guided strategies improve clinical outcomes in PDAC.

Humans↗

PubMed1993

The segmental Bauplan of the rostral zone of the head in vertebrates.

Observations in a wide selection of lower vertebrate embryos have confirmed classical descriptions concerning segmentation of the early head mesoderm. The premandibular (PM) segment is seen as the most rostral representative of a continuous rostro-caudal series of condensations in the paraxial mesoderm, luminisations within which are secondary and variable in occurrence and form. The premandibular condensations are typically in continuity across the midline; the confluence, which comes to lie behind Rathke's pouch, marks the site of first mesoderm formation behind the oral membrane. The underlying consistency of pre-otic segmental pattern throughout the vertebrates is frequently obscured by superimposed variation in morphological detail between species, reflecting the dynamic nature of the morphogenetic tissue processes. Luminisation is one such morphogenetic epiphenomenon. Variations in it account for the terminal (Platt's) vesicle and "proboscis pores": such structures cannot therefore be safely used to infer evolutionary homologies. Many previous difficulties facing segmentation theory are explained as the result of failure to take account of the dynamic nature of the responsible morphogenetic events.

Animals↗

PubMed2003

Ecological dynamics of mutualist/antagonist communities.

One approach to understanding how mutualisms function in community settings is to model well-studied pairwise interactions in the presence of the few species with which they interact most strongly. In nature, such species are often specialized antagonists of one or both mutualists. Hence, these models can also shed light on the problem of when and how mutualisms are able to persist in the face of exploitation. We used spatial stochastic simulations to model the ecological dynamics of obligate, species-specific mutualisms between plants and pollinating seed parasite insects (e.g., yuccas and yucca moths) in the presence of one of two obligate antagonist species: flower-feeding insects (florivores) or insects that parasitize seeds but fail to pollinate (exploiters). Our results suggest that mutualisms can persist surprisingly well in the presence of highly specialized antagonists but that they exhibit distinctly different temporal and spatial dynamics when antagonists are present. In our models, antagonists tend to induce oscillations in the mutualist populations. As the number of per capita visits by antagonists increase, the system's oscillatory dynamics become more extreme, finally leading to the extinction of one or more of the three species. When the antagonists exhibit high per capita visitation frequencies and long dispersal distances, significant spatial patchiness emerges within these tripartite interactions. We found surprisingly little difference between the ecological effects of florivores and exploiters, although in general florivores tended to drive themselves (and sometimes the mutualists) to extinction at parameter values at which the exploiters were able to persist. These theoretical results suggest several testable hypotheses regarding the ecological and evolutionary persistence of mutualisms. More broadly, they point to the critical importance of studying the dynamics of pairwise interactions in community contexts.

Animals↗

PubMed2005

Evolutionary innovations in the fossil record: the intersection of ecology, development, and macroevolution.

The origins of evolutionary innovations have been intensively studied, but relatively little is known about their large-scale ecological patterns. For post-Paleozoic benthic marine invertebrates, which have the richest and most densely sampled fossil record, order-level taxa tend to appear first in onshore, disturbed habitats, even in groups that are now exclusively deep-water (so that present-day distributions are not reliable indicators of original environments). New results presented here show that the onshore-origination pattern is robust to shifts in taxonomic methods and to new paleontological discoveries, and the few available studies suggest that this pattern can also be seen in terms of excursions in morphospace or the acquisition of derived character states, without reference to taxonomic categories. The environmental pattern at high levels contrasts significantly with the origin of low-level novelties (such as defined genera and families) in crinoids, echinoids, and bryozoans, where first appearances tend to conform to their clade-specific bathymetric diversity gradients. This discordance seems to eliminate potential driving mechanisms that simply scale up within-population genetic or ecological processes. Little is known about the factors that promote the onshore-offshore expansion of orders across the continental shelf, or that drive some clades to abandon ancestral habitats for an exclusively deep-water distribution. The origin of evolutionary innovation must ultimately reside in developmental changes, but the onshore-origination bias could emerge from two different dynamics: the pattern could be primarily genetic and developmental, i.e., innovations truly arise onshore; or primarily ecological, i.e., innovations arise randomly but preferentially survive onshore. Whatever the ultimate driving mechanisms, these macroevolutionary patterns show that theories of large-scale evolutionary novelty must include an ecological dimension.

Animals↗

PubMed2026

Evolutionary expansion of the NF-Y gene family in bivalves and divergent subunit responses to thermal and pathogenic stress in the noble scallop.

Nuclear factor Y (NF-Y) is a conserved eukaryotic transcription factor complex that specifically interacts with the CCAAT motif. Prior research has demonstrated that this gene family participates in various biological processes, encompassing growth, development, and stress responses, across a broad spectrum of organisms. However, research on the role of the NF-Y family in bivalves remains limited. In this study, we comprehensively identified the NF-Y family in 34 bivalve species, and further investigated its expression in the noble scallop Chlamys nobilis. A total of 296 NF-Y genes were identified and classified into three subfamilies, NF-YA, NF-YB, and NF-YC. Phylogenetic analysis revealed that NF-YA and NF-YC have remained relatively conserved, whereas NF-YB has undergone significant expansion. Additionally, while substantial disparities in gene copy numbers exist across species, the motif composition and exon-intron structures within each subfamily demonstrate notable conservation. Tissue expression profiling revealed distinct expression patterns among CnNF-Y genes, with several members exhibiting relatively high transcript abundance in gonadal tissues. Furthermore, qRT-PCR results demonstrated that CnNF-YA2, CnNF-YB6, and CnNF-YC were significantly and continuously upregulated under heat stress. Conversely, several genes, particularly CnNF-YA2, CnNF-YB3, and CnNF-YB4, exhibited dynamic transcriptional responses to Vibrio parahaemolyticus exposure. These findings enhance our understanding of the evolutionary trajectory and functional diversification of the NF-Y gene family in bivalves, laying a theoretical foundation for future research on thermal adaptation, immune regulation, and molecular breeding in scallops.

Animals↗

PubMedDate not supplied

The relationship of family dynamics/social support to patient functioning in IDDM patients on intensive insulin therapy.

A 6 month pilot study was conducted to examine the relationship between family dynamics/social support and patient functioning in diabetic patients on intensive insulin therapy. Intensified therapy was associated with improvements in the DUHP symptom score, MHI psychological well-being score, and in the DUHP social functioning score. In diabetic patients, regardless of therapy, extreme family dynamics were correlated with higher DUHP symptom scores and lower MHI psychological well-being scores at the initial measurement time. However, over the 6 month study period, extreme family dynamics were predictive of improvements in the DUHP symptoms score and in the quality of friendships in diabetic patients on intensive insuline therapy. In diabetic patients, regardless of therapy, higher levels of social support correlated with higher levels of psychological and social functioning at the initial measurement time, and with improvements in quality of family life over the 6 month measurement time. Higher social support was also associated with improvements in quantity of friends and the DUHP social functioning score in diabetic patients on intensive insulin therapy. The study also generated empiric support for co-evolutionary models of disease states/family dynamics/treatment systems by showing that 6 month changes in family dynamics were predicted by the initial FACES adaptability measure and the initial mean monthly glucose value. Intensified therapy predicted lower family cohesion and more family rigidity over the 6 month study period. These findings also suggest, when combined with the result that diabetic patients from more cohesive families experienced a rise in monthly mean glucose values, that some diabetic patients may become trapped in a vicious cycle which perpetuates poor glucose control and extreme family dynamics.

Adaptation, Psychological↗

PubMed2026

Genome-wide characterization of the bZIP gene family in Rattus norvegicus and expression profiling analysis during brain development.

BACKGROUND: The brown rat (Rattus norvegicus) serves as a cornerstone model organism in biomedical research, particularly for understanding physiological homeostasis and stress responses. The basic leucine zipper (bZIP) transcription factor family is a pivotal regulatory network involved in growth, organogenesis, and neurodevelopment. Despite its importance, a systematic characterization of the bZIP gene family in rats has remained elusive. RESULTS: In this study, we performed a genome-wide identification of 61 RnbZIP genes, which were categorized into 10 distinct subfamilies based on phylogenetic relationships and chromosomal localization. Structural analysis revealed conserved motif arrangements within subfamilies, while collinearity analysis identified significant gene duplication events-predominantly tandem and segmental duplications-that have driven the evolutionary expansion of the RnbZIP family. Quantitative analysis showed that members within the same subfamily shared 45%-92% sequence similarity (calculated using the BLOSUM62 scoring matrix), and all duplicated gene pairs underwent strong purifying selection (Ka/Ks < 1). Comparative genomics across seven rodent species further underscored the evolutionary conservation and divergence of these factors. Expression profiling across diverse organs and brain developmental stages indicated that RnbZIP genes exhibit high tissue specificity. Notably, 10 candidate genes, including RnbZIP01, RnbZIP02, and RnbZIP08, demonstrated dynamic expression patterns during brain maturation, suggesting their essential roles in neurodevelopmental processes. CONCLUSIONS: Our findings provide a comprehensive structural and evolutionary framework for the RnbZIP gene family, highlighting their potential regulatory functions in rat organogenesis and brain development. This study establishes a valuable resource for further functional characterization of specific bZIP members in mammalian neurological systems.

Animals↗

PubMed2026

Discovery and evolution of endogenous retroviruses in the genome of crab-eating macaque (Macaca fascicularis).

Endogenous retroviruses (ERVs) are a dynamic and biologically significant component of vertebrate genomes, with integration events spanning deep evolutionary time. The crab-eating macaque (Macaca fascicularis) is an important non-human primate model for biomedical research because of its close phylogenetic relationship to humans and its conservation status as an endangered species. However, the ERV complement of its genome has not been systematically characterized. Using the current highest-quality chromosome-level genome assembly for this species, we performed a genome-wide, homology-based survey of relatively intact ERV proviruses in M. fascicularis. We identified 106 proviral loci distributed across all chromosomes. Phylogenetic reconstruction based on conserved reverse transcriptase domains classified these elements into β-, γ-, and unclassified lineages, with β- and γ-retroviral lineages predominating. LTR divergence-based dating indicated that these proviruses represent multiple waves of historical retroviral activity and span a broad range of integration ages. This curated dataset provides a high-confidence reference set for investigating the evolutionary history and genomic impact of preserved ERV proviruses in an endangered primate model; however, it does not include degraded ERV fragments or solo LTRs.

Animals↗

PubMed1989

Genetic control of the immune repertoire in nematode infections.

Mammals vary considerably, both within and between species, in the way in which their innate and adaptive immune systems respond to infections. An understanding of the processes involved in such variability will not only contribute to explaining heterogeneity in susceptibility and pathology, but will also be relevant to vaccination. This will be particularly important for the new generation of vaccines that are likely to be composed of one or a few cloned or synthesized antigens. For helminth infections, this could have particular relevance to hypersensitivity responses. The adaptive immune response is fundamentally constrained by the genetic constitution of an individual, and the need to avoid reactivity to self. This will have important implications for the dynamic relationship between host defences and parasite evasion mechanisms at both physiological and evolutionary levels. In this review, Malcolm Kennedy examines the genetic control of the specificity of the immune response to nematode infections, and in particular, the role of the major histocompatibility complex.

Journal Article↗

PubMed2006

Dynamic expression of the LIM-homeodomain gene Lhx15 through larval brain development of the sea lamprey (Petromyzon marinus).

LIM-homeodomain genes encode a family of transcription factors with highly conserved roles in the patterning and regionalisation of the vertebrate brain. The expression of one of those genes, Lhx15, in the embryonic lamprey brain, characterises precise functional subdivisions. In order to analyse the non-embryonic development of the lamprey brain, we chose this gene to perform in situ hybridisations in Petromyzon marinus larvae of different ages. We demonstrate the usefulness of Lhx15 to follow the development and morphogenesis of brain structures and show the dynamical expression of this gene through time. Furthermore, we provide evidence for the evolutionary conservation of the expression of this gene in the spinal cord, notochord and urogenital system.

Animals↗

PubMed2005

Spatial dynamics and molecular ecology of North American rabies.

Rabies, caused by a single-stranded RNA virus, is arguably the most important viral zoonotic disease worldwide. Although endemic throughout many regions for millennia, rabies is also undergoing epidemic expansion, often quite rapid, among wildlife populations across regions of Europe and North America. A current rabies epizootic in North America is largely attributable to the accidental introduction of a particularly well-adapted virus variant into a naive raccoon population along the Virginia/West Virginia border in the mid-1970s. We have used the extant database on the spatial and temporal occurrence of rabid raccoons across the eastern United States to construct predictive models of disease spread and have tied patterns of emergence to local environmental variables, genetic heterogeneity, and host specificity. Rabies will continue to be a remarkable model system for exploring basic issues in the temporal and spatial dynamics of expanding infectious diseases and examining ties between disease population ecology and evolutionary genetics at both micro- and macro-evolutionary time scales.

Algorithms↗

PubMed2004

Genetic diversity and evolution of hepatitis C virus--15 years on.

In the 15 years since the discovery of hepatitis C virus (HCV), much has been learned about its role as a major causative agent of human liver disease and its ability to persist in the face of host-cell defences and the immune system. This review describes what is known about the diversity of HCV, the current classification of HCV genotypes within the family Flaviviridae and how this genetic diversity contributes to its pathogenesis. On one hand, diversification of HCV has been constrained by its intimate adaptation to its host. Despite the >30 % nucleotide sequence divergence between genotypes, HCV variants nevertheless remain remarkably similar in their transmission dynamics, persistence and disease development. Nowhere is this more evident than in the evolutionary conservation of numerous evasion methods to counteract the cell's innate antiviral defence pathways; this series of highly complex virus-host interactions may represent key components in establishing its 'ecological niche' in the human liver. On the other hand, the mutability and large population size of HCV enables it to respond very rapidly to new selection pressures, manifested by immune-driven changes in T- and B-cell epitopes that are encountered on transmission between individuals with different antigen-recognition repertoires. If human immunodeficiency virus type 1 is a precedent, future therapies that target virus protease or polymerase enzymes may also select very rapidly for antiviral-resistant mutants. These contrasting aspects of conservatism and adaptability provide a fascinating paradigm in which to explore the complex selection pressures that underlie the evolution of HCV and other persistent viruses.

Biological Evolution↗

PubMed1986

An analysis of migratory systems: 2. Operational framework.

"This is the second in a series of three interrelated papers which aim to combine evolutionary migration models with stochastic utility theory. The first paper dealt with migratory dynamics. Here the details are given of a choice model, established by McFadden, which can be used in conjunction with migratory dynamics thus providing an explicit link between the macroproperties of the population system and human behaviour. First, the structure of transition probabilities is derived under a two-level decision to migrate. An argument is then given about the empirical form of these probabilities, and the discussion closes with a method which can be used for their maximum likelihood estimation."

Behavior↗

PubMed1990

Quantum mechanics and cellular information processing: the self-assembly paradigm.

Biological cells have greater information processing efficiency than the programmable computers used to model them. In part this is due to the larger number of interactions that can contribute to function. General arguments suggest that systems in which quantum features play a prominent role are more powerful than classical physical-dynamical analogs. A hypothetical model, involving macromolecular self-assembly, is used to illustrate how the parallelism inherent in the quantum mechanical wave function could play a role in cellular pattern processing. Signals impinging on the external membrane of the cell trigger the release of specifically shaped macromolecules. These aggregate into a mosaic shape features that reflect different groupings of the signal input patterns. The shape features are in turn read out and connected to effector actions by adaptor molecules. The self-assembly model fits into a more general hierarchical scheme of biological information processing in which macroscopic signals are transduced to mesoscopic and then microphysical representations, processed largely at the microphysical level, and then amplified for macroscopic action. The physical dynamics are controlled by proteins and other macromolecules that are molded through the evolutionary process of variation and selection. The organizational requirements for evolutionary moldability and for efficient information processing function are completely consistent. They include high dimensionality, multiplicity of weak interactions, and hierarchical-compartmental structure.

Biological Evolution↗