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PubMed1980

Regulatory gene adaptation: an evolutionary model.

There is increasing support for the notion that changes in regulatory loci have played a major role in eukaryotic evolution. Assuming a model of genetic regulation based upon presently accepted views of the organisation of the eukaryotic genome and basic models of evolutionary genetics, one can provide a context for speculation about the advantages and disadvantages of adaptation via regulatory genes. As additional information is obtained on particular regulatory systems, the evolutionary genetic model can be modified and expanded.

Adaptation, Biological↗

PubMed2026

Interpreting cancer genetics through a two-step "evolutionary cascade hypothesis": bridging neutral and selective perspectives.

BACKGROUND: DNA mutations are the fundamental engines of cancer, driving its initiation and progression. The forces that fuel malignancy are also the architects of evolution, shaping life through genetic variations. Mutations, in fact, can emerge naturally from endogenous processes, such as oxidative DNA damage or errors in replication, as well as induced by external factors, including cosmic radiation and chemical carcinogens. MAIN BODY: A key question in cancer research is whether tumor evolution is primarily governed by selective bottlenecks, neutral evolution, or dynamic genetic plasticity. In this work, we examine cancer as a disease driven by evolutionary processes rooted in fundamental biological requirements, including sustained proliferation and nutrient utilization. We hypothesize that the accumulation of mutations activates an evolutionary switch, enabling tumor cells to acquire an enhanced capacity for survival, adaptation, and growth at rates far exceeding typical evolutionary timescales. We propose the "evolutionary cascade hypothesis," a unifying framework that integrates these models into a coherent sequence. At its core lies the failure of DNA repair mechanisms, representing a critical transition in cancer progression. This shift marks the transition from an initial non-Darwinian, neutral phase to a Darwinian, more deterministic phase. CONCLUSIONS: As predictive models of tumor evolution advance through genomic big data and artificial intelligence-driven analysis, the future of cancer treatment may extend beyond targeting individual mutations to disrupting the underlying evolutionary mechanisms that sustain malignancy. This paradigm shift could redefine therapeutic strategies and ultimately improve patient outcomes.

Humans↗

PubMed2001

Genetic algorithm-based model of evolutionary dynamics of class II transposable elements.

We propose a new conceptual framework to study the dynamics of transposable elements. Based on a genetic algorithm, our model is designed as a self-organizing system. Our results show that transposable elements could emerge from a single endonuclease gene. The DNA repair mechanisms appear to condition the emergence success of class II TEs. Antagonist selective forces acting on transposable elements and their hosts induce by their opposition differences in the sequence evolution of the functional domains and of the copies.

Algorithms↗

PubMed2001

West Mediterranean islands (Corsica, Balearic islands, Sardinia) and the Basque population: contribution of HLA class I molecular markers to their evolutionary history.

The genetic structure of Balearic islands (Corsica and Sardinia), situated on the same trans-Mediterranean maritime routes and having very similar histories, were compared and their position among the neighbouring Caucasian populations was inferred. For this purpose, three HLA loci (HLA-A, -B and -Cw) were typed at the DNA level in these populations and the allelic and haplotypic frequencies were estimated. Because previous studies have shown common genetic features in the Sardinians and Basques, HLA-Cw molecular typing was also performed in a sample of French Basques in order to establish the haplotypic structure of this population for a more accurate comparison with the three others. By its allelic composition, the Corsican population has an intermediate position between the two other islander populations. Its close relationship with the Sardinian population, however, was clearly revealed by the phylogenetic analysis which also suggests a proximity with eastern Mediterranean peoples, whereas the Balearic islands are more narrowly related to Spain and western Europe. Peculiarities were observed in the distributions of some common haplotypes in the populations of the islands that confirm the results of the phylogenetic analysis and could be related to their history. Noteworthy is the presence of the HLA-A30-Cw*0501-B18 haplotype at frequencies approximately 2% in Corsica and the Balearic islands, yet the estimated frequencies of this haplotype are much lower than in the Sardinian and Basque populations.

Evolution, Molecular↗

PubMed2000

From genotype to phenotype: buffering mechanisms and the storage of genetic information.

DNA sequence variation is abundant in wild populations. While molecular biologists use genetically homogeneous strains of model organisms to avoid this variation, evolutionary biologists embrace genetic variation as the material of evolution since heritable differences in fitness drive evolutionary change. Yet, the relationship between the phenotypic variation affecting fitness and the genotypic variation producing it is complex. Genetic buffering mechanisms modify this relationship by concealing the effects of genetic and environmental variation on phenotype. Genetic buffering allows the build-up and storage of genetic variation in phenotypically normal populations. When buffering breaks down, thresholds governing the expression of previously silent variation are crossed. At these thresholds, phenotypic differences suddenly appear and are available for selection. Thus, buffering mechanisms modulate evolution and regulate a balance between evolutionary stasis and change. Recent work provides a glimpse of the molecular details governing some types of genetic buffering.

Animals↗

PubMed1993

[Molecular-genetic analysis of expression features of the evolutionary-conservative neurogene Nc73EF of Drosophila melanogaster].

Molecular-genetic analysis of the Nc (neural conserved) genome sequence of Drosophila melanogaster located at the position 73EF of Drosophila melanogaster was performed. The Nc73EF sequence was shown to be expressed in the nervous system of Drosophila. We constructed the restriction map of this sequence and revealed the main RNA-coding fragment in the 5'-3' orientation. The RNA-dot analysis data demonstrated that expression of the Nc73EF transcripts took place mainly in the nervous system. Hybridization with the human brain poly(A)+RNA confirmed the basic RNA-coding fragment to be evolutionary conservative. Southern blot analysis showed this fragment to be unique in the Drosophila genome. Northern blots detected three transcripts of this DNA fragment.

Animals↗

PubMed2001

Evolutionary self-organization of cell-free genetic coding.

Genetic encoding provides a generic construction scheme for biomolecular functions. This paper addresses the key problem of coevolution and exploitation of the multiple components necessary to implement a replicable genetic encoding scheme. Extending earlier results on multicomponent replication, the necessity of spatial structure for the evolutionary stabilization of the genetic coding system is established. An individual-based stochastic model of interacting molecules in three-dimensional space is presented that allows the evolution of genetic coding to be analyzed explicitly. A massively parallel configurable computer (NGEN) is used to implement the model, on the time scale of millions of generations, directly in electronic hardware. The spatial correlations between components of the genetic coding system are analyzed and found to be essential for evolutionary stability.

Animals↗

PubMed1991

An evolutionary perspective on salt, hypertension, and human genetic variability.

Natural selection for electrolyte conservation has likely been the norm throughout human evolutionary history. However, the current patterns of excessive dietary salt intake create the potential for salt overload. Under these conditions, hypertension may be considered an expected pathological response to an evolutionarily new constraint. The transatlantic Middle Passage may have created a genetic bottleneck for salt conservation in African-Americans. Although the initial consequences of this important historical event probably constricted genetic variability and further magnified the potential for salt-sensitive hypertension, the Middle Passage undoubtedly also served as a more generalized major source of environmental stress and may have stimulated subsequent hereditary diversity in the survivors of this holocaust and their descendants. Accelerated rates of mutation, genetic recombination, and transposable genetic elements in conjunction with enhanced opportunities for gene flow, new selective pressures, and drift have all contributed to the tremendous heterogeneity of contemporary African-Americans. It is unlikely that a single genetic event, even of the severity of the Middle Passage, can account comprehensively for the apparent susceptibility of this macroethnic group to high blood pressure and hypertension.

Biological Evolution↗

PubMed2002

Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models.

MOTIVATION: The information model chosen to store biological data affects the types of queries possible, database performance, and difficulty in updating that information model. Genetic sequence data for pharmacogenetics studies can be complex, and the best information model to use may change over time. As experimental and analytical methods change, and as biological knowledge advances, the data storage requirements and types of queries needed may also change. RESULTS: We developed a model for genetic sequence and polymorphism data, and used XML Schema to specify the elements and attributes required for this model. We implemented this model as an ontology in a frame-based representation and as a relational model in a database system. We collected genetic data from two pharmacogenetics resequencing studies, and formulated queries useful for analysing these data. We compared the ontology and relational models in terms of query complexity, performance, and difficulty in changing the information model. Our results demonstrate benefits of evolving the schema for storing pharmacogenetics data: ontologies perform well in early design stages as the information model changes rapidly and simplify query formulation, while relational models offer improved query speed once the information model and types of queries needed stabilize.

Algorithms↗

PubMed1996

Frequency of migrants and migratory activity are genetically correlated in a bird population: evolutionary implications.

Most migratory bird populations are composed of individuals that migrate and individuals that remain resident. While the role of ecological factors in maintaining this behavioral dimorphism has received much attention, the importance of genetic constraints on the evolution of avian migration has not yet been considered. Drawing on the recorded migratory activities of 775 blackcaps (Sylvia atricapilla) from a partially migratory population in southern France, we tested two alternative genetic models about the relationship between incidence and amount of migratory activity. The amount of migratory activity could be the continuous variable "underlying" the phenotypic expression of migratory urge, or, alternatively, the expression of both traits could be controlled by two separate genetic systems. The distributions of migratory activities in five different cohorts and the inheritance pattern derived from selective breeding experiments both indicate that incidence and amount of migratory activity are two aspects of one trait. Thus, all birds without measurable activity have activity levels at the low end of a continuous distribution, below the limit of expression or detection. The phenotypic dichotomy "migrant-nonmigrant" is caused by a threshold which may not be fixed but influenced both genetically and environmentally. This finding has profound implications for the evolution of migration: the transition from migratoriness to residency should not only be driven by selection favoring resident birds but also by selection for lower migratory activity. This potential for selection on two aspects, residency and migration distance, of the same trait may enable extremely rapid evolutionary changes to occur in migratory behavior.

Animals↗

PubMed1996

Selection by somatic signals: the advertisement of phenotypic state through costly intercellular signals.

We develop a model of intercellular signalling, to explore the possibility that the signals exchanged between cells within a body may be subject to many of the same evolutionary pressures as signals exchanged between individuals whose genetic interests conflict. Evolutionary signalling theory maintains that signals, to be reliable indicators of need, intention or quality must be more costly than would be required merely to transmit a message. Cost guarantees that poor quality individuals are less able to display the high magnitude signals produced by the higher quality individuals. Receivers have been favoured by natural selection to attend only to the costliest signals, and thereby acquire honest information from the signaller. Hence the extravagant, costly ornamentation found among males of many species, ensures that females can accurately choose among them on the basis of their qualities. However, because somatic cells are normally perfectly genetically related, and are often denied access to the germ line, there will be minimal genetic conflicts of interest. This appears to imply that reliable intercellular signals should be produced without the need for cost to ensure their reliability. Nevertheless, we show that whenever cells vary in their phenotypic qualities in ways relevant to the fitness of the body, and given that there exists a class of cell that remains "ignorant' of its phenotypic state, costly intercellular signalling will evolve as a form of quality control. Specifically, we show that given variation in the cell population, signal cost will aid the identification and removal of cells that over-represent their true phenotypic state, and which therefore could lower fitness. Cells that under-represent their state are simply outcompeted by other cells. The cells of a body employ signals in a variety of intercellular interactions, including the development of the nervous system, the formation of neuromuscular junctions, and during the establishment of the immune repetoire. In each of these cases, cells may employ costly signals to advertise their phenotypic quality to other cells, and we review the evidence in support of this hypothesis: in effect, the cells may possess a molecular counterpart to the peacock's tail.

Animals↗

PubMed2005

A non-stationary model for functional mapping of complex traits.

SUMMARY: Understanding the genetic control of growth is fundamental to agricultural, evolutionary and biomedical genetic research. In this article, we present a statistical model for mapping quantitative trait loci (QTL) that are responsible for genetic differences in growth trajectories during ontogenetic development. This model is derived within the maximum likelihood context, implemented with the expectation-maximization algorithm. We incorporate mathematical aspects of growth processes to model the mean vector and structured antedependence models to approximate time-dependent covariance matrices for longitudinal traits. Our model has been employed to map QTL that affect body mass growth trajectories in both male and female mice of an F2 population derived from the Large and Small mouse strains. The results from this model are compared with those from the autoregressive-based functional mapping approach. Based on results from computer simulation studies, we suggest that these two models are alternative to one another and should be used simultaneously for the same dataset.

Aging↗

PubMed2003

The evolution of transcriptional regulation in eukaryotes.

Gene expression is central to the genotype-phenotype relationship in all organisms, and it is an important component of the genetic basis for evolutionary change in diverse aspects of phenotype. However, the evolution of transcriptional regulation remains understudied and poorly understood. Here we review the evolutionary dynamics of promoter, or cis-regulatory, sequences and the evolutionary mechanisms that shape them. Existing evidence indicates that populations harbor extensive genetic variation in promoter sequences, that a substantial fraction of this variation has consequences for both biochemical and organismal phenotype, and that some of this functional variation is sorted by selection. As with protein-coding sequences, rates and patterns of promoter sequence evolution differ considerably among loci and among clades for reasons that are not well understood. Studying the evolution of transcriptional regulation poses empirical and conceptual challenges beyond those typically encountered in analyses of coding sequence evolution: promoter organization is much less regular than that of coding sequences, and sequences required for the transcription of each locus reside at multiple other loci in the genome. Because of the strong context-dependence of transcriptional regulation, sequence inspection alone provides limited information about promoter function. Understanding the functional consequences of sequence differences among promoters generally requires biochemical and in vivo functional assays. Despite these challenges, important insights have already been gained into the evolution of transcriptional regulation, and the pace of discovery is accelerating.

Animals↗

PubMed2004

Phylogenetic analysis based on genome-scale metabolic pathway reaction content.

Phylogenetic classifications based on single genes such as rRNA genes do not provide a complete and accurate picture of evolution because they do not account for evolutionary leaps caused by gene transfer, duplication, deletion and functional replacement. Here, we present a whole-genome-scale phylogeny based on metabolic pathway reaction content. From the genome sequences of 42 microorganisms, we deduced the metabolic pathway reactions and used the relatedness of these contents to construct a phylogenetic tree that represents the similarity of metabolic profiles (relatedness) as well as the extent of metabolic pathway similarity (evolutionary distance). This method accounts for horizontal gene transfer and specific gene loss by comparison of whole metabolic subpathways, and allows evaluation of evolutionary relatedness and changes in metabolic pathways. Thus, a tree based on metabolic pathway content represents both the evolutionary time scale (changes in genetic content) and the evolutionary process (changes in metabolism).

Archaea↗

PubMed1999

Lineage selection and the evolution of multistage carcinogenesis.

A wide array of proto-oncogenes and tumour suppressor genes are involved in the prevention of cancer. Each form of cancer requires mutations in a characteristic group of genes, but no single group controls all cancers. This lack of generality shows that the control of cancer is not an ancient, fixed property of cells. By contrast, it supports a dynamic evolutionary model, whereby genetic controls over unregulated cell growth are recruited independently through evolutionary time in different tissues within different taxa. The complexity of this genetic control can be predicted from a population genetic model of lineage selection driven by the detrimental fitness effects of cancer. Cancer occurs because the genetic control of cell growth is vulnerable to somatic mutations (or 'hits'), particularly in large, continuously dividing tissues. Thus, compared to small rodents, humans must have evolved more complex genetic controls over cell growth in at least some of their tissues because of their greater size and longevity; an expectation relevant to the application of mouse data to humans. Similarly, the 'two-hit' model so successfully applied to retinoblastoma, which originates in a small embryonic tissue, is unlikely to be generally applicable to other human cancers; instead, more complex scenarios are expected to dominate, with complexity depending upon a tissue's size and its pattern of proliferation.

Animals↗

PubMed1996

Interpreting genetic variability: the effects of shared evolutionary history.

Data from different individuals at a single locus are positively correlated because of the shared genealogy of the sampled genes. This paper illustrates the qualitative effects on genealogical trees of assumptions about population demography, and it considers the consequences for genetic variability. An understanding of these effects is invaluable in the interpretation of data and for inferences about population history. In contrast, traditional genetic measures of diversity and approximation methods do not seem well suited for addressing the problem.

Animals↗

PubMed1996

Evolutionary adaptationism: another biological approach to criminal and antisocial behaviour.

Although in a sense "genetic', the conceptual framework of evolutionary psychology, behavioural ecology and sociobiology is distinct from that of behaviour genetics. Considerable confusion has resulted from failures to recognize the distinctions. These disciplines are primarily concerned with the characterization of evolved adaptations, which are usually species-typical and environmentally contingent, so theory and research in these fields mainly concerns environmental rather than genetic sources of behavioural variation. Heritable behavioural variation is in general neither predicted by nor supportive of adaptationist theories. One might even say that substantial heritability of an apparently consequential attribute is a datum that challenges the tenets of adaptationism. Behaviour genetics and evolutionary adaptationism have had only limited mutual influence, but increasing knowledge of the processes by which genotypes affect behavioural phenotypes should facilitate development of a more synthetic approach.

Adaptation, Psychological↗

PubMed2006

Tandem repetitive D domains of the sperm ligand zonadhesin evolve faster in the paralogue than in the orthologue comparison.

Gene duplication is regarded as an important evolutionary mechanism creating genetic and phenotypic novelty. At the same time, the evolutionary mechanisms following gene duplication have been a subject of much debate. Here we analyze the sequence evolution of zonadhesin, a mammalian sperm ligand that binds to the oocyte zona pellucida in a species-specific manner. In pig, rabbit, and primates, precursor zonadhesin comprises, among others, one partial and four complete tandem repetitive D domains. The mouse precursor is distinguished by 20 additional partial D3 domains consisting of 120 amino acids each. This gene structure allows sequence comparison in both paralogues and orthologues. Detailed sequence analysis reveals that D domains evolve faster across paralogues than orthologues. Moreover, at the codon level, partial D3 paralogues of mouse show evidence of positive selection, whereas the corresponding orthologues do not. Individual posttranslational motif patterns and positive selection point to neofunctionalization of partial D3 paralogues of mouse, rather than subfunctionalization. However, as we found additional evidence for homogenization by partial gene conversion, sequence evolution of partial D3 paralogues of mouse might be better described as a combination of divergent and convergent evolution. So far, the divergence at the codon level has outbalanced the convergence at the level of smaller fragments. The probable driving force behind the evolutionary patterns observed is sexual selection. We finally discuss whether the functional determination influences the evolutionary regime acting on sperm ligands and egg receptors, respectively.

Amino Acid Motifs↗