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PubMed2026

Retrotransposon activation during spermatogenesis achieves massive ecDNA biogenesis but rare integration.

Retrotransposon mobilization in germline cells enables the rewriting of genetic information to drive genome innovation, species evolution, and adaptation through the generation of de novo mutations. However, uncontrolled mobilization can cause DNA breaks and genome instability, often leading to sterility. How retrotransposon mobilization that can be retained for genome evolution persists despite negative outcomes of retrotransposon activity remains poorly understood. Here, we used Drosophila spermatogenesis as a model to investigate retrotransposon mobilization dynamics. Although many retrotransposon families are transcriptionally active, we found that the LTR retrotransposon nomad completes the full mobilization cascade (including mRNA export, protein translation, and reverse transcription) to produce double-stranded DNA (dsDNA) the most efficiently. Strikingly, despite successfully generating dsDNA, nomad rarely achieves genomic reintegration. Instead, its newly synthesized DNA predominantly forms extrachromosomal circular DNA (ecDNA). These findings show that retrotransposon-derived DNA largely remains as ecDNA. This could prevent widespread genomic integration during spermatogenesis, potentially preserving genome stability with the presence of limited retrotransposon activity.

Animals↗
PubMed2002

Structure, form, and function of flight in engineering and the living world.

By combining appearance and behavior in animals with physical laws, we can get an understanding of the adaptation and evolution of various structures and forms. Comparisons can be made between animal bodies and various technical constructions. Technical science and theory during the latest decades have resulted in considerable insight into biological adaptations, but studies on structures, forms, organs, systems, and processes in the living world, used in the right way, have also aided the engineer in finding wider and better solutions to various problems, among them in the design of micro-air vehicles (MAVs). In this review, I discuss the basis for flight and give some examples of where flight engineering and nature have evolved similar solutions. In most cases technology has produced more advanced structures, but sometimes animals are superior. I include how different animals have solved the problem of producing lift, how animal wings meet the requirements of strength and rigidity, how wing forms are adapted to various flight modes, and how flight kinematics are related to flight behavior and speed. The dynamics of vorticity is summarized. There are a variety of methods for the determination of flight power; it has been estimated adequately by lifting-line theory, by physiological measurements, and from mass loss and food intake. In recent years alternative methods have been used, in which the mechanical power for flight is estimated from flight muscle force used during the downstroke. Refinements of these methods may create new ways of estimating flight power more accurately. MAVs operate at the same Reynolds numbers as large insects and small birds and bats. Therefore, studies on animal flight are valuable for MAV design, which is discussed here.

Adaptation, Biological↗
PubMed2006

Studying phenotypic evolution using multivariate quantitative genetics.

Quantitative genetics provides a powerful framework for studying phenotypic evolution and the evolution of adaptive genetic variation. Central to the approach is G, the matrix of additive genetic variances and covariances. G summarizes the genetic basis of the traits and can be used to predict the phenotypic response to multivariate selection or to drift. Recent analytical and computational advances have improved both the power and the accessibility of the necessary multivariate statistics. It is now possible to study the relationships between G and other evolutionary parameters, such as those describing the mutational input, the shape and orientation of the adaptive landscape, and the phenotypic divergence among populations. At the same time, we are moving towards a greater understanding of how the genetic variation summarized by G evolves. Computer simulations of the evolution of G, innovations in matrix comparison methods, and rapid development of powerful molecular genetic tools have all opened the way for dissecting the interaction between allelic variation and evolutionary process. Here I discuss some current uses of G, problems with the application of these approaches, and identify avenues for future research.

Biological Evolution↗
PubMed2000

Statistical methods for detecting molecular adaptation.

The past few years have seen the development of powerful statistical methods for detecting adaptive molecular evolution. These methods compare synonymous and nonsynonymous substitution rates in protein-coding genes, and regard a nonsynonymous rate elevated above the synonymous rate as evidence for darwinian selection. Numerous cases of molecular adaptation are being identified in various systems from viruses to humans. Although previous analyses averaging rates over sites and time have little power, recent methods designed to detect positive selection at individual sites and lineages have been successful. Here, we summarize recent statistical methods for detecting molecular adaptation, and discuss their limitations and possible improvements.

Journal Article↗
PubMed2026

Comparative Genomics Reveals Convergent Evolution Between Avivorous Bats (Ia io and Nyctalus aviator).

Investigating the genetic basis of dietary specialization can provide insights into the evolution of niche breadth. In this study, we employed comparative genomics to investigate the adaptive mechanisms enabling two bat species (Nyctalus aviator and Ia io) to shift from insectivory to seasonal bird consumption (avivorous bats). Our findings revealed adaptation related to immune response and lipid metabolism in avivorous bat species. Avivorous bats exhibit strong positive selection and convergent evolution in immune-related genes, which are under heightened selective pressure compared to those of non-avivorous bats. These species also display significantly fewer endogenous retroviral elements. These findings emphasized the significance of immune-driven adaptive evolution in avivory. Additionally, our results showed that the dietary evolution of avivorous bats is accompanied by convergent evolution associated with the lipid metabolism. Notably, CEPT1, the upstream gene required for the activation of the PPAR pathway, underwent positive selection and convergence, which may have affected lipid metabolism. These adaptations may enable avivorous bat species to face the challenge of immune response and nutrition during dietary niche expansion. These findings not only provide comprehensive insights into the adaptive evolution driving the unique diet of avivorous bats but also offered novel perspectives on the molecular mechanisms underlying ecological niche evolution in a dietary context.

Animals↗
PubMed2004

Pleiotropy as a mechanism to stabilize cooperation.

Most genes affect many traits. This phenomenon, known as pleiotropy, is a major constraint on evolution because adaptive change in one trait may be prevented because it would compromise other traits affected by the same genes. Here we show that pleiotropy can have an unexpected effect and benefit one of the most enigmatic of adaptations--cooperation. A spectacular act of cooperation occurs in the social amoeba Dictyostelium discoideum, in which some cells die to form a stalk that holds the other cells aloft as reproductive spores. We have identified a gene, dimA, in D. discoideum that has two contrasting effects. It is required to receive the signalling molecule DIF-1 that causes differentiation into prestalk cells. Ignoring DIF-1 and not becoming prestalk should allow cells to cheat by avoiding the stalk. However, we find that in aggregations containing the wild-type cells, lack of the dimA gene results in exclusion from spores. This pleiotropic linkage of stalk and spore formation limits the potential for cheating in D. discoideum because defecting on prestalk cell production results in an even greater reduction in spores. We propose that the evolution of pleiotropic links between cheating and personal costs can stabilize cooperative adaptations.

Animals↗
PubMed2003

Evolution of phage with chemically ambiguous proteomes.

BACKGROUND: The widespread introduction of amino acid substitutions into organismal proteomes has occurred during natural evolution, but has been difficult to achieve by directed evolution. The adaptation of the translation apparatus represents one barrier, but the multiple mutations that may be required throughout a proteome in order to accommodate an alternative amino acid or analogue is an even more daunting problem. The evolution of a small bacteriophage proteome to accommodate an unnatural amino acid analogue can provide insights into the number and type of substitutions that individual proteins will require to retain functionality. RESULTS: The bacteriophage Qbeta initially grows poorly in the presence of the amino acid analogue 6-fluorotryptophan. After 25 serial passages, the fitness of the phage on the analogue was substantially increased; there was no loss of fitness when the evolved phage were passaged in the presence of tryptophan. Seven mutations were fixed throughout the phage in two independent lines of descent. None of the mutations changed a tryptophan residue. CONCLUSIONS: A relatively small number of mutations allowed an unnatural amino acid to be functionally incorporated into a highly interdependent set of proteins. These results support the 'ambiguous intermediate' hypothesis for the emergence of divergent genetic codes, in which the adoption of a new genetic code is preceded by the evolution of proteins that can simultaneously accommodate more than one amino acid at a given codon. It may now be possible to direct the evolution of organisms with novel genetic codes using methods that promote ambiguous intermediates.

Allolevivirus↗
PubMed2005

Disturbance induces the contrasting evolution of reinforcement and dispersiveness in directed and random movers.

Spatial models commonly assume that dispersal rates are constant across individuals and environments and that movement directions are unbiased. These random-movement assumptions are inadequate to capture the range of dispersal behaviors revealed in diverse case studies. We examine an alternative assumption of directed movement, in which dispersal is a conditional and directional response by individuals to varying environmental conditions. Specifically, we assume individuals bias their movements to climb spatial fitness gradients. We compare the consequences of random and directed movement for local adaptation, the evolution of dispersal, and the reinforcement process. The implications of each movement strategy depend on the nature of environmental disturbance, and we examine the outcomes for undisturbed environments and with uncorrelated and autocorrelated disturbances. Both movement strategies offer advantages over sedentary life histories by allowing colonization of suitable habitats. However, random movement eventually becomes costly in stable environments because it inhibits local adaptation. In contrast, directed movement accelerates local adaptation. In disturbed environments, random movement offers bet-spreading advantages by distributing offspring across habitats. Despite being a more targeted strategy, an intermediate amount of directed movement provides similar bet-spreading benefits. These fitness consequences have implications for the evolution of dispersal. Dispersiveness is lost by random movers in undisturbed environments, is maintained in polymorphism with infrequent disturbances, and evolves when disturbances are uncorrelated. Directed movement becomes selectively neutral in the absence of disturbance, evolves when disturbances are autocorrelated, and is maintained in polymorphism with uncorrelated disturbances. Disturbance also determines the outcome of the reinforcement process for each strategy. For example, directed movers show no progress toward reinforcement in undisturbed environments, evolve random mating with uncorrelated disturbances, and can evolve assortative mating in infrequently disturbed environments.

Animals↗
PubMed1985

Trends in the functional morphology and sensorimotor control of feeding behavior in salamanders: an example of the role of internal dynamics in evolution.

Organisms are self-producing and self-maintaining, or "autopoietic" systems. Therefore, the course of evolution and adaptation of an organism is strongly determined by its own internal properties, whatever role "external" selection may play. The internal properties may either act as constraints that preclude certain changes or they open new pathways: the organism canalizes its own evolution. As an example the evolution of feeding mechanisms in salamanders, especially in the lungless salamanders of the family Plethodontidae, is discussed. In this family a large variety of different feeding mechanisms is found. The authors reconstruct this evolutionary process as a series of "bifurcation points" of either constraints or opportunities forming a sequence of preconditions for the formation of a high-speed projectile tongue characteristic of tropical salamanders. Furthermore, it is shown how parallel evolution of seemingly unrelated domains within an organism such as respiratory physiology, life history biology and pattern of ontogeny has rather direct relevance to the feeding biology, thus demonstrating that organisms always evolve as wholes.

Animals↗
PubMed1995

Molecular evolution of the duplicated Amy locus in the Drosophila melanogaster species subgroup: concerted evolution only in the coding region and an excess of nonsynonymous substitutions in speciation.

From the analysis of restriction maps of the Amy region in eight sibling species belonging to the Drosophila melanogaster species subgroup, we herein show that the patterns of duplication of the Amy gene are almost the same in all species. This indicates that duplication occurred before speciation within this species subgroup. From the nucleotide sequence data, we show a strong within-species similarity between the duplicated loci in the Amy coding region. This is in contrast to a strong similarity in the 5' and 3' flanking regions within each locus (proximal or distal) throughout the species subgroup. This means that concerted evolution occurred only in the Amy coding region and that differentiated evolution between the duplication occurred in the flanking regions. Moreover, when comparing the species, we also found a significant excess of nonsynonymous substitutions. In particular, all the fixed substitutions specific to D. erecta were found to be nonsynonymous. We thus conclude that adaptive protein evolution occurred in the lineage of D. erecta that is a "specialist" species for host plants and probably also occurs in the process of speciation in general.

Amino Acid Sequence↗
PubMed2004

Allee effects, immigration, and the evolution of species' niches.

Theoretical studies of adaptation to sink environments (with conditions outside the niche requirements of a species) have shown that immigration from source habitats can either facilitate or inhibit local adaptation. Here, we examine the influence of immigration on the evolution of local adaptation, given an Allee effect (i.e., at low densities, absolute fitness increases with population density). We consider a deterministic model for evolution at a haploid locus, and a stochastic individual-based model for evolution of a quantitative trait, and several kinds of Allee effects. We demonstrate that increased immigration can greatly facilitate adaptive evolution in the sink; with greater immigration, local population sizes rise, and because of the Allee effect, there is a positive indirect effect of immigration on local fitness. This makes it easier for alleles of modest effect to be captured by natural selection, transforming the sink into a locally adapted population that can persist without immigration.

Adaptation, Biological↗
PubMed1999

The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes.

Angiosperms have dominated the Earth's vegetation since the mid-Cretaceous (90 million years ago), providing much of our food, fibre, medicine and timber, yet their origin and early evolution have remained enigmatic for over a century. One part of the enigma lies in the difficulty of identifying the earliest angiosperms; the other involves the uncertainty regarding the sister group of angiosperms among extant and fossil gymnosperms. Here we report a phylogenetic analysis of DNA sequences of five mitochondrial, plastid and nuclear genes (total aligned length 8,733 base pairs), from all basal angiosperm and gymnosperm lineages (105 species, 103 genera and 63 families). Our study demonstrates that Amborella, Nymphaeales and Illiciales-Trimeniaceae-Austrobaileya represent the first stage of angiosperm evolution, with Amborella being sister to all other angiosperms. We also show that Gnetales are related to the conifers and are not sister to the angiosperms, thus refuting the Anthophyte Hypothesis. These results have far-reaching implications for our understanding of diversification, adaptation, genome evolution and development of the angiosperms.

Biological Evolution↗
PubMed2003

[Relationships between plant reproductive strategy and disturbance].

Plant reproductive strategy in life history is related to plant adaptation or evolution, ecosystem degradation or restoration, and biodiversity conservation, which are the components of theoretic and applied ecological studies. In this article, several issues concerning the relationships between plant reproductive strategy in life history and disturbance, including Grime's classification of plant reproductive strategies, adaptations of plant vegetative reproduction to disturbances, adaptations of seed morphological traits to disturbance, roles of soil seed bank in disturbance adaptation, and dispersal and germination adaptation of diaspores to disturbance, were briefly reviewed. China's study on relationships between plant reproductive strategy in life history and disturbance in arid zone was also reviewed and discussed.

Ecosystem↗
PubMed2024

Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones.

Cancer progression is an evolutionary process driven by the selection of cells adapted to gain growth advantage. We present a formal study on the adaptation of gene expression in subclonal evolution. We model evolutionary changes in gene expression as stochastic Ornstein-Uhlenbeck processes, jointly leveraging the evolutionary history of subclones and single-cell expression data. Applying our model to sublines derived from single cells of a mouse melanoma revealed that sublines with distinct phenotypes are underlined by different patterns of gene expression adaptation, indicating non-genetic mechanisms of cancer evolution. Sublines previously observed to be resistant to anti-CTLA4 treatment showed adaptive expression of genes related to invasion and non-canonical Wnt signaling, whereas sublines that responded to treatment showed adaptive expression of genes related to proliferation and canonical Wnt signaling. Our results suggest that clonal phenotypes emerge as the result of specific adaptivity patterns of gene expression. A record of this paper's transparent peer review process is included in the supplemental information.

Animals↗
PubMed1989

New approaches to structural evolution of limb bones in primates.

Structural analysis of primate limb bones using engineering beam theory can reduce complex biological forms to a few readily interpretable and functionally relevant parameters. Several methods of obtaining and analyzing these structural parameters are described, including computed tomography, multiple plane radiography, photon absorptiometry, and automated digital analysis. Examples of applications of these data to problems in primate adaptation and evolution include improved estimation of body mass in fossil species, investigation of relative fore- and hindlimb mechanical loadings ('dominance'), and study of more subtle within and between species differences in behavior as reflected in variations in limb bone shape. In addition, it is shown that combined analyses of diaphyseal and articular structure can provide information on aspects of structural evolution of primate limb bones not evident from independent analysis of either type of characteristic alone.

Animals↗
PubMed1991

Evolution in molecular structure and adaptive variance in metabolism.

1. A hypothesis is advanced to the effect that all metabolites, even minor ones, are expressed as a result of stimuli and are directed against or support actions on receptor systems. 2. In particular the hypothesis emphasizes the dynamic character of the secondary metabolite pattern as a function of physiological or environmental conditions and that the variations observed reflect the evolution of receptors. 3. Predictions based on this principle are experimentally verifiable. 4. The hypothesis has major implications in the entire area of life sciences.

Biological Evolution↗
PubMed2000

Canalization as a non-genetic source of adaptiveness during morphogenesis: experimental evidence from analysis of reproductive development in Sorghum bicolor.

In Sorghum bicolor, perturbations in reproductive development observed following salt-treatment also influence progeny grown in the absence of NaCl. However, a developmental reversion of these modifications may be observed throughout two successive generations. This response, termed canalization, does not spontaneously occur following growth in the absence of NaCl, but is triggered by the level of perturbation in parental expression of reproductive characters. Moreover, canalization is not specific to the perturbed character, but it includes modifications in reproductive development as a whole. A decrease in developmental variability coincides with amplitude of the developmental reversion. This phenomenon is interpreted as an evidence for orientation of the developmental process towards the lowest free-energy state of the 'epigenetic landscape'. Involvement of this phenomenon of canalization in developmental stability, adaptiveness, and evolution is discussed. Moreover, these results point to the need for a posteriori methods of investigations in order to analyze self-organized transformations in biological systems.

Adaptation, Physiological↗