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PubMed2026

Evolutionary Conservation and Reproductive Expression of ABC Transporter Genes in Two Sphenomorphus Skinks.

ATP-binding cassette (ABC) transporters represent one of the largest membrane protein superfamilies in vertebrates, playing essential roles in translocating diverse substrates across membranes. However, knowledge of ABC transporter genes in reptiles remains limited. In this study, we conducted a comprehensive genome-wide identification and characterization of the ABC gene family in oviparous Sphenomorphus incognitus and viviparous Sphenomorphus indicus. A total of 45 ABC genes were identified in each species and classified into seven subfamilies (ABCA-ABCG). Comparative and phylogenetic analyses revealed a generally conserved gene repertoire, with limited duplication events observed mainly in the ABCA and ABCG subfamilies, whereas other subfamilies (e.g., ABCE, ABCF, and ABCD) remained highly conserved. Interestingly, a lineage-specific duplication of ABCC2 was identified in lizards. Oviductal expression profiling revealed distinct temporal patterns of ABC gene expression across reproductive stages. Several genes, including ABCG1, ABCC3, and ABCD4, exhibited conserved expression trajectories across both species, suggesting shared transcriptional regulation. In contrast, ABCA1, ABCB1, and ABCG2 showed species-specific expression patterns, indicating regulatory divergence between the two lizard species. Overall, ABC gene expression was more dynamic in S. incognitus than in S. indicus. In summary, although the ABC transporter family is structurally conserved, it exhibits lineage-specific evolutionary changes and divergent transcriptional regulation in lizard oviducts. This study provides a foundation for understanding the diversity and regulation of ABC transporter genes in reptiles.

Animals↗
PubMed2000

Spatiotemporal reorganization of growth rates in the evolution of ontogeny.

Heterochrony, evolutionary changes in rate or timing of development producing parallelism between ontogeny and phylogeny, is viewed as the most common type of evolutionary change in development. Alternative hypotheses such as heterotopy, evolutionary change in the spatial patterning of development, are rarely entertained. We examine the evidence for heterochrony and heterotopy in the evolution of body shape in two clades of piranhas. One of these is the sole case of heterochrony previously reported in the group; the others were previously interpreted as cases of heterotopy. To compare ontogenies of shape, we computed ontogenetic trajectories of shape by multivariate regression of geometric shape variables (i.e., partial warp scores and shape coordinates) on centroid size. Rates of development relative to developmental age and angles between the trajectories were compared statistically. We found a significant difference in developmental rate between species of Serrasalmus, suggesting that heterochrony is a partial explanation for the evolution of body shape, but we also found a significant difference between their ontogenetic transformations; the direction of the difference between them suggests that heterotopy also plays a role in this group. In Pygocentrus we found no difference in developmental rate among species, but we did find a difference in the ontogenies, suggesting that heterotopy, but not heterochrony, is the developmental basis for shape diversification in this group. The prevalence of heterotopy as a source of evolutionary novelty remains largely unexplored and will not become clear until the search for developmental explanations looks beyond heterochrony.

Animals↗
PubMedDate not supplied

The cusp of evolution and development: a model of cichlid tooth shape diversity.

Tooth shape is a hallmark of repeated evolutionary radiations among cichlid fishes from East Africa. Cusp shape and number vary both within populations and among closely related species with different feeding behaviors and ecologies. Here, we use histology and scanning electron microscopy to chart the developmental trajectory of tooth shape differences in fishes from Lake Malawi. We demonstrate that species with bi- or tricuspid adult (replacement) teeth initially possess a first-generation unicuspid dentition. Notably, the timing of turnover from first-generation to replacement teeth differs among species and is correlated with feeding ecology. Next, we use field data for cichlid species with adult unicuspid, bicuspid, and tricuspid teeth to demonstrate a strong and positive relationship between the number of teeth in a row and tooth shape. We discuss cichlid tooth ontogeny in the context of morphogenetic models designed to explain the developmental basis of tooth shape variation in mammals. We suggest that the dramatic differences in cichlid dentitions can be explained by variation in the expression of common activators and inhibitors acting at multiple stages of odontogenesis.

Animals↗
PubMed2026

Deconstructing empirical fitness seascapes across scales of granularity.

The fitness landscape metaphor remains resonant in evolutionary theory and has facilitated the birth of newer concepts, like the fitness seascape, that consider the role of environmental context in shaping the dynamics of evolution. Since its emergence, the seascape has appeared in numerous studies examining how different and fluctuating environments shape evolutionary outcomes. Despite growing interest, we lack comprehensive examinations of how environmental context shapes features of fitness seascapes. In this study, we address this gap by deconstructing empirical fitness seascapes across scales of granularity: loci, locus interactions (epistasis), alleles, trajectories, and entire seascapes. For each, we examine how environmental context influences qualitative and quantitative aspects of seascapes, and find that they change appreciably, with patterns specific to individual systems of study. We also quantify how much each scale varies across environments, and find that certain scales tend to be more sensitive to context than others. In summary, we reflect on the implications of the seascape metaphor for the incorporation of environmental effects into theoretical population genetics, for understanding how the environment shapes evolution in disease systems, and for contemporary bioengineering efforts.

Genetic Fitness↗
PubMed2004

Adaptive evolution of social traits: origin, trajectories, and correlations of altruism and mobility.

Social behavior involves "staying and helping," two individual attributes that vary considerably among organisms. Investigating the ultimate causes of such variation, this study integrates previously separate lines of research by analyzing the joint evolution of altruism and mobility. We unfold the network of selective pressures and derive how these depend on physiological costs, eco-evolutionary feedbacks, and a complex interaction between the evolving traits. Our analysis highlights habitat saturation, both around individuals (local aggregation) and around unoccupied space (local contention), as the key mediator of altruism and mobility evolution. Once altruism and mobility are allowed to evolve jointly, three general insights emerge. First, the cost of mobility affects the origin of altruism, determining whether and how quickly selfishness is overcome. Second, the cost of altruism determines which of two qualitatively different routes to sociality are taken: an evolutionary reduction of mobility, resulting in higher habitat saturation, is either preceded or followed by the adaptive rise of altruism. Third, contrary to conventional expectations, a positive correlation between evolutionarily stable levels of altruism and mobility can arise; this is expected when comparing populations that evolved under different constraints on mobility or that differ in other life-history traits.

Adaptation, Physiological↗
PubMed2026

Stem Cell Differentiation Disperses Transcriptional Clusters via a Conserved Surface-Condensate Trajectory.

Stem cells exhibit exceptionally prominent transcriptional clusters, which dissolve with progressing differentiation. Although these clusters are assigned central roles in embryonic gene regulation, their formation and loss during differentiation remain poorly understood. This study reveals that these prominent clusters disperse along a conserved trajectory in mouse embryonic stem cells, fruit fly testes, and zebrafish embryos. Imaging and lattice simulations show that these clusters form via surface condensation on H3K27ac-marked super-enhancer regions, which act as genomic scaffolds. Upon differentiation, partial loss of these active epigenetic marks and transcription-driven unfolding lead to dispersal of the prominent clusters. The block copolymer-based lattice simulations explain this process as a conserved trajectory through a three-dimensional state space, governed by surface condensation principles that extend beyond canonical liquid-liquid phase separation. This work marks surface condensation as a biophysical mechanism for the dynamic organization of stem cell-specific transcriptional hubs and demonstrates evolutionary conservation in several organisms. By uncovering a conserved biophysical mechanism for transcriptional organization in development, our work illustrates how polymer properties can contribute to the control of cell identity and fate.

Animals↗
PubMed1997

What demographers can learn from fruit fly actuarial models and biology.

Historically demographers have viewed the results of actuarial studies of nonhuman species, particularly those on invertebrates such as fruit flies, as largely irrelevant to investigations on human populations. In this paper I present life table data from large scale studies on the Mediterranean fruit fly, and show that they provide important insights into fundamental aspects of mortality relevant to human populations: the trajectory of mortality at older ages, sex mortality differentials, the concept of maximal life span, and demographic heterogeneity and selection. An overriding theme of the paper is the need for demographers to acquire a heightened awareness of new developments in biology including areas such as evolutionary ecology, experimental demography, and molecular medicine.

Age Distribution↗
PubMed2004

Chaotic dynamics of a behavior-based miniature mobile robot: effects of environment and control structure.

To study the regularity and complexity of autonomous behavior, the flow of sensory information obtained in autonomous mobile robots under various conditions was analyzed as a complex system. Sensory information time series Xn was collected from a miniature mobile robot during free navigation, and plotted on the return map, the graph of X(n+tau) vs. Xn. The plot exhibited a characteristic trajectory, representing the regularity of the time series. Correlation integral and Lyapunov exponent analysis also showed properties of deterministic chaos; the presence of fractal dimension and positive Lyapunov exponent. Analysis of sensory information obtained in the robot with three different neural controllers revealed that the autonomous robot behaves in such a way that the flow of sensory information is governed by a deterministic rule, and this pattern is unique to each controller. Furthermore, the analysis in various environments exhibited that transitions from one trajectory to another on the return map occur during the course of autonomous behavior. The fractal and Lyapunov dimensions calculated in various conditions indicate that these dimension could be utilized to quantify the complexity of autonomous behavior and the relative difficulty of tasks. Analyses at different evolutionary stage revealed that behavioral performance correlates with fractal dimension. These studies using a miniature mobile robot that allowed to idealize the experimental conditions demonstrated firmly that the complex analysis could be utilized in evaluation and optimization of autonomous systems and the behavior.

Behavior↗
PubMedDate not supplied

Variation of tooth number in mammalian dentition: connecting genetics, development, and evolution.

A major question in modern biology is how gene mutations affect development and are translated into macroevolutionary changes in morphology. Variations in tooth number, a strategy used by many mammals to develop specialized dentitions, has been an important factor for species diversification. Changes in the number of teeth tend to occur in the reverse of the order teeth are formed during development, which also characterizes the general pattern of tooth loss observed during the evolution of placental mammals. To understand how changes at the molecular level affect the distinct stages of tooth development, we analyzed the ontogenesis of tooth growth arrest in sciurids and mice and in single and double knockout mutant mice. We show that the complexity of the genetic network that governs tooth development can change during ontogenetic trajectory, and these changes may be related to macroevolutionary changes. Furthermore, we show that the variation in tooth number in the affected members of human families bearing mutations in the MSX1 and PAX9 genes can help to understand how the genetic variations within a population can modulate evolutionary changes in dental patterning.

Animals↗
PubMed2003

Invited review: Theories of aging.

Several factors (the lengthening of the average and, to a lesser extent, of the maximum human life span; the increase in percentage of elderly in the population and in the proportion of the national expenditure utilized by the elderly) have stimulated and continue to expand the study of aging. Recently, the view of aging as an extremely complex multifactorial process has replaced the earlier search for a distinct cause such as a single gene or the decline of a key body system. This minireview keeps in mind the multiplicity of mechanisms regulating aging; examines them at the molecular, cellular, and systemic levels; and explores the possibility of interactions at these three levels. The heterogeneity of the aging phenotype among individuals of the same species and differences in longevity among species underline the contribution of both genetic and environmental factors in shaping the life span. Thus, the presence of several trajectories of the life span, from incidence of disease and disability to absence of pathology and persistence of function, suggest that it is possible to experimentally (e.g., by calorie restriction) prolong functional plasticity and life span. In this minireview, several theories are identified only briefly; a few (evolutionary, gene regulation, cellular senescence, free radical, and neuro-endocrineimmuno theories) are discussed in more detail, at molecular, cellular, and systemic levels.

Aging↗
PubMed2026

Archaic ancestry inference in imputed ancient human genomes.

When modern humans expanded from Africa into Eurasia, they interbred with archaic hominins such as Neanderthals and Denisovans. This introgression shaped human evolution, yet most insights have been gained from present-day genomes, leaving little known about how archaic variants evolved after interbreeding. Ancient genomes offer a direct view of this process, but low coverage and poor quality have limited their use. Recent advances in genotype imputation offer a way to overcome these challenges by reconstructing missing information from reference panels and recovering evolutionary signals from low-coverage data. Here, we show that imputation enables accurate detection and quantification of archaic introgression in ancient genomes, improves local archaic ancestry inference, and that regions of archaic ancestry are imputed with especially high accuracy. We further demonstrate that imputed genomes can reconstruct the trajectories of introgressed haplotypes, distinguish populations across time and geography, and identify both known and additional candidates for adaptive introgression.

Humans↗
PubMedDate not supplied

Early life events and their consequences for later disease: a life history and evolutionary perspective.

Biomedical science has little considered the relevance of life history theory and evolutionary and ecological developmental biology to clinical medicine. However, the observations that early life influences can alter later disease risk--the "developmental origins of health and disease" (DOHaD) paradigm--have led to a recognition that these perspectives can inform our understanding of human biology. We propose that the DOHaD phenomenon can be considered as a subset of the broader processes of developmental plasticity by which organisms adapt to their environment during their life course. Such adaptive processes allow genotypic variation to be preserved through transient environmental changes. Cues for plasticity operate particularly during early development; they may affect a single organ or system, but generally they induce integrated adjustments in the mature phenotype, a process underpinned by epigenetic mechanisms and influenced by prediction of the mature environment. In mammals, an adverse intrauterine environment results in an integrated suite of responses, suggesting the involvement of a few key regulatory genes, that resets the developmental trajectory in expectation of poor postnatal conditions. Mismatch between the anticipated and the actual mature environment exposes the organism to risk of adverse consequences-the greater the mismatch, the greater the risk. For humans, prediction is inaccurate for many individuals because of changes in the postnatal environment toward energy-dense nutrition and low energy expenditure, contributing to the epidemic of chronic noncommunicable disease. This view of human disease from the perspectives of life history biology and evolutionary theory offers new approaches to prevention, diagnosis and intervention.

Biological Evolution↗
PubMed2004

Facial heights: evolutionary relevance of postnatal ontogeny for facial orientation and skull morphology in humans and chimpanzees.

Facial heights, i.e. the vertical distances between the superior and inferior limits of facial compartments, contribute to the orientation of the viscerocranium in the primate skull. In humans, vertical facial variation is among the main sources of diversity and frequently associated with an integrated suite of other cranio-mandibular traits. Facial heights and kyphosis are also important factors in interspecific variation and models of hominoid evolution. The ontogenetic determination of adult facial orientation and its relation to phylogenetic variation are unclear, but crucial in all previously mentioned respects. We addressed these issues in a sample of 175 humans and chimpanzees with Procrustes based geometric morphometrics, testing hypotheses of interspecific similarity in postnatal ontogenetic trajectories, early versus later ontogenetic facial pattern determination, and a developmental model of morphological integration. We analyzed the contribution of postnatal morphogenesis to adult vertical facial variation by partitioning morphological variation into a portion of pure growth allometry and a non-allometric fraction. A statistically significant difference of growth-allometries revealed that in both species growth established the adult skull proportions by vertical facial expansion, but while in chimpanzees the complete viscerocranium showed reorientation, in humans only the lower face was modified. In both species the results support a hypothesis of early facial pattern determination. A coincident emergence of morphological traits favors a hypothesis of developmental integration of the face, excluding traits of the basi- and neurocranium. Interspecific differences in integration may have implications for evolutionary studies. The present findings indicate that growth establishes the adult skull proportions and integrates principal facial orientation patterns, already there in early postnatal ontogeny.

Adult↗
PubMed1998

Biodemographic trajectories of longevity.

Old-age survival has increased substantially since 1950. Death rates decelerate with age for insects, worms, and yeast, as well as humans. This evidence of extended postreproductive survival is puzzling. Three biodemographic insights--concerning the correlation of death rates across age, individual differences in survival chances, and induced alterations in age patterns of fertility and mortality--offer clues and suggest research on the failure of complicated systems, on new demographic equations for evolutionary theory, and on fertility-longevity interactions. Nongenetic changes account for increases in human life-spans to date. Explication of these causes and the genetic license for extended survival, as well as discovery of genes and other survival attributes affecting longevity, will lead to even longer lives.

Aging↗
PubMed2006

Flexibility and enzymatic cold-adaptation: a comparative molecular dynamics investigation of the elastase family.

Molecular dynamics simulations of representative mesophilic and psycrophilic elastases have been carried out at different temperatures to explore the molecular basis of cold adaptation inside a specific enzymatic family. The molecular dynamics trajectories have been compared and analyzed in terms of secondary structure, molecular flexibility, intramolecular and protein-solvent interactions, unravelling molecular features relevant to rationalize the efficient catalytic activity of psychrophilic elastases at low temperature. The comparative molecular dynamics investigation reveals that modulation of the number of protein-solvent interactions is not the evolutionary strategy followed by the psycrophilic elastase to enhance catalytic activity at low temperature. In addition, flexibility and solvent accessibility of the residues forming the catalytic triad and the specificity pocket are comparable in the cold- and warm-adapted enzymes. Instead, loop regions with different amino acid composition in the two enzymes, and clustered around the active site or the specificity pocket, are characterized by enhanced flexibility in the cold-adapted enzyme. Remarkably, the psycrophilic elastase is characterized by reduced flexibility, when compared to the mesophilic counterpart, in some scattered regions distant from the functional sites, in agreement with hypothesis suggesting that local rigidity in regions far from functional sites can be beneficial for the catalytic activity of psychrophilic enzymes.

Acclimatization↗
PubMed1997

The effects of length trajectory on the mechanical power output of mouse skeletal muscles.

The effects of length trajectory on the mechanical power output of mouse soleus and extensor digitorum longus (EDL) muscles were investigated using the work loop technique in vitro at 37 degrees C. Muscles were subjected to sinusoidal and sawtooth cycles of lengthening and shortening; for the sawtooth cycles, the proportion of the cycle spent shortening was varied. For each cycle frequency examined, the timing and duration of stimulation and the strain amplitude were optimized to yield the maximum power output. During sawtooth length trajectories, power increased as the proportion of the cycle spent shortening increased. The increase in power was attributable to more complete activation of the muscle due to the longer stimulation duration, to a more rapid rise in force resulting from increased stretch velocity and to an increase in the optimal strain amplitude. The power produced during symmetrical sawtooth cycles was 5-10 % higher than during sinusoidal work loops. Maximum power outputs of 92 W kg-1 (soleus) and 247 W kg-1 (EDL) were obtained by manipulating the length trajectory. For each muscle, this was approximately 70 % of the maximum power output estimated from the isotonic force-velocity relationship. We have found a number of examples suggesting that animals exploit prolonging the shortening phase during activities requiring a high power output, such as flying, jet-propulsion swimming and vocalization. In an evolutionary context, increasing the relative shortening duration provides an alternative to increasing the maximum shortening velocity (Vmax) as a way to increase power output.

Animals↗
PubMed2024

Decoding the trajectory of antibiotic resistance genes in saline and alkaline soils: Insights from different fertilization regimes.

The soil salinity and alkalinity play an important role in the occurrence and proliferation of antibiotic resistance genes (ARGs). Yet, little is known the underlying mechanism by which soil salinity and alkalinity affect antibiotic resistance evolution. Here we investigated the ARGs variation in soil salinity and alkalinity environments created by different fertilization, and explored the biological mechanisms that salinity and alkalinity alter the evolutionary paradigm of antibiotic resistance. The results showed the soil treated by organic fertilizer exhibited a low salinity, neutral level (TSD 239.20 μS/cm, pH 7.17). The ARG abundance in the OF treatment was the highest, keeping an average of 67.83 TPM. Beside the effect of direct input of organic fertilizer at the beginning, it was important to note that, ARGs abundance during planting showed significant correlations with pH and electric conductivity. We observed that changes in microbial survival strategies under different salinity and alkalinity conditions further affected ARG hosts abundance. Indoor experiments demonstrated that there was a survival trade-off between the growth of resistant bacteria and the evolution of antibiotic resistance in salinity and alkalinity environments. Meta-genomic and Meta-transcriptomic analysis consistently demonstrated bacterial antibiotic resistance was primarily associated with pyruvate, energy and lipid metabolic pathways. The functional gene related to salinity and alkalinity, like cysH, cysK, plsB and plsC showed negative correlations with MDR. Prokaryotic transcription assays validated these relations. This study well explains the prevalence of soil ARGs after different fertilization regimes and will give a deeper understanding for the effect of soil salinity and alkalinity on antibiotic resistance evolution.

Soil↗
PubMed2003

Protein sequences yield a proteomic code.

Analysis of crystallized protein structures suggests that globular proteins are organized as consecutively connected units of 25-35 residues. These units are closed loops, that is returns of the polypeptide chain trajectory to a close contact with itself. This universal feature of apparently polymer-statistical nature is a basis for a principally novel view on the globular proteins as loop fold structures. The same unit size has been detected in protein sequences translated from complete prokaryotic genomes by positional autocorrelation analysis, which strongly indicates the evolutionary connection of the units. The units are further characterized by prototype sequences matching to their numerous derivatives in the translated genomes. The matches to five strongest prokaryotic prototypes and three prototypes of C. elegans are identified in the sequences of crystallized proteins, and their structures analyzed. Corresponding segments of the polypeptide chains in majority of cases form closed loops, though evolutionary fate of every prototype element is shown to be rather diverse. Then loop ends can be separated by a sequence-wise distant segments and stabilized by the spatial interactions in the context of the overall globular structure. The units belong to a presumably limited spectrum of the sequence prototypes, full repertoire of which would constitute a proteomic code.

Amino Acid Motifs↗