Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Evolutionary trajectories”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19Linked to original sources
PubMed2001

Developmental effects of selective breeding for an infantile trait: the rat pup ultrasonic isolation call.

This article describes how continued selection for divergent levels of the 10-day-old infant rat's ultrasonic vocal (USV) response to isolation affects the time course of development of that and other possible co-selected traits from 3 to 21 days postnatally. Since selective breeding for an infantile trait has not been reported before, we collected from colleagues a number of predicted outcomes that reflect the wide range of current opinion on the relationship between microevolutionary and developmental processes. After 15 generations of selective breeding, we found widely divergent USV responses between 10-day-old High USV line (300 USV/2 min) and low USV line (15 USV/2 min) pups. The developmental trajectory of USV responses at 3 and 7 days of age also was markedly altered in both these lines in comparison to the randomly bred controls, but was much less affected in 14-, 18-, or 21-day-old pups, contrary to all predictions. The development of other behavioral responses to isolation generally remained unaffected by the continued selection as did physical traits, measures of temperature regulation and classic developmental milestones. Only two traits showed evidence of co-selection: High line pups showed more urination/defecation in response to isolation from 10 days on, and more rapid ear canal opening at 10 days. These and other findings are presented and discussed in relation to the developmental and evolutionary concepts on which the different predictions were based.

Age Factors↗
PubMed2006

Similar folds with different stabilization mechanisms: the cases of Prion and Doppel proteins.

BACKGROUND: Protein misfolding is the main cause of a group of fatal neurodegenerative diseases in humans and animals. In particular, in Prion-related diseases the normal cellular form of the Prion Protein PrP (PrPC) is converted into the infectious PrPSc through a conformational process during which it acquires a high beta-sheet content. Doppel is a protein that shares a similar native fold, but lacks the scrapie isoform. Understanding the molecular determinants of these different behaviours is important both for biomedical and biophysical research. RESULTS: In this paper, the dynamical and energetic properties of the two proteins in solution is comparatively analyzed by means of long time scale explicit solvent, all-atom molecular dynamics in different temperature conditions. The trajectories are analyzed by means of a recently introduced energy decomposition approach (Tiana et al, Prot. Sci. 2004) aimed at identifying the key residues for the stabilization and folding of the protein. Our analysis shows that Prion and Doppel have two different cores stabilizing the native state and that the relative contribution of the nucleus to the global stability of the protein for Doppel is sensitively higher than for PrP. Moreover, under misfolding conditions the Doppel core is conserved, while the energy stabilization network of PrP is disrupted. CONCLUSION: These observations suggest that different sequences can share similar native topology with different stabilizing interactions and that the sequences of the Prion and Doppel proteins may have diverged under different evolutionary constraints resulting in different folding and stabilization mechanisms.

Amino Acid Sequence↗
PubMed2004

Reassessment of the environmental mechanisms controlling developmental polyphenism in spadefoot toad tadpoles.

Identifying the environmental mechanism(s) controlling developmental polyphenism is the first step in gaining a mechanistic and evolutionary understanding of the factors responsible for its expression and evolution. Tadpoles of the spadefoot toad Spea multiplicata can display either a "typical" omnivorous or a carnivorous phenotype. Exogenous thyroxine and feeding on conspecific tadpoles have been accepted as triggers for development of the carnivorous phenotype on the basis of a series of studies in the early 1990s. I repeated the thyroxine and conspecific-feeding assays and demonstrated that neither exogenous thyroxine nor feeding on conspecifics induces the carnivorous phenotype. Previous researchers used simple ratio statistics to argue that field-collected carnivores and thyroxine-treated tadpoles are similar, and my results supported these claims if I used the same simple ratio methodology. However, investigation of trait developmental trajectories and allometries for field-collected carnivores and thyroxine-treated and conspecific-fed tadpoles show that these phenotypes are profoundly different.

Adaptation, Physiological↗
PubMed2005

Maternal hormones as a tool to adjust offspring phenotype in avian species.

Avian eggs contain substantial amounts of maternal hormones and so provide an excellent model to study hormone-mediated maternal effects. We review this new and rapidly evolving field, taking an ecological and evolutionary approach and focusing on effects and function of maternal androgens in offspring development. Manipulation of yolk levels of androgens within the physiological range indicates that maternal androgens affect behaviour, growth, morphology, immune function and survival of the offspring, in some cases even long after fledging. Descriptive and experimental studies show systematic variation in maternal androgen deposition both within and among clutches, as well as in relation to the sex of the embryo. We discuss the potential adaptive value of maternal androgen transfer at all these three levels. We conclude that maternal androgen deposition in avian eggs provides a flexible mechanism of non-genetic inheritance, by which the mother can favour some offspring over others, and adjust their developmental trajectories to prevailing environmental conditions, producing different phenotypes. However, the literature is less consistent than often assumed and at all three levels, the functional explanations need further experimental testing. The field would greatly benefit from an analysis of the underlying physiological mechanisms.

Androgens↗
PubMed1996

Discrete clutch sizes, local mate competition, and the evolution of precise sex allocation.

Optimal sex allocation under a population structure with local mate competition has been studied mainly in deterministic models that are based on the assumption of continuous clutch sizes; Hamilton's (1967) model is the classic example. When clutch sizes are small, however, this assumption is not appropriate. When taking the discrete nature of eggs into account it becomes critically important whether females control only the mean sex ratio ("binomial" females) or the variance as well ("precise" females). As both types of sex ratio control have been found, it is of interest to investigate their evolutionary stability. In particular, it may be questioned whether perfect control of the sex ratio is always favoured by natural selection when mating groups are small. Models based on discrete clutch sizes are developed to determine evolutionarily stable (ES) sex ratios. It is predicted that when all females are of the binomial type they should produce a lower proportion of daughters than predicted by Hamilton's model, especially when clutch size and foundress number are small. When all females are of the precise type, the ES number of sons should generally be either a stable mixed strategy or a pure strategy, but there are special cases (for two foundresses and particular clutch sizes) where the ES number of sons lies in a trajectory of neutrally stable mixed strategies; the predicted mean sex ratios can be either higher or lower than predicted by Hamilton's model. The existence of ES mixed strategies implies that individual females do not necessarily have to produce sex ratios with perfect precision; some level of imperfection can be tolerated (i.e., will not be selected against). When the population consists of both binomial and precise females, the latter always have a selective advantage. This advantage of precision does not disappear when precision approaches fixation in the population. The latter result contradicts the conclusions of Taylor and Sauer (1980) which is due to their way of expressing selective advantage; they define selective advantage as the between-generation increase per allele, which will always become vanishingly small when an allele reaches fixation, irrespective of fitness differences.

Animals↗
PubMed2006

Mutation-biased adaptation in a protein NK model.

Evolutionary trends responsible for systematic differences in genome and proteome composition have been attributed to GC:AT mutation bias in the context of neutral evolution or to selection acting on genome composition. A possibility that has been ignored, presumably because it is part of neither the Modern Synthesis nor the Neutral Theory, is that mutation may impose a directional bias on adaptation. This possibility is explored here with simulations of the effect of a GC:AT bias on amino acid composition during adaptive walks on an abstract protein fitness landscape called an "NK" model. The results indicate that adaptation does not preclude mutation-biased evolution. In the complete absence of neutral evolution, a modest GC:AT bias of realistic magnitude can displace the trajectory of adaptation in a mutationally favored direction, to such a degree that amino acid composition is biased substantially and persistently. Thus, mutational explanations for evolved patterns need not presuppose neutral evolution.

Adaptation, Physiological↗
PubMed2006

Learning, climate and the evolution of cultural capacity.

Patterns of environmental variation influence the utility, and thus evolution, of different learning strategies. I use stochastic, individual-based evolutionary models to assess the relative advantages of 15 different learning strategies (genetic determination, individual learning, vertical social learning, horizontal/oblique social learning, and contingent combinations of these) when competing in variable environments described by 1/f noise. When environmental variation has little effect on fitness, then genetic determinism persists. When environmental variation is large and equal over all time-scales ("white noise") then individual learning is adaptive. Social learning is advantageous in "red noise" environments when variation over long time-scales is large. Climatic variability increases with time-scale, so that short-lived organisms should be able to rely largely on genetic determination. Thermal climates usually are insufficiently red for social learning to be advantageous for species whose fitness is very determined by temperature. In contrast, population trajectories of many species, especially large mammals and aquatic carnivores, are sufficiently red to promote social learning in their predators. The ocean environment is generally redder than that on land. Thus, while individual learning should be adaptive for many longer-lived organisms, social learning will often be found in those dependent on the populations of other species, especially if they are marine. This provides a potential explanation for the evolution of a prevalence of social learning, and culture, in humans and cetaceans.

Adaptation, Physiological↗
PubMed1996

X-ray crystallographic studies of alanine-65 variants of carbonic anhydrase II reveal the structural basis of compromised proton transfer in catalysis.

The three-dimensional structures of A65F, A65L, A65H, A65T, A65S, and A65G human carbonic anhydrase II (CAII) variants have been solved by X-ray crystallographic methods to probe the importance of residue 65 and the structural implications of its evolutionary drift in the greater family of carbonic anhydrase isozymes. Structure-activity relationships in this series of CAII variants are correlated with those established for other carbonic anhydrase isozymes. We conclude that a bulky side chain at position 65 hinders the formation of an effective solvent bridge between zinc-bound water and H64 and thereby hinders solvent-mediated proton transfer between these two groups [Jackman, J. E., Merz, K. M., Jr., & Fierke, C. A. (1996) Biochemistry 35, 16421-16428]. Despite the introduction of a polar hydroxyl group at this position, smaller side chains such as serine or threonine substituted for A65 do not perturb the formation of a solvent bridge between H64 and zinc-bound solvent. Thus, the evolution of residue 65 size is one factor affecting the trajectory of catalytic proton transfer.

Alanine↗
PubMed2000

Forward modeling allows feedback control for fast reaching movements.

Delays in sensorimotor loops have led to the proposal that reaching movements are primarily under pre-programmed control and that sensory feedback loops exert an influence only at the very end of a trajectory. The present review challenges this view. Although behavioral data suggest that a motor plan is assembled prior to the onset of movement, more recent studies have indicated that this initial plan does not unfold unaltered, but is updated continuously by internal feedback loops. These loops rely on a forward model that integrates the sensory inflow and motor outflow to evaluate the consequence of the motor commands sent to a limb, such as the arm. In such a model, the probable position and velocity of an effector can be estimated with negligible delays and even predicted in advance, thus making feedback strategies possible for fast reaching movements. The parietal lobe and cerebellum appear to play a crucial role in this process. The ability of the motor system to estimate the future state of the limb might be an evolutionary substrate for mental operations that require an estimate of sequelae in the immediate future.

Journal Article↗
PubMed2001

Possible consequences of genes of major effect: transient changes in the G-matrix.

Understanding the process of evolutionary divergence requires knowledge of the strength, form, and targets of selection, as well as the genetic architecture of the divergent traits. Quantitative genetic approaches to understanding multivariate selection and genetic response to selection have proven to be powerful tools in this endeavor, particularly with respect to short-term evolution. However, the application of quantitative genetic theory over periods of substantial phenotypic change is controversial because it requires that the requisite genetic parameters remain constant over the period of time in question. We show herein how attempts to determine the stability of key genetic parameters may be misled by the 'many genes of small effect' type of genetic architecture generally assumed in quantitative genetics. The presence of genes of major effect (GOMEs) can alter the genetic variance-covariance matrix dramatically for brief periods of time, significantly alter the rate and trajectory of multivariate evolution, and thereby mislead attempts to reconstruct or predict long term evolution.

Biological Evolution↗
PubMed2003

Correlated evolution of life-history with size at maturity in Daphnia pulicaria: patterns within and between populations.

Explaining the repeated evolution of similar sets of traits under similar environmental conditions is an important issue in evolutionary biology. The extreme alternative classes of explanations for correlated suites of traits are optimal adaptation and genetic constraint resulting from pleiotropy. Adaptive explanations presume that individual traits are free to evolve to their local optima and that convergent evolution represents particularly adaptive combinations of traits. Alternatively, if pleiotropy is strong and difficult to break, strong selection on one or a few particularly important characters would be expected to result in consistent correlated evolution of associated traits. If pleiotropy is common, we predict that the pattern of divergence among populations will consistently reflect the within-population genetic architecture. To test the idea that the multivariate life-history phenotype is largely a byproduct of strong selection on body size, we imposed divergent artificial selection on size at maturity upon two populations of the cladoceran Daphnia pulicaria, chosen on the basis of their extreme divergence in body size. Overall, the trajectory of divergence between the two natural populations did not differ from that predicted by the genetic architecture within each population. However, the pattern of correlated responses suggested the presence of strong pleiotropic constraints only for adult body size and not for other life-history traits. One trait, offspring size, appears to have evolved in a way different from that expected from the within-population genetic architecture and may be under stabilizing selection.

Animals↗
PubMed2004

The effective size of mixed sexually and asexually reproducing populations.

Using the transition matrix of inbreeding and coancestry coefficients, the inbreeding (N(eI)), variance (N(eV)), and asymptotic (N(e lambda)) effective sizes of mixed sexual and asexual populations are formulated in terms of asexuality rate (delta), variance of asexual (C) and sexual (K) reproductive contributions of individuals, correlation between asexual and sexual contributions (rho(ck)), selfing rate (beta), and census population size (N). The trajectory of N(eI) toward N(e lambda) changes crucially depending on delta, N, and beta, whereas that of N(eV) is rather consistent. With increasing asexuality, N(e lambda) either increases or decreases depending on C, K, and rho(ck). The parameter space in which a partially asexual population has a larger N(e lambda) than a fully sexual population is delineated. This structure is destroyed when N(1 - delta) < 1 or delta > 1 - 1/N. With such a high asexuality, tremendously many generations are required for the asymptotic size N(e lambda) to be established, and N(e lambda) is extremely large with any value of C, K, and rho(ck) because the population is dominated eventually by individuals of the same genotype and the allelic diversity within the individuals decays quite slowly. In reality, the asymptotic state would occur only occasionally, and instantaneous rather than asymptotic effective sizes should be practical when predicting evolutionary dynamics of highly asexual populations.

Alleles↗
PubMed2004

The temporal organization of posture changes during the first year of independent walking.

Although the development of upright posture has received considerable attention, the quiet stance of infants in their first months of learning this fundamental behavior has not been well studied. The purpose of the present study was to characterize the time evolutionary properties, or temporal organization, of these infants' unperturbed upright stance as well as to elucidate how somatosensory information influences that organization. Six healthy, full-term infants were tested monthly from walk onset until 9 months of independent walking experience while standing either independently or touching a static surface. The structure of sway was assessed through stabilogram-diffusion analysis using an exponential Ornstein-Uhlenbeck characterization. The results of this analysis revealed two new insights into postural development. First, the developmental changes in quiet stance involved a decreased rate at which sway decays to maximal variance, rather than an attenuation of the magnitude of that variance. Specifically, measures indexing amount of sway variance were significantly reduced when touching a static surface as compared with an independent stance condition, but revealed no change with increased walking experience. Further, a reduction in the average rate constant of decay indicated an increased influence of long time-scale sway corrections on the overall sway trajectory. Second, it was shown that, at early walk ages, the use of touch both reduced the amount of variance and shifted the rate constant of sway towards longer time-scale displacements. Taken in the context of previous research, these results support our conclusion that early postural development embodies the dual tasks of calibrating sensorimotor relations for estimation of self-motion as well as identification and tuning of control system properties.

Age Factors↗
PubMed2005

Variation in continuous reaction norms: quantifying directions of biological interest.

Thermal performance curves are an example of continuous reaction norm curves of common shape. Three modes of variation in these curves--vertical shift, horizontal shift, and generalist-specialist trade-offs--are of special interest to evolutionary biologists. Since two of these modes are nonlinear, traditional methods such as principal components analysis fail to decompose the variation into biological modes and to quantify the variation associated with each mode. Here we present the results of a new method, template mode of variation (TMV), that decomposes the variation into predetermined modes of variation for a particular set of thermal performance curves. We illustrate the method using data on thermal sensitivity of growth rate in Pieris rapae caterpillars. The TMV model explains 67% of the variation in thermal performance curves among families; generalist-specialist trade-offs account for 38% of the total between-family variation. The TMV method implemented here is applicable to both differences in mean and patterns of variation, and it can be used with either phenotypic or quantitative genetic data for thermal performance curves or other continuous reaction norms that have a template shape with a single maximum. The TMV approach may also apply to growth trajectories, age-specific life-history traits, and other function-valued traits.

Animals↗
PubMed2026

Dissecting fluctuating selection: A unified population and quantitative genetics framework.

One of the longstanding debates in evolutionary biology is the effect of fluctuating selection on genetic changes in populations. However, the extent to which these periodic forces influence organisms at both genomic and phenotypic levels remains unclear. Despite the compelling evidence of fluctuating selection from recent studies, there is a disconnect between empirical and theoretical findings concerning the underlying mechanisms due to the limited evidence regarding the scale and processes that generate genome-wide oscillations. This study aims to elucidate how both genetic factors (e.g. heritability, number of causative loci) and ecological factors (e.g. season length, the difference in the phenotypic optima between seasons, population size dynamics) drive fluctuating selection and to identify the parameters that produce consistent oscillatory patterns. We developed a modeling framework integrating quantitative and population genetics to simulate a population under various selection regimes. We applied spectral analysis to detect periodicity, indicating cyclical selective environments. Our simulations highlight the conditions sustaining oscillations in allele frequencies over time. Spectral analysis successfully identifies the periodic patterns from allele frequency trajectories, even under highly complex selection regimes. Not only does our study clarify the conditions that yield oscillatory behaviors, but these parameters can also potentially be estimated in natural populations, providing a possibility of empirically testing these models.

Fluctuating selection↗
PubMed2026

Dissecting fluctuating selection: A unified population and quantitative genetics framework.

One of the longstanding debates in evolutionary biology is the effect of fluctuating selection on genetic changes in populations. However, the extent to which these periodic forces influence organisms at both genomic and phenotypic levels remains unclear. Despite the compelling evidence of fluctuating selection from recent studies, there is a disconnect between empirical and theoretical findings concerning the underlying mechanisms due to the limited evidence regarding the scale and processes that generate genome-wide oscillations. This study aims to elucidate how both genetic factors (e.g. heritability, number of causative loci) and ecological factors (e.g. season length, the difference in the phenotypic optima between seasons, population size dynamics) drive fluctuating selection and to identify the parameters that produce consistent oscillatory patterns. We developed a modeling framework integrating quantitative and population genetics to simulate a population under various selection regimes. We applied spectral analysis to detect periodicity, indicating cyclical selective environments. Our simulations highlight the conditions sustaining oscillations in allele frequencies over time. Spectral analysis successfully identifies the periodic patterns from allele frequency trajectories, even under highly complex selection regimes. Not only does our study clarify the conditions that yield oscillatory behaviors, but these parameters can also potentially be estimated in natural populations, providing a possibility of empirically testing these models.

Fluctuating selection↗
PubMed2026

Revisiting the genome assembly of Lupinus species reveals differential diploidization after a shared whole-genome duplication.

Accurate genome assemblies are essential for comparative genomics, yet Hi-C-guided scaffolding can introduce structural errors that misrepresent chromosome architecture and bias evolutionary inferences. Here, we identified pervasive scaffolding errors-including artificial fusions, internal inversions, and incomplete contig mounting-in 2 previously published Lupinus genomes (L. cosentinii and L. digitatus) using a segmentation method based on long terminal repeat (LTR) retrotransposon density. We reassembled both genomes, producing chromosome-level references of 472.7 Mb (16 chromosomes) and 427.2 Mb (21 chromosomes), with BUSCO completeness >98.5%. Synteny validation and reapplication of LTR profiling confirmed that all prior errors were resolved. Using these corrected genomes together with 4 additional Lupinus species and 2 outgroup legumes, we investigated postpolyploid evolution. Synonymous substitution rate (Ks) analysis revealed a genus-specific whole-genome duplication (WGD) event (Ks = 0.17) shared by all 6 Lupinus species. The proportion of WGD-derived genes varied markedly, from 60% in L. digitatus to only 36% in L. mutabilis, indicating differential diploidization. While all species retained a core set of WGD duplicates enriched in cytoskeleton organization, ion transport, and defense responses, each exhibited lineage-specific functional trajectories: cell wall modification in L. cosentinii and L. digitatus, nitrogen metabolism in L. albus and L. angustifolius, flower development in L. luteus, and stress/lipid metabolism in L. mutabilis. Our corrected assemblies provide optimal references for Lupinus comparative genomics, and our findings demonstrate that a shared WGD event can lead to both conserved and highly divergent postpolyploid fates, likely underpinning adaptive diversification within the genus.

Lupinus↗
PubMed1989

Embryonic development of axon pathways in the Drosophila CNS. II. Behavior of pioneer growth cones.

We have identified the neurons that pioneer the major CNS axon tracts in the Drosophila embryo and determined their trajectory and fasciculation choices using serial section electron microscopy. Although Drosophila pioneer neurons make choices similar to those of their grasshopper homologs, there are interesting differences that reflect the much smaller nervous system size and the much faster rate of development characteristic of Drosophila. For example, where 2 longitudinal tracts are pioneered independently in grasshopper, only one is formed in Drosophila. This change is due to a change in fasciculation affinity of the pCC growth cone. Additionally, the intersegmental (IS) nerve is pioneered by a different neuron in Drosophila (aCC) than in the grasshopper (U1) because the smaller Drosophila CNS places the IS nerve within filopodial reach of the aCC soma, while in the grasshopper it is not. Drosophila growth cones explore a much more confined neuropil volume than do grasshopper growth cones but can also sample a larger fraction of the CNS as well. For this reason, some cell-cell recognition events critical to pathfinding in the grasshopper embryo may not be as essential in Drosophila. Nevertheless, many specific cellular affinities have been retained through the evolutionary divergence of these 2 species.

Animals↗