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Results for “phenotypic trajectory”

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PubMed1981

The estimation of epistasis in components of fitness in experimental populations of Drosophila melanogaster I. A two-stage maximum likelihood model.

Laboratory populations of Drosophila melanogaster bearing the Curly and Plum marked second chromosome inversions were observed in selection experiments for ten discrete generations. Maximum likelihood estimates of the relative fitnesses of Curly, Plum, Curly-Plum, and wild phenotypes were obtained from selection trajectories. Using these estimates, measures of multiplicative and additive epistasis were calculated. These were partitioned into pre-sampling and post-sampling components, and both were found to be significant. In several cases the sign of the epistasis of the two components was reversed, and the direction of net epistasis depended on the particular inversion. The significance of partitioning epistasis into components is discussed in the light of two locus population genetic theory.

Animals↗

PubMed1996

Development of second-order vestibular projections in the chicken embryo.

The results reviewed here demonstrate that vestibulospinal and vestibulo-ocular interneurons in the chicken embryo are organized into coherent clusters, each of which occupies a unique spatial domain and has a characteristic axon trajectory. Moreover, the vestibulo-ocular clusters have specific termination patterns in the extraocular motoneuron pools and may to some extent have specific functions. The axon trajectories and termination patterns are established accurately during early development. This suggests the presence of selective mechanisms that ensure the generation of an appropriately specific connectivity pattern. The correlation of cluster domains with unique fields of regulatory gene expression at early stages suggests a mechanistic link between the position of a vestibular interneuron and the differentiation of its axon trajectory, termination pattern, and neurotransmitter phenotype.

Animals↗

PubMed1993

Development of Drosophila wing sensory neurons in mutants with missing or modified cell surface molecules.

The neurons of the sensory receptors on the wing of Drosophila melanogaster have highly characteristic axon projections in the central nervous system (CNS). The morphology of these projections was studied in flies bearing mutations that affect cell surface molecules thought to be important in axon guidance. The animals used were mutant for the fasciclinI (fasI), fasciclinII (fasII), fasciclinIII (fasIII) and neurally altered carbohydrate (nac) genes. Axon populations were visualized by staining with DiI and light-reacting the dye with diaminobenzidine to yield permanent preparations. The fasI, fasII and fasIII mutants as well as the nac mutant display altered axonal trajectories in the CNS. One phenotype seen in fasII mutants and in animals mutant for both fasI and fasIII was extra branching within the axon projection pattern. A second phenotype observed was a reduction or complete loss of one of the tracts, apparently due to the axons shifting to a neighboring tract. This was seen in the most extreme form in nac mutants and to a lesser degree in fasIII mutants. To determine if the mutations discussed here affected axon guidance, wing discs were analyzed using the antibody 22C10 to label sensory neurons in the wing during metamorphosis. Both misrouting of axons and the appearance of ectopic neurons in the wing were observed. In the fasI:fasIII, the fasII and the nac mutants, there was misrouting of sensory axons in the developing wing. In addition, the fasII and nac mutants displayed ectopic sensory neurons in the wing. This implies that the cell surface molecules missing (fasciclins) or modified (by the nac gene product), in these mutants may play a role in both neurogenesis and axon guidance.

Animals↗

PubMed2002

A logistic mixture model for characterizing genetic determinants causing differentiation in growth trajectories.

The logistic or S-shaped curve of growth is one of the few universal laws in biology. It is certain that there exist specific genes affecting growth curves, but, due to a lack of statistical models, it is unclear how these genes cause phenotypic differentiation in growth and developmental trajectories. In this paper we present a statistical model for detecting major genes responsible for growth trajectories. This model is incorporated with pervasive logistic growth curves under the maximum likelihood framework and, thus, is expected to improve over previous models in both parameter estimation and inference. The power of this model is demonstrated by an example using forest tree data, in which evidence of major genes affecting stem growth processes is successfully detected. The implications for this model and its extensions are discussed.

Crosses, Genetic↗

PubMed2006

Substance use disorder trajectory classes: diachronic integration of onset age, severity, and course.

BACKGROUND: Substance use disorders (SUDs) may be characterized by onset age, severity, substance type, course, and outcomes. SUD phenotypes in the literature typically consider each of these features in isolation. Conceptual frameworks and data collection procedures for assessing SUD phenotypes are increasingly "diachronic" in approach, providing for characterizations "throughout time". The recent availability of statistical procedures for the identification of latent classes offers the possibility of developing SUD phenotypes integrating these developmental features. This article illustrates the utilization of SAS-TRAJ mixture modeling to characterize variations in SUD symptom trajectories to define phenotypes. METHODS: The subjects were 332 adult males with SUDs. Their course of symptoms from early adolescence through middle adulthood was retrospectively determined. Symptom trajectories were defined by the number of DSM-IV SUD symptoms by year of age. SAS-TRAJ mixture models identified trajectory classes. Model development, evaluation, and selection using this approach are discussed. RESULTS: Among these men with SUDs, six trajectory classes were identified, including groups characterized by early-onset and severe SUD symptoms persisting into adulthood, an early-onset group similar in adolescence but improving in adulthood, and other groups with symptoms emerging later with varying degrees of severity and persistence. The SUD trajectory classes were significantly different on comorbid psychopathology, particularly childhood disruptive behavior disorders. CONCLUSION: The results present a new method for the comprehensive depiction of heterogeneity in SUD symptoms. Future studies may determine the extent to which SUDs phenotypes based on the course of symptom development inform etiology, prevention and treatment research.

Adolescent↗

PubMed2025

Resource presentation dictates genetic and phenotypic adaptation in yeast.

BACKGROUND: Environments shape adaptive trajectories of populations, often leading to adaptive parallelism in identical, and divergence in different environments. However, how does the likelihood of these possibilities change with minute changes in the environment remain unclear. RESULTS: In this study, we evolved Saccharomyces cerevisiae in environments which differed only in the manner in which the sugar source is presented to the population. In one set of populations, carbon was presented as a mixture of glucose-galactose, and in the other, as melibiose, a glucose-galactose disaccharide. Since the two environments differed in how the two monosaccharides are packaged, we call these environments 'synonymous'. Our results show that even subtle environmental differences can lead to differing phenotypic responses between the two sets of evolved populations. However, despite different adaptive responses, pleiotropic effects of adaptation are largely predictable. We also show that distinct genomic targets of adaptation between the two sets of evolved populations are functionally convergent. CONCLUSION: This study highlights how subtle environmental differences dictate phenotypic and genetic adaptation of populations. Additionally, these results also suggest the predictive potential of ancestor's fitness in understanding pleiotropic responses. Our work underscores the importance of studying more such environments to understand the generality of adaptive responses in populations.

Saccharomyces cerevisiae↗

PubMed1996

Modelling phenotypic plasticity. II. Do genetic correlations matter?

Predictions of the evolutionary trajectory of reaction norms and interpretation of empirical results are usually based on two mathematically equivalent ways of partitioning phenotypic variance into its genetic, environmental, and interaction components: the genotype by environment interaction estimated by means of an analysis of variance, or the interenvironment genetic correlation (i.e. the genetic correlation between the expressions of the same trait in two environments). Both these quantities are supposed to indicate the amount of genetic variability for plasticity in natural population. I point out that not only are the qualitative predictions based on these statistical methods sometimes in conflict with each other, but that both may fail to predict rates of evolution and equilibria under some circumstances, because they ignore the details of the genetic machinery. It is shown that, ultimately, the only way to predict reliably the evolution of plasticity is actually to know its specific genetic basis and the genotypic constitution of the population, however inconvenient this may be from both theoretical and empirical standpoints. The discussion is framed in terms of a simple one-locus two-allele model that mimics the real case of the pennant/vestigial system describing plasticity of wing length to temperature in Drosophila melanogaster.

Alleles↗

PubMed2005

Interaction of rearing environment and reproductive tactic on gene expression profiles in Atlantic salmon.

Organisms that share the same genotype can develop into divergent phenotypes, depending on environmental conditions. In Atlantic salmon, young males of the same age can be found either as sneakers or immature males that are future anadromous fish. Just as the organism-level phenotype varies between divergent male developmental trajectories, brain gene expression is expected to vary as well. We hypothesized that rearing environment can also have an important effect on gene expression in the brain and possibly interact with the reproductive tactic adopted. We tested this hypothesis by comparing brain gene expression profiles of the two male tactics in fish from the same population that were reared in either a natural stream or under laboratory conditions. We found that expression of certain genes was affected by rearing environment only, while others varied between male reproductive tactics independent of rearing environment. Finally, more than half of all genes that showed variable expression varied between the two male tactics only in one environment. Thus, in these fish, very different molecular pathways can give rise to similar macro-phenotypes depending on rearing environment. This result gives important insights into the molecular underpinnings of developmental plasticity in relationship to the environment.

Animals↗

PubMed2004

Defining a never-smoker: results from the nonsmokers survey.

The U.S. Centers for Disease Control defines a never-smoker as someone who has smoked < 100 cigarettes per lifetime. In an attempt to explore differences among nonsmokers and to validate this cutpoint, we surveyed 69 nonsmokers who had smoked between 1 and 200 cigarettes in their lifetime on their experiences during the time they smoked. Of the 7 who classified themselves as ex-smokers, 2 met DSM-IV criteria for nicotine dependence, compared with none who classified themselves as never-smokers. No respondents provided data permitting the computation of a Fagerstrom Test for Nicotine Dependence (FTND) score. Withdrawal effects were minimal, but craving, tolerance, and subjective effects showed a pattern of significant differences that were most prominent between those who smoked only 1 cigarette and those who smoked at least a pack. Our data indicate a graded effect but also suggest that 19 cigarettes per lifetime is a more conservative cutpoint than 99 for defining the never-smoker phenotype. Further investigation of the smoking trajectory and characteristics associated with development of signs of dependence in never- vs. ever-smokers may help refine this cutpoint and shed light on what protects some people who experiment with smoking from becoming chronic users.

Adult↗

PubMed2026

Sex-specific ethylene responses drive floral sexual plasticity in Cannabis sativa.

Cannabis sativa L. exhibits pronounced sexual plasticity in which both XX and XY plants can undergo floral phenotypic sex reversal in response to ethylene modulation, yet the underlying molecular mechanisms remain poorly defined. Here, we present the most extensive multi-omic analysis of ethylene-induced sex change in C. sativa to date, integrating over 130 RNA-seq libraries, ethylene pathway metabolite quantification, and whole-genome sequencing across three XX and XY genotypes. Treatments with silver thiosulfate and ethephon induced more than 80% phenotypic conversion, but transcriptomic responses diverged sharply between XX and XY plants. Profiling 47 ERGs revealed 14 high-confidence candidates, including CsACS1, CsACO5, CsERF1, and CsMTN, with sex-specific and temporal expression patterns that show dynamic ethylene mediation of plasticity. Early transcriptional activation occurred prior to the emergence of flowers, within 18 h of sex-change treatments and the photoperiod-induced transition to flowering. As opposite-sex floral tissues emerged, ethylene-related gene expression shifted accordingly within developing floral organs, with distinct sets of genes stabilizing the opposite-sex phenotype in XX and XY plants. Several candidates were located in non-recombining regions of the X chromosome or were absent from the Y chromosome, and most exhibited low nucleotide diversity, consistent with functional constraint. These results provide a high-resolution view of ethylene-responsive sexual plasticity in cannabis and show that the shared capacity for sex reversal in XX and XY plants is implemented through distinct regulatory trajectories that produce opposite-sex floral phenotypes. This work expands the mechanistic understanding of sex expression in dioecious species and identifies candidate genes relevant to the development of sex-stable cultivars.

Ethylenes↗

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↗

PubMedDate not supplied

Developmental drive: an important determinant of the direction of phenotypic evolution.

Over any period of evolutionary time, the prevailing ontogenetic trajectory within a lineage may either recur unchanged from generation to generation (stasis) or alter (developmental reprogramming). A key question about reprogramming is whether it exhibits intrinsic biases in favor of some sorts of change and against others, which may be referred to respectively as "drive" and "constraint." A simple logical argument suggests that both drive and constraint should be common, and conversely that cases of equiprobable modification in various phenotypic directions should be relatively rare. These proposals, that drive and constraint exist and that they are common, appear to be widely accepted, even among neo-Darwinians, who are sometimes portrayed as rejecting them. What is more controversial is that developmental drive (and constraint) can have a powerful influence on the direction of evolutionary change. It is argued that such an influence will occur, and indeed may be pervasive.

Developmental Biology↗

PubMed1982

In vitro-constructed RP4-prime plasmids mediate orientated mobilization of the Proteus morganii chromosome.

RP4-prime plasmids containing inserts of Proteus morganii strain 2815 chromosomal DNA (0.5-13 megadaltons in size) were constructed in vitro. When introduced into the latter organism, the hybrid plasmids promoted transfer of chromosomal markers in an orientated manner, with recombinant frequencies from 10(-4) to 10(-6) per donor. Transconjugants expressed the tetracycline-resistant phenotype of the plasmids. Plasmid-guided trajectories overlapped and a circular map of chromosome markers was constructed. Correspondence between size of inserted chromosomal DNA in hybrid plasmids and numbers of markers transferred suggested that homology played a role in chromosome mobilization by these plasmids.

Chromosome Mapping↗

PubMed2026

Virulent Parasites Emerge in Hosts With Rising Temperatures.

Climate change is increasing the risk of emerging parasites. However, whether more virulent variants will spread during climate-driven outbreaks remains unclear. Here, we aimed to explore the short-term trajectory of parasite evolution-at the phenotypic and genomic scales-across environmentally relevant temperatures in a thermally mismatched host-parasite interaction. We experimentally evolved a wild parasitic bacterium (Leucobacter musarum), across the thermal range (20°C-30°C) and extremes (35°C) of Cabo Verde-the site of field collection-in a Caenorhabditis elegans host strain. Starting from a single bacterial isolate, we then tracked phenotypic and de novo genomic changes that arose across replicate populations following ten passages of experimental evolution. We found that at 25°C, warm for the host but an average temperature for the parasite, host-mediated selection favoured higher virulence and genomic diversification by the end of the experiment. At hot temperatures, towards the limit of host survival, virulence was maintained across all parasite populations. Parasites evolved at hot temperatures also displayed a latent virulence boost, deadlier once hosts experienced a heatwave. Patterns of molecular evolution were constrained to parallel changes in fewer loci at extreme temperatures. Our findings suggest that shifting environmental temperatures will leave phenotypic and genomic signatures on evolving parasites.

Animals↗

PubMed2001

Control of interneuron fate in the developing spinal cord by the progenitor homeodomain protein Dbx1.

Spinal interneurons help to coordinate motor behavior. During spinal cord development, distinct classes of interneurons are generated from progenitor cells located at different positions within the ventral neural tube. V0 and V1 interneurons derive from adjacent progenitor domains that are distinguished by expression of the homeodomain proteins Dbx1 and Dbx2. The spatially restricted expression of Dbx1 has a critical role in establishing the distinction in V0 and V1 neuronal fate. In Dbx1 mutant mice, neural progenitors fail to generate V0 neurons and instead give rise to interneurons that express many characteristics of V1 neurons-their transcription factor profile, neurotransmitter phenotype, migratory pattern, and aspects of their axonal trajectory. Thus, a single progenitor homeodomain transcription factor coordinates many of the differentiated properties of one class of interneurons generated in the ventral spinal cord.

Animals↗

PubMed2003

Genetic linkage analysis of longitudinal hypertension phenotypes using three summary measures.

BACKGROUND: Longitudinal data often have multiple (repeated) measures recorded along a time trajectory. For example, the two cohorts from the Framingham Heart Study (GAW13 Problem 1) contain 21 and 5 repeated measures for hypertension phenotypes as well as epidemiological risk factors, respectively. Direct modelling of a large number of serially and biologically correlated traits in the context of linkage analysis can be prohibitively complex. Alternatively, we may consider using univariate transformation for linkage analysis of longitudinal repeated measures. RESULTS: We evaluated the utility of three conventional summary measures (mean, slope, and principal components) for genetic linkage analysis of longitudinal phenotypes by analyzing the chromosome 10 data of the Framingham Heart Study. Except for the temporal slope, all of the summary methods and the multivariate analysis identified the previously reported region, marker GATA64A09, for systolic blood pressure or high blood pressure. Further analysis revealed that this region may harbor gene(s) affecting human blood pressure at multiple stages of life. CONCLUSION: We conclude that mean and principal components are feasible alternatives for genetic linkage analysis of longitudinal phenotypes, but the slope might have a separate genetic basis from that of the original longitudinal phenotypes.

Adult Children↗

PubMed2005

Estimation of direct and maternal genetic and permanent environmental effects for weights from birth to 356 days of age in a herd of Japanese Black cattle using random regression.

A total of 11,815 weight records from 23,94 Japanese Black calves was used to estimate direct, maternal, direct permanent environmental, and maternal permanent environmental effects on growth from birth to 356 d of age. The data were collected from a herd of Japanese Black cattle in Shiroshi city, Miyagi prefecture, Japan. A random regression model, including parity of dam and year-season of calving-sex of calf as fixed effects and animal, dam, animal permanent environmental, and maternal permanent environmental as random effects, was fitted to the data using Legendre polynomials for age of calf. Direct heritability estimates increased from 0.38 at birth to 0.65 at 120 d of age, decreased to 0.38 at 300 d, and then increased again up to 0.47 at 356 d. The ratio of animal permanent environmental variance to phenotypic variance decreased from 0.41 at birth to 0.12 at 90 d, and then increased gradually up to 0.40 at 270 d and oscillated around this value up to the end of the test period. Maternal genetic heritabilities increased from 0.04 at birth to 0.09 at 120 d and then decreased to 0.06 thereafter, whereas the variance ratios due to maternal permanent environment were fairly constant across the age trajectory, fluctuating around the value of 0.03. Direct genetic, phenotypic, maternal genetic, animal permanent environmental, and maternal permanent environmental correlations between different ages were all positive, and they generally decreased as the interval between ages increased. These correlations were lower between weights from nonadjacent ages than those between weights from adjacent ages. Results suggest that selection on preweaning weights would have a positive effect on weights at later ages.

Animals↗

PubMed2026

Mirror worlds: The shared regulatory architecture of cell fate in development and cancer.

Lineage plasticity has emerged as a central mechanism through which cancer cells adapt to therapeutic pressure, evade immune surveillance, and acquire aggressive phenotypes. Although recognized across tumor types, the regulatory principles governing how cancer cells reprogram cellular identity remain incompletely understood. In this review, we propose that lineage plasticity in cancer reflects the redeployment of regulatory frameworks established during normal development. Rather than representing a stochastic byproduct of genomic instability, cancer plasticity frequently unfolds within gene regulatory architectures that also govern cell fate specification, lineage commitment, and controlled state transitions during embryogenesis and tissue homeostasis. Developmental transcription factors, including members of the SOX family, FOXA1, ASCL1, NKX2-1, and epithelial-mesenchymal transition regulators, function as lineage gatekeepers during development but are repurposed in cancer to destabilize lineage commitment and enable phenotypic switching. Similarly, epigenetic regulators that guide developmental trajectories, including chromatin remodeling complexes, Polycomb group proteins, and DNA methylation machinery, are frequently dysregulated or redistributed in tumors, altering the repression of lineage-stabilizing and alternative lineage programs and thereby weakening epigenetic barriers to lineage transitions. Together, these observations support a model in which development and cancer operate as mirror regulatory systems: one establishing and stabilizing cellular identity, the other exploiting the same regulatory architecture to permit adaptive reprogramming under selective pressure. We further discuss how emerging single-cell and spatial multi-omics technologies, integrated with artificial intelligence-based modeling, enable mapping of cell state landscapes and transitional trajectories, transforming lineage plasticity from a descriptive phenomenon into a measurable and predictable property of tumor evolution.

Humans↗