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How organisms evolve under extreme environmental changes is a critical question in the face of global climate change. Genetic accommodation is an evolutionary process by which natural selection acts on novel phenotypes generated through repeated encounters with extreme environments. In this study, polyphenic and monophenic strains of theblackmutant tobacco hornworm,Manduca sexta, were evolved via genetic accommodation of heat stress-induced phenotypes, and the molecular differences between the two strains were explored. Transcriptomic analyses showed that epigenetic and hormonal differences underlie the differences between the two strains and their distinct responses to temperature. DNA methylation had diverged between the two strains potentially mediating genetic assimilation. Juvenile hormone (JH) signaling in the polyphenic strain was temperature sensitive, whereas in the monophenic strain, JH signaling remained low at all temperatures. Although 20-hydroxyecdysone titers were elevated under heat shock conditions in both strains, the strains did not differ in the titers. Tyrosine hydroxylase was also found to differ between the two strains at different temperatures, and its expression could be modulated by topical application of a JH analog. Finally, heat shock of unselectedblackmutants demonstrated that the expression of the JH-response gene,Krüppel-homolog 1(Kr-h1), increased within the first 30 min of heat shock, suggesting that JH levels respond readily to thermal stress. Our study highlights the critical role that hormones and epigenetics play during genetic accommodation and potentially in the evolution of populations in the face of climate change. 

Aposematic coloration offers an opportunity to explore the molecular mechanisms underlying canalization. In this study, the role of epigenetic regulation underlying robustness was explored in the aposematic coloration of the milkweed bug,Oncopeltus fasciatus. Polycomb(Pc) andEnhancer of zeste(E(z)), which encode components of the Polycomb repressive complex 1 (PRC1) and PRC2, respectively, andjing, which encodes a component of the PRC2.2 subcomplex, were knocked down in the fourth instar ofO. fasciatus. Knockdown of these genes led to alterations in scutellar morphology and melanization. In particular, whenPcwas knocked down, the adults developed a highly melanized abdomen, head and forewings at all temperatures examined. In contrast, theE(z)andjingknockdown led to increased plasticity of the dorsal forewing melanization across different temperatures. Moreover,jingknockdown adults exhibited increased plasticity in the dorsal melanization of the head and the thorax. These observations demonstrate that histone modifiers may play a key role during the process of canalization to confer robustness in the aposematic coloration. 

We investigate the dynamic characteristics of Covid-19 daily infection rates in Taiwan during its initial surge period, focusing on 79 districts within the seven largest cities. By employing computational techniques, we extract 18 features from each district-specific curve, transforming unstructured data into structured data. Our analysis reveals distinct patterns of asymmetric growth and decline among the curves. Utilizing theoretical information measurements such as conditional entropy and mutual information, we identify major factors of order-1 and order-2 that influence the peak value and curvature at the peak of the curves, crucial features characterizing the infection rates. Additionally, we examine the impact of geographic and socioeconomic factors on the curves by encoding each of the 79 districts with two binary characteristics: North-vs-South and Urban-vs-Suburban. Furthermore, leveraging this data-driven understanding at the district level, we explore the fine-scale behavioral effects on disease spread by examining the similarity among 96 age-group-specific curves within urban districts of Taipei and suburban districts of New Taipei City, which collectively represent a substantial portion of the nation’s population. Our findings highlight the implicit influence of human behaviors related to living, traveling, and working on the dynamics of Covid-19 transmission in Taiwan. 

For a large ensemble of complex systems, a Many-System Problem (MSP) studies how heterogeneity constrains and hides structural mechanisms, and how to uncover and reveal hidden major factors from homogeneous parts. All member systems in an MSP share common governing principles of dynamics, but differ in idiosyncratic characteristics. A typical dynamic is found underlying response features with respect to covariate features of quantitative or qualitative data types. Neither all-system-as-one-whole nor individual system-specific functional structures are assumed in such response-vs-covariate (Re–Co) dynamics. We developed a computational protocol for identifying various collections of major factors of various orders underlying Re–Co dynamics. We first demonstrate the immanent effects of heterogeneity among member systems, which constrain compositions of major factors and even hide essential ones. Secondly, we show that fuller collections of major factors are discovered by breaking heterogeneity into many homogeneous parts. This process further realizes Anderson’s “More is Different” phenomenon. We employ the categorical nature of all features and develop a Categorical Exploratory Data Analysis (CEDA)-based major factor selection protocol. Information theoretical measurements—conditional mutual information and entropy—are heavily used in two selection criteria: C1—confirmable and C2—irreplaceable. All conditional entropies are evaluated through contingency tables with algorithmically computed reliability against the finite sample phenomenon. We study one artificially designed MSP and then two real collectives of Major League Baseball (MLB) pitching dynamics with 62 slider pitchers and 199 fastball pitchers, respectively. Finally, our MSP data analyzing techniques are applied to resolve a scientific issue related to the Rosenberg Self-Esteem Scale. 

Without assuming any functional or distributional structure, we select collections of major factors embedded within response-versus-covariate (Re-Co) dynamics via selection criteria [C1: confirmable] and [C2: irrepaceable], which are based on information theoretic measurements. The two criteria are constructed based on the computing paradigm called Categorical Exploratory Data Analysis (CEDA) and linked to Wiener–Granger causality. All the information theoretical measurements, including conditional mutual information and entropy, are evaluated through the contingency table platform, which primarily rests on the categorical nature within all involved features of any data types: quantitative or qualitative. Our selection task identifies one chief collection, together with several secondary collections of major factors of various orders underlying the targeted Re-Co dynamics. Each selected collection is checked with algorithmically computed reliability against the finite sample phenomenon, and so is each member’s major factor individually. The developments of our selection protocol are illustrated in detail through two experimental examples: a simple one and a complex one. We then apply this protocol on two data sets pertaining to two somewhat related but distinct pitching dynamics of two pitch types: slider and fastball. In particular, we refer to a specific Major League Baseball (MLB) pitcher and we consider data of multiple seasons. 

All features of any data type are universally equipped with categorical nature revealed through histograms. A contingency table framed by two histograms affords directional and mutual associations based on rescaled conditional Shannon entropies for any feature-pair. The heatmap of the mutual association matrix of all features becomes a roadmap showing which features are highly associative with which features. We develop our data analysis paradigm called categorical exploratory data analysis (CEDA) with this heatmap as a foundation. CEDA is demonstrated to provide new resolutions for two topics: multiclass classification (MCC) with one single categorical response variable and response manifold analytics (RMA) with multiple response variables. We compute visible and explainable information contents with multiscale and heterogeneous deterministic and stochastic structures in both topics. MCC involves all feature-group specific mixing geometries of labeled high-dimensional point-clouds. Upon each identified feature-group, we devise an indirect distance measure, a robust label embedding tree (LET), and a series of tree-based binary competitions to discover and present asymmetric mixing geometries. Then, a chain of complementary feature-groups offers a collection of mixing geometric pattern-categories with multiple perspective views. RMA studies a system’s regulating principles via multiple dimensional manifolds jointly constituted by targeted multiple response features and selected major covariate features. This manifold is marked with categorical localities reflecting major effects. Diverse minor effects are checked and identified across all localities for heterogeneity. Both MCC and RMA information contents are computed for data’s information content with predictive inferences as by-products. We illustrate CEDA developments via Iris data and demonstrate its applications on data taken from the PITCHf/x database. 

We develop Categorical Exploratory Data Analysis (CEDA) with mimicking to explore and exhibit the complexity of information content that is contained within any data matrix: categorical, discrete, or continuous. Such complexity is shown through visible and explainable serial multiscale structural dependency with heterogeneity. CEDA is developed upon all features’ categorical nature via histogram and it is guided by all features’ associative patterns (order-2 dependence) in a mutual conditional entropy matrix. Higher-order structural dependency of k(≥3) features is exhibited through block patterns within heatmaps that are constructed by permuting contingency-kD-lattices of counts. By growing k, the resultant heatmap series contains global and large scales of structural dependency that constitute the data matrix’s information content. When involving continuous features, the principal component analysis (PCA) extracts fine-scale information content from each block in the final heatmap. Our mimicking protocol coherently simulates this heatmap series by preserving global-to-fine scales structural dependency. Upon every step of mimicking process, each accepted simulated heatmap is subject to constraints with respect to all of the reliable observed categorical patterns. For reliability and robustness in sciences, CEDA with mimicking enhances data visualization by revealing deterministic and stochastic structures within each scale-specific structural dependency. For inferences in Machine Learning (ML) and Statistics, it clarifies, upon which scales, which covariate feature-groups have major-vs.-minor predictive powers on response features. For the social justice of Artificial Intelligence (AI) products, it checks whether a data matrix incompletely prescribes the targeted system.