Aphasia due to right hemisphere infarction in a patient with situs inversus after carotid artery stenting: a case report.

BACKGROUND: Situs inversus (SI) is a rare congenital anomaly in which systemic organs and vessels are positioned in a mirror image of their normal positions. An interesting issue regarding individuals with such a condition is whether they also have reversed brain asymmetries. Most of studies on this issue indicate that, similarly to many people with normal visceral alignment, patients with SI have a left hemispheric dominance for language functions. CASE PRESENTATION: We report a rare occurrence of anomalous cerebral dominance for language in a patient with complete situs inversus. The right-handed patient developed aphasia after carotid stenting, and brain magnetic resonance imaging showed cerebral infarction in the right parietal lobe. CONCLUSION: Anomalous cerebral dominance for language and visceral situs inversus in our patient both may result from a single, genetically coded atypicality of developmental gradient.

Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids.

The shift from outcrossing to self-fertilization is one of the main evolutionary transitions in plants and has broad effects on evolutionary trajectories. In Brassicaceae, the ability to inhibit self-fertilization is controlled by 2 genes, SCR and SRK, tightly linked within the S-locus. A series of small non-coding RNAs also encoded within the S-locus regulates the transcriptional activity of SCR alleles, resulting in a linear dominance hierarchy between them. In Brassicaceae, natural allopolyploid species are often self-compatible (SC) even when one of the progenitor species is self-incompatible, but the reason why polyploid lineages tend to lose self-incompatibility (SI) and the timing of the loss of SI (immediately after ancestral hybridization between the progenitor species, or at a later stage after the formation of allopolyploid lineages) have generally remained elusive. We used a series of synthetic diploid and tetraploid hybrids obtained between self-fertilizing Capsella orientalis and outcrossing Capsella grandiflora to test whether the breakdown of SI could be observed immediately after hybridization, and whether the occurrence of SC phenotypes could be explained by the dominance interactions between S-haplotypes inherited from the parental lineages. We used RNA-sequencing data from young inflorescences to measure allele-specific expression of the SCR gene and infer dominance interactions in the synthetic hybrids. We then evaluated the seed set from autonomous self-pollination in the synthetic hybrids. Our results demonstrate that self-compatibility of the hybrids depends on the relative dominance between S-alleles inherited from the parental species, confirming that SI can be lost instantaneously upon formation of the ancestral allopolyploid lineage. They also confirm that the epigenetic regulation that controls dominance interactions between S-alleles can function between subgenomes in allopolyploids. Together, our results illustrate how a detailed knowledge of the mechanisms controlling SI can illuminate our understanding of the patterns of co-variation between the mating system and changes in ploidy.

The noncoding circular RNA circHomer1 regulates developmental experience-dependent plasticity in mouse visual cortex.

Circular RNAs (circRNAs) are noncoding RNAs abundant in brain tissue, and many are derived from activity-dependent, linear mRNAs encoding for synaptic proteins, suggesting that circRNAs may directly or indirectly play a role in regulating synaptic development, plasticity, and function. However, it is unclear if the circular forms of these RNAs are similarly regulated by activity and what role these circRNAs play in developmental plasticity. Here, we employed transcriptome-wide analysis comparing differential expression of both mRNAs and circRNAs in juvenile mouse primary visual cortex (V1) following monocular deprivation (MD), a model of developmental plasticity. Among the differentially expressed mRNAs and circRNAs following 3-day MD, the circular and the activity-dependent linear forms of the Homer1 gene, circHomer1 and Homer1a respectively, were of interest as their expression changed in opposite directions: circHomer1 expression increased while the expression of Homer1a decreased following MD. Knockdown of circHomer1 prevented the depression of closed-eye responses normally observed after 3-day MD. circHomer1-knockdown led to a reduction in average dendritic spine size prior to MD, but critically there was no further reduction after 3-day MD, consistent with impaired structural plasticity. circHomer1-knockdown also prevented the reduction of surface AMPA receptors after 3-day MD. Synapse-localized puncta of the AMPA receptor endocytic protein Arc increased in volume after MD but were smaller in circHomer1-knockdown neurons, suggesting that circHomer1 regulates plasticity through mechanisms of activity-dependent AMPA receptor endocytosis. Thus, activity-dependent circRNAs regulate developmental synaptic plasticity, and our findings highlight the essential role of circHomer1 in V1 plasticity induced by short-term MD.

Sex-specific life-history trait expression in hybrids of a cave- and surface-dwelling fish (Poecilia mexicana, Poeciliidae).

Evaluating the fitness of hybrids can provide important insights into genetic differences between species or diverging populations. We focused on surface- and cave-ecotypes of the widespread Atlantic molly Poecilia mexicana and raised F1 hybrids of reciprocal crosses to sexual maturity in a common-garden experiment. Hybrids were reared in a fully factorial 2 × 2 design consisting of lighting (light vs. darkness) and resource availability (high vs. low food). We quantified survival, ability to realize their full reproductive potential (i.e., completed maturation for males and 3 consecutive births for females) and essential life-history traits. Compared to the performance of pure cave and surface fish from a previous experiment, F1s had the highest death rate and the lowest proportion of fish that reached their full reproductive potential. We also uncovered an intriguing pattern of sex-specific phenotype expression, because male hybrids expressed cave molly life histories, while female hybrids expressed surface molly life histories. Our results provide evidence for strong selection against hybrids in the cave molly system, but also suggest a complex pattern of sex-specific (opposing) dominance, with certain surface molly genes being dominant in female hybrids and certain cave molly genes being dominant in male hybrids.

The genetic architecture of polygenic local adaptation and its role in shaping barriers to gene flow.

We consider how the genetic architecture underlying locally adaptive traits determines the strength of a barrier to gene flow in a mainland-island model. Assuming a general life cycle, we derive an expression for the effective migration rate when local adaptation is due to genetic variation at many loci under directional selection on the island, allowing for arbitrary fitness and dominance effects across loci. We show how the effective migration rate can be combined with classical single-locus diffusion theory to accurately predict multilocus differentiation between the mainland and island at migration-selection-drift equilibrium and determine the migration rate beyond which local adaptation collapses, while accounting for genetic drift and weak linkage. Using our efficient numerical tools, we then present a detailed study of the effects of dominance on barriers to gene flow, showing that when total selection is sufficiently strong, more recessive local adaptation generates stronger barriers to gene flow. We then study how heterogeneous genetic architectures of local adaptation affect barriers to gene flow, characterizing adaptive differentiation at migration-selection balance for different distributions of fitness effects. We find that a more heterogeneous genetic architecture generally yields a stronger genome-wide barrier to gene flow and that the detailed genetic architecture underlying locally adaptive traits can have an important effect on observable differentiation when divergence is not too large. Lastly, we study the limits of our approach as loci become more tightly linked, showing that our predictions remain accurate over a large biologically relevant domain.

Astrocyte-derived dominance winning reverses chronic stress-induced depressive behaviors.

Individuals with low social status are at heightened risk of major depressive disorder (MDD), and MDD also influences social status. While the interrelationship between MDD and social status is well-defined, the behavioral causality between these two phenotypes remains unexplored. Here, we investigated the behavioral relationships between depressive and dominance behaviors in male mice exposed to chronic restraint stress and the role of medial prefrontal cortex (mPFC) astrocytes in these behaviors. Chronic restraint stress induced both depressive and submissive behaviors. Chemogenetic mPFC astrocyte activation significantly enhanced dominance in chronic stress-induced submissive mice by increasing the persistence of defensive behavior, although it did not affect depressive behaviors. Notably, repetitive winning experiences following mPFC astrocyte stimulation exerted anti-depressive effects in chronic restraint stress-induced depressive mice. These data indicate that mPFC astrocyte-derived winning experience renders anti-depressive effects, and may offer a new strategy for treating depression caused by low status in social hierarchies by targeting mPFC astrocytes.

Species-specific behavioural responses to environmental variation as a potential species coexistence mechanism in ants.

A fundamental question of ecology is why species coexist in the same habitat. Coexistence can be enabled through niche differentiation, mediated by trait differentiation. Here, behaviour constitutes an often-overlooked set of traits. However, behaviours such as aggression and exploration drive intra- and interspecific competition, especially so in ants, where community structure is usually shaped by aggressive interactions. We studied behavioural variation in three ant species, which often co-occur in close proximity and occupy similar dominance ranks. We analysed how intra- and allospecific aggression, exploration and foraging activity vary under field conditions, namely with temperature and over time. Behaviours were assessed for 12 colonies per species, and four times each during several months. All behavioural traits consistently differed among colonies, but also varied over time and with temperature. These temperature-dependent and seasonal responses were highly species-specific. For example, foraging activity decreased at high temperatures in Formica rufibarbis, but not in Lasius niger; over time, it declined strongly in L. niger but much less in F. rufibarbis. Our results suggest that, owing to these species-specific responses, no species is always competitively superior. Thus, environmental and temporal variation effects a dynamic dominance hierarchy among the species, facilitating coexistence via the storage effect.

Relationship between dominance hierarchy steepness and rank-relatedness of benefits in primates.

In animal social groups, the extent to which individuals consistently win agonistic interactions and their ability to monopolize resources represent 2 core aspects of their competitive regime. However, whether these two aspects are closely correlated within groups has rarely been studied. Here, we tested the hypothesis that hierarchy steepness, which is generally used to represent power differentials between group members, predicts the variation in the distribution of fitness-related benefits (i.e. fecundity, infant survival, mating success, and feeding success) in relation to individual dominance ranks. We tested this hypothesis in primate groups using comparative phylogenetic meta-analytical techniques. Specifically, we reviewed published and unpublished studies to extract data on individual dominance ranks, their access to fitness-related benefits, and hierarchy steepness. We collected and included in our analysis a total of 153 data points, representing 27 species (including 2 chimpanzee sub-species). From these, we used 4 common methods to measure individual dominance ranks and hierarchy steepness, i.e. D ij -based normalized David's scores, randomized Elo-ratings, and David's scores and Elo-ratings estimated in Bayesian frameworks. We found that hierarchy steepness had no effect on the strength of the relationship between dominance rank and access to fitness-related benefits. Our results suggest that hierarchy steepness does not reflect between-group variation in the extent to which individual dominance affects the acquisition of fitness-related benefits in primates. Although the ability to win agonistic encounters is essential, we speculate that other behavioral strategies adopted by individuals may play crucial roles in resource acquisition in animal competitive regimes.

Global increase of lianas in tropical forests.

Lianas profoundly affect tropical forests dynamics, reducing productivity and carbon storage, which underscores the importance of monitoring change in their abundance in projecting the future of the global terrestrial carbon store. While increasing liana populations are documented within the Neotropics, the global consistency of these patterns is questioned, and remains to be determined. To evaluate pantropical trends in liana abundance comprehensively and quantitatively, we conducted a systematic literature review and meta-analysis. This approach allowed us to synthesize data from published longitudinal studies examining liana trends across the tropics. We calculated standardized effect sizes and standard errors, and applied a Bayesian hierarchical meta-analytic model to adjust for publication bias. Our analysis reveals an overall pan-tropical increase in lianas abundance, occurring at an average rate of 1.7 ± 0.7 SE% per year (~10% to 24% per decade). This upward trend, confirmed to be robust against publication bias, extends beyond Neotropical regions, indicating a widespread phenomenon. Although a global trend of increasing liana abundance is evident, significant local variation exist, attributable to differences in life cycle stages, abundance metrics, forest successional stages, and biogeographical realms. Notably, increases in stem density of saplings and biomass of canopy lianas, especially in old-growth forests, point to global climatic drivers and heightened turnover rates in tropical forests as factors promoting sustained liana growth in the canopy and clonal colonization in the understory. These trends suggest that the rise in liana abundance may not only persist but could also intensify under climate change. Considering both previous and current research on lianas, our findings confirm growing concerns about lianas' expanding impact on pan-tropical carbon storage, highlighting their significant potential effect on global carbon dynamics.

Molecular concepts to explain heterosis in crops.

Heterosis describes the superior performance of hybrid plants compared with their genetically distinct parents and is a pillar of global food security. Here we review the current status of the molecular dissection of heterosis. We discuss how extensive intraspecific structural genomic variation between parental genotypes leads to heterosis by genetic complementation in hybrids. Moreover, we survey how global gene expression complementation contributes to heterosis by hundreds of additionally active genes in hybrids and how overdominant single genes mediate heterosis in several species. Furthermore, we highlight the prominent role of the microbiome in improving the performance of hybrids. Taken together, the molecular understanding of heterosis will pave the way to accelerate hybrid productivity and a more sustainable agriculture.

The Influence of the Dominant Leg in Body Asymmetries in Children and Adolescent Male Soccer Players.

The current study aimed to examine (a) whether the dominant leg (DL) was associated with the contralateral side of functional scoliosis and (b) if any of the postural asymmetries' evaluation variables may be a reliable predictor of the functional scoliosis development in young male soccer players. Six hundred-nine (n = 609) male soccer players (age: 10.8 ± 2.7 years; height: 147 ± 17 cm; weight: 43.4 ± 14.6 kg; DL: Right 81.6%, Left 14%, Both 4.4%) participated in this study. The spinal asymmetries evaluation included thoracic kyphosis, lumbar lordosis, truncal rotation, shoulders alignment from posterior view, anterior and posterior pelvic tilt, anterior superior iliac spine (ASIS), hamstring tightness, and lower extremities discrepancy. A significant association was observed between the DL and the truncal rotation side: χ2(4) = 30.84, p = 0.001, V = 0.16. Participants with longer left legs were likelier to present a spinal asymmetry (OR = 1.18). The participants with higher left shoulders were 2.13 times more likely to have spinal asymmetry than the participants with normal shoulders level. Participants with left ASIS higher were 3.08 times more likely to present asymmetry than those with normally aligned ASIS levels. There was also a significant association between the DL and the side of truncal rotation: χ2(2) = 13.30, p = 0.001, V = 0.449. Logistic regression analysis for the functional scoliotic group and truncal rotation side demonstrated that the taller participants and participants with shorter right legs were more likely to have asymmetry on the left side (OR = 1.29, OR = 0.32). Participants with greater right hamstring stiffness were likelier to have a truncal rotation on the right side (OR = 0.93). Participants with higher left shoulders were 0.20 times less likely to have a truncal rotation on the left side than the participants with normal shoulders level. In conclusion, leg dominance in children and in youth soccer players may be a factor causing truncal rotation on the contralateral side. Additional causes, such as leg length discrepancy and pelvic tilt, may progressively lead to functional scoliosis.

Directional-Specific Modulation of Postural Control and Stepping Kinematics in Multidirectional Gait Initiation.

Daily living activities present a diverse array of task and environmental constraints, highlighting the critical role of adapting gait initiation (GI) for an individual's quality of life. This study investigated the effects of GI directions, obstacle negotiation, and leg dominance on anticipatory postural adjustments and stepping kinematics. Fourteen active, young, healthy individuals participated in GI across 4 directions-forward, medial 45°, lateral 45°, and lateral 90°-with variations in obstacle presence and leg dominance. Results revealed a consistent decreasing trend in maximum center of pressure displacement, anticipatory postural adjustment duration, step distance, and swing leg velocity with lateral shifts in GI directions, yet the step duration and swing leg heel trajectory were not affected by GI directions except in lateral 90° GI. Center of pressure displacements were intricately scaled to directional propulsive forces generation, and the stepping kinematics were influenced by the directional modifications in movements. With obstacles, modifications in anticipatory postural adjustment metrics and stepping kinematics reflected the obstacle clearance movements. The dominant leg GI exhibited longer step durations and greater movement variability in medial 45° GI. The current investigation of GI factors expands our existing understanding of GI dynamics and offers valuable insights applicable to fall prevention and gait rehabilitation strategies.

Chasing the chill: Unveiling the dynamic flavors and textures of ice cream formulations.

In this study, nine commercial ice creams and four prototypes were assessed. For the sensory analysis, quantitative descriptive analysis (QDA), and temporal dominance of sensations (TDS) methodology were used. According to the QDA results, full-composition ice cream showed significantly higher differences (p < .05) in terms such as vanilla and sweet flavors, brightness, creamy texture and appearance, and viscosity, exhibiting longer melting times. Functional ice creams showed significantly higher differences (p < .05) in terms like viscosity, creamy texture, and appearance. On the other hand, agave fructans in prototype ice creams were found to be able to reduce fat, but not fat and sugar simultaneously, showing a significant decrease (p < .05) in terms such as hardness, crystallized texture, gummy texture, and porosity. Based on the PCA results, the analysis accounted for 75.28% of data variability. Full-composition ice creams and one functional ice cream were related to terms such as viscosity, fatty sensation, creamy texture and appearance, dense, gummy, among others. The rest of the commercial ice creams were related to vanilla and caramel flavor and smell, artificial aftertaste, aerated, porosity, among others. Prototype ice creams were related to hard texture, salty and milk flavor, and crystallized texture. Based on the results of the TDS method, all formulations were found to be significantly dominant (5%) in terms such as vanilla flavor and sweet flavor at the beginning of the test. Formulations containing butyric fat and/or vegetable fat, or agave fructans were significantly dominant (5%) in fatty sensation.

Dominance analysis to assess solute contributions to multicomponent phase equilibria.

Phase separation in aqueous solutions of macromolecules underlies the generation of biomolecular condensates in cells. Condensates are membraneless bodies, representing dense, macromolecule-rich phases that coexist with the dilute, macromolecule-deficient phases. In cells, condensates comprise hundreds of different macromolecular and small molecule solutes. How do different solutes contribute to the driving forces for phase separation? To answer this question, we introduce a formalism we term energy dominance analysis. This approach rests on analysis of shapes of the dilute phase boundaries, slopes of tie lines, and changes to dilute phase concentrations in response to perturbations of concentrations of different solutes. The framework is based solely on conditions for phase equilibria in systems with arbitrary numbers of macromolecules and solution components. Its practical application relies on being able to measure dilute phase concentrations of the components of interest. The dominance framework is both theoretically facile and experimentally applicable. We present the formalism that underlies dominance analysis and establish its accuracy and flexibility by deploying it to analyze phase diagrams probed in simulations and in experiments.

Evaluation of The Effect of Ocular Dominance on Macular Microcirculation via Swept-Source Optical Coherence Tomography Angiography.

PURPOSE: To determine the existence of differences in the retinal microcirculation of dominant and non-dominant eyes, as well as of interocular differences in macular microcirculation, using swept-source optical coherence tomography angiography (OCTA). METHODS: In total, 122 eyes of 61 individuals were enrolled in this cross-sectional study. Measurements were taken using the swept-source optical coherence tomography Triton device (Topcon Corp, Tokyo, Japan) coupled with non-invasive OCTA technology. Macular perfusion parameters were assessed, including superficial vascular complex, vascular density of the deep vascular complex, vascular density of the choriocapillaris vascular complex, superficial foveal avascular zone and deep foveal avascular zone. Ocular dominance was determined among individuals with healthy eyes using the hole-in-the-card test. RESULTS: Ocular dominance was found in 68.9% of right eyes and 31.1% of left eyes. The mean age of the subjects was 34.45 ± 16.48 years (range: 18-73 years). We found that 16 (30.76%) males and 22 (31.42%) females had left-eye dominance (p > 0.05). None of the OCTA parameters differed between the eyes based on dominance (p > 0.05). Central macular thickness and sub-foveal choroidal thickness did not show significant differences (p > 0.05). When comparing interocular parameters, a significant difference was observed only in the inferior sector of the superficial vascular complex (p = 0.04). CONCLUSION: There was no significant difference in OCTA parameters between dominant and non-dominant eyes. There was no predominant interocular difference in the measurements.

Seasonal and vertical patterns of water availability and variability determine plant reproductive phenology.

BACKGROUND AND AIMS: Changing precipitation regimes can influence terrestrial plants and ecosystems. However, plant phenological responses to changing precipitation temporal patterns and the underlying mechanisms are largely unclear. This study was conducted to explore the effects of seasonal precipitation redistribution on plant reproductive phenology in a temperate steppe. METHODS: A field experiment with control (C), advanced (AP) and delayed (DP) growing-season precipitation peaks, and the combination of AP and DP (ADP) were employed. Seven dominant plant species were selected and divided into two functional groups (early- vs. middle-flowering species, shallow- vs. deep-rooted species) to monitor reproductive phenology including budding, flowering, and fruiting date, as well as reproductive duration for four growing seasons from 2015 to 2017, and 2022. KEY RESULTS: The AP, but not DP treatment advanced the phenological (i.e., budding, flowering, and fruiting) dates and lengthened the reproductive duration across the 4 growing seasons and 7 monitored species. In addition, the phenological responses showed divergent patterns among different plant functional groups, which could be attributed to shifts in soil moisture and its variability in different months and soil depths. Moreover, species with lengthened reproductive duration increased phenological overlap with other species, which could have a negative impact on their dominance under the AP treatment. CONCLUSIONS: Our findings reveal that changing precipitation seasonality could have considerable impacts on plant phenology by affecting soil water availability and variability. Incorporating these two factors simultaneously in the phenology models will help us understand the response of plant phenology under intensified changing precipitation scenarios. In addition, the observations of decreased dominance for the species with lengthened reproductive duration suggest that changing reproductive phenology can have a potential to affect community composition in grasslands under global change.

Multi-scale beta-diversity patterns in testate amoeba communities: species turnover and nestedness along a latitudinal gradient.

The relationship between species diversity and spatial scale is a central topic in spatial community ecology. Latitudinal gradient is among the core mechanisms driving biodiversity distribution on most scales. Patterns of ß-diversity along latitudinal gradient have been well studied for aboveground terrestrial and marine communities, whereas soil organisms remain poorly investigated in this regard. The West Siberian Plain is a good model to address diversity scale-dependence since the latitudinal gradient does not overlap with other possible factors such as elevational or maritime. Here, we collected 111 samples following hierarchical sampling (sub-zones, ecosystem types, microhabitat and replicate samples) and performed multi-scale partitioning of ß-diversity of testate amoeba assemblages as a model of study. We found that among-ecosystem ß-diversity is a leading scale in testate amoeba assemblages variation. Rare species determine ß-diversity at all scale levels especially in the northern regions, where rare taxa almost exclusively accounted for the diversity at the ecosystem level. ß-Diversity is generally dominated by the turnover component at all scales in lower latitudes, whereas nestedness prevailed at among-ecosystem scale in higher latitudes. These findings indicate that microbial assemblages in northern latitudes are spatially homogeneous and constrained by historical drivers at larger scales, whereas in southern regions, it is dominated by the turnover component both at the microhabitat and ecosystem scales and therefore determined by recent vegetation and environmental heterogeneity. Overall, we have provided the evidence for the existence of negative latitudinal gradient for among-ecosystem ß-diversity but not for among-microhabitat and among-sample ß-diversity for terrestrial testate amoeba communities.

Lateralization of acquisition and consolidation in direction but not amplitude of a motor skill task.

Previous research suggests that the neural processes underlying specification of movement direction and amplitude are independently represented in the nervous system. However, our understanding of acquisition and consolidation processes in the direction and distance learning remains limited. We designed a virtual air hockey task, in which the puck direction is determined by the hand direction at impact, while the puck distance is determined by the amplitude of the velocity. In two versions of this task, participants were required to either specify the direction or the distance of the puck, while the alternate variable did not contribute to task success. Separate groups of right-handed participants were recruited for each task. Each participant was randomly assigned to one of two groups with a counter-balanced arm practice sequence (right to left, or left to right). We examined acquisition and, after 24 h, we examined two aspects of consolidation: 1) same hand performance to test the durability and 2) the opposite hand to test the effector-independent consolidation (interlimb transfer) of learning. The distance task showed symmetry between hands in the extent of acquisition as well as in both aspects of consolidation. In contrast, the direction task showed asymmetry in both acquisition and consolidation: the dominant right arm showed faster and greater acquisition and greater transfer from the opposite arm training. The asymmetric acquisition and consolidation processes shown in the direction task might be explained by lateralized control and mapping of direction, an interpretation consistent with previous findings on motor adaptation paradigms.

Revisiting Dominance in Population Genetics.

Dominance refers to the effect of a heterozygous genotype relative to that of the two homozygous genotypes. The degree of dominance of mutations for fitness can have a profound impact on how deleterious and beneficial mutations change in frequency over time as well as on the patterns of linked neutral genetic variation surrounding such selected alleles. Since dominance is such a fundamental concept, it has received immense attention throughout the history of population genetics. Early work from Fisher, Wright, and Haldane focused on understanding the conceptual basis for why dominance exists. More recent work has attempted to test these theories and conceptual models by estimating dominance effects of mutations. However, estimating dominance coefficients has been notoriously challenging and has only been done in a few species in a limited number of studies. In this review, we first describe some of the early theoretical and conceptual models for understanding the mechanisms for the existence of dominance. Second, we discuss several approaches used to estimate dominance coefficients and summarize estimates of dominance coefficients. We note trends that have been observed across species, types of mutations, and functional categories of genes. By comparing estimates of dominance coefficients for different types of genes, we test several hypotheses for the existence of dominance. Lastly, we discuss how dominance influences the dynamics of beneficial and deleterious mutations in populations and how the degree of dominance of deleterious mutations influences the impact of inbreeding on fitness.

Deep learning can predict subgenome dominance in ancient but not in neo/synthetic polyploidized genomes.

Deep learning offers new approaches to investigate the mechanisms underlying complex biological phenomena, such as subgenome dominance. Subgenome dominance refers to the dominant expression and/or biased fractionation of genes in one subgenome of allopolyploids, which has shaped the evolution of a large group of plants. However, the underlying cause of subgenome dominance remains elusive. Here, we adopt deep learning to construct two convolutional neural network (CNN) models, binary expression model (BEM) and homoeolog contrast model (HCM), to investigate the mechanism underlying subgenome dominance using DNA sequence and methylation sites. We apply these CNN models to analyze three representative polyploidization systems, Brassica, Gossypium, and Cucurbitaceae, each with available ancient and neo/synthetic polyploidized genomes. The BEM shows that DNA sequence of the promoter region can accurately predict whether a gene is expressed or not. More importantly, the HCM shows that the DNA sequence of the promoter region predicts dominant expression status between homoeologous gene pairs retained from ancient polyploidizations, thus predicting subgenome dominance associated with these events. However, HCM fails to predict gene expression dominance between new homoeologous gene pairs arising from the neo/synthetic polyploidizations. These results are consistent across the three plant polyploidization systems, indicating broad applicability of our models. Furthermore, the two models based on methylation sites produce similar results. These results show that subgenome dominance is associated with long-term sequence differentiation between the promoters of homoeologs, suggesting that subgenome expression dominance precedes and is the driving force or even the determining factor for sequence divergence between subgenomes following polyploidization.