Reproductive inequality in humans and other mammals.

To address claims of human exceptionalism, we determine where humans fit within the greater mammalian distribution of reproductive inequality. We show that humans exhibit lower reproductive skew (i.e., inequality in the number of surviving offspring) among males and smaller sex differences in reproductive skew than most other mammals, while nevertheless falling within the mammalian range. Additionally, female reproductive skew is higher in polygynous human populations than in polygynous nonhumans mammals on average. This patterning of skew can be attributed in part to the prevalence of monogamy in humans compared to the predominance of polygyny in nonhuman mammals, to the limited degree of polygyny in the human societies that practice it, and to the importance of unequally held rival resources to women's fitness. The muted reproductive inequality observed in humans appears to be linked to several unusual characteristics of our species-including high levels of cooperation among males, high dependence on unequally held rival resources, complementarities between maternal and paternal investment, as well as social and legal institutions that enforce monogamous norms.

Estimating bonobo (Panpaniscus) and chimpanzee (Pantroglodytes) evolutionary history from nucleotide site patterns.

Admixture appears increasingly ubiquitous in the evolutionary history of various taxa, including humans. Such gene flow likely also occurred among our closest living relatives: bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). However, our understanding of their evolutionary history has been limited by studies that do not consider all Pan lineages or do not analyze all lineages simultaneously, resulting in conflicting demographic models. Here, we investigate this gap in knowledge using nucleotide site patterns calculated from whole-genome sequences from the autosomes of 71 bonobos and chimpanzees, representing all five extant Pan lineages. We estimated demographic parameters and compared all previously proposed demographic models for this clade. We further considered sex bias in Pan evolutionary history by analyzing the site patterns from the X chromosome. We show that 1) 21% of autosomal DNA in eastern chimpanzees derives from western chimpanzee introgression and that 2) all four chimpanzee lineages share a common ancestor about 987,000 y ago, much earlier than previous estimates. In addition, we suggest that 3) there was male reproductive skew throughout Pan evolutionary history and find evidence of 4) male-biased dispersal from western to eastern chimpanzees. Collectively, these results offer insight into bonobo and chimpanzee evolutionary history and suggest considerable differences between current and historic chimpanzee biogeography.

Effective Manipulation of a Colossal Second-Order Transverse Response in an Electric-Field-Tunable Graphene Moiré System.

The second-order nonlinear transport illuminates a frequency-doubling response emerging in quantum materials with a broken inversion symmetry. The two principal driving mechanisms, the Berry curvature dipole and the skew scattering, reflect various information including ground-state symmetries, band dispersions, and topology of electronic wave functions. However, effective manipulation of them in a single system has been lacking, hindering the pursuit of strong responses. Here, we report on the effective manipulation of the two mechanisms in a single graphene moiré superlattice, AB-BA stacked twisted double bilayer graphene. Most saliently, by virtue of the high tunability of moiré band structures and scattering rates, a record-high second-order transverse conductivity ∼ 510 µm S V-1 is observed, which is orders of magnitude higher than any reported values in the literature. Our findings establish the potential of electrically tunable graphene moiré systems for nonlinear transport manipulations and applications.

Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection.

BACKGROUND: Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures. RESULTS: Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection. CONCLUSIONS: Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.

Identification of skewed X chromosome inactivation using exome and transcriptome sequencing in patients with suspected rare genetic disease.

BACKGROUND: X-chromosome inactivation (XCI) is an epigenetic process that occurs during early development in mammalian females by randomly silencing one of two copies of the X chromosome in each cell. The preferential inactivation of either the maternal or paternal copy of the X chromosome in a majority of cells results in a skewed or non-random pattern of X inactivation and is observed in over 25% of adult females. Identifying skewed X inactivation is of clinical significance in patients with suspected rare genetic diseases due to the possibility of biased expression of disease-causing genes present on the active X chromosome. The current clinical test for the detection of skewed XCI relies on the methylation status of the methylation-sensitive restriction enzyme (Hpall) binding site present in proximity of short tandem polymorphic repeats on the androgen receptor (AR) gene. This approach using one locus results in uninformative or inconclusive data for 10-20% of tests. Further, recent studies have shown inconsistency between methylation of the AR locus and the state of inactivation of the X chromosome. Herein, we develop a method for estimating X inactivation status, using exome and transcriptome sequencing data derived from blood in 227 female samples. We built a reference model for evaluation of XCI in 135 females from the GTEx consortium. We tested and validated the model on 11 female individuals with different types of undiagnosed rare genetic disorders who were clinically tested for X-skew using the AR gene assay and compared results to our outlier-based analysis technique. RESULTS: In comparison to the AR clinical test for identification of X inactivation, our method was concordant with the AR method in 9 samples, discordant in 1, and provided a measure of X inactivation in 1 sample with uninformative clinical results. We applied this method on an additional 81 females presenting to the clinic with phenotypes consistent with different hereditary disorders without a known genetic diagnosis. CONCLUSIONS: This study presents the use of transcriptome and exome sequencing data to provide an accurate and complete estimation of X-inactivation and skew status in a cohort of female patients with different types of suspected rare genetic disease.

The natural history of luck: A synthesis study of structured population models.

Chance pervades life. In turn, life histories are described by probabilities (e.g. survival and breeding) and averages across individuals (e.g. mean growth rate and age at maturity). In this study, we explored patterns of luck in lifetime outcomes by analysing structured population models for a wide array of plant and animal species. We calculated four response variables: variance and skewness in both lifespan and lifetime reproductive output (LRO), and partitioned them into contributions from different forms of luck. We examined relationships among response variables and a variety of life history traits. We found that variance in lifespan and variance in LRO were positively correlated across taxa, but that variance and skewness were negatively correlated for both lifespan and LRO. The most important life history trait was longevity, which shaped variance and skew in LRO through its effects on variance in lifespan. We found that luck in survival, growth, and fecundity all contributed to variance in LRO, but skew in LRO was overwhelmingly due to survival luck. Rapidly growing populations have larger variances in LRO and lifespan than shrinking populations. Our results indicate that luck-induced genetic drift may be most severe in recovering populations of species with long mature lifespan and high iteroparity.

High Nucleotide Skew Palindromic DNA Sequences Function as Potential Replication Origins due to their Unzipping Propensity.

Locations of DNA replication initiation in prokaryotes, called "origins of replication", are well-characterized. However, a mechanistic understanding of the sequence dependence of the local unzipping of double-stranded DNA, the first step towards replication initiation, is lacking. Here, utilizing a Markov chain model that was created to address the directional nature of DNA unzipping and replication, we model the sequence dependence of local melting of double-stranded linear DNA segments. We show that generalized palindromic sequences with high nucleotide skews have a low kinetic barrier for local melting near melting temperatures. This allows for such sequences to function as potential replication origins. We support our claim with evidence for high-skew palindromic sequences within the replication origins of mitochondrial DNA, bacteria, archaea and plasmids.

Strength of Sexual Selection and Sex Roles Vary between Social Groups in a Coral Reef Cardinalfish.

AbstractThe strength and direction of sexual selection can vary among populations. However, spatial variability is rarely explored at the level of the social group. Here we investigate sexual selection and sex roles in the paternally mouthbrooding, socially monogamous, and site-attached pajama cardinalfish, Sphaeramia nematoptera. Females were larger and more aggressive and had a longer dorsal fin filament, indicating reversed sex roles. At the scale of social groups, we show that the Bateman gradient and reproductive variance depend on the sex ratio and size of groups. In small and medium-sized groups with balanced or male-biased sex ratios, Bateman gradients were steeper for females, whereas gradients were equally steep for both sexes in large groups or when the sex ratio was female biased. For both sexes, reproductive variance increased with group size and with a higher male-to-female sex ratio. In S. nematoptera, mating opportunities outside the socially monogamous pair appear to impact sexual selection. We conclude that strength and direction of sexual selection can be masked by social dynamics in group-living species when considering only population and large-scale demographic processes.

To Prosper, Live Long: Understanding the Sources of Reproductive Skew and Extreme Reproductive Success in Structured Populations.

AbstractIn many species, a few individuals produce most of the next generation. How much of this reproductive skew is driven by variation among individuals in fixed traits, how much by external factors, and how much by random chance? And what does it take to have truly exceptional lifetime reproductive output (LRO)? In the past, we and others have partitioned the variance of LRO as a proxy for reproductive skew. Here we explain how to partition LRO skewness itself into contributions from fixed trait variation, four forms of "demographic luck" (birth state, fecundity luck, survival trajectory luck, and growth trajectory luck), and two kinds of "environmental luck" (birth environment and environment trajectory). Each of these is further partitioned into contributions at different ages. We also determine what we can infer about individuals with exceptional LRO. We find that reproductive skew is largely driven by random variation in lifespan, and exceptional LRO generally results from exceptional lifespan. Other kinds of luck frequently bring skewness down rather than increasing it. In populations where fecundity varies greatly with environmental conditions, getting a good year at the right time can be an alternate route to exceptional LRO, so that LRO is less predictive of lifespan.

A female-biased gene expression signature of dominance in cooperatively breeding meerkats.

Dominance is a primary determinant of social dynamics and resource access in social animals. Recent studies show that dominance is also reflected in the gene regulatory profiles of peripheral immune cells. However, the strength and direction of this relationship differs across the species and sex combinations investigated, potentially due to variation in the predictors and energetic consequences of dominance status. Here, we investigated the association between social status and gene expression in the blood of wild meerkats (Suricata suricatta; n = 113 individuals), including in response to lipopolysaccharide, Gardiquimod (an agonist of TLR7, which detects single-stranded RNA in vivo) and glucocorticoid stimulation. Meerkats are cooperatively breeding social carnivores in which breeding females physically outcompete other females to suppress reproduction, resulting in high reproductive skew. They therefore present an opportunity to disentangle the effects of social dominance from those of sex per se. We identify a sex-specific signature of dominance, including 1045 differentially expressed genes in females but none in males. Dominant females exhibit elevated activity in innate immune pathways and a larger fold-change response to LPS challenge. Based on these results and a preliminary comparison to other mammals, we speculate that the gene regulatory signature of social status in the immune system depends on the determinants and energetic costs of social dominance, such that it is most pronounced in hierarchies where physical competition is important and reproductive skew is large. Such a pattern has the potential to mediate life history trade-offs between investment in reproduction versus somatic maintenance.

Demographic inference for spatially heterogeneous populations using long shared haplotypes.

We introduce a modified spatial Λ-Fleming-Viot process to model the ancestry of individuals in a population occupying a continuous spatial habitat divided into two areas by a sharp discontinuity of the dispersal rate and effective population density. We derive an analytical formula for the expected number of shared haplotype segments between two individuals depending on their sampling locations. This formula involves the transition density of a skew diffusion which appears as a scaling limit of the ancestral lineages of individuals in this model. We then show that this formula can be used to infer the dispersal parameters and the effective population density of both regions, using a composite likelihood approach, and we demonstrate the efficiency of this method on a range of simulated data sets.

Illumination matters Part III: Impact of light obstruction on illuminance from flexible ureteroscopes - a comparative PEARLS analysis.

PURPOSE: Artifacts from poor ureteroscopes' light design with shadowing and dark areas in the field of view have been reported. The aim was to quantify effects of light obstruction in a kidney calyx model. METHODS: We evaluated a series of contemporary flexible ureteroscopes including the Storz Flex-Xc and Flex-X2s, Olympus V3 and P7, Pusen 7.5F and 9.2F, as well as OTU Wiscope using an enclosed 3D-printed pink in vitro kidney calyx model submerged in saline, where the field of light was intentionally partially obstructed alternatively at 12, 3, 6, and 9 o'clock. A color spectrometer was used for illuminance measurements at a 45° opening position in the background of the model. RESULTS: Overall and mean background illuminance for each obstructive situation were significantly different between scopes for both 50% and 100% brightness settings (ANOVA p < 0.001). At 50% brightness setting, almost all scopes had their highest and lowest background illuminance with the 6 o'clock and 3 o'clock obstructive situation, respectively. At 100% brightness setting, these became 6 o'clock and 12 o'clock obstructive situations. Considering each obstructive situation individually, the Flex-Xc was consistently the scope with highest background illuminance and the Pusen 7.5F the lowest. Background illuminance for each obstructive situation varied significantly for each scope individually, with the greatest range of variability for Pusen 7.5F and V3. CONCLUSIONS: Illuminance performance of ureteroscopes within an obstructed calyx model differ significantly for various obstructive situations. Urologists should be aware of this to help guide their choice of ureteroscope.

Flexible Bayesian semiparametric mixed-effects model for skewed longitudinal data.

BACKGROUND: In clinical trials and epidemiological research, mixed-effects models are commonly used to examine population-level and subject-specific trajectories of biomarkers over time. Despite their increasing popularity and application, the specification of these models necessitates a great deal of care when analysing longitudinal data with non-linear patterns and asymmetry. Parametric (linear) mixed-effect models may not capture these complexities flexibly and adequately. Additionally, assuming a Gaussian distribution for random effects and/or model errors may be overly restrictive, as it lacks robustness against deviations from symmetry. METHODS: This paper presents a semiparametric mixed-effects model with flexible distributions for complex longitudinal data in the Bayesian paradigm. The non-linear time effect on the longitudinal response was modelled using a spline approach. The multivariate skew-t distribution, which is a more flexible distribution, is utilized to relax the normality assumptions associated with both random-effects and model errors. RESULTS: To assess the effectiveness of the proposed methods in various model settings, simulation studies were conducted. We then applied these models on chronic kidney disease (CKD) data and assessed the relationship between covariates and estimated glomerular filtration rate (eGFR). First, we compared the proposed semiparametric partially linear mixed-effect (SPPLM) model with the fully parametric one (FPLM), and the results indicated that the SPPLM model outperformed the FPLM model. We then further compared four different SPPLM models, each assuming different distributions for the random effects and model errors. The model with a skew-t distribution exhibited a superior fit to the CKD data compared to the Gaussian model. The findings from the application revealed that hypertension, diabetes, and follow-up time had a substantial association with kidney function, specifically leading to a decrease in GFR estimates. CONCLUSIONS: The application and simulation studies have demonstrated that our work has made a significant contribution towards a more robust and adaptable methodology for modeling intricate longitudinal data. We achieved this by proposing a semiparametric Bayesian modeling approach with a spline smoothing function and a skew-t distribution.

Transient vertical diplopia following ibuprofen intake: a case report.

Ibuprofen, a commonly used over-the-counter medication, is widely recognized for its effective pain relief properties but is also associated with various adverse effects, including rare ocular and neurological manifestations. We report a case of a 27-year-old male who experienced transient vertical diplopia following a standard ibuprofen dosage for back pain. Symptoms resolved promptly upon discontinuation of the drug, with normal findings on extensive clinical and laboratory evaluations. The clinical presentation, suggestive of skew deviation, implies central toxicity. This case underscores the potential for diplopia associated with NSAIDs like ibuprofen to be underdiagnosed and offers valuable insights into the central toxicity of ibuprofen. Further research is warranted to elucidate the underlying mechanisms and optimize patient care in similar scenarios.

Assessing Variance in Male Reproductive Skew Based on Long-Term Data in Free-Ranging Rhesus Macaques.

The unequal share in male reproduction (male reproductive skew) has been reported across primate species. To explain the distribution of male reproduction within groups various skew models have been applied to primates, however the "dynamic tug-of-war" model first accounted for the specifics of primate sociality. This model assumes that an increase in the number of competing males, a high degree of female cycle synchrony and their interaction will result in a lower degree of male reproductive skew. Here, we first tested the predictors of this model in rhesus macaques (Macaca mulatta) using long-term demographic and genetic data (up to 9 groups over 22 seasons) of the Cayo Santiago population (Puerto Rico). We also tested an extended version including group size and sex ratio and their interaction with female cycle synchrony. Finally, we investigated which male attributes determine the probability to become a top sire (highest paternity share per group and season). Confirming studies, male rhesus macaques exhibited low to medium degrees of reproductive skew based on the multinomial index, M. Unlike predicted, reproductive skew was higher in groups with more males. The extended analysis suggested that reproductive skew increased with group size in more male-biased groups, but decreased with group size in female-biased groups indicating that the numbers of male and female group members matter. We detected no effect of female cycle synchrony on the variance of reproductive skew. Finally, only maternal rank predicted the probability to become a top sire as long as males resided in their natal group. Together, our results did not support predictions by the dynamic skew model in rhesus macaques, but strengthen studies suggesting that other factors in addition to male-male competition predict male reproductive output in rhesus macaques. Future skew studies should consider female choice and alternative male mating strategies.

GRINS: Genetic elements that recode assembly-line polyketide synthases and accelerate their diversification.

Assembly-line polyketide synthases (PKSs) are large and complex enzymatic machineries with a multimodular architecture, typically encoded in bacterial genomes by biosynthetic gene clusters. Their modularity has led to an astounding diversity of biosynthesized molecules, many with medical relevance. Thus, understanding the mechanisms that drive PKS evolution is fundamental for both functional prediction of natural PKSs as well as for the engineering of novel PKSs. Here, we describe a repetitive genetic element in assembly-line PKS genes which appears to play a role in accelerating the diversification of closely related biosynthetic clusters. We named this element GRINS: genetic repeats of intense nucleotide skews. GRINS appear to recode PKS protein regions with a biased nucleotide composition and to promote gene conversion. GRINS are present in a large number of assembly-line PKS gene clusters and are particularly widespread in the actinobacterial genus Streptomyces While the molecular mechanisms associated with GRINS appearance, dissemination, and maintenance are unknown, the presence of GRINS in a broad range of bacterial phyla and gene families indicates that these genetic elements could play a fundamental role in protein evolution.

A Complex Environmental Water-Level Detection Method Based on Improved YOLOv5m.

The existing methods for water-level recognition often suffer from inaccurate readings in complex environments, which limits their practicality and reliability. In this paper, we propose a novel approach that combines an improved version of the YOLOv5m model with contextual knowledge for water-level identification. We employ the adaptive threshold Canny operator and Hough transform for skew detection and correction of water-level images. The improved YOLOv5m model is employed to extract the water-level gauge from the input image, followed by refinement of the segmentation results using contextual priors. Additionally, we utilize a linear regression model to predict the water-level value based on the pixel height of the water-level gauge. Extensive experiments conducted in real-world environments encompassing daytime, nighttime, occlusion, and lighting variations demonstrate that our proposed method achieves an average error of less than 2 cm.

Main Factors Shaping Amino Acid Usage Across Evolution.

The standard genetic code determines that in most species, including viruses, there are 20 amino acids that are coded by 61 codons, while the other three codons are stop triplets. Considering the whole proteome each species features its own amino acid frequencies, given the slow rate of change, closely related species display similar GC content and amino acids usage. In contrast, distantly related species display different amino acid frequencies. Furthermore, within certain multicellular species, as mammals, intragenomic differences in the usage of amino acids are evident. In this communication, we shall summarize some of the most prominent and well-established factors that determine the differences found in the amino acid usage, both across evolution and intragenomically.

Unequal Reproduction Early in a Social Transition: Insights from Invasive Wasps.

AbstractIn eusocial insects, nestmate queens can differ in their reproductive output, causing asymmetries in the distribution of mutual benefits. However, little is known about how reproductive success is partitioned in incipiently polygynous species, which would provide clues about the evolutionary forces shaping the emergence of polygyny. Here, we leverage a recent transition from predominantly single-queen (monogyne) to multiple-queen (polygyne) colonies in an invasive yellowjacket species to investigate whether queens in incipiently polygyne colonies invest equally in reproductive effort or vary in their relative investment in each caste. We excavated nine polygyne Vespula pensylvanica colonies in Hawaii and used restriction site-associated DNA sequencing to infer the parentage of worker, male, and gyne (daughter queen) pupae from each nest comb. In four colonies with at least eight gyne pupae, a single queen produced most or all gynes. These queens had no male offspring and few worker offspring, suggesting that a subset of nestmate queens might exploit the collective benefits of newly polygyne societies. In contrast to most queens, gyne producers had offspring distributed nonrandomly across nest combs. Nestmate queens generally exhibited low relatedness levels. Our results suggest that rapid, ecologically driven transitions to polygyny among unrelated queens may, at their onset, be vulnerable to reproductive asymmetries that are likely evolutionarily unstable. More broadly, this study contributes to the understanding of social evolution by uncovering asymmetric partitioning of reproduction in a population with newly evolved polygyny and raises questions about the future trajectories of introduced populations.

Queen fecundity, worker entourage and cuticular chemistry in the ant Formica fusca.

Cooperative breeding entails conflicts over reproductive shares that may be settled in different ways. In ants, where several queens simultaneously reproduce in a colony, both queens and workers may influence the reproductive apportionment and offspring quality. Queens may vary in their intrinsic fecundity, which may influence the size of the worker entourage attending individual queens, and this may eventually dictate the reproductive output of a queen. We tested whether the reproductive success of queens is affected by the size of their worker entourage, their fecundity at the onset of the reproductive season, and whether the queen cuticular hydrocarbon profile carries information on fecundity. We show that in the ant Formica fusca both queen fecundity and egg hatching success increase with the size of their entourage, and that newly hatched larvae produced by initially highly fecund queens are smaller. Furthermore, higher relatedness among workers increased queen fecundity. Finally, the queens that received a large worker entourage differed in the cuticular chemistry from those that received a small worker entourage. Our results thus show that workers play a pivotal role in determining queen fitness, that high intracolony relatedness among workers enhances the overall reproductive output in the colony, and that queen fecundity is reflected in their cuticular hydrocarbon profile.