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opencc-by-4.0Sep 2022View details →

Data and Source codes: Ancestral sex-role plasticity facilitates the evolution of same-sex sexual behavior

This repository provides access to the tracking data and analysis code used for the manuscript: Ancestral sex-role plasticity facilitates the evolution of same-sex sexual behavior by Nobuaki Mizumoto1, Thomas Bourguignon1, and Nathan W. Bailey2 1 Okinawa Institute of Science & Technology Graduate University, Onna-son, Okinawa, Japan 2 School of Biology, University of St Andrews, St Andrews, U.K. published in the Proceedings of the National Academy of Sciences of the United States of America.

Multilevel selection on social network traits differs between sexes in experimental populations of forked fungus beetles

Both individual and group behavior can influence individual fitness, but multilevel selection is rarely quantified on social behaviors. Social networks provide a unique opportunity to study multilevel selection on social behaviors, as they describe complex social traits and patterns of interaction at both the individual and group levels. In this study, we used contextual analysis to measure the consequences of both individual network position and group network structure on individual fitness in experimental populations of forked fungus beetles (Bolitotherus cornutus) with two different resource distributions. We found that males with high individual connectivity (strength) and centrality (betweenness) had higher mating success. However, group network structure did not influence their mating success. Conversely, we found that individual network position had no effect on female reproductive success but that females in populations with many social interactions experienced lower reproductive success. The strength of individual-level selection in males and group-level selection in females intensified when resources were clumped together, showing that habitat structure influences multilevel selection. Individual and emergent group social behavior both influence variation in components of individual fitness but impact male mating success and female reproductive success differently, setting up intersexual conflicts over patterns of social interactions at multiple levels.

Data from: Sex-dependent effects of parental age on offspring fitness in a cooperatively breeding bird

Parental age can have considerable effects on offspring phenotypes and health. However, intergenerational effects may also have longer-term effects on offspring fitness. Few studies have investigated parental age effects on offspring fitness in natural populations while also testing for sex- and environment-specific effects. Further, longitudinal parental age effects may be masked by population-level processes such as the selective disappearance of poor-quality individuals. Here, we used multi-generational data collected on individually marked Seychelles warblers (Acrocephalus sechellensis) to investigate the impact of maternal and paternal age on offspring lifespan and lifetime reproductive success. We found negative effects of maternal age on female offspring lifespan and lifetime reproductive success, which were driven by within-mother effects. There was no difference in annual reproductive output of females born to older versus younger mothers, suggesting that the differences in offspring lifetime reproductive success were driven by effects on offspring lifespan. In contrast, there was no association between paternal age and female offspring lifespan or either maternal or paternal age and male offspring lifespan. Lifetime reproductive success, but not annual reproductive success, of male offspring increased with maternal age, but this was driven by between-mother effects. No paternal age effects were found on female offspring's lifetime reproductive success but there was a positive between-father effect on male offspring's lifetime reproductive success. We did not find strong evidence for environment-dependent parental age effects. Our study provides evidence for parental age effects on the lifetime fitness of offspring and shows that such effects can be sex-dependent. These results add to the growing literature indicating the importance of intergenerational effects on long-term offspring performance and highlight that these effects can be an important driver of variation in longevity and fitness in the wild.

Limited sex differences in plastic responses suggest evolutionary conservatism of thermal reaction norms: A meta-analysis in insects

Temperature has a profound effect on the growth and development of ectothermic animals. However, the extent to which ecologically-driven selection pressures can adjust thermal plastic responses in growth schedules is not well understood. Comparing temperature-induced plastic responses between sexes provides a promising but underexploited approach to evaluating the evolvability of thermal reaction norms: males and females share largely the same genes and immature environments but typically experience different ecological selection pressures. We proceed from the idea that substantial sex differences in plastic responses could be interpreted as resulting from sex-specific life-history optimization, whereas similarity among the sexes should rather be seen as evidence of an essential role of physiological constraints. In this study, we performed a meta-analysis of sex-specific thermal responses in insect development times, using data on 161 species with comprehensive phylogenetic and ecological coverage. As a reference for judging the magnitude of sex-specificity in thermal plasticity, we compared the magnitude of sex differences in plastic responses to temperature with those in response to diet. We show that sex-specific responses of development times to temperature variation are broadly similar. We also found no strong evidence for sex-specificity in thermal responses to depend on the magnitude or direction of sex differences in development time. Sex differences in temperature-induced plastic responses were systematically less pronounced than sex differences in responses induced by variations in larval diet. Our results point to the existence of substantial constraints on the evolvability of thermal reaction norms in insects as the most likely explanation. If confirmed, the low evolvability of thermal response is an essential aspect to consider in predicting evolutionary responses to climate warming.

opencc-by-4.0Oct 2022View details →

Mitochondrial influence on sex-specific phenotypes within natural populations

Data and scripts for the manuscript entitled "Mitochondrial influence on sex-specific phenotypes within natural populations" submitted to Evolution.

Genotypic sex shapes maternal care in the African Pygmy mouse, Mus minutoides

Sexually dimorphic behaviours, such as parental care, have long been thought to be mainly driven by gonadal hormones. In the past two decades, a few studies have challenged this view, highlighting the direct influence of the sex chromosome complement (XX vs XY or ZZ vs ZW). The African pygmy mouse, Mus minutoides, is a wild mouse species with naturally occurring XY sex reversal induced by a third, feminizing X* chromosome, leading to three female genotypes: XX, XX* and X*Y. Here, we show that sex reversal in X*Y females shapes a divergent maternal care strategy (maternal aggression, pup retrieval and nesting behaviours) from both XX and XX* females. Although neuroanatomical investigations were inconclusive, we show that the dopaminergic system in the anteroventral periventricular nucleus of the hypothalamus is worth investigating further as it may support differences in pup retrieval behaviour between females. Combining behaviours and neurobiology in a rodent subject to natural selection, we evaluate potential candidates for the neural basis of maternal behaviours and strengthen the underestimated role of the sex chromosomes in shaping sex differences in brain and behaviours. All things considered, we further highlight the emergence of a third sexual phenotype, challenging the binary view of phenotypic sexes.

opencc-by-4.0Feb 2014View details →

Supplementary material 2 from: Steinberg E, Nieves M, Mudry M (2014) Multiple sex chromosome systems in howler monkeys (Platyrrhini, Alouatta). Comparative Cytogenetics 8(1): 43-69. https://doi.org/10.3897/compcytogen.v8i1.6716

Supplementary Figure S. (doi: 10.3897/CompCytogen.v8i1.6716.app2) File format: Microsoft Word file (doc).:

opencc-zeroMay 2024View details →

Position in the laying order has sex-specific consequences for reproductive success in adult black-headed gulls

Mothers who produce multiple offspring within one reproductive attempt often allocate resources differentially; some maternally-derived substances are preferentially allocated to last-produced offspring and others to first-produced offspring. The combined effect of these different allocation regimes on the overall fitness of offspring produced early or late in the sequence is not well understood, partly because production order is often coupled with birth order, making it difficult to separate effects of pre-natal maternal allocation from those of post-natal social environments. In addition, very little is known about the influence of laying order on fitness in later-life. In this study, we used a semi-natural captive colony of black-headed gulls to test whether an offspring's position in the laying order affected its early life survival and later life reproductive success, independent of its hatching order. Later-laid eggs were less likely to hatch, but among those that did, survival to adulthood was greater than that of first-laid eggs. In adulthood, the laying order of females did not affect their likelihood of breeding in the colony, but male offspring hatched from last-laid eggs were significantly less likely to gain a breeding position than earlier-laid males. In contrast, later-laid female parents hatched lower proportions of their clutches than first-laid females, but hatching success was unrelated to the laying order of male parents. Our results indicate that gull mothers induce complex and sex-specific effects on both the early survival of their offspring and on long-term reproductive success through laying order effects among eggs of the same breeding attempt.

opencc-by-4.0May 2024View details →

A comprehensive catalog of approxiamte short tandem repeat regions on autosomes and sex chromosomes of the human genome GRCh38

To obtain a general TR catalog across the human genome, we identified genomic intervals with a stretch of approximate repetitions of a DNA motif ranging from 1-6bp on GRCh38 autosomes and sex chromosomes by using STRfinder (v1.0), and each STR region was annotated based on gencode.V38 (https://www.gencodegenes.org/human/release_38.html). To end up, we successfully found 1,656,159 TR intervals, covering 1.107653% (34.2 Mbp) of GRCh38 (https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta).

opencc-zeroMay 2024View details →

Data from: Female-biased population sex ratios caused by genetic rather than ecological mechanisms in dwarf willow (Salix herbacea L.)

Biased sex ratios among reproductive individuals are common in plants, but the underlying mechanisms, as well as the evolutionary consequences, are not well understood. The classical theory of Düsing and Fisher predicts an equal primary sex ratio at seed production, based on the selective advantage of the rare sex. Biased sex ratios among reproductive plants can arise from sexual dimorphism in survival and flowering. Sex ratio biases can also be present from the seed stage; in these cases, assumptions of Düsing's and Fisher's theory, for example, random mating or demographic equilibrium, are thought to be violated. We investigated mechanisms leading to female-biased sex ratios in the arctic-alpine dwarf willow Salix herbacea L. We studied sex ratios in three natural populations over three years as well as in 29 crosses (full-sib families) under controlled conditions over four growth periods. We tested whether sex ratio was associated with habitat parameters (elevation and snowmelt time), or with germination, survival or flowering, and whether females and males differed in size or flowering that may cause observation bias. We detected a strong and consistent female bias, both in natural populations (sex ratio [proportion of females]: 0.71-0.82) and in our controlled experiment (overall sex ratio: 0.70-0-72). Female bias became more pronounced with increasing elevation. Our data did not support sexual dimorphism in size or flowering. Family sex ratios varied largely (from 0.25 to 1), including many female-biased families, unbiased families and two male-biased families. Families with lower germination, seedling establishment, survival or flowering did not have stronger female bias, indicating that intrinsically higher survival or flowering in females does not explain overall female bias. Synthesis: Our results suggest that sex ratio bias in S. herbacea is already present in seeds and does not arise through intrinsic differences between sexes. Candidate mechanisms that can lead to both overall female bias and variation in sex ratio among families are meiotic drive or cyto-nuclear interactions. The pioneer habit of Salix may lead to non-equilibrium population dynamics that allow for the long-term persistence of variable genetic sex ratio distortion systems that arise from genetic conflict.

Figure 2 in Phallus eversion sexing in Phrynops geoffroanus (Testudines: Chelidae): a new non-invasive approach

Figure 2. Frequency polygon between success rate and phallus eversion methods in Phrynops geoffroanus.

Figure 1 in Phallus eversion sexing in Phrynops geoffroanus (Testudines: Chelidae): a new non-invasive approach

Figure 1. Phrynops geoffroanus in (A) ventral view of the male; (B) Ventral view of the female; Greater tail prominence in female (B) and absence of plastron concavity in both sexes.

Figure 3 in Phallus eversion sexing in Phrynops geoffroanus (Testudines: Chelidae): a new non-invasive approach

Figure 3. Timing of stimulus time required for phallus eversion in Phrynops geoffroanus, for methods 4 and 5.

Figure 4 in Phallus eversion sexing in Phrynops geoffroanus (Testudines: Chelidae): a new non-invasive approach

Figure 4. Phrynops geoffroanus' phallus eversion in three stages: (A) primary with only the apical portion; (B) partial engorgement; (C) total engorgement; (D) engorgement with apical exposure.

opencc-by-4.0Jun 2024View details →

Real-world comprehensive genomic and immune profiling reveals distinct age- and sex-based genomic and immune landscapes in tumors of patients with non-small cell lung cancer

Wallen ZD, Ko H, Nesline MK, Hastings SB, Strickland KC, Previs RA, Zhang S, Pabla S, Conroy J, Jackson JB, Saini KS, Jensen TJ, Eisenberg M, Caveney B, Sathyan P, Severson EA, Ramkissoon SH. Real-world comprehensive genomic and immune profiling reveals distinct age- and sex-based genomic and immune landscapes in tumors of patients with non-small cell lung cancer. Front Immunol. 2024 Jun 21;15:1413956. doi: <a href="https://doi.org/10.3389/fimmu.2024.1413956">10.3389/fimmu.2024.1413956</a>. PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38975340/">38975340</a>; PMCID: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11224431/">PMC11224431</a>. ABSTRACT Younger patients with non-small cell lung cancer (NSCLC) (<50 years) represent a significant patient population with distinct clinicopathological features and enriched targetable genomic alterations compared to older patients. However, previous studies of younger NSCLC suffer from inconsistent findings, few studies have incorporated sex into their analyses, and studies targeting age-related differences in the tumor immune microenvironment are lacking. We performed a retrospective analysis of 8,230 patients with NSCLC, comparing genomic alterations and immunogenic markers of younger and older patients while also considering differences between male and female patients. We defined older patients as those ≥65 years and used a 5-year sliding threshold from <45 to <65 years to define various groups of younger patients. Additionally, in an independent cohort of patients with NSCLC, we use our observations to inform testing of the combinatorial effect of age and sex on survival of patients given immunotherapy with or without chemotherapy. We observed distinct genomic and immune microenvironment profiles for tumors of younger patients compared to tumors of older patients. Younger patient tumors were enriched in clinically relevant genomic alterations and had gene expression patterns indicative of reduced immune system activation, which was most evident when analyzing male patients. Further, we found younger male patients treated with immunotherapy alone had significantly worse survival compared to male patients ≥65 years, while the addition of chemotherapy reduced this disparity. Contrarily, we found younger female patients had significantly better survival compared to female patients ≥65 years when treated with immunotherapy plus chemotherapy, while treatment with immunotherapy alone resulted in similar outcomes. These results show the value of comprehensive genomic and immune profiling (CGIP) for informing clinical treatment of younger patients with NSCLC and provides support for broader coverage of CGIP for younger patients with advanced NSCLC. DATA AVAILABILITY:  De-identified, individual-level patient data, genomic variants, and individual immune gene expression data used in the manuscript can be found in this repository (https://zenodo.org/record/11396552). An R markdown file with R code used to perform the analyses and generate figures is also provided in the repository along with the data. All versions of software used are provided in the Methods section of the manuscript. Raw sequencing data were derived from routine clinical testing of real-world patients and cannot be shared publicly. Data for immune gene expression signatures are not publicly available due to a non‑provisional patent filing covering the methods used to generate and analyze these data but are available from the corresponding author on reasonable request.

opencc-zeroJun 2024View details →

Pesticide exposure triggers sex-specific inter- and trans-generational effects conditioned by past sexual selection

Environmental variation often induces plastic responses in organisms that can trigger changes in subsequent generations through non-genetic inheritance mechanisms. Such transgenerational plasticity thus consists of environmentally-induced non-random phenotypic modifications that are transmitted through generations. Transgenerational effects may vary according to the sex of the organism experiencing the environmental perturbation, the sex of their descendants, or both, but whether they are affected by past sexual selection is unknown. Here we use experimental evolution on an insect model system to conduct a first test of the involvement of sexual selection history in shaping transgenerational plasticity in the face of rapid environmental change (exposure to pesticides). We manipulated evolutionary history in terms of the intensity of sexual selection for over 80 generations before exposing individuals to the toxicant. We found that sexual selection history constrained adaptation under rapid environmental change. We also detected intergenerational and transgenerational effects of pesticide exposure in the form of increased fitness and longevity. These cross-generational influences of toxicants were sex-dependent (they affected only male descendants), and intergenerational, but not transgenerational, plasticity was modulated by sexual selection history. Our results highlight the complexity of intragenerational, intergenerational, and transgenerational influences of past selection and environmental stress on phenotypic expression.

Figure 3 in Response of Invasive Longhorn Beetles (Coleoptera: Lamiinae) to Known Cerambycid Aggregation-Sex Pheromones in the Puna District of Hawaii Island

Figure 3. Mean (± SE) numbers of PLB (Lagocheirus obsoletus) caught in traps baited with solvent control, fuscumol acetate, or monochamol (experiment 1). Means with an asterisk are significantly different than the solvent control (max-t test, p <0.05).

Figure 2 in Response of Invasive Longhorn Beetles (Coleoptera: Lamiinae) to Known Cerambycid Aggregation-Sex Pheromones in the Puna District of Hawaii Island

Figure 2. Mean (± SE) numbers of QLB (Acalolepta aesthetica) caught in traps baited with solvent control, fuscumol, fuscumol acetate, geranylacetone, or a blend of the three compounds (experiment 2). There were no significant differences between the treatments and the solvent control (max-t test, p> 0.05).

Figure 1 in Response of Invasive Longhorn Beetles (Coleoptera: Lamiinae) to Known Cerambycid Aggregation-Sex Pheromones in the Puna District of Hawaii Island

Figure 1. Mean (± SE) numbers of QLB (Acalolepta aesthetica) caught in traps baited with solvent control, fuscumol acetate, or monochamol (experiment 1). There were no significant differences between the treatments and the solvent control (max-t test, p> 0.05).

Figure 4 in Response of Invasive Longhorn Beetles (Coleoptera: Lamiinae) to Known Cerambycid Aggregation-Sex Pheromones in the Puna District of Hawaii Island

Figure 4. Mean (± SE) numbers of PLB (Lagocheirus obsoletus) caught in traps baited with solvent control, fuscumol, fuscumol acetate, geranylacetone, or a blend of the three compounds (experiment 2). Means with an asterisk are significantly different than the solvent control (max-t test, p <0.05).