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Fig. 6 in Description of new Ceratitis species (Diptera: Tephritidae) from Africa, or how morphological and DNA data are complementary in discovering unknown species and matching sexes
Fig. 6. Ceratitis serrata De Meyer, 1996. a. Head, frontal view. b. Head and thorax, anterodorsal view. c. Thorax, lateral view. d. Thorax, dorsal view. e. Abdomen, dorsal view. Scale bars: A = 0.5 mm; B–D = 1 mm.
Fig. 3 in Description of new Ceratitis species (Diptera: Tephritidae) from Africa, or how morphological and DNA data are complementary in discovering unknown species and matching sexes
Fig. 3. Ceratitis taitaensis De Meyer & Copeland sp. nov. a. Head and thorax, anterodorsal view. b. Thorax, lateral view. c. Thorax, dorsal view. d. Abdomen, dorsal view. e. Male wing. f. Female wing. g. Female aculeus. h. Aculeus tip. Scale bars: A–F = 1 mm; G–H = 0.1mm.
Fig. 4 in Description of new Ceratitis species (Diptera: Tephritidae) from Africa, or how morphological and DNA data are complementary in discovering unknown species and matching sexes
Fig. 4. Ceratitis sawahilensis De Meyer & Virgilio sp. nov. a. Head and thorax, anterodorsal view. b. Thorax, lateral view. c. Thorax, dorsal view. d. Abdomen, dorsal view. e. Wing. f. Habitus image (credit: S.A. Marshall). g. Female aculeus. h. Aculeus tip. Scale bars: A–F = 1 mm; G–H = 0.1 mm.
Fig. 2 in Description of new Ceratitis species (Diptera: Tephritidae) from Africa, or how morphological and DNA data are complementary in discovering unknown species and matching sexes
Fig. 2. Ceratitis pallidula De Meyer, Mwatawala & Virgilio sp. nov. a. Head and thorax, anterodorsal view. b. Head and thorax, lateral view. c. Thorax, dorsal view. d. Abdomen, dorsal view. e. Wing. Scale bars = 1 mm.
Fig. 1. — a–f in Description of new Ceratitis species (Diptera: Tephritidae) from Africa, or how morphological and DNA data are complementary in discovering unknown species and matching sexes
Fig. 1. — a–f. Ceratitis quilicii De Meyer, Mwatawala & Virgilio sp. nov. Ƌ. a. Head and thorax, anterodorsal view. b. Head and thorax, lateral view. c. Thorax, dorsal view. d. Midleg, anterior view. e. Wing. f. Midtibia, anterior view. — g. C. rosa Karsch, 1887 s.str. midtibia, anterior view. Scale bars = 1 mm.
Data from: Neo-sex chromosomes and demography shape genetic diversity in the critically endangered Raso lark
Generally small effective population sizes expose island species to inbreeding and loss of genetic variation. The Raso lark has been restricted to a single islet for ~500 years, with a population size of a few hundred. To investigate the factors shaping genetic diversity in the species, we assembled a reference genome for the related Eurasian skylark and then assessed genomic diversity and demographic history using RAD-seq data (26 Raso lark samples and 52 samples from its two most closely related mainland species). Genetic diversity in the Raso lark is lower than in its mainland relatives, but is nonetheless considerably higher than anticipated given its recent population size. This is partly explained by an unusual and dramatic effect of enlarged neo-sex chromosomes, which preserve high heterozygosity across 13% of the genome in females, and account for half of the overall genetic diversity in the population. In addition, by reconstructing past demography we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Nevertheless, relatedness analyses suggest that the population is at risk of inbreeding depression. Our findings are particularly important in that they reveal the hidden effects of genome architecture in shaping diversity estimates, and hence demonstrate the value of a reference genome and population genomic analyses over conventional metrics to study diversity in non-model and endangered species.
Genome-wide association summary statistics for sex- and age-specific analysis of chronic back pain
<p>The dataset comprises summary-level statistics for age- and sex-specific genome-wide association study of chronic back pain (cBP) in individuals of European descent from UK Biobank (<a href="https://www.ukbiobank.ac.uk/">https://www.ukbiobank.ac.uk/</a>). The study was carried out under UK Biobank approved project #18219. </p> <p><strong>The dataset accompanies the paper (please cite if using the dataset):</strong></p> <p><a href="https://pubmed.ncbi.nlm.nih.gov/33021770/">Freidin, Maxim B.; Tsepilov, Yakov A.; Stanaway, Ian B.; Meng, Weihua; Hayward, Caroline; Smith, Blair H.; Khoury, Samar; Parisien, Marc; Bortsov, Andrey; Diatchenko, Luda; Børte, Sigrid; Winsvold, Bendik S.; Brumpton, Ben M.; Zwart, John-Anker; HUNT All-In Pain; Aulchenko, Yurii S.; Suri, Pradeep; Williams, Frances M.K. Sex- and age-specific genetic analysis of chronic back pain. Pain. 2020. doi:10.1097/j.pain.0000000000002100.</a></p> <p>The phenotype of cBP was defined as back pain for 3+ months. Linear mixed-effects additive model was fitted adjusting for age, genotyping array type, and 10 genetic PCs provided by UK Biobank. The following filters were applied: minor allele frequency >0.001, genotyping and individual call rates >0.98%, imputation quality score (INFO) >0.7. GWAS were carried out in males and females separately in the whole sample (<strong>allages</strong>) as well as in groups of younger than 65 years (<strong>under65</strong>) and 65+ years old (<strong>65plus</strong>) as detailed in the paper. Accordingly, 6 files are deposited here, corresponding to each group. </p> <p><strong>Column headers:</strong></p> <p>SNP, SNP rsID </p> <p>CHR, chromosome</p> <p>BP, genomic position (GRCh37 build)</p> <p>EA, effect allele (coded as "1")</p> <p>OTHER, other allele (coded as "0")</p> <p>A1FREQ, frequency of effect allele</p> <p>INFO, imputation quality</p> <p>BETA, effect size (for effect allele)</p> <p>SE, standard error of effect size</p> <p>PVAL, p-value for association</p>
Sex, shells, and weaponry: Coercive reproductive tactics in the Painted Turtle, Chrysemys picta
<p><strong>Abstract. </strong>Males and females have divergent reproductive interests arising from their unequal investments in offspring. This sexual conflict drives an antagonistic arms-race that influences sex-specific reproductive success. Alternative reproductive tactics are expected in long-lived species for which the reproductive strategy that maximizes mating success could differ across body sizes. The mating strategy of the painted turtle (<em>Chrysemys picta</em>) has been characterized as an elaborate and amiable male courtship display during which males use their elongate foreclaws to stroke females, coupled with female mate choice. Contrary to this long-held understanding, <em>in situ</em> field observations and experimental trials from our long-term study in Algonquin Provincial Park, Canada, demonstrate that males also exhibit an alternative, coercive mating strategy. Males are equipped with sexually-size dimorphic tomiodonts, tooth-like cusps of the beak, as well as a weaponized anterior shell, with which they wound the head and neck of females. Behavioral trials during the breeding periods showed that male reproductive tactics shift from courtship (foreclaw display) to coercion (striking, biting, and forced submergence) across ontogeny, and male size predicts the occurrence and frequency of coercive behavior. We found phenotype-behavior matching whereby small males invest in putatively ornamental foreclaws used for courtship and large males invest in weaponry for coercion, challenging existing knowledge of this well-studied species. As a group with a long evolutionary history and varied mating systems, Testudines are a particularly interesting taxon in which to ask questions about mating system evolution.</p>
Gestational Cd exposure in the CD-1 mouse induces sex-specific hepatic insulin insensitivity, obesity and metabolic syndrome in adult female offspring
<p>There is compelling evidence that developmental exposure to some toxic metals increases risk for obesity and obesity-related morbidity including cardiovascular disease and type 2 diabetes in adults. To explore the hypothesis that developmental Cd exposure increased risk of obesity later in life, male and female CD-1 mice were maternally exposed to 500 ppb CdCl<sub>2</sub> in drinking water during a human gestational equivalent period (GD0 - PND10). Hallmark indicators of metabolic disruption, hepatic steatosis, and metabolic syndrome were evaluated prior to birth through adulthood. Blood Cd levels in dams were similar to those observed in human pregnancy cohorts. There were no observed impacts of exposure on dams or pregnancy-related outcomes. Results of glucose and insulin tolerance testing revealed that Cd-exposure impaired glucose homeostasis in young adult offspring. Exposure-related increases in circulating triglycerides and hepatic steatosis were apparent only in females. By PND120, Cd-exposed females had become 30% heavier with 700% more perigonadal fat than unexposed control females. There was no evidence of dyslipidemia, steatosis, increased weight gain, nor increased adiposity in Cd-exposed male offspring. Hepatic transcriptome analysis at PND1, PND21, and PND42 revealed evidence for female-specific increases in oxidative stress and mitochondrial dysfunction with significant early disruption of retinoic acid signaling and altered insulin receptor signaling consistent with hepatic insulin sensitivity in adult females. The observed steatosis and metabolic syndrome-like phenotypes resulting from exposure to 500 ppb CdCl<sub>2</sub> during the pre- and perinatal period of development equivalent to human gestation indicate that Cd acts developmentally as a sex-specific delayed obesogen.</p>
Sex-based population structure of ectoparasites from Neotropical bats
<p>The structure and composition of populations may be molded by multiple evolutionary and ecological mechanisms, with natural selection affecting sex ratios, as well as the distributions of each sex throughout the environment. To address sex-based aspects of population structure, I evaluated sex ratios, co-occurrence of the sexes, correlations of abundance of the sexes, and dispersion of individuals of each sex for each of 34 host-ectoparasite associations from Paraguayan bats. Of the 34 host-ectoparasite associations, 23 exhibited positive co-occurrence, 27 exhibited positive correlation of abundances, 4 exhibited male sex bias, 1 exhibited female sex bias, 27 had clumped distributions of males, and 26 had clumped distributions of females. No associations exhibited negative co-occurrence, negative correlation of abundance, or hyper-dispersed males or females. There was no evidence for sexual segregation, sex-based niche partitioning, or intrasexual selection in any host-ectoparasite association. Previously proposed mechanisms (e.g. pre-partum sex bias, local mate competition, or mortality from host grooming) fail to explain observed patterns of sex bias. For ectoparasites of hosts that occupy permanent roost sites, sex-specific behaviour related to reproduction may make females more susceptible to off-host predation and less likely to be present in samples from bats captured away from the roost.</p>
Time spent in distinct life-history stages has sex-specific effects on reproductive fitness in wild Atlantic salmon
<p><span>In species with complex life cycles, life history theory predicts that fitness is affected by conditions encountered in previous life history stages. Here, we use a four-year pedigree to investigate if time spent in two distinct life history stages has sex-specific reproductive fitness consequences in anadromous Atlantic salmon (<i>Salmo salar</i>). We determined the amount of years spent in fresh water as juveniles (freshwater age, FW, measured in years), and years spent in the marine environment as adults (sea age, SW, measured in sea winters) on 264 sexually mature adults collected on a river spawning ground. We then estimated reproductive fitness as the number of offspring (reproductive success) and the number of mates (mating success) using genetic parentage analysis (>5000 offspring). Sea age is significantly and positively correlated with reproductive and mating success of both sexes whereby older and larger individuals gained the highest reproductive fitness benefits (females: 62.2% increase in offspring/SW and 34.8% increase in mate number/SW; males: 201.9% offspring/SW and 60.3% mates/SW). Younger freshwater age was significantly related to older sea age and thus increased reproductive fitness, but only among females (females: -33.9% offspring/FW and -32.4% mates/FW). This result implies that females can obtain higher reproductive fitness by transitioning to the marine environment earlier. In contrast, male mating and reproductive success was unaffected by freshwater age and more males returned at a younger age than females despite the reproductive fitness advantage of later sea age maturation. Our results show that the timing of transitions between juvenile and adult phases has a sex-specific consequence on female reproductive fitness, demonstrating a life-history trade-off between maturation and reproduction in wild Atlantic salmon.</span></p>
FIGURE 6 in Support for the underrepresented sex: new descriptions of scutacarid males (Acari, Heterostigmatina)
FIGURE 6. Scanning electron micrographs of the genital apparatus and legs IV of an Imparipes dispar male covered with fungal spores: a. Posterior view of the genital apparatus and legs IV, b. detail of the two adhesive pads on the tarsus of leg IV, c. dorsal view of the tarsus and partly tibia of leg IV. Abbreviations: adp = adhesive pads, gp = genital plate, sp = spore (s).
Human pan-body age- and sex-specific molecular phenomena inferred from public transcriptome data using machine learning - Data
<p>Expression data used in manuscript <i>Human pan-body age- and sex-specific molecular phenomena inferred from public transcriptome data using machine learning</i></p>
Paper data and code of manuscript: Intraspecific variation on heat tolerance in a model ectotherm: effects of body mass, cell size, oxygen and sex
<p>When using the data or code from this manuscript, please cite it as:</p><p><strong>Leiva FP</strong>, Santos M, Rezende E, & Verberk WCEP. 2021. Paper data and code of manuscript: Intraspecific variation on heat tolerance in a model ectotherm: effects of body mass, cell size, oxygen and sex. Zenodo. <a href="https://doi.org/10.5281/zenodo.5120028">https://doi.org/10.5281/zenodo.5120028</a>.</p>
Sex and Age Impact CD4+ T Cell Susceptibility to HIV In Vitro Through Cell Activation Dynamics
<p>Cellular composition and the responsiveness of the immune system evolve upon aging and are influenced by biological sex. CD4+ T cells from women living with HIV exhibit a decreased viral replication ex vivo compared to men's. We, thus, hypothesized that these findings could be recapitulated in vitro and infected primary CD4+ T cells with HIV-based vectors pseudotyped with VSV-G or HIV envelopes. We used cells isolated from twenty donors to interrogate the effect of sex and age on permissiveness over a six-day activation kinetics. Our data identified an increased permissiveness to HIV between 24 and 72 h post-stimulation. Sex- and age-based analyses at these time points showed an increased susceptibility to HIV of the cells isolated from males and from donors over 50 years of age, respectively. A parallel assessment of surface markers' expression revealed higher frequencies of activation marker CD69 and of immune checkpoint inhibitors (PD-1 and CTLA-4) in the cells from highly permissive donors. Furthermore, positive correlations were identified between the expression kinetics of CD69, PD-1 and CTLA-4 and HIV expression kinetics. The cell population heterogeneity was assessed using a single-cell RNA-Seq analysis and no cell subtype enrichment was identified according to sex. Finally, transcriptomic analyses further highlighted the role of activation in those differences with enriched activation and cell cycle gene sets in male and older female cells. Altogether, this study brought further evidence about the individual features affecting HIV replication at the cellular level and should be considered in latency reactivation studies for an HIV cure.</p>
Species and sex specific chemical composition in a concealed gland from an internal gland-like tissue of an African frog family
<p><span>Intraspecific chemical communication in frogs is understudied and the few published cases are limited to externally visible and male-specific breeding glands. Frogs of the family Odontobatrachidae, a West African endemic complex of five morphologically cryptic species, have large, fatty gland-like strands along their lower mandible. We investigated the general anatomy of this strand and analyzed its chemical composition. We found the strand to be present in males and females of all species. The strand varies in markedness, with well-developed strands usually found in reproductively active individuals. Although the strands are situated under the skin, they are connected to particular skin sections, the vocal sac in male frogs and a respective area in females. Gas-chromatography/mass spectrometry and multivariate analysis revealed, that the strands contain sex- and species-specific chemical profiles, which are consistent across geographically distant populations. The profiles varied between reproductive and non-reproductive individuals. Our results indicate that the gland-like strand in the Odontobatrachidae comprise a so far overlooked type of breeding related organ, potentially a gland, that most likely plays a role in the mating and/or breeding behavior of the five Odontobatrachus species. Our results highlight the relevance of multimodal signaling in anurans, and indicate that chemical signaling may not be restricted to sexually dimorphic, apparent skin glands.</span></p>
Experimental evolution under varying sex ratio and behavioral plasticity in response to perceived competitive environment independently affect calling effort in male crickets
<p>The operational sex ratio (OSR) is a key component influencing the magnitude of sexual selection driving the evolution of male sexual traits, but males often also retain the ability to plastically modulate trait expression depending on the current environment. Here we employed an experimental evolution approach to determine whether the OSR affects the evolution of male calling effort in decorated crickets, a costly sexual trait, and whether plasticity in calling effort is altered by the OSR under which males have evolved. Calling effort of males from two selection regimes maintained at different OSRs over 18–20 generations (male- versus female-biased) was recorded at two different levels of perceived competition, in the absence of rivals or in the presence of an experimentally muted competitor. The effect of the OSR on the evolution of male calling effort was modest and in the opposite direction predicted by theory. Instead, the immediate competitive environment strongly influenced male calling effort as males called more in the presence of a rival, revealing considerable plasticity in this trait. This increased calling effort came at a cost, however, as males confined with a muted rival experienced significantly higher mortality.</p>
Data from: Sex-specific effects of inbreeding in juvenile brown trout
<p>Inbreeding depression, i.e., the reduction of health and vigour in individuals with high inbreeding coefficients, is expected to increase with environmental, social, or physiological stress. It has therefore been predicted that sexual selection and the associated stress usually lead to higher inbreeding depression in males than in females. However, sex-specific differences in life history may reverse that pattern during certain developmental stages. In some salmonids, for example, female juveniles start developing their gonads earlier than males who instead grow faster. We tested whether the sexes are differently affected by inbreeding during that time. To study the effects of inbreeding coefficients that may be typical for natural populations of brown trout (<em>Salmo trutta</em>), and also to control for potentially confounding maternal or paternal effects, we sampled males and females from the wild, used their gametes in a block-wise full-factorial breeding design to produce 60 full-sib families, released the offspring as yolk-sac larvae into the wild, sampled them 6 months later, identified their genetic sex, and used microsatellites to assign them to their parents. We used whole-genome resequencing to calculate the kinship coefficients for each breeding pair and hence the expected average inbreeding coefficient per family. Juvenile growth could be predicted from these expected inbreeding coefficients and the genetic sex: Females reached lower body sizes with increasing inbreeding coefficient, while no such link could be found in males. This sex-specific inbreeding depression led to the overall pattern that females were on average smaller than males by the end of their first summer.</p>
Low sex drive and choosy females: Fungal infections are a reproductive downfall for male house flies
<p>Many entomopathogenic fungi cause infections that kill their insect host. Little is understood about changes in the reproductive investment that occur during an infection by a lethal disease over the waning life of an insect. Life history theory suggests the host will respond by investing resources into fighting the disease or increasing reproduction. Here, we investigate how the reproductive life of adult house flies, <em>Musca domestica</em>, is impacted by its host-specific fungal pathogen, <em>Entomophthora muscae</em>. Specifically, we test how the week-long infection alters the mating behavior of virgin adult male house flies. We find that the pathogen significantly decreases male libido; an effect which grows stronger over the course of the infection. Furthermore, females were significantly less likely to choose an infected male, reducing male mating success. Additionally, we assessed sperm viability to understand the reproductive costs for monandrous females to mate with infected males. Analyses revealed that sperm quality decreases as early as three days post-infection. These results show that <em>E. muscae</em>, which can have a prevalence near 100% in wild populations, causes severe lifetime reproductive costs to male house flies. Understanding how host-pathogen interactions affect host life history is crucial for elucidating all the negative effects pathogen virulence exerts on hosts.</p>
Sex chromosomes and hormones independently influence healthy brain development but act similarly after cranial radiation
<h2><strong>Description</strong></h2> <p>Biological sex influences prevalence of developmental disorders through sex hormones and sex chromosomes. However, our understanding of their impacts in neurodevelopment and response to injury remains limited. In this project, we use high resolution magnetic resonance imaging (MRI) to investigate the four core genotype mouse model (FCG) that separates the influences of sex hormones and sex chromosomes during normal brain development and after cranial radiation therapy. </p> <p>Sex differences are attributed to either sex hormones or sex chromosomes. This can be distinguished by the FCG model which decouples the sex determining region (SRY) from the Y chromosome by moving SRY onto an autosome. This gives us four core sex genotypes: XX NULL, XY NULL, XX SRY, and XY SRY.</p> <p>This dataset represents the <em>most comprehensive mouse brain imaging study</em> employing the FCG model to date with 5 timepoints (P14, P23, P42, P63, P98), Ccl2 wildtype (+/+) and knockouts (-/-), irradiation (7Gy) and sham (0Gy) mice. All in all, a total of <strong>1071 images</strong>! The results presented here is published in PNAS.</p> <p>In vivo MRI scans were obtained using a 7-T MRI scanner (Bruker BioSpin, Ettlingen, Germany) equipped with four cryocoils for simultaneous imaging of four mice. The scans were performed with the following settings: T1-weighted, 3D-gradient echo sequence, 75μm isotropic resolution, TR=26ms, TE=8.25ms, flip angle=26°, field of view=25×22×22mm, and matrix size=334×294×294.</p> <p>All structural MR images are stored in <strong>images.tar.gz</strong>. Images were segmented and registered using an automated pipeline which are stored in <strong>labels.tar.gz</strong>. The consensus average and labels are <strong>final_average.mnc </strong>and <strong>final_labels.mnc</strong>, respectively. Extracted structure volumes alongside the metadata are included in <strong>df_micevolumes.csv</strong>. Structural MRIs are in MINC format and the <strong>readme.txt</strong> provides further information on this dataset. </p> <p>The authors express their sincere gratitude for the research funding recieved from the Canadian Institutes of Health Research (158622, 168037) and the Ontario Institute for Cancer Research (IA-024) with funding from the Government of Ontario and Restracomp from the SIckKids Research Training Centre.</p> <p><strong>Publication</strong>: https://www.pnas.org/doi/10.1073/pnas.2404042121</p> <h2><strong>Code/Software </strong></h2> <p><strong>MINC</strong><br>https://www.bic.mni.mcgill.ca/ServicesSoftware/MINC</p> <p><strong>RMINC</strong><br>https://github.com/Mouse-Imaging-Centre/RMINC</p> <p><strong>PydPiper</strong><br>https://github.com/Mouse-Imaging-Centre/pydpiper/tree/v2.0.19.1</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.