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opencc-by-4.0Mar 2020View details →

Data file: a qualitative social media content analysis of the Dutch #breakthesilence campaign on negative and traumatic experiences of labour and birth

Data file with typed out quotes from the Dutch #breakthesilence campaign analysed for the study 'Left powerless: a qualitative social media content analysis of the Dutch #breakthesilence campaign on negative and traumatic experiences of labour and birth'.

opencc-zeroJul 2020View details →

Data from: De novo gene birth, horizontal gene transfer and gene duplication as sources of new gene families associated with the origin of a symbiosis in Amanita

By introducing novel capacities and functions, new genes and gene families may play a crucial role in ecological transitions. Mechanisms generating new gene families include de novo gene birth, horizontal gene transfer and neofunctionalization following a duplication event. The ectomycorrhizal (ECM) symbiosis is a ubiquitous mutualism and the association has evolved repeatedly and independently many times among the fungi, but the molecular dynamics enabling its emergence remain elusive. We developed a phylogenetic workflow to first understand if gene families unique to ECM Amanita fungi and absent from closely related asymbiotic species are functionally relevant to the symbiosis, and then to systematically infer their origins. We identified 109 gene families unique to ECM Amanita species. Genes belonging to unique gene families are under strong purifying selection and are upregulated during symbiosis, compared to genes of conserved or orphan gene families. The origins of seven of the unique gene families are strongly supported as either de novo gene birth (two gene families), horizontal gene transfer (four), and gene duplication (one). An additional 34 families appear new because of their selective retention within symbiotic species. Among the 109 unique gene families, the most upregulated gene in symbiotic cultures encodes an ACC deaminase, an enzyme capable of downregulating the synthesis of the plant hormone ethylene. Ethylene is a common negative regulator of plant-microbial mutualisms.

opencc-zeroSep 2020View details →

Endometrioma ethanol sclerotherapy could increase IVF live birth rate in women with moderate-severe endometriosis

Objective: To examine the impact of ethanol sclerotherapy (EST) for endometrioma on in vitro fertilization (IVF) cumulative live birth rates (CLBR) in women with moderate-severe endometriosis. Methods: This retrospective cohort study included women with moderate-severe endometriosis (revised American Fertility Society stage III-IV) and endometrioma who underwent IVF with the ultra-long agonist protocol. We compared two groups: women undergoing EST for endometrioma before IVF (EST group), and women whose endometrioma was left in situ during IVF (No-EST group). The primary outcome was the CLBR per IVF cycle, including fresh and frozen embryo transfers. The secondary endpoints included the complication rate, number of mature oocytes retrieved, clinical pregnancy rate and pregnancy loss rate. Results: Seventy-four women were included in the study, with 37 in the EST group and 37 in the No-EST group, representing 67 and 69 IVF cycles, respectively. The population and cycle characteristics were comparable between the two groups, especially the ovarian response to stimulation. The CLBR was significantly increased in the EST group compared to the No-EST group (31.3% vs. 14.5%, p = 0.03). The clinical and biochemical pregnancy rates were significantly increased in the EST group (37.3% vs. 15.9%, p = 0.01 and 43.3% vs. 23.2%, p = 0.01, respectively). Multivariate analysis revealed a significantly increased chance of live birth in women exposed to EST before IVF with an adjusted OR of 2.68 (95% confidence interval, CI: 1.13–6.36, p = 0.02). In the EST group, we reported one major complication Clavien and Dindo classification grade III, complication involving an ovarian abscess that required a laparoscopic drainage. Conclusions: EST is an interesting technique to improve IVF success rates in women with moderate-severe endometriosis. EST could be discussed before IVF in infertile women.

opencc-zeroSep 2020View details →

Data for: Birth order as a source of within-genotype diversification in the clonal duckweed, Spirodela polyrhiza (Araceae: Lemnoideae)

Organismal persistence attests to adaptive response to environmental variation. Diversification bet hedging, in which risk is reduced at the cost of expected fitness, is increasingly recognized as an adaptive response, yet mechanisms by which a single genotype generates diversification remain obscure. The clonal greater duckweed, Spirodela polyrhiza (L.), facultatively expresses a seed-like but vegetative form, the "turion", that allows survival through otherwise lethal conditions. Turion reactivation phenology is a key fitness component, yet little is known about turion reactivation phenology in the field, or sources of variation. Here, using floating traps deployed in the field, we find a remarkable extent of variation in natural reactivation phenology that cannot be explained solely by spring cues, occurring over a period of at least 200 days. Under controlled laboratory conditions, we find support for the hypothesis that turion phenology is influenced jointly by phenotypic plasticity to temperature and diversification within clones. Turion "birth order" consistently accounted for a difference in reactivation time of 46 days at temperatures between 10° and 18°C, with early birth-order turions reactivating more rapidly than late birth-order turions. These results should motivate future work to formally evaluate turion phenology variance as a bet-hedging trait.

opencc-zeroOct 2020View details →

Data from: Vaginal host immune-microbiome interactions in a cohort of primarily African-American women who ultimately underwent spontaneous preterm birth or delivered at term

Background: Recent studies suggest that alterations in the vaginal microbiome allow for the assessment of the risk for spontaneous preterm birth (PTB), the leading cause of neonatal morbidity and mortality worldwide. However, the associations between the local immune response and the vaginal microbiome are still poorly understood. Herein, we characterize the vaginal host immune-microbiome interactions in women who ultimately underwent PTB and in those who delivered at term. Methods: Vaginal fluid samples from 52 pregnant women (of whom 18 underwent PTB and 34 delivered at term) were collected from 10-32 weeks in a case-control study. Concentrations of 33 immune mediators were determined using sensitive and specific immunoassays. The previously published 16S rRNA gene sequence and bacterial phylotype data of these subjects were utilized in this study. Linear mixed effects models were utilized to test associations between vaginal immune mediator concentrations and bacterial phylotype relative abundances. Results: 1) Specific immune mediators (β-defensins 2 and 3, IL-1β, CXCL10, CCL2, CCL3, SLPI, and VEGF) correlated with 18 different vaginal bacterial phylotypes in the overall study population; 2) vaginal concentrations of CXCL10, CCL2, CCL3, SLP1 and VEGF negatively correlated with non-Lactobacillus members of the vaginal microbiome; 3) vaginal concentrations of CXCL10 were negatively correlated with 15 bacterial phylotypes, most of which are typical members of Community State Type IV of the vaginal microbiome, such as Gardnerella vaginalis, Megasphaera sp. type 1, and Atopobium vaginae; 4) Gemella spp. were negatively correlated with vaginal concentrations of VEGF, CCL2, CCL3, SLPI, and CXCL10; 5) when comparing PTB cases to term controls, five soluble immune mediators (CCL26, CCL22 and CCL2, CXCL10 and IL-16), and especially CCL26, were negatively correlated with five typical members of Community State Type IV: Sneathia sanguinegens, Parvimonas micra, Veillonellaceae, BVAB2, and Gemella spp; and 6) Sneathia sanguinegens had stronger negative associations with all five soluble immune mediators (CCL26, CCL22 and CCL2, CXCL10 and IL-16) in PTB cases than in term controls. Conclusions: The assessment of vaginal host immune-microbiome interactions revealed that specific soluble immune mediators, mainly CXCL10, negatively correlated with typical members of Community State Type IV of the vaginal microbiome. In addition, this assessment particularly showed that Sneathia sanguinegens had stronger negative associations with different immune mediators, including CXCL10 and CCL26, in women who ultimately had a PTB compared to those who delivered at term. These findings provide insight into the vaginal host immune-microbiome interactions in normal and complicated pregnancies.

opencc-zeroDec 2014View details →

Data from: Onset of autumn shapes the timing of birth in Pyrenean chamois more than onset of spring

1. In seasonal environments, birth dates are a central component for a species' life history, with potential long-term fitness consequences. Yet our understanding of selective pressures of environmental changes on birth dates is limited in wild mammals due to the difficulty of data collection. In a context of rapid climate change, the question of a possible mismatch between plant phenology and birth phenology also remains unanswered for most species. 2. We assessed whether and how the timing of birth in a mountain mammal (isard, Rupicapra pyrenaica) tracked changes in plant growing season, accounting for maternal traits, individual heterogeneity, and population density. We not only focused on spring conditions but also assessed to what extent onset of autumn can be a driver of phenological biological events and compared the magnitude of the response to the magnitude of the environmental changes. We relied on a 22-year study based on intensively monitored marked individuals of known age. 3. Births were highly synchronized (80% of kids born within 25 days) and highly repeatable (84%; among-females variation of 9.6 days, withinfemale variation of 4.2 days). Individual phenotypic plasticity allows females to respond rapidly to inter-annual changes in plant phenology but did not prevent the existence of a mismatch: a 10-day advance in the autumn or spring plant phenology led to 3.9 and 1.3 days advance in birth dates, respectively. 4. Our findings suggest that plant phenology may act as a cue to induce important stages of the reproductive cycle (e.g., conception and gestation length), subsequently affecting parturition dates, and stressed the importance of focusing on long-term changes during spring for which females may show much lower adaptive potential than during autumn. These results also question the extent to which individual plasticity along with high heterogeneity among individuals will allow species to cope with demographic consequences of climate changes.

opencc-zeroDec 2016View details →

Data from: Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: birth, death, and adaptation

Across insect genomes, the size of the cytochrome P450 monooxygenase (CYP) gene superfamily varies widely. CYPome size variation has been attributed to reciprocal adaptive radiations in insect detoxification genes in response to plant biosynthetic gene radiations driven by coevolution between herbivores and their chemically defended hostplants. Alternatively, variation in CYPome size may be due to random "birth and death" processes, whereby exponential increase via gene duplications is limited by random decay via gene death or transition via divergence. We examined CYPome diversification in the genomes of seven Lepidoptera species varying in host breadth from monophagous (Bombyx mori) to highly polyphagous (Amyelois transitella). CYPome size largely reflects the size of Clan 3, the clan associated with xenobiotic detoxification, and to some extent phylogenetic age. Consistently across genomes, families CYP6, CYP9, and CYP321 are most diverse and CYP6AB, CYP6AE, CYP6B, CYP9A, and CYP9G are most diverse among subfamilies. Higher gene number in subfamilies is due to duplications occurring primarily after speciation and specialization ("P450 blooms"), and the genes are arranged in clusters, indicative of active duplicating loci. In the parsnip webworm, Depressaria pastinacella, gene expression levels in large subfamilies are high relative to smaller subfamilies. Functional and phylogenetic data suggest a correlation between highly dynamic loci (reflective of extensive gene duplication, functionalization, and in some cases loss) and the ability of enzymes encoded by these genes to metabolize hostplant defenses, consistent with an adaptive, nonrandom process driven by ecological interactions.

opencc-zeroDec 2014View details →

Data from: Birth date predicts alternative life-history pathways in a fish with sequential reproductive tactics

In species with plastic expression of alternative reproductive tactics (ARTs), individuals of the same sex, usually males, can adopt different reproductive tactics depending on factors such as body size. The 'birth date hypothesis' proposes that condition-dependent expression of ARTs may ultimately depend on birth date, because individuals born at different times of the year may achieve different sizes and express different reproductive tactics accordingly. However, this has rarely been tested. Here, we tested this hypothesis in a fish with ARTs, the peacock blenny (Salaria pavo). A long-term (6 years) mark–recapture study demonstrated that ARTs in the peacock blenny were sequential and that males may follow at least two alternative life-history pathways: a nest-holder pathway, in which males express the nest-holder tactic from their first breeding season onwards, and a parasitic pathway, where males reproduce on their first breeding season as sneaker males and subsequently as nest-holders. We have found evidence of a birth date effect on the expression of ARTs in the peacock blenny. Males following the nest-holder pathway are born earlier and are larger at the first breeding season than males following the parasitic pathway, but they have similar growth curves. The mechanisms underlying a birth date effect are far from clear and might be diverse. We have not found support for a mechanism of body size threshold triggering sexual maturation and subsequent ARTs. A mechanism of tactic determination that is strictly based on timing of first maturation is also unlikely. A proxy of lifetime reproductive success shows crossing (body size associated) fitness curves for the two main life-history pathways.

opencc-zeroDec 2017View details →

Data from: Human birth seasonality: latitudinal gradient and interplay with childhood disease dynamics

More than a century of ecological studies have demonstrated the importance of demography in shaping spatial and temporal variation in population dynamics. Surprisingly, the impact of seasonal recruitment on infectious disease systems has received much less attention. Here, we present data encompassing 78 years of monthly natality in the USA, and reveal pronounced seasonality in birth rates, with geographical and temporal variation in both the peak birth timing and amplitude. The timing of annual birth pulses followed a latitudinal gradient, with northern states exhibiting spring/summer peaks and southern states exhibiting autumn peaks, a pattern we also observed throughout the Northern Hemisphere. Additionally, the amplitude of United States birth seasonality was more than twofold greater in southern states versus those in the north. Next, we examined the dynamical impact of birth seasonality on childhood disease incidence, using a mechanistic model of measles. Birth seasonality was found to have the potential to alter the magnitude and periodicity of epidemics, with the effect dependent on both birth peak timing and amplitude. In a simulation study, we fitted an susceptible-exposed-infected-recovered model to simulated data, and demonstrated that ignoring birth seasonality can bias the estimation of critical epidemiological parameters. Finally, we carried out statistical inference using historical measles incidence data from New York City. Our analyses did not identify the predicted systematic biases in parameter estimates. This may be owing to the well-known frequency-locking between measles epidemics and seasonal transmission rates, or may arise from substantial uncertainty in multiple model parameters and estimation stochasticity.

opencc-zeroDec 2011View details →

Data from: Body size evolution on islands: are adult size variations in tiger snakes a non-adaptive consequence of selection on birth size?

Mean adult size has been used as the traditional measure of body size to explain trends of insular gigantism and dwarfism in a wide array of taxa. However, patterns of variation in body size at birth have received surprisingly little attention, leaving open the possibility that adult body-size differences are nonadaptive consequences of selection acting on neonate body size. Here I used an empirical and correlative approach to test this hypothesis in a mosaic of 12 island and mainland snake populations in Australia. Data collected on 597 adult and 1,084 neonate tiger snakes showed that (1) both adult and neonate mean body sizes varied strongly across populations; (2) prey diversity and size convincingly explained birth-size variations: birth size—notably, gape size—correlated with prey size; (3) neonate snout-vent length was significantly correlated with neonate gape size; and (4) neonate snout-vent length was significantly correlated with adult snout-vent length. Postnatal growth rates recorded under common-garden conditions differed across populations and were correlated with mean prey size. These data collectively suggest that (1) prey size is the main driver for the evolution of body size at birth in gape-limited predators, (2) adult size variations may reflect selective forces acting on earlier life stages, and (3) adult size variations may also reflect resource availability during ontogeny (notably, prey diversity).

opencc-zeroDec 2015View details →

Data from: Birth dates vary with fixed and dynamic maternal features, offspring sex, and extreme climatic events in a high-latitude marine mammal

Reproductive synchrony tends to be widespread in diverse species of plants and animals, especially at higher latitudes. However, for long-lived mammals, birth dates for different individuals can vary by weeks within a population. A mother's birth timing can reveal useful information about her reproductive abilities and have important implications for the characteristics and survival of her offspring. Despite this, our current knowledge of factors associated with variation in birth dates is modest. We used long-term data for known-age Weddell seals in Antarctica and a Bayesian hierarchical modeling approach to study how birth dates varied with fixed and temporally varying features of mothers, whether sex allocation varied with birth timing, and annual variation in birth dates. Based on birth dates for 4465 pups born to 1117 mothers aged 4–31, we found that diverse features of mothers were associated with variation in birth dates. Maternal identity was the most important among these. Unlike most studies, which have reported that birth dates occur earlier as mothers age, we found that birth dates progressively occurred earlier in the year in the early part of a mother's reproductive life, reached a minimum at age 16, and then occurred later at later ages. Birth dates were positively related to a mother's age at primiparity and recent reproductive effort. The earliest birth dates were for pups born to prime-age mothers who did not reproduce in the previous year but began reproduction early in life, suggesting that females in the best condition gave birth earlier than others. If so, our finding that male pups tended to be born earlier than females provides support for the Trivers–Willard sex-allocation model. Average birth dates were quite consistent across years, except for 2 years that had notable delays and occurred during the period when massive icebergs were present and disrupted the ecosystem.

Figure 3 in Live birth in the Devonian period

Figure 3 | Materpiscis gen. nov. a, Diagram showing position of embryo and yolk sac within the mother. b, Artist's reconstruction of Materpiscis gen. nov. giving birth (by B. Choo).

Figure 2 in Live birth in the Devonian period

Figure 2 | Holotype of Materpiscis attenboroughi gen. et sp. nov. (WAM 07.12.1). a–e, SEM images of umbilical cord. a, Umbilicus section. b, Image showing a vascular canal (v). c, image showing pit (p). d, Image showing possible

Figure 1 in Live birth in the Devonian period

Figure 1 | Holotype of Materpiscis attenboroughi gen. et sp. nov. (WAM 07.12.1). a, Body with embryo. The boxed area is magnified in panel

Figure 1 in Live birth in the Devonian period

Figure 1 | Holotype of Materpiscis attenboroughi gen. et sp. nov. (WAM 07.12.1). a, Body with embryo. The boxed area is magnified in panel c. b, Embryo at early preparation. c, d, Umbilical cord and embryo at later preparation. e, Adult skull roof in dorsal view. f, Adult left marginal. h, Dermal armour restored in lateral view. i, Left adult tooth plates in mesial view. g, Austroptyctodus gardineri (WAM 86.9.662) showing embryos. ADL, anterior dorsolateral plate; AL, anterior lateral plate; Ce, central; df.bas, dorsal fin basal plate of adult; haem, haemal arch; Ifg, inferognathal; MD, median dorsal plate; Mg, marginal; neur, neural arch; Nu, nuchal; PNu, paranuchal plate; PRO, preorbital; PTO, postorbital; Sgn, supragnathal; SM, submarginal plate; umb, umbilical cord.

opencc-by-4.0Jul 2023View details →

The limits of the constant-rate birth-death prior for phylogenetic tree topology inference

Birth-death models are stochastic processes describing speciation and extinction through time and across taxa, and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under constant-rate birth-death (crBD) tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between crBD and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which crBD differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used crBD priors with those that used other non-BD Bayesian and non-Bayesian methods, we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using crBD in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios, but also highlights that empirically observed phylogenetic imbalance is highly improbable under crBD, leading to systematic bias in data sets with limited information content.