Find research datasets worth reusing

opencc-zeroMar 2023View details →

Genetic insights into the age-specific biological mechanisms governing human ovarian ageing

There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modelling framework, which determines the time-dependency of DNA variant-age-at-onset associations, without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the sign of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages, and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age-dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modelling of large-scale biobank data.

opencc-zeroMar 2023View details →

Genetic variation in sexual size dimorphism is associated with variation in sex-specific plasticity in Drosophila

The difference in body size between females and males, or sexual size dimorphism (SSD), is ubiquitous, and yet we have a poor understanding of the developmental-genetic mechanisms that generate it, and how these mechanisms may vary within and among species. Such an understanding of the genetic architecture of SSD is important if we are to evaluate alternative models of SSD evolution, but is difficult to describe because SSD is a characteristic of populations, not individuals. Here, we overcome this challenge by using isogenic lineages of Drosophila to measure SSD for 196 genotypes. We demonstrate extensive genetic variation for SSD, primarily driven by higher levels of genetic variation for body size among females than males. While we observe a general increase in SSD with sex-averaged body size (pooling for sex) among lineages, the vast majority of variation in SSD is independent of sex-averaged body size, and shows a strong genetic correlation with sex-specific plasticity, such that increased female-biased SSD is associated with increased body-size plasticity in females. Our data are consistent with the condition-dependence hypothesis of sexual dimorphism, and suggest that SSD in Drosophila is a consequence of selection on the developmental-genetic mechanisms that regulate the plasticity of body size.

opencc-zeroMar 2023View details →

Strong habitat-specific phenotypic plasticity but no genome-wide differentiation across a rainforest gradient in an African butterfly

Habitat-specific thermal responses are well documented in various organisms and likely determine the vulnerability of populations to climate change. However, the underlying roles of genetics and plasticity that shape such habitat-specific patterns are rarely investigated together. Here we examined the thermal plasticity of the butterfly Bicyclus dorothea originating from rainforest and ecotone habitats in Cameroon under common garden conditions. We also sampled wild-caught butterflies from forest and ecotone sites and used RADseq to explore genome-wide population differentiation. We found differences in the level of phenotypic plasticity across habitats. Specifically, ecotone populations exhibited greater sensitivity in wing eyespot features with variable development temperatures relative to rainforest populations. Known adaptive roles of wing eyespots in Bicyclus species suggest that this morphological plasticity is likely under divergent selection across environmental gradients. However, we found no distinct population structure of genome-wide variation between habitats, suggesting high levels of ongoing gene flow between habitats is homogenizing most parts of the genome.

Data from: Trait-specific indirect effects underlie variation in the response of spiders to cannibalistic social partners

Organisms may respond in different ways to the risk posed by conspecifics, but the cause of such variation remains elusive. Here, we use a half-sib/full-sib design to evaluate the contribution of (indirect) genetic or environmental effects to the behavioral response of the cannibalistic wolf spider Lycosa fasciiventris (Dufour, 1835) towards conspecific cues. Spiders showed variation in relative occupancy time, activity, and velocity on patches with or without conspecific cues, but direct genetic variance was only found for occupancy time. These three traits were correlated and could be lumped in a principal component: spiders spending more time in patches with conspecific cues moved less and at a lower rate in those areas. Genetic and/or environmental components of carapace width and weight loss in the social partner were significantly correlated with the principal component of focal individuals. Individual Variation in these traits may reflect the quality and/or quantity of cues produced by social partners, hence focal individuals were likely behaving along a continuum of strategies in response to the risk posed by social partners. Therefore, environmental and genetic trait variation in the social partners may be key to maintain trait diversity in focal individuals, even in the absence of direct genetic variation.

opencc-by-4.0Jan 2023View details →

Data for 'Assessing the value of biodiversity-specific footprinting metrics linked to South American soy trade'

Underlying data for publication 'Assessing the value of biodiversity-specific footprinting metrics linked to South American soy trade'.

Data for: Dispersal-limited symbionts exhibit unexpectedly wide variation in host specificity

A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macroevolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode versus multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. Comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts.

Data and codes from: Taxon-specific responses to landscape-scale and long-term implementation of environmentally friendly rice farming

<ol> <li> Rice feeds about half of the world's population. The intensification of rice farming has threatened biodiversity and ecosystem services, such as pest control. A growing body of evidence suggests that environmentally friendly rice farming (EFF) can be effective in biodiversity conservation. However, its dependence on spatial and temporal scales of EFF implementation and surrounding seminatural habitats has remained largely unknown. </li> <li> We evaluated the effects of three types of EFF (organic farming, winter flooding and Integrated Pest Management [IPM]) against conventional farming on plants, spiders, and waterbirds in Japan. Through systematic surveys of 254 rice fields across rice production areas, we monitored EFF implementation at field and landscape scales, considering the time since transition to EFF and the surrounding seminatural areas. </li> <li> EFF implementation at the field scale, such as organic farming, was found to have positive effects on plant richness and spider abundance, whereas the percent area of EFF fields within a 200-m radius positively affected Ardeidae abundance. However, as the percent area of surrounding semi-natural habitats increased, the difference in the plant richness between organic and other fields decreased. </li> <li>Prolonged implementation periods of IPM or winter flooding, together with a reduction of more than 50% in synthetic fertilisers and pesticides from conventional agriculture, led to an increase in the spider abundance. Conversely, no clear positive effect of longer implementation periods of organic farming resulted in similar spider abundance in the three EFF types after 20 years.</li> <li> Synthesis and applications. This suggests that the benefits of environmentally friendly rice farming depend on their spatial and temporal scales and the surrounding seminatural areas. We propose that such a context dependency should be considered in future policy. Our findings also provide a starting point for future research to test the mixed biodiversity benefits of EFF across cropland types and around the world. </li> </ol>

Data and code for: Sex-specific trait architecture in a sexually size dimorphic spider

Sexual dimorphism, or sex-specific trait expression, may evolve when selection favours different optima for the same trait between sexes, i.e., under antagonistic selection. Intra-locus sexual conflict exists when the sexually dimorphic trait under antagonistic selection is based on genes shared between sexes. A common assumption is that the presence of sexual-size dimorphism (SSD) indicates that sexual conflict has been, at least partly, resolved via decoupling of the trait architecture between sexes. However, whether and how decoupling of the trait architecture between sexes has been realised often remains unknown. We tested for differences in architecture of adult body size between sexes in a species with extreme SSD, the African hermit spider (Nephilingis cruentata), where adult female body size greatly exceeds that of males. Specifically, we estimated the sex-specific importance of genetic and maternal effects on adult body size among individuals that we laboratory-reared for up to eight generations. Quantitative genetic model estimates indicated that size variation in females is to a larger extent explained by direct genetic effects than by maternal effects, but in males to a larger extent by maternal than by genetic effects. We conclude that this sex-specific body-size architecture enables body-size evolution to proceed much more independently than under a common architecture to both sexes.

Data from: Sex-specific selection patterns in a dioecious insect-pollinated plant

This is an experimental research project which aims at understanding how natural and sexual selection gradients (and differentials) vary according to sex in a dioecious insect-pollinated species, Silene dioica. Moreover, Bateman gradients are estimated using two sampling methods for genotyped offspring acquisition. The following dataset was obtained on the whole flowering season and includes: <ul> <li>individual information (population cohort etc.)</li> <li>18 floral traits (using mean for repeated measures)</li> <li>female reproductive success</li> <li>male reproductive success (clean results from CERVUS, with and without paternity share)</li> <li>male and female mating success (estimating with different sampling methods)</li> </ul>

Regional and global climate risks for reef corals: incorporating species-specific vulnerability and exposure to climate hazards

Climate change is driving rapid and widespread erosion of the environmental conditions that formerly supported species persistence. Existing projections of climate change typically focus on forecasts of acute environmental anomalies and global extinction risks. The current projections also frequently consider all species within a broad taxonomic group together without differentiating species-specific patterns. Consequently, we still know little about the explicit dimensions of climate risk (i.e., species-specific vulnerability, exposure and hazard) that are vital for predicting future biodiversity responses (e.g., adaptation, migration) and developing management and conservation strategies. Here, we use reef corals as model organisms (n = 741 species) to project the extent of regional and global climate risks of marine organisms into the future. We characterise species-specific vulnerability based on the global geographic range and historical environmental conditions (1900–1994) of each coral species within their ranges and quantify the projected exposure to climate hazard beyond the historical conditions as climate risk. We show that many coral species will experience a complete loss of pre-modern climate analogs at the regional scale and across their entire distributional ranges, and such exposure to hazardous conditions is predicted to pose substantial regional and global climate risks to reef corals. Although high-latitude regions may provide climate refugia for some tropical corals until the mid-21st century, they will not become a universal haven for all corals. Notably, high-latitude specialists and species with small geographic ranges remain particularly vulnerable as they tend to possess limited capacities to avoid climate risks (e.g., via adaptive and migratory responses). Predicted climate risks are amplified substantially under the SSP5-8.5 compared with the SSP1-2.6 scenario, highlighting the need for stringent emission controls. Our projections of both regional and global climate risks offer unique opportunities to facilitate climate action at spatial scales relevant to conservation and management.

opencc-zeroMay 2023View details →

Data from: Behaviour-specific spatiotemporal patterns of habitat use by sea turtles revealed using biologging and supervised machine learning

<ol> <li>Conservation of threatened species and anthropogenic threat mitigation commonly rely on spatially managed areas selected according to habitat preference. Since the impact of threats can be behaviour-specific, such information could be incorporated into spatial management to improve conservation outcomes. However, collecting spatially explicit behavioural data is challenging.</li> <li>Using multi-sensor biologging tags containing high-resolution movement sensors (e.g., accelerometer, magnetometer, GPS) and animal-borne video cameras, combined with supervised machine learning, we developed a method to automatically identify and geolocate typically ambiguous behaviours for the poorly understood flatback turtle Natator depressus. Subsequently, we evaluated behaviour-specific spatiotemporal patterns of habitat use.</li> <li>Boosted regression trees successfully identified the presence of foraging and resting in 7074 dives (AUC > 0.9), using dive features representing characteristics of locomotory activity, body posture, and three-dimensional dive paths validated by ancillary video data. Foraging was characterised by dives with longer duration, variable depth, tortuous bottom phases; resting was characterised by dives with decreased locomotory activity and longer duration bottom phases.</li> <li>Foraging and resting showed minimal spatial segregation based on 50% and 95% utilisation distributions. Expected diel patterns of behaviour-specific habitat use were superseded by the extreme tides at the near-shore study site. Turtles rested in areas close to the subtidal and intertidal boundary within larger overlapping foraging areas, allowing efficient access to intertidal food resources upon inundation at high tides when foraging was ~25% more likely.</li> <li> Synthesis and applications: Using supervised machine learning and biologging tools, we show the potential for dynamic spatial management of flatback turtles to mitigate behaviour-specific threats by prioritising protection of important locations at pertinent times. Although results are a species-specific response to a super-tidal environment, our approach can be generalised to a broad range of taxa and study systems, facilitating a conceptual advance in spatial management.</li> </ol>

opencc-by-4.0May 2025View details →

The essential clathrin adaptor protein complex-2 is tumor suppressive specifically in vivo

Full Immunoblots from publication

opencc-zeroMay 2023View details →

Survival and cause-specific mortality in adult females of a northern migratory ungulate

Survival of ungulates can vary seasonally due to changing environmental conditions, e.g., weather or predation pressure. The wild forest reindeer (Rangifer tarandus fennicus, 'WFR') migrate between calving and wintering grounds. The annual cycle of female WFR includes four main seasons (wintering, calving, rutting and autumn migration) during which they are subject to different conditions, but almost nothing is known about their survival or mortality patterns. We measured survival in 305 GPS-tagged female WFR in two subpopulations in Finland (2010–2022). Data were analysed for inter-annual and seasonal patterns in survival and cause-specific mortality (predation, traffic, accidents and unknown causes) with known-fate models. Inter-annual survival in Suomenselkä (mean 0.90) showed an increasing trend during the study and was higher than in Kainuu (mean 0.84) which showed a declining trend. Seasonal variation in survival was population dependent. Survival was lowest in Kainuu during the winter while in Suomenselkä, it was lowest during autumn migration. Concerning cause-specific mortality, seasonal variation mirrored variation in predation that was the primary cause of mortality (55% of cases). Wolves (Canis lupus) killed the majority of predated individuals (58%). Predation rates were two times higher in Kainuu where the wolf density was higher. We provide the first adult survival estimates for WFR and show that the seasonal variation in survival is clearly different between these two northern ungulate populations. This indicates that seasonal variation in survival is determined by site-dependent factors and cannot be generalised across populations.

opencc-by-4.0May 2023View details →

Additional raw data in `Cell-type-specific co-expression inference from single cell RNA-sequencing data'.

This repository holds the additional raw data used to generate figures in the publication "Cell-type-specific co-expression inference from single cell RNA-sequencing data" (preprint version: <a href="http://source%20code%20repo%20for%20%60cell-type-specific%20co-expression%20inference%20from%20single%20cell%20rna-sequencing%20data%27./">https://www.biorxiv.org/content/10.1101/2022.12.13.520181v1</a>). Table of contents: <ul> <li>Figure_1B.rds:  <ul> <li>raw data of Figure 1B </li> <li>co-expression estimates of 500*499/2 gene pairs across 100 replicates for 7 methods under two settings of sequencing detph variations</li> </ul> </li> <li>Supplementary_Figure_1B.rds:  <ul> <li>raw data of Supplementary Figure 1B </li> <li>co-expression estimates of 500*499/2 gene pairs across 100 replicates for 7 methods under two settings of sequencing detph variations</li> </ul> </li> <li>Supplementary_Figure_2.rds:  <ul> <li>raw data of Supplementary Figure 2 </li> <li>empirical power evaluated for 4999 gene pairs and 6 methods</li> </ul> </li> <li>Figure_3B.rds:  <ul> <li>raw data of Figure 3B</li> <li>co-expression estimates of a network of 500 genes for 9 methods across 100 replicates</li> </ul> </li> <li>Additional_Raw_Data.xlsx <ul> <li>raw data of Figure 3A: (geometric mean expression levels, co-expression estimates) for 4999 gene pairs and 11 methods</li> <li>raw data of Figure 3C: running times for 11 methods</li> <li>raw data of Supplementary Figure 3: (geometric mean expression levels, co-expression estimates) for 4999 gene pairs and 11 methods under two settings of sequencing detph variations</li> </ul> </li> </ul>

opencc-zeroJun 2023View details →

Data for: Sex-specific transgenerational plasticity: Developmental temperatures of mothers and fathers have different effects on sons and daughters

Each parent can influence offspring phenotypes via provisioning of the zygote or sex-specific DNA methylation. Transgenerational plasticity may therefore depend on environmental conditions experienced by each parent. We tested this hypothesis by conducting a fully factorial experiment across three generations of guppies (Poecilia reticulata), determining the effects of warm (28°C) and cold (21°C) thermal backgrounds of mothers and fathers on mass and length, and thermal performance (sustained [Ucrit] and sprint swimming speeds, citrate synthase and lactate dehydrogenase activities; 18, 24, 28, 32 and 36°C test temperatures) of sons and daughters. Offspring sex was significant for all traits except for sprint speed. Warmer mothers produced sons and daughters with reduced mass and length, and warmer fathers produced shorter sons. Ucrit of male offspring was greatest when both parents were raised at 28°C, and warmer fathers produced daughters with greater Ucrit. Similarly, warmer fathers produced sons and daughters with greater metabolic capacities. We show that thermal variation experienced by parents can modify offspring phenotypes, and that predicting the impacts of environmental change on populations would require knowledge of the thermal background of each mothers and fathers, particularly where sexes are spatially segregated.

opencc-by-4.0Jun 2023View details →

Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Mapping MGEs in oral plaque biofilms at high specificity

We stained for the GFP gene in samples that contained mixtures of plaque and GFP-transformed E. coli. We mapped mefE, an AMR gene located on a plasmid and encoding an antibiotic efflux pump, in the plaque metagenomic data of volunteer A but not volunteer B. To test the efficacy of gel embedding and clearing, we used orthogonal FISH probes, designed to not target any sequence in the plaque. We identified a T7-like prophage via metagenomic analysis and developed probes targeting its capsB gene, which encodes the minor capsid protein. We identified a highly prevalent prophage of the class Caudoviricetes with a large terminase gene, termL, and were able to design a large set of FISH probes to stain in three different colors simultaneously. We identified three non-plasmid AMR genes within metagenome assembled genomes: patA, patB, and adeF.

opencc-by-nc-sa-4.0Jun 2023View details →

Software Requirements Specifications from the RE@UTS Group

This repository contains a list of requirements specifications procured by the requirements engineering laboratory at the University of Technology Sydney (RE@UTS) for reuse in research. These artifacts represent a diverse set of domains and formats, offering a heterogeneous benchmark for studies in requirements engineering.

opencc-by-4.0Jun 2023View details →

OntoMaturity Specification

Material used as a basis for building the OntoMaturity ontology.

opencc-by-4.0Jun 2023View details →

OntoMaturity ontology specification

Material used as a basis for building the OntoMaturity ontology.