Find research datasets worth reusing

opencc-zeroApr 2024View details →

Ecological divergence despite common mating sites: Genotypes and symbiotypes shed light on cryptic diversity in the black bean aphid species complex

Different host plants represent ecologically dissimilar environments for phytophagous insects. The resulting divergent selection can promote the evolution of specialized host races, provided that gene flow is reduced between populations feeding on different plants. In black bean aphids belonging to the Aphis fabae complex, several morphologically cryptic taxa have been described based on their distinct host plant preferences. However, host choice and mate choice are largely decoupled in these insects: they are host-alternating and migrate between specific summer host plants and shared winter hosts, with mating occurring on the shared hosts. This provides a yearly opportunity for gene flow among aphids using different summer hosts, and raises the question if and to what extent the ecologically defined taxa are reproductively isolated. Here, we analyzed a geographically and temporally structured dataset of microsatellite genotypes from A. fabae that were mostly collected from their main winter host Euonymus europaeus, and additionally from another winter host and fourteen summer hosts. The data reveals multiple, strongly differentiated genetic clusters, which differ in their association with different summer and winter hosts. The clusters also differ in the frequency of infection with two heritable, facultative endosymbionts, separately hinting at reproductive isolation and divergent ecological selection. Furthermore, we found evidence for occasional hybridization among genetic clusters, with putative hybrids collected more frequently in spring than in autumn. This suggests that similar to host races in other phytophagous insects, both prezygotic and postzygotic barriers including selection against hybrids maintain genetic differentiation among A. fabae taxa, despite a common mating habitat.

opencc-zeroApr 2024View details →

Standing and shed litters alter plant growth in disturbed and undisturbed soils differently

Plant species affect key ecosystem processes like nutrient cycling and overall ecosystem productivity through their litter. The outcome of litter effects is largely determined by its decomposability, which directly effects soil properties. If litter remains standing or unshed (i.e. marcescent), its final decomposability can be increased by photodegradation of recalcitrant structures (like lignin). If the litter is immediately shed, its decomposability largely depends on its original nutrient content. Moreover, plant species may affect soil also through other, more direct effects. It is however unknown whether marcescent and immediately shed litters affect soil, and by that plants, differently, whether direct effects of plants on soil interact with those of marcescent and shed litters, and whether these interactions are consistent under different soil conditions. We set up a pot experiment, where we tested the effects of originally marcescent and shed litters (both added on the soil surface of the pots) on three grassland species (Bromus erectus, Filipendula vulgaris, and Plantago media) in contrasting soils from long-term stable ancient grassland and grassland restored on arable land 20 years before. We also tested how litter types and plant species affect soil chemical properties and microbial community (characterised by PLFA markers). Marcescent litter contained a lower amount of nutrients, but still increased plant biomass more than shed litter, although only for F. vulgaris (likely due to mobilisation of soil nutrients). The effect of litter on soil chemical properties and microbial community was low. These were largely affected by the plant species growing in the pot. The effect of these species on the microbial community was stronger in the undisturbed soil of ancient grasslands, while plant species affected mainly chemical properties in disturbed soil of restored grasslands. B. erectus slowed down the decomposition of both litter types in restored grassland soil. The effect of marcescent litter on living plants was significant but species-specific and depended on soil conditions. Marcescence seems to have a stronger effect on plants in disturbed soil, which indicates its importance for recovery of the ecosystem after disturbance.

opencc-by-4.0Dec 2023View details →

Figure 1 in Genetic difference between two Schistosoma japonicum isolates with contrasting cercarial shedding patterns revealed by whole genome sequencing

Figure 1. Map of geographical locations of research sites.

opencc-by-4.0Jul 2024View details →

The early evolution of the BA.2.86 VOI sheds light on the origins of highly divergent SARS-CoV-2 lineages

Alignments corresponding to the D1-D4.1 datasets. Five different datasets (named here D1, D2, D3, D4 and D4.4) comprising complete SARS-CoV-2 genomes (low-coverage excluded, Ns ≤ 5%) were compiled from assemblies retrieved from GISAID. Genomes within these datasets were collated at different time points, aligned and sequentially subsampled under a phylogenetically-informed approach.

opencc-by-4.0Jul 2021View details →

CLDF Dataset derived from Syrjänen et al.'s "Shedding more light on language classification" from 2013

Cite the source of the dataset as: <blockquote> Syrjänen, K.; Honkola, T.; Korhonen, K.; Lehtinen, J.; Vesakoski, O. &amp; Wahlber, N. Shedding more light on language classification using basic vocabularies and phylogenetic methods. Diachronica, 2013, 30, 323-352 </blockquote>

opencc-by-4.0Dec 2016View details →

Fig. 1 in Effect of temperature changes on the cercarial-shedding rate of two trematodes

Fig. 1. Flow diagram of experimental procedure for cercariae emergence assays.

opencc-zeroAug 2021View details →

A comprehensive approach to detect hybridization sheds light on the evolution of Earth's largest lizards

Hybridization between species occurs more frequently in vertebrates than traditionally thought, but distinguishing ancient hybridization from other phenomena that generate similar evolutionary patterns remains challenging. Here, we used a comprehensive workflow to discover evidence of ancient hybridization between the Komodo dragon (Varanus komodoensis) from Indonesia and a common ancestor of an Australian group of monitor lizards known colloquially as sand monitors. Our data comprise >300 nuclear loci, mitochondrial genomes, phenotypic data, fossil and contemporary records, and past/present climatic data. We show that the four sand monitor species share more nuclear alleles with V. komodoensis than expected given a bifurcating phylogeny, likely as a result of hybridization between the latter species and a common ancestor of sand monitors. Sand monitors display phenotypes that are intermediate between their closest relatives and V. komodoensis. Biogeographic analyses suggest that V. komodoensis and ancestral sand monitors co-occurred in northern Australia. In agreement with the fossil record, this provides further evidence that the Komodo dragon once inhabited the Australian continent. Our study shows how different sources of evidence can be used to thoroughly characterize evolutionary histories that deviate from a treelike pattern, that hybridization can have long-lasting effects on phenotypes, and that detecting hybridization can improve our understanding of evolutionary and biogeographic patterns.

opencc-zeroOct 2022View details →

Gastrointestinal helminths increase Bordetella bronchiseptica shedding and host variation in supershedding

Co-infected hosts, individuals that carry more than one infectious agent at any one time, have been suggested to facilitate pathogen transmission, including the emergence of supershedding events. However, how the host immune response mediates the interactions between co-infecting pathogens and how these affect the dynamics of shedding remains largely unclear. We used laboratory experiments and a modeling approach to examine temporal changes in the shedding of the respiratory bacterium Bordetella bronchiseptica in rabbits with one or two gastrointestinal helminth species. Experimental data showed that rabbits co-infected with one or both helminths shed significantly more B. bronchiseptica, by direct contact with an agar petri dish than rabbits with bacteria alone. Co-infected hosts generated supershedding events of higher intensity and more frequently than hosts with no helminths. To explain this variation in shedding an infection-immune model was developed and fitted to rabbits of each group. Simulations suggested that differences in the magnitude and duration of shedding could be explained by the effect of the two helminths on the relative contribution of neutrophils and specific IgA and IgG to B. bronchiseptica neutralization in the respiratory tract. However, the interactions between infection and immune response at the scale of analysis that we used could not capture the rapid variation in the intensity of shedding of every rabbit. We suggest that fast and local changes at the level of respiratory tissue probably played a more important role. This study indicates that co-infected hosts are an important source of variation in shedding, and provides a quantitative explanation of the role of helminths in the dynamics of respiratory bacterial infections.

opencc-zeroNov 2022View details →

Data from: The endocast of Euparkeria sheds light on the ancestral archosaur nervous system

Understanding the evolution of the tetrapod brain is essential to trace the history of ecomorphological diversification of modern clades. While previous studies focused on the morphological transformation of the nervous system along the dinosaur-bird transition, little is known about the brain anatomy of archosauriformes and early archosaurs. Here, we describe the endocast of Euparkeria capensis, a small-bodied, terrestrial archosauriform closely related to Archosauria, with the goal of resolving the current uncertainties surrounding the ancestral condition of the archosaurian nervous system. The endocast of Euparkeria is sigmoidal, with large olfactory bulbs, an expanded cerebral hemisphere and an elongated flocculus. We suggest that this pivotal taxon was an active predator with a remarkable olfactory acuity. Overall, the endocast of Euparkeria resembles the ones observed in phytosaurs, crocodilians and early dinosaurs, implying that modern crocodilians retain an archosaurian plesiomorphic brain morphology.

opencc-by-4.0Nov 2022View details →

Electron microscopy files (SBFSEM & TEM) for "Syncytial nerve net in a ctenophore sheds new light on the early evolution of nervous systems"

4 electron microscopy datasets: 1) SBFSEM data of 1-day old ctenophore Mnemiopsis leidyi (animal 1) 2) SBFSEM data of 1-day old ctenophore Mnemiopsis leidyi (animal 2) 3) SBFSEM data of 1-day old ctenophore Mnemiopsis leidyi (animal 3) 4) TEM data of nerve net of 1-day old ctenophore Mnemiopsis leidyi

opencc-zeroNov 2022View details →

Fine-scale temporal dynamics of flower visitors sheds light on the pollination strategy of a dioecious palm in the Ecuadorian Andes

Background: Dioecious plants generally display sexual dimorphism in male and female floral traits, potentially attracting slightly different pollinator communities. The sharing of common floral visitors between male and female flowers and their timing of visits to both sexes is of critical importance to ensure plant's reproductive success. Palm inflorescences are visited by abundant and diverse insect communities, yet the temporal patterns of insect visits on both sexes remain poorly known. Results: We report 59 morphospecies in the arthropod community, dominated by three beetle families: Staphylinidae, Nitidulidae and Curculionidae. Male inflorescences were more abundantly visited than female, but visitors of the later were taxonomically more diverse. Among the 16 pollinator candidates identified, 9 visited both inflorescence sexes synchronously at dusk /night whereas the others did so asynchronously during the day. Conclusion: Our study provides new insights into the pollination mechanism of P. aequatorialis. We found evidence of differential pollinator attraction between floral sexes, which may be explained by the sexual dimorphism of both flowers. Synchronicity in dusk/night visits of both inflorescence sexes suggests a sexual synchronization of the signal used to attract pollinators.

opencc-zeroNov 2022View details →

Plastid phylogenomics shed light on intergeneric relationships and spatiotemporal evolutionary history of Melocanninae (Poaceae: Bambusoideae)

Melocanninae is sister to other subtribes of Paleotropical woody bamboos with some 90 species mainly concentrated in Asia. However, phylogenetic relationships within the subtribe are poorly known. Here, we filled the gaps in complete plastome data of Melocanninae, reconstructed the phylogeny of Melocanninae, and further estimated divergence time and ancestral distribution range. Our results showed that the two major genera, Cephalostachyum and Schizostachyum, were paraphyletic. Species of Cephalostachyum were resolved in two successive basal clades, while Annamocalamus was embedded in the Schizostachyum clade. Different plastid regions provided inconsistent signals for the relationship of Melocanna and Pseudostachyum. Conservative loci supported a successive divergence rather than sister relationship between them and the difference may be caused by long-branch attraction. We infer that Melocanninae originated in the East Himalaya to northern Myanmar in the early Miocene. Three routes were revealed in forming its present biogeographic pattern: in situ diversification on the Asian mainland; dispersing southwest to Sri Lanka and to the Western Ghats in South India; and spreading southeast to Malesia and Oceania via the Indo-China Peninsula. The rapid uplift of the Tibetan Plateau and the intensification of Asian monsoons since the Miocene and the sea-level-fall events since the late Miocene might be potential driving forces for diversification of Melocanninae and, particularly the latter event, for the species radiation of Schizostachyum.

opencc-zeroJan 2023View details →

Data from: Genomic loci involved in sensing environmental cues and metabolism affect seasonal coat shedding in Bos taurus and Bos indicus cattle

Seasonal shedding of winter hair at the start of summer is well-studied in wild and domesticated populations. However, the genetic influences on this trait and their interactions are poorly understood. We use data from 13,364 cattle with 36,899 repeated phenotypes to investigate the relationship between hair shedding and environmental variables, single nucleotide polymorphisms, and their interactions to understand quantitative differences in seasonal shedding. Using de-regressed estimated breeding values from a repeated records model in a genome-wide association analysis (GWAA) and meta-analysis of year-specific GWAA gave remarkably similar results. These GWAA identified hundreds of variants associated with seasonal hair shedding. There were especially strong associations on chromosomes 5 and 23. Genotype-by-environment interaction GWAA identified 1,040 day-length-by-genotype interaction associations and 17 apparent temperature-by-genotype interaction associations with hair shedding, highlighting the importance of day length on hair shedding. Accurate genomic predictions of hair shedding were created for the entire dataset, Angus, Hereford, Brangus, and multi-breed datasets. Loci related to metabolism and light-sensing have a large influence on seasonal hair shedding. This is one of the largest genetic analyses of a phenological trait and provides insight for both agriculture production and basic science.

opencc-by-4.0May 2023View details →

Reproducibility Package for Predictive Limitations of Physics-Informed Neural Networks in Vortex Shedding

This archive contains the repro-pack for the paper at <a href="http://github.com/barbagroup/jcs_paper_pinn">https://github.com/barbagroup/jcs_paper_pinn</a>.

opencc-by-4.0May 2023View details →

Reproducibility Package (Raw Data) for Predictive Limitations of Physics-Informed Neural Networks in Vortex Shedding

Raw data results from the simulations using PINN methods and PetIBM for the paper at: https://github.com/barbagroup/jcs_paper_pinn

The Safety of Molnupiravir (EIDD-2801) and Its Effect on Viral Shedding of SARS-CoV-2 (END-COVID)

ClinicalTrials.gov study NCT04405739. IPD Sharing: Not stated. Countries: 1. Publications: 1.

A Study to Evaluate the Safety, Tolerability, Immunogenicity and Vaccine-like Viral Shedding of MEDI-534, Against Respiratory Syncytial Virus (RSV) and Parainfluenza Virus Type 3 (PIV3), in Healthy 6

ClinicalTrials.gov study NCT00686075. IPD Sharing: Not stated. Countries: 9. Publications: 1.

Single-arm Trial to Evaluate the Biodistribution and Shedding of Talimogene Laherparepvec

ClinicalTrials.gov study NCT02014441. IPD Sharing: Not stated. Countries: 2. Publications: 1.

A Phase 1/2A Study to Evaluate the Safety, Immunogenicity, and Shedding of MEDI-560 in Infants 1 to < 12 Months of Age

ClinicalTrials.gov study NCT00508651. IPD Sharing: Not stated. Countries: 1. Publications: 1.

A Study to Evaluate the Shedding and Safety of Trivalent Influenza Virus Vaccine Live, Intranasal in Infants and Young Children

ClinicalTrials.gov study NCT00344305. IPD Sharing: Not stated. Countries: 1. Publications: 1.