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Research Data Management in Selected Health Research Institutions in Uganda

This data set was collected from Researchers in three purposively selected health reseach Institutions in Uganda. The purpose of the study was to explore compliance to FAIR data princiles and Open science initiative given the increasing dependence on donor funding and need to fulfill the requirement for good research practices.

opencc-zeroNov 2023View details →

Predator selection on multicomponent warning signals in an aposematic moth

Aposematic prey advertise their unprofitability with conspicuous warning signals that are often composed of multiple color patterns. Many species show intraspecific variation in these patterns even though selection is expected to favor invariable warning signals that enhance predator learning. However, if predators acquire avoidance to specific signal components, this might relax selection on other aposematic traits and explain variability. Here we investigated this idea in the aposematic moth Amata nigriceps that has conspicuous black and orange coloration. The size of the orange spots in the wings is highly variable between individuals, whereas the number and width of orange abdominal stripes remain consistent. We produced artificial moths that varied in the proportion of orange in the wings or the presence of abdominal stripes. We presented these to a natural avian predator, the noisy miner (Manorina melanocephala), and recorded how different warning signal components influenced their attack decisions. When moth models had orange stripes on the abdomen, birds did not discriminate between different wing signals. However, when the stripes on the abdomen were removed, birds chose the model with smaller wing spots. In addition, we found that birds were more likely to attack moths with a smaller number of abdominal stripes. Together, our results suggest that bird predators primarily pay attention to the abdominal stripes of A. nigriceps, and this could relax selection on wing coloration. Our study highlights the importance of considering individual warning signal components if we are to understand how predation shapes selection on prey warning coloration.

opencc-zeroNov 2023View details →

Data for: Pollinator and habitat-mediated selection as potential contributors to ecological speciation in two closely related species

In ecological speciation, incipient species diverge due to natural selection that is ecologically based. In flowering plants, different pollinators could mediate that selection (pollinator-mediated divergent selection) or other features of the environment that differ between habitats of two species could do so (environment-mediated divergent selection). Although these mechanisms are well understood, they have received little rigorous testing, as few studies of divergent selection across sites of closely related species include both floral traits that influence pollination and vegetative traits that influence survival. This study employed common gardens in sites of the two parental species and a hybrid site, each containing advanced generation hybrids along with the parental species, to test these forms of ecological speciation in plants of the genus Ipomopsis. Three vegetative traits (specific leaf area, leaf trichomes, and photosynthetic water-use efficiency) and five floral traits (corolla length and width, anther insertion, petal color, nectar production) were analyzed for impacts on fitness components (survival to flowering and seeds per flower, respectively). These traits exhibited strong clines across the elevational gradient in the hybrid zone, with narrower clines in theory reflecting stronger selection or higher genetic variance. Plants with long corollas and inserted anthers had higher seeds per flower at the I. tenuituba site, whereas selection favored the reverse condition at the I. aggregata site, a signature of divergent selection. In contrast, no divergent selection due to variation in survival was detected on any vegetative trait. Selection within the hybrid zone most closely resembled selection within the I. aggregata site. Across traits, the strength of divergent selection was not significantly correlated with width of the cline, which was better predicted by evolvability (standardized genetic variance). These results support the role of pollinator-mediated divergent selection in ecological speciation and illustrate the importance of genetic variance in determining divergence across hybrid zones.

Dataset of comprehensive Full-notch creep tests (FNCT) of selected high-density polyethylene (PE-HD) materials

The dataset provided in this repository comprises data obtained from a series of full-notch creep tests (FNCT) performed on selected high-density polyethylene (PE-HD) materials (for further details, see section 1 Materials in this document) in accordance with the corresponding standard ISO 16770 [1]. The FNCT is one of the mechanical testing procedures used to characterize polymer materials with respect to their environmental stress cracking (ESC) behavior. It is widely applied for PE-HD materials, that are predominantly used for pipe and container applications. It is based on the determination of the time to failure for a test specimen under constant mechanical load in a well-defined and temperature controlled liquid environment. The test device used here also allows for continuous monitoring of applied force, specimen elongation and temperature.

Ontogeny of hepatic metabolism in two broiler lines divergently selected for the ultimate pH of the Pectoralis major muscle

Nutrient availability during early stages of development (embryogenesis and the first week of life) can have long-term effects on physiological functions and bird metabolism. The embryo develops in a closed structure and depends entirely on the nutrients and energy available in the egg. The aim of this study was to describe the ontogeny of pathways governing hepatic metabolism that mediates many physiological functions in the pHu+ and pHu- chicken lines, which are divergently selected for the ultimate pH of meat, a proxy for muscle glycogen stores, and which differ in the nutrient content and composition of eggs. Our study provides the first detailed description of the evolution of different hepatic metabolic pathways during the early development of embryos and post-hatching chicks. We found a metabolic orientation for the pHu+ line towards proteolysis, glycogen degradation, ATP synthesis and autophagy, likely in response to a higher energy requirement compared with pHu- embryos. The metabolic orientations specific to the pHu+ and pHu- lines are established very early, probably in relation with their different genetic background and available nutrients.

opencc-zeroNov 2023View details →

Code and data for Bayesian joint species distribution model selection for community-level prediction

Code and data for reproducing the analysis in the manuscript "Bayesian joint species distribution model selection for community-level prediction." Provided data include percent cover observations for 39 modeled vascular plant species within boreal forest understory communities and environmental model covariates. R code is provided to generate model inputs, apply alternative models, generate out-of-sample predictions, and calculate associated community and species log scores and alternative model evaluation metrics. Further, R source code is provided to implement the multinomial joint species distribution model defined in the manuscript. Details on the data, its processing, and the alternative model definitions and structure can be found in the main text of the manuscript. Provided data are currently being used in ongoing analyses and coordination with authors may be warranted to avoid duplicate publication. Potential users are encouraged to consider collaboration with authors when useful and appropriate. Misinterpretation of data may occur if used outside the context of the original analysis. All data are made available in their current state. While significant efforts have been made to ensure data accuracy, complete accuracy cannot be guaranteed. Data may be updated periodically. It is the responsibility of the data user to check for updated versions of the data.

Raw Data: Higher seed yield through selection for reduced seed shattering in Italian ryegrass

Raw data used for publication "Higher seed yield through selection for reduced seed shattering in Italian ryegrass (Lolium multiflorum Lam.)" This dataset accompanies the article with the same title published on bioRxiv https://doi.org/10.1101/2023.12.01.569550

opencc-zeroDec 2023View details →

Selection for evasive mimicry imposed by an arthropod predator

It has long been hypothesized that a species that is relatively easy to catch by predators may face selection to resemble a species that is harder to catch. Several experiments using avian predators have since supported this "evasive mimicry" hypothesis. However, the sudden movement of artificial evasive prey in each of the above experiments may have startled the predators, generating an avoidance response unrelated to difficulty of capture. Additionally, in the above experiments, the catchability of prey was all or nothing, while in nature predators may occasionally catch evasive prey or fail to catch slower species, which might inhibit learning. Here, using mantids as predators, we conducted an experimental test of the evasive mimicry hypothesis that circumvents these limitations, using live painted calyptrate flies with modified evasive capabilities as prey. We found that mantids readily learned to avoid pursuing the more evasive prey types. Warning signals based on evasiveness and their associated mimicry may be widespread phenomena in nature. These findings not only further support its plausibility but demonstrate that even arthropod predators can select for it.

Figure 2 in Geographic variation in select species of the bat genus Platyrrhinus

Figure 2. Box plots of the centroid size by species/sex. (A) dorsal view of Platyrrhinus dorsalis, (B) ventral view of P. dorsalis, (C) dorsal view of P. umbratus, and (D) ventral view of P. umbratus. Sex: females = gray and males = light blue. Color box limits indicate the first (25%) and third (75%) quartile, the thick black line indicates the median centroid size, and open circles represent outliers.

Figure 1 in Geographic variation in select species of the bat genus Platyrrhinus

Figure 1. Dorsal (A) and ventral (B) views of a Platyrrhinus cranium illustrating the landmarks used in geometric morphometric analyses.

Figure 5 in Geographic variation in select species of the bat genus Platyrrhinus

Figure 5. Principal Component Analysis (PCA) of Platyrrhinus umbratus obtained from the (A) dorsal and (B) ventral views of the cranium. Specimens of each group is represented by a dot (nigellus: black; umbratus: blue).

Figure 4 in Geographic variation in select species of the bat genus Platyrrhinus

Figure 4. Principal Component Analysis (PCA) of Platyrrhinus dorsalis obtained from the (A) dorsal and (B) ventral views of the cranium. Specimens of each group is represented by a dot (chocoensis: gray; dorsalis: red).

Figure 3 in Geographic variation in select species of the bat genus Platyrrhinus

Figure 3. Box plots of the centroid size by groups, showing dorsal (A) and ventral (B) views of Platyrrhinus dorsalis, and dorsal (C) and (D) ventral views of P. umbratus. Groups: chocoensis = gray, dorsalis = red, nigellus = black,and umbratus = blue. Color box limits indicate the first (25 %) and third (75 %) quartile,the thick black line indicates the median centroid size, and open circles represent outliers.

opencc-zeroDec 2022View details →

Data for: Hunting mode and habitat selection mediate the success of human hunters

As a globally widespread apex predator, humans have unprecedented lethal and non-lethal effects on prey populations and ecosystems. Yet compared to non-human predators, little is known about the drivers and consequences of human hunting behavior. Here, we characterized the hunting modes, habitat selection, and harvest success of 483 rifle hunters in California using high-resolution GPS data. We used Hidden Markov Models to characterize fine-scale behavior, and k-means clustering to group hunters by hunting mode, on the basis of their time spent in each behavioral state. Hunters exhibited three distinct and successful hunting modes ("coursing", "stalking", and "sit-and-wait"), with stalking as the most successful strategy. Across hunting modes, there was variation in patterns of selection for roads, topography, and habitat cover, with important differences in habitat use of successful and unsuccessful hunters across modes. Our study indicates that hunters can successfully employ a diversity of harvest strategies, and that hunting success is mediated by the interacting effects of hunting mode and landscape features. Such results highlight the breadth of human hunting modes, even within a single hunting technique, and lend insight into the varied ways that humans exert predation pressure on wildlife.

opencc-zeroDec 2023View details →

Sexual selection on a female copulatory device in an insect with nuptial gifts

Male genitalia are rapidly evolving structures, often driven by sexual selection to increase fertilization success. Although sexual selection on females can be strong in systems where males provide offspring care or feed their mates, sometimes resulting in the evolution of female ornamentation, there are no actual estimates of direct sexual selection on female genitalia. In a New Zealand ground weta, Hemiandrus pallitarsis (Orthoptera: Ensifera, Anostostomatidae), females possess a genitalic device (the accessory organ) that is necessary for successful copulation and the acquisition of glandular food-gifts from males. These nutritious gifts are known to result in sexual competition among females in other ensiferan species. In ground weta, the gifts are probably important in avoiding starvation during a months-long period when caring for (their lifetime production of) eggs and offspring. Here, we test the hypothesis that the accessory organ is a sexually selected device in H. pallitarsis by measuring the female Bateman gradient, Jones index, and directional sexual selection on the accessory organ. Using newly developed and characterized microsatellite loci, we analyze offspring and/or stored sperm to estimate female mating frequency for the first time in ground weta. As predicted, we found both a positive Bateman gradient and Jones index for females, and evidence of directional sexual selection on accessory organ length. Although organ length does not correlate well with female fecundity, it may increase mating success by indicating her condition and thus quality of her offspring care.

opencc-by-4.0Dec 2023View details →

Transport Starter Data Kit: Historical socio-transport data for selected countries in Africa, Asia, and South America

This Transport Starter Data Kit contains historical annual data (1990–2021) on passenger activity, freight activity, vehicle stock, energy intensity, and load factor segregated by mode and fuel, where available. Additionally, historical data on population (total, urban, rural, growth) and GDP (total, agriculture, construction, mining, manufacturing, service, energy, growth) are included in the kit, within the 'Data' tab. The historical data can be used as a foundation for transport-energy modelling and/or to identify areas of improvement. This data was verified through consultation with relevant stakeholders before publishing. The definition used for each vehicle mode is found in the 'Definitions' tab, and the description of each data observation status is found in the 'Notes' tab. All data sources are linked where possible.Countries included: Angola, Burundi, Benin, Burkina Faso, Brazil, Botswana, Central African Republic, Côte d'Ivoire, Cameroon, Democratic Republic of the Congo, Congo, Colombia, Djibouti, Algeria, Egypt, Eritrea, Ethiopia, Gabon, Ghana, Guinea, Gambia, Guinea-Bissau, Equatorial Guinea, Indonesia, Kenya, Cambodia, Republic of Korea, Lao People's Democratic Republic, Liberia, Libya, Lesotho, Morocco, Mali, Myanmar, Mozambique, Mauritania, Malawi, Malaysia, Namibia, Niger, Nigeria, Philippines, Rwanda, Sudan, Senegal, Sierra Leone, Somalia, South Sudan, Eswatini, Chad, Togo, Thailand, Tunisia, Taiwan Province of China, United Republic of Tanzania, Uganda, Viet Nam, South Africa, Zambia, Zimbabwe.

opencc-zeroDec 2023View details →

Competitors alter selection on alpine plants exposed to experimental climate change

Investigating how climate change alters selection regimes is a crucial step towards understanding the potential of populations to evolve in the face of changing conditions. Previous studies have mainly focused on understanding how changing climate directly influences selection, while the role of species' interactions has received little attention. Here, we used a transplant experiment along an elevation gradient to estimate how climate warming and competitive interactions lead to shifts in directional phenotypic selection on morphology and phenology of four alpine plants. We found that warming generally imposed novel selection, with the largest shifts in regimes acting on specific leaf area and flowering time across species. Competitors instead weakened the selection acting on traits that was imposed directly by warming. Weakened or absent selection in the presence of competitors was largely associated with the suppression of absolute means and variation of fitness. Our results suggest that although climate change can impose strong selection, competitive interactions within communities might act to limit selection and thereby stymie evolutionary responses in alpine plants facing climate change.

opencc-by-4.0Jan 2024View details →

Data for: Making 1H-1H couplings more accessible and accurate with selective 2DJ NMR experiments aided by 13C satellites

1H-1H coupling constants are one of the primary sources of information for NMR structural analysis. Several selective 2DJ experiments have been proposed that allow their individual measurement at pure shift resolution. However, all these experiments fail in the not uncommon case when coupled protons have very close chemical shifts. Firstly, the coupling between protons with overlapping multiplets is inaccessible due to the inability of a frequency-selective pulse to invert just one of them. Secondly, the strong coupling condition affects the accuracy of coupling measurements involving third spins. These shortcomings impose a limit on the effectiveness of state-of-the-art experiments, such as G-SERF or PSYCHEDELIC. Here, we introduce two new and complementary selective 2DJ experiments that we coin SERFBIRD and SATASERF. These experiments overcome the aforementioned issues by utilizing the 13C satellite signals at natural isotope abundance, which resolve the chemical shift degeneracy. We demonstrate the utility of these experiments on the tetrasaccharide stachyose and the challenging case of norcamphor, for the latter achieving measurement of all JHH couplings while only few were accessible with PSYCHEDELIC. The new experiments are applicable to any organic compound and will prove valuable for configurational and conformational analyses. This deposit contains Bruker pulse sequences of the SERFBIRD and SATASERF experiments, and the Bruker NMR experimental data. See the readme.pdf file for an overview of the latter.

opencc-by-4.0Jan 2024View details →

Heterogeneous selectivity and morphological evolution of marine clades during the Permian-Triassic mass extinction

This is a supplementary repository, including the dataset and codes we used in this manuscript. we developed a new method, called DeepMorph to analyze the morphological evolution of six marine clades (i.e., ammonoids, bivalves, brachiopods, gastropods, ostracods, and conodonts  ) during the Permian-Triassic mass extinction events. The taxonomy dataset was uploaded and contains 599 genera and 656 images, spanning from the latest Permian (Changhsingian) to the earliest Triassic (Induan).