Find research datasets worth reusing

Long-range inhibition synchronizes and updates prefrontal task activity

Trial-by-trial physiology data (synchrony measurements and population activity vectors used to compute population vector similarity) supporting Cho et al., 2023. Any use of this data should cite this DOI as well as the associated publication.

Brief introduction to parameterization of downward longwave radiation based on long-term baseline surface radiation measurements in China

This short vidio is used to briefly introduce the contents of the article "Parameterization of downward longwave radiation based on long-term baseline surface radiation measurements in China".

opencc-zeroMar 2023View details →

Long-term effect of forest harvesting on boreal species assemblages under climate change

Logging is the main human disturbance impacting biodiversity in forest ecosystems. However, the impact of forest harvesting on biodiversity is modulated by abiotic conditions through complex relationships that remain poorly documented. Therefore, the interplay between forest management and climate change can no longer be ignored. Our aim was to study the expected long-term variations in the assemblage of bird and beetle communities following modifications in forest management under different climate change scenarios. We developed species distribution models to predict the occurrence of 88 species of birds and beetles in eastern Canadian boreal forests over the next century. We simulated three climate scenarios (baseline, RCP4.5 and RCP8.5) under which we varied the level of harvesting. We also analyzed the regional assemblage dissimilarity by decomposing it into balanced variations in species occupancy and occupancy gradient. We predict that forest harvesting will alter the diversity by increasing assemblage dissimilarity under all the studied climate scenarios, mainly due to species turnover. Species turnover intensity was greater for ground-dwelling beetles, probably because they have lower dispersal capacity than flying beetles or birds. A good dispersal capacity allows species to travel more easily between ecosystems across the landscape when they search for suitable habitats after a disturbance. Regionally, an overall increase in the probability of occupancy is projected for bird species, whereas a decrease is predicted for beetles, a variation that could reflect differences in ecological traits between taxa. Our results further predict a decrease in the number of species that increase their occupancy after harvest under the most severe climatic scenario for both taxa. We anticipate that under severe climate change, increasing forest disturbance will be detrimental to beetles associated with old forests but also with young forests after disturbances.

HairSplitter: separating strains in metagenome assemblies with long reads

Datasets, command lines and assemblies analyzed in the manuscript "HairSplitter: separating strains in metagenome assemblies with long reads".

Dataset from publication: Long-term changes in bloom dynamics of Southern and Central Baltic cold-water phytoplankton

This data set contains the output of the numerical ocean model GETM used in the publication "Long-term changes in bloom dynamics of Southern and Central Baltic cold-water phytoplankton"

Dataset for manuscript "Host-related and environmental factors influence long-term ectoparasite infestation dynamics of mouse lemurs in northwestern Madagascar" to be published in the American Journal of Primatology

This Excel-file contains three datasets, corresponding to the initial raw dataset resulting from all ectoparasite inspections (n = 2,241), the merged dataset used for host-related and temporal modeling (n = 1940), and the even more condensed dataset with one datapoint per individual used for climatic modeling (n = 583), respectively.

A long-term (1981-2020) 1-km daily extreme and mean near surface air temperature product over Yellow River Basin of China

The dataset includes the semless 1-km daily extreme and mean near surface air temperature products over Yellow River Basin of China. The fourth version is from 1 January 2011 to 31 Decmber 2020.

opencc-zeroMar 2023View details →

Migration statistics and animal biometrics for mule deer that migrated long-distances (2011–2020), Wyoming, USA

Billions of animals migrate to track seasonal pulses in resources. Optimally timing migration is a key strategy, yet the ability of animals to compensate for phenological mismatches en route is largely unknown. We studied a population of mule deer (Odocoileus hemionus) in Wyoming that lack reliable cues on their desert winter range, causing them to start migration 70 days ahead to 52 days behind the wave of spring green-up. By adjusting movement speed and stopover use, however, individual deer arrive at the summer range within an average 6-day window. Late migrants move 2.5 times faster and spend 72% less time on stopovers than early migrants, which allows them to catch the green wave. Ungulates, and potentially other migratory species, possess cognitive abilities to recognize where they are in space and time relative to key resources. Such behavioral capacity may allow migratory taxa to maintain foraging benefits amid rapidly changing phenology.

Dataset for "Seismic background level (SBL) growth can reveal slowly developing long-term eruption precursors"

Ichihara M, Ohminato T, Konstantinou KI, Yamakawa K, Watanabe A, Takeo M (2023) Seismic background level (SBL) growth can reveal slowly developing long-term eruption precursors. Scientific Report (revised) Matlab fig files for Figures 1--6 and Figures in Supporting Information in the above manuscript.

opencc-zeroMar 2023View details →

Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests

Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The pre-human extent of these grasslands is a topic of vigorous debate, with conventional wisdom holding that they are anthropogenic in nature and emerging evidence supporting that grasslands were a component of the pre-human Central Highlands vegetation. Here, we shed light on the temporal dynamics of Madagascar's vegetative composition by conducting a population genomic investigation of Goodman's mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar's eastern rainforests and in the Central Highlands, which makes them a valuable indicator species. Population divergences among forest-dwelling mammals can serve as a proxy for habitat fragmentation and patterns of post-divergence gene flow can reveal potential migration corridors consistent with a wooded grassland mosiac. We used RADseq data to infer phylogenetic relationships, population structure, demographic models of post-divergence gene flow, and population size change through time. These analyses offer evidence that open habitats are an ancient component of the Central Highlands, and that wide-spread forest fragmentation occurred naturally during a period of decreased precipitation near the last glacial maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Notably, though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may be more vulnerable from paleoclimatic changes.

Brazilian Starter Data Kit Update to Support the Paper "Integrated Long-Term Expansion Planning and Short-Term Operation Assessment for Decarbonisation Pathways in Brazil Considering Utility-Scale Storage"

This dataset presents updates on the Brazilian starter data kit, considering current load profile data and specific renewable energy sources production, using public data from official Brazilian power system agents. The dataset contains the input data and respective files to run OSeMOSYS and Flextool, including the utility-scale storage model. Additionally, this dataset contains the results of the study "Integrated Long-Term Expansion Planning and Short-Term Operation Assessment for Decarbonisation Pathways in Brazil Considering Utility-Scale Storage". This study evaluates the increase in variable renewable energy in Brazil and its integration with Storage systems.

opencc-by-4.0Apr 2023View details →

Fibertools: fast and accurate m6A calling using single-molecule long-read sequencing (ML data)

Fibertools is a convolutional neural network that permits the fast and accurate identification of endogenous and exogenous N6-methyladenine (m6A)-marked bases using single-molecule long-read sequencing. This dataset (ML data) provides training and validation data for training fibertools supervised and semi-supervised CNN models for three long-read chemistries.

opencc-by-4.0Jul 2022View details →

Long-term soil erosion monitoring in China using the RUSLE model based on Google Earth Engine

This dataset contains soil erosion maps in China at 500m resolution from 2010 to 2020. The dataset is stored in GeoTif format with the unit of t/(km2 · a).

Effects of long-term mowing on leaf- and root-associated bacterial community structures are linked to functional traits in 11 plant species from a temperate steppe

<ol> <li>Long-term mowing can cause morphological stuntedness of plants, thus reducing grassland productivity and exacerbating grassland degradation. Although plant microbiomes can enhance plant resistance against disturbance, considerable uncertainty exists regarding how mowing and mowing-induced plant trait plasticity affect plant microbiomes in natural grasslands. </li> <li>Here we examined the responses of leaf-/root-associated bacterial (LAB/RAB) communities of 11 dominant herbaceous perennials (6 replicates per species) to a 17-year mowing treatment in a temperate grassland. We also measured leaf/root physiological and morphological traits and analyzed the relationships among mowing practice, bacterial community structures, and leaf/root trait parameters. </li> <li>We found that both leaf and root functional traits showed interspecific variations (variations across different plant species), while only the leaf traits exhibited intraspecific variation (treatment-induced variations within plant species) between the treatments. Similarly, the LAB community structure was more sensitive to mowing but less influenced by host species identity, compared to the RAB community. The RAB community structure was primarily shaped by host species identity, while mowing was a secondary influencing factor. </li> <li> The different patterns of LAB and RAB communities in response to mowing could be specifically explained by the inter-/intraspecific variations of the related leaf and root traits. The LAB community was strongly correlated with the leaf traits which exhibited mowing-induced plasticity (intraspecific variation), with the correlations with nitrogen resorption efficiency and aboveground dry weight being the greatest. The root traits were important indicators of bacterial community structure in the root compartment across the hosts, rather than between the treatments. Root tissue density showed the strongest interspecific variation, and was identified as an overwhelming driver of the RAB community. The shifts in LAB/RAB communities under mowing were largely attributed to the increased proportions of Actinobacteria. The high mowing sensitivity of the LAB community was associated with the enrichment of soil-derived Actinobacteria in leaves under mowing. Actinobacteria were also the main keystone taxa in the bacterial community networks under mowing. </li> <li>Our results demonstrate that the magnitude of plant-associated microbial community response to long-term mowing is plant compartment- and trait-variation-dependent, and advance our understanding of the leaf/root microbiome-trait relationships in complex plant communities.</li> </ol>

opencc-by-4.0Dec 2022View details →

Code and data for "Two-way coupled long-wave isentropic ocean-atmosphere dynamics"

This repository contains the code and data needed to replicate the figures and simulations in the JFM Paper: "Two-way coupled long-wave isentropic ocean-atmosphere dynamics". Please see the readme.txt file for details. Edit: -v3 added a jfm_pysonly.zip which contains only the Python scripts to create the figures to allow for a faster separate download -v2 updated with JFM paper DOI https://doi.org/10.1017/jfm.2023.131 in file headers

Drought neutralizes positive effects of long-term grazing on grassland productivity through altering plant-soil interactions

Livestock grazing is among the most intensive land-use activities in grasslands and can affect plant communities directly or indirectly via grazing-induced soil legacies. Under climate change, grasslands are threatened globally by recurrent drought. However, the extent to which drought influences grazing-induced soil legacy effects on plant biomass production and community composition remains largely unexplored. We grew five naturally co-occurring plant species (three dominants and two subordinates) in mixed communities in a glasshouse experiment in live and sterilized soil that had or had not been subjected to 19 years of grazing; these plant communities were then exposed to a subsequent drought. We tested the treatment effects on plant community biomass, proportional aboveground biomass of individual species, arbuscular mycorrhizal (AM) fungal root colonization, and soil nutrient availability. Under drought-free conditions, soils from grazed plots produced significantly higher plant aboveground and total community biomass compared to soils from ungrazed plots. In contrast, plant aboveground and total community biomass were similar between grazed and ungrazed soils under drought conditions. Similarly, soils from grazed plots increased the proportional biomass of dominant species but decreased the proportion of subordinate species; however, the proportional biomass of dominant and subordinate species was similar between grazed and ungrazed soils under drought conditions. Soil NO3--N in grazed soil was significantly higher compared to ungrazed soil. Drought dramatically increased soil NO3--N in sterilized soil and had a more pronounced increase in grazed soil than in ungrazed soil. Arbuscular mycorrhizal fungal root colonization from grazed soil was lower compared to ungrazed soil. Drought significantly increased the soil available phosphorus concentration, as well as plant community AM fungal root colonization. Synthesis. Our study suggests that drought can neutralize positive grazing effects on plant community biomass production via altered plant-soil interactions. Also, we found that drought can alleviate the negative effects of grazing legacies on subordinate species by reducing the competitiveness of dominant species. Our study provides new insights for understanding the underlying mechanisms of grazing effects on grassland productivity under climate change.

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>

Long-term nitrogen deposition inhibits soil priming effects by enhancing phosphorus limitation in a subtropical forest

It is widely accepted that phosphorus (P) limits microbial metabolic processes and thus soil organic carbon (SOC) decomposition in tropical forests. Global change factors like elevated atmospheric nitrogen (N) deposition can enhance P limitation, raising concerns about the fate of SOC. However, how elevated N deposition affects the soil priming effect (PE) (i.e., fresh C inputs induced changes in SOC decomposition) in tropical forests remains unclear. We incubated soils exposed to nine years of experimental N deposition in a subtropical evergreen broadleaved forest with two types of 13C-labeled substrates of contrasting bioavailability (glucose and cellulose) with and without P amendments. We found that N deposition decreased soil total P and microbial biomass P, suggesting enhanced P limitation. In P unamended soils, N deposition significantly inhibited the PE. In contrast, adding P significantly increased the PE under N deposition and by a larger extent for the PE of cellulose (PEcellu) than the PE of glucose (PEglu). Relative to adding glucose or cellulose solely, adding P with glucose alleviated the suppression of soil microbial biomass and C-acquiring enzymes induced by N deposition, whereas adding P with cellulose attenuated the stimulation of acid phosphatase induced by N deposition. Across treatments, the PEglu increased as C-acquiring enzyme activity increased, whereas the PEcellu increased as acid phosphatase activity decreased. This suggests that P limitation, enhanced by N deposition, inhibits the soil PE through varying mechanisms depending on substrate bioavailability; that is, P limitation regulates the PEglu by affecting soil microbial growth and investment in C acquisition, whereas regulates the PEcellu by affecting microbial investment in P acquisition. These findings provide new insights for tropical forests impacted by N loading, suggesting that expected changes in C quality and P limitation can affect the long-term regulation of the soil PE.

A high-quality, long-read genome assembly of the whitelined sphinx moth (Lepidoptera: Sphingidae: Hyles lineata)

The sphinx moth genus Hyles comprises 29 described species inhabiting all continents except Antarctica. The genus diverged relatively recently (40 – 25 mya), arising in the Americas and rapidly establishing a cosmopolitan distribution. The whitelined sphinx moth, Hyles lineata, represents the oldest extant lineage of this group and is one of the most widespread and abundant sphinx moths in North America. Hyles lineata exhibits the large body size and adept flight control characteristic of the sphinx moth family (Sphingidae), but is unique in displaying extreme larval color variation and broad host plant use. These traits, in combination with its broad distribution and high relative abundance within its range, have made H. lineata a strong model organism for studying phenotypic plasticity, plant-herbivore interactions, physiological ecology, and flight control. Despite being one of the most well-studied sphinx moths, little data exists on genetic variation or regulation of gene expression. Here we report a high-quality draft genome showing high contiguity (N50 of 14.2 Mb) and completeness (98.2% of Lepidoptera BUSCO genes), an important first characterization to facilitate such studies. We also annotate the core melanin synthesis pathway genes and confirm that they have high sequence conservation with other moths and are most similar to those of another, well-characterized sphinx moth, the tobacco hornworm (Manduca sexta).