Find research datasets worth reusing

Fig. 1 in Long-term changes in avian relative abundances in relation to human disturbance in a tropical dry forest in central Myanmar

Fig. 1. Map of Chatthin Wildlife Sanctuary with land-cover changes; flooded dipterocarp forest (FL), mixed deciduous forest (MD) and young dipterocarp forest (YI) in Chatthin Wildlife Sanctuary between 1999 and 2020 and locations of bird survey points.

Fig 4 in Long-term changes in avian relative abundances in relation to human disturbance in a tropical dry forest in central Myanmar

Fig 4. Seasonal (y-axis) and long-term trends of abundances of six avian guilds in Chatthin Wildlife Sanctuary from 1999 to 2020. Redder = higher abundances, white/paler = lower abundances, and grey = no data.

Figures 5–6 in Pepsis elegans Lepeletier (Hymenoptera: Pompilidae: Pepsinae)-a secretive spider wasp and century-long conundrum

Figures 5–6. Habitus photos of Pepsis elegans and host. 5) Pepsis elegans. Female with dried mud plastered on her pronotum, mesonotum, mesoscutellum, propodeum, tegulae, forewings, mid-femora, mid- and hind tibiae, especially hind tibial teeth, and hind tarsi, Pryor, Mayes County, Oklahoma. Photograph © Robert Webster. 6) Ummidia audouini. Adult female immobilized by sting of "big black wasp," lying dorsal side upward on Mississippi River delta soil in Bolivar County, Mississippi. © Blake Layton, Jr.

Figures 3–4 in Pepsis elegans Lepeletier (Hymenoptera: Pompilidae: Pepsinae)-a secretive spider wasp and century-long conundrum

Figures 3–4. Localities of Pepsis spp. 3) Pepsis elegans. Females searched for host spiders on the ground, obtained nectar from flowers, and were attracted to artificial light at night near this mesic open woodland, Pryor, Mayes County, Oklahoma. Photograph © Robert Webster. 4) Pepsis cerberus, P. elegans, P. novitia. Geographic location map in Nearctic Region (based on Brimley 1936; Hurd 1952; Krombein 1952; Johnston 2000; Bond and Opell 2002; Vardy 2005; Leavengood et al. 2011; Bond and Godwin 2013; Hamilton et al. 2016; Norden 2017; Godwin and Bond 2021; Durand, pers. comm.; BugGuide.net; flickr.com; iNaturalist.org; gbif.org; SCAN; and specimen records from 36 insect collections as indicated in Materials and Methods). Black lines represent range limits of potential host spider genera. Solid black line represents geographic limit of Ummidia (Halonoproctidae) species (Godwin and Bond 2021). Dashed black line represents geographic limit of Aphonopelma (Theraphosidae) species (Hamilton et al. 2016). Dotted black line represents geographic limit of Eucteniza Ausserer (Euctenizidae) species (Bond and Godwin 2013). Dash-dotted black line represents geographic limit of Entychides Simon (Euctenizidae) species (Bond and Opell 2002).

Figures 1–2. Pepsis elegans. 1 in Pepsis elegans Lepeletier (Hymenoptera: Pompilidae: Pepsinae)-a secretive spider wasp and century-long conundrum

Figures 1–2. Pepsis elegans. 1) Female imbibing nectar from Asclepias incarnata L. (Apocynaceae), near Skiatook, Tulsa County, Oklahoma. Note dried mud on forewings. Photograph © Thomas Shahan. 2) Female host-searching on foot path, Webster's Garden, Pryor, Mayes County, Oklahoma. Note dried mud on forewings. Photograph © Robert Webster.

opencc-zeroDec 2023View details →

The role of tropical rainfall in driving range dynamics for a long-distance migratory bird

Predicting how the range dynamics of migratory species will respond to climate change requires a mechanistic understanding of the factors that operate across the annual cycle to control the distribution and abundance of a species. Here we use multiple lines of evidence to reveal that environmental conditions during the nonbreeding season influence range dynamics across the lifecycle of a migratory songbird, the American redstart (Setophaga ruticilla). Using long-term data from the nonbreeding grounds and breeding origin estimated from stable hydrogen isotopes in tail feathers, we found that the relationship between nonbreeding season survival and migration distance is mediated by precipitation, but only during dry years. A long-term drying trend throughout the Caribbean is associated with higher mortality for individuals from the northern portion of the species' breeding range, resulting in an approximate 500 km southward shift in breeding origins of this Jamaican population over the past 30 years. This shift in connectivity is mirrored by changes in the redstarts breeding distribution of abundance. These results demonstrate that the climatic effects on demographic processes originating during the tropical nonbreeding season is actively shaping range dynamics in a migratory bird.

opencc-by-4.0Dec 2022View details →

Data from "Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar"

Data from : 'Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar' An Vanden Broeck*, Tim Meese*, Pieter Verschelde, Karen Cox, Berthold Heinze, Dieter Deforce, Ellen De Meester and Filip Van Nieuwerburgh   Related publication: Vanden Broeck, A.*, Meese, T.*, Verschelde, P. et al. Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar. BMC Biol 22, 30 (2024). https://doi.org/10.1186/s12915-024-01816-1 <ul> <li>* These authors contributed equally.</li> </ul> -------------------------------------------------- Background: Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar (Populus nigra cv. 'Italica' Duroi) offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome. Results: We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH-context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe any biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring's' phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment. Conclusions: Genome-wide cytosine methylation patterns in symmetrical GC-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in GC-context can be used as bio-markers to infer a common ancestor and thus to investigate the environmental history of a specific Lombardy poplar on short time-scales. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.   ADDITIONAL FILES Additional file 1. CSV-file with information on the Lombardy poplar trees samples used for whole genome bisulfite sequencing (WGBS) in the two methylome experiments (metadata). The raw fastq datafiles obtained by whole genome bisulfite sequencing (WGBS) are available at the <a href="https://www.ncbi.nlm.nih.gov/geo/">Gene Expression Omnibus (GEO) database</a> (submission  GSE225596). Additional file 2. CSV-file with mapping statistics, bisulfite conversion rates and percentages of cytosine methylation for each DNA-sample analyzed by whole genome bisulfite sequencing (WGBS). (processed data). Additional file 3. CSV-file with the total list of GO terms that were enriched in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (processed data). Additional file 4. POWERPOINT-file. Heatmaps with GO terms over-represented in promoters containing DMRs in CpG-context per between-group pairwise comparison. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively). A. HUN4 versus ITS3; B. HUN4 versus UKD2, C; ITS3 versus SPC1; D. HUN4 versus SCP1,  E. SPC1 versus UKD2 Additional file 5. CSV-file with the raw data of the bud set observations in the common garden experiment (raw data). Additional file 6. HTML-file with the R source codes to reproduce the results of the bud set analysis (code, R script). Additional file 7. A text-file representing the Snakefile (i.e. a readable Python-based workflow) including the different steps and rules of the bioinformatics of the WGBS data analyses (code, Snakefile). Additional file 8. RMD-file with the code to reproduce the analyses to identify differential methylated predefined regions (code, R script). Additional file 9. R-script with the code to reproduce the clustering and visualizing of the GO enrichment results (code, R script). Supporting files 1. Zip-folder with: i) excel-files listing the genes in DMRs, and ii) PNG-files with the ‘Biological Coefficient of Variation (BCV)’-plots between any of the six pairwise comparisons of Lombardy poplars grouped per ortet and identified with Bioconductor package edgeR. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (processed data). Supporting files 2. Zip-folder with PNG-files representing heatmaps and excel-files with clustered GO terms significant over-represented in promoters and gene regions located in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively. The files were obtained with the Bioconductor package simplifyEnrichment (processed data). --------------------------------------------------------- Version 3: <ul> <li>Renaming of file names according to the publisher's guidelines</li> <li>Additional file 2 includes also bisulfite conversion rates per sample</li> </ul>

opencc-by-4.0Dec 2023View details →

'Twitter Is Dead, Long Live X!' A Decade of Microblog Research and Implications for Knowledge and Research

Talk at the <a href="https://www.digital-philosophy.org/" target="_blank" rel="noopener">Philosophy [in:of:for:and] Digital Knowledge Infrastructures</a> online workshop 2023 (28/09/2023).

opencc-zeroDec 2023View details →

Mixed population trends inside a California protected area: Evidence from long-term community science monitoring

Protected areas are one of the most widespread and accepted conservation interventions, yet their population trends are rarely compared to regional trends to gain insight into their effectiveness. Here, we leverage two long-term community science datasets to demonstrate mixed effects of protected areas on long-term bird population trends. We analyzed 31 years of bird transect data recorded by community volunteers across all major habitats of Stanford University's Jasper Ridge Biological Preserve to determine the population trends for a sample of 66 species. We found that nearly a third of species experienced long-term declines, and on average, all species declined by 12%. Further, we averaged species trends by conservation status and key life history attributes to identify correlates and possible drivers of these trends. Observed increases in some cavity-nesters and declines of scrub-associated species suggest that long-term fire suppression may be a key driver, reshaping bird communities through changes in forest and chaparral structure and composition. Additionally, we compared our results to those of the North American Breeding Bird Survey's Central California Coast region (n = 55 species) to place Jasper Ridge in a broader context. Most species experienced similar directional population trends inside vs. outside of the preserve, and only eight species (14.5%) did better inside this small, protected area. Therefore, we must identify relevant management strategies for declining populations and explicitly consider how existing protected areas target and manage each species. Further, this analysis underscores the importance of local and national community science for revealing nuanced long-term bird population trends.

opencc-by-4.0Sep 2023View details →

Data for "Long-term disgust habituation with limited generalisation in care home workers"

Anonymised data for the manuscript "Long-term disgust habituation with limited generalisation in care home workers". For use with scripts in the linked GitHub repository.

opencc-by-4.0Apr 2023View details →

Post-hypnotic safety suggestion improves stress coping with long-lasting effects

Effective coping with acute stress is important to promote mental health and to build stress resilience. Interventions improving stress coping usually require long training periods. In this study, we present a hypnosis-based intervention that produces long-term effects after a single hypnosis session. In that session, we established a post-hypnotic safety suggestion that participants can activate afterwards with a cue. We tested 60 participants in our study who all received the hypnosis session and a stress task. The safety group used the post-hypnotic safety cue during acute stress (Trier Social Stress Test, TSST). The control group used a neutral trigger instead. We measured subjective stress responses via self-reports and physiological stress responses via saliva and blood samples as well as heart rate. One week later, all participants filled in an online survey to measure long-term effects of the post-hypnotic safety suggestion. We found that participants using the post-hypnotic safety cue during the TSST reported significantly lower stress compared to the control group. The safety group also reported significantly fewer negative thoughts concerning their TSST performance than the control group during the stress recovery phase and one week later. All participants indicated that the post-hypnotic safety suggestion still worked one week after its establishment. Suggestibility did not affect the efficacy of the post-hypnotic safety suggestion. Our findings demonstrate that post-hypnotic safety suggestions improve stress coping with long-lasting effects, which makes it a promising intervention to promote mental health and establish stress resilience in just one hypnosis session. The manuscript is published in Scientific Reports on February 12, 2024 and available here: https://doi.org/10.1038/s41598-024-54071-3

opencc-zeroJan 2024View details →

Energetic trade-offs in migration decision-making, reproductive effort, and subsequent parental care in a long-distance migratory bird

Migratory species trade-off long-distance movement with survival and reproduction, but the spatiotemporal scales at which these decisions occur is relatively unknown. Technological and statistical advances allow fine-scale study of animal decision-making, improving our understanding of possible causes and therefore conservation management. We quantified effects of reproductive preparation during spring migration on subsequent breeding outcomes, breeding outcomes on autumn migration characteristics, and autumn migration characteristics on subsequent parental survival in Greenland white-fronted geese (Anser albifrons flavirostris). These are long-distance migratory birds with a ~50% population decline from 1999 to 2022. We deployed GPS-acceleration devices on adult females to quantify up to five years of individual decision-making throughout the annual cycle. Weather and habitat-use affected time spent feeding and overall dynamic body acceleration (i.e., energy expenditure) during spring and autumn. Geese that expended less energy and fed longer during spring were more likely to successfully reproduce. Geese with offspring expended more energy and fed for less time during autumn, potentially representing adverse fitness consequences of breeding. These behavioural comparisons among Greenland white-fronted geese improve our understanding of fitness trade-offs underlying abundance. We provide a reproducible framework for full annual cycle modelling using location and behaviour data, applicable to similarly studied migratory animals.

opencc-zeroFeb 2024View details →

Developmental temperature, more than long-term evolution, defines thermal tolerance in an Estuarine Copepod

Climate change is resulting in increasing ocean temperatures and salinity variability, particularly in estuarine environments. Tolerance of temperature and salinity change interact and thus may impact organismal resilience. Populations can respond to multiple stressors in the short-term (i.e., plasticity) or over longer timescales (i.e., adaptation). However, little is known about the short- or long-term effects of elevated temperature on the tolerance of acute temperature and salinity changes. Here we characterized the response of the near-shore and estuarine copepod, Acartia tonsa, to temperature and salinity stress. Copepods originated from one of two sets of replicated >40 generation-old temperature adapted lines: Ambient (AM, 18°C) and ocean warming (OW, 22°C). Copepods from these lines were subjected to one and three generations at the reciprocal temperature. Copepods from all treatments were then assessed for differences in acute temperature and salinity tolerance. Development (one generation), three generations, and >40 generations of warming increased thermal tolerance compared to Ambient conditions, with development in OW resulting in equal thermal tolerance to three and >40 generations of OW. Strikingly, developmental OW and >40 generations of OW had no effect on low salinity tolerance relative to Ambient. By contrast, when environmental salinity was reduced first, copepods had lower thermal tolerances. These results highlight a critical role for plasticity in the copepod climate response and suggest that salinity variability may reduce copepod tolerance to subsequent warming.

opencc-zeroFeb 2024View details →

Rare, long-distance dispersal underpins genetic connectivity in the pink sea fan, Eunicella verrucosa

Characterising patterns of genetic connectivity in marine species is of critical importance given the anthropogenic pressures placed on the marine environment. For sessile species, population connectivity can be shaped by many processes, such as pelagic larval duration, oceanographic boundaries, and currents. This study combines restriction-site associated DNA sequencing (RADseq) and passive particle dispersal modelling to delineate patterns of population connectivity in the pink sea fan, Eunicella verrucosa, a temperate octocoral. Individuals were sampled from 20 sites covering most of the species' northeast Atlantic range, and a site in the northwest Mediterranean Sea to inform on connectivity across the Atlantic-Mediterranean transition. Using 7,510 neutral SNPs, a geographic cline of genetic clusters was detected, partitioning into: Ireland, Britain, France, Spain (Atlantic), and Portugal and Spain (Mediterranean). Evidence of significant inbreeding was detected at all sites, a finding not detected in a previous study of this species based on microsatellite loci. Genetic connectivity was characterised by an isolation by distance pattern (IBD) (r2 = 0.78, p<0.001), which persisted across the Mediterranean-Atlantic boundary. In contrast, exploration of ancestral population assignment using the program ADMIXTURE indicated genetic partitioning across the Bay of Biscay, which we suggest represents a natural break in the species' range, possibly linked to a lack of suitable habitat. As the pelagic larval duration (PLD) is unknown, passive particle dispersal simulations were run for 14 and 21 days. For both modelled PLDs, inter-annual variations in particle trajectories suggested that in a long-lived, sessile species, range-wide IBD is driven by rare, longer dispersal events which act to maintain gene flow. These results suggest that oceanographic patterns may facilitate range-wide stepping-stone genetic connectivity in E. verrucosa, and highlight that both oceanography and natural breaks in a species' range should be considered in the designation of ecologically coherent MPA networks.

opencc-by-4.0Jul 2021View details →

Long time series (2001-2015) high-resolution crop yield and water productivity dataset of China

A long-term data series, at 1-km resolution, of crop yield (kg/ha) and crop water productivity (kg/m3) for maize and wheat across China, based on the MOD16 ET product, multiple remotely sensed crop physiological and environmental indicators, and crop phenological information, using a random forest algorithm. Results showed that MOD16 products are an accurate alternative to eddy covariance flux tower data to describe crop evapotranspiration (maize and wheat RMSE: 4.42 and 3.81 mm/8d, respectively) and the proposed yield estimation model showed accuracy at local (maize and wheat rRMSE: 26.81 and 21.80%, respectively) and regional (maize and wheat rRMSE: 15.36 and 17.17%, respectively) scales. These high-resolution crop yield and CWP datasets generated in this study revealed spatiotemporal patterns of agricultural production in China and may be applied to many scenarios, including understanding effects of climate change on agricultural production capacity in China under increasing demand for food security to optimize agricultural production strategies.

opencc-zeroMar 2024View details →

Repeatedly experiencing the McGurk effect induces long-lasting changes in auditory speech perception

In the McGurk effect, presentation of incongruent auditory and visual speech evokes a fusion percept different than either component modality. We show that repeatedly experiencing the McGurk effect for 14 days induces a change in auditory-only speech perception: the auditory component of the McGurk stimulus begins to evoke the fusion percept, even when presented on its own without accompanying visual speech. This perceptual change, termed fusion-induced recalibration (FIR), was talker-specific and syllable-specific and persisted for a year or more in some participants without any additional McGurk exposure. Participants who did not experience the McGurk effect did not experience FIR, showing that recalibration was driven by multisensory prediction error. A causal inference model of speech perception incorporating multisensory cue conflict accurately predicted individual differences in FIR. Just as the McGurk effect demonstrates that visual speech can alter the perception of auditory speech, FIR shows that these alterations can persist for months or years. The ability to induce seemingly permanent changes in auditory speech perception will be useful for studying plasticity in brain networks for language and may provide new strategies for improving language learning.

Figs 8, 9 in The role of museums in safeguarding biodiversity: A happy end of the century-long saga of Tritogenia zuluensis (Beddard, 1907) (Oligochaeta: Tritogeniidae)

Figs 8, 9. Labels: (8) a, b – original by I. Trägårdh, referring to collection locality and preservation method; c – species name, collection area and date ('Natal Stanford Hill' refers to another specimen, possibly to M. papillatus); (9) label referring to Microchaetus colletti and Microchaetus zululensis, the species identified by Beddard, with the added comment: 'see P.Z.S. 1907 August'.

Figs 2–4 in The role of museums in safeguarding biodiversity: A happy end of the century-long saga of Tritogenia zuluensis (Beddard, 1907) (Oligochaeta: Tritogeniidae)

Figs 2–4. Tritogenia zuluensis (Beddard, 1907): (2, 3) lectotype, anterior part of the body, ventrally (2) and specimen dissected dorsally (3); (4) paralectotype, specimen dissected dorsally. Abbreviations: C – clitellum, Dbv – dorsal blood vessel, G – gizzard, Gp – genital papillae, I – intestine, Tp – tubercula pubertatis. Scale bars = 1 cm.

Figs 5–7 in The role of museums in safeguarding biodiversity: A happy end of the century-long saga of Tritogenia zuluensis (Beddard, 1907) (Oligochaeta: Tritogeniidae)

Figs 5–7. Tritogenia zuluensis (Beddard, 1907), re-examined specimen 'GNM Oligochaeta 16' described by Michaelsen (1907) as Microchaetus zulu, accepted as a synonym of zuluensis by Michaelsen (1913): (5) whole specimen, ventrally; (6) anterior part of specimen; (7) anterior part dissected. Abbreviations: G – gizzard, Gg – genital glands, Gp – genital papillae. Scale bars = 1 cm.

Fig. 1 in The role of museums in safeguarding biodiversity: A happy end of the century-long saga of Tritogenia zuluensis (Beddard, 1907) (Oligochaeta: Tritogeniidae)

Fig. 1. Reproduction of the historical drawing of Microchaetus zuluensis Beddard, 1907 (text-fig. 85), the anterior part of the body, with misleading indication of the simple segmentation.