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opencc-zeroJul 2023View details →

Warmer springs increase potential for temporal reproductive isolation among habitat patches in subalpine flowering plants

<ol> <li>Flowering phenology can vary considerably even at fine spatial scales, potentially leading to temporal reproductive isolation among habitat patches. Climate change could alter flowering synchrony, and hence temporal isolation, if plants in different microhabitats vary in their phenological response to climate change. Despite the importance of temporal isolation in determining patterns of gene flow, and hence population genetic structure and local adaptation, little is known about how changes in climate affect temporal isolation within populations.</li> <li>Here, we use flowering phenology and floral abundance data of 50 subalpine plant species over 44 years to test whether temporal isolation between habitat patches is affected by spring temperature. For each species and year, we analyzed temporal separation in peak flowering and flowering overlap between habitat patches separated by 5 to 950 m.</li> <li>Across our study species, warmer springs were associated with more temporal differentiation in flowering peaks among habitat patches, and less flowering overlap, increasing potential for temporal isolation within populations.</li> <li> Synthesis. By reducing opportunities for mating among plants in nearby habitat patches, our results suggest that warmer springs may reduce opportunities for gene flow within populations, and, consequently, the capacity of plant populations to adapt to environmental changes.</li> </ol>

Temporal dynamics of soil fungi in a pyrodiverse dry-sclerophyll forest

Fire is a major evolutionary and ecological driver that shapes biodiversity in forests. While above-ground community responses to fire have been well-documented, those below-ground are much less understood. However, below-ground communities, including fungi, play key roles in forests and facilitate the recovery of other organisms after fire. Here, we used internal transcribed spacer (ITS) meta-barcoding data from forests with three different times since fire [short (3 years), medium (13–19 years) and long (>26 years)] to characterize the temporal responses of soil fungal communities across functional groups, ectomycorrhizal exploration strategies and inter-guild associations. Our findings indicate that fire effects on fungal communities are strongest in the short to medium term, with clear distinctions between communities in forests with a short time (3 years) since fire, a medium time (13–19 years) and a long time (>26 years) since fire. Ectomycorrhizal fungi were disproportionately impacted by fire relative to saprotrophs, but the direction of the response varied depending on morphological structures and exploration strategies. For instance, short-distance ectomycorrhizal fungi increased with recent fire, while medium-distance (fringe) ectomycorrhizal fungi decreased. Further, we detected strong, negative inter-guild associations between ectomycorrhizal and saprotrophic fungi but only at medium and long times since fire. Given the functional significance of fungi, the temporal changes in fungal composition, inter-guild associations and functional groups after fire demonstrated in our study may have functional implications that require adaptive management to curtail.

Data for: Leveraging spatio-temporal genomic breeding value estimates of dry matter yield and herbage quality in ryegrass via random regression models

Joint modeling of correlated multi-environment and multi-harvest data of perennial crop species may offer advantages in prediction schemes and a better understanding of the underlying dynamics in space and time. The goal of the present study was to investigate the relevance of incorporating the longitudinal dimension of within-season multiple measurements of forage perennial ryegrass traits in a reaction norm model setup that additionally accounts for genotype-environment interactions (G×E). Genetic parameters and accuracy of genomic breeding value (gEBV) predictions were investigated by fitting three random regression models (gRRM) using Legendre polynomial functions to the data. Genomic DNA sequencing of family pools of diploid perennial ryegrass was performed using DNA nanoball-based technology and yielded 56,645 single nucleotide polymorphisms which were used to calculate the allele frequency-based genomic relationship matrix. Biomass yield's estimated additive genetic variance and heritability values were higher in later harvests. The additive genetic correlations were moderate to low in early measurements and peaked at intermediates, with fairly stable values across the environmental gradient, except for the initial harvest data collection. This led to the conclusion that complex (G×E) arises from spatial and temporal dimensions in the early season, with lower re-ranking trends thereafter. In general, modeling the temporal dimension with a second-order orthogonal polynomial improved the accuracy of gEBV prediction for nutritive quality traits, but no gain in prediction accuracy was detected for dry matter yield. This study leverages the flexibility and usefulness of gRRM models for perennial ryegrass breeding and can be readily extended to other multi-harvest crops.

Takeout gene expression is associated with temporal kin recognition

A key component of parental care is avoiding killing and eating your own offspring. Many organisms commit infanticide of young but switch to parental care at the time when their own offspring would be expected, known as temporal kin recognition. It is unclear why such indirect kin recognition is so common across taxa. One possibility is that conserved mechanisms that regulate timing and feeding in other contexts are co-opted to enable the evolution of temporal kin recognition. Here we determine whether takeout, a gene implicated in coordinating feeding, influences temporal kin recognition in the subsocial beetle the roundneck sexton beetle, Nicrophorus orbicollis. We find that takeout expression is not associated with non-parental feeding changes resulting from hunger, or in the general switch to the full parental care repertoire. However, beetles that accepted and provided care to their offspring had a higher takeout expression than beetles that committed infanticide. Together, these data support the idea that the evolution of temporal kin recognition may be enabled by co-option of mechanisms that integrate feeding behaviour in other contexts.

opencc-by-4.0Aug 2023View details →

Date set for the manuscript: Exploring the temporal dynamics of methane ebullition in a subtropical freshwater reservoir

The dataset supports the findings of the manuscript entitled ‘Exploring the Temporal Dynamics of Methane Ebullition in a Subtropical Freshwater Reservoir’. The results of the manuscript are based on continuous in-situ measurements conducted at Passaúna Reservoir, located in the southern part of Brazil (South America). The monitoring was carried out from 2017 to 2020, during which a comprehensive set of environmental variables was obtained from various studies. The primary objective of the manuscript was to comprehend the temporal dynamics of ebullition flux in the reservoir. Therefore, time series data of ebullition and relevant environmental variables were analyzed across different time scales, ranging from minutes to daily resolutions. Statistical and data driven models were tested to predict ebullition at varying time scales, considering the influence of environmental variables. The findings are discussed in the manuscript. Here, xlsx files and Matlab scripts are provided. The xlsx files contain time series data for environmental variables ('Environmental_Variables_TimeSeries') and ebullition flux ('Ebullition_Flux_TimeSeries'). Separate sheets were utilized for different time intervals, namely 5 minutes (dt=5min), 10 minutes (dt=10min), 1 hour (dt=1hr), and 1 day (dt=1d). Explanations and units are provided within the column labels, while 'NaN' denotes missing data. Matlab scripts for all the empirical models that were tested, as outlined in the manuscript's supporting information (Tables S1 and S2), have been made available (detailed in the following table). These scripts were developed using MatLab R2023a. <table> <tbody> <tr> <td> File (.m) </td> <td> Description </td> </tr> <tr> <td> Main scripts </td> </tr> <tr> <td> TableS1_Empirical_Models_Literature </td> <td> Empirical models from the literature tested. (Table S1 in the manuscript) </td> </tr> <tr> <td> TableS2_FirstPart_Reffited_Models </td> <td> Empirical models from the literature refitted. (Table S2 in the manuscript) </td> </tr> <tr> <td> TableS2_SecondPart_New_Models </td> <td> New empirical models implemented. (Table S2 in the manuscript) </td> </tr> <tr> <td> TableS2_SecondPart_New_Models_GAM_Timescales </td> <td> Generalized additive models (GAM) applied to predict ebullition at different timescales. (Table S2 in the manuscript). </td> </tr> <tr> <td> PredictedR2_GAM_models </td> <td> Calculate the predicted R-squared for GAM. </td> </tr> <tr> <td> Functions (need for the main scripts) </td> </tr> <tr> <td> load_TimeSeries </td> <td> Import time series of environmental variables from excel sheets into MatLab. </td> </tr> <tr> <td> load_EbullitionTS </td> <td> Import time series of ebullition from excel sheets into MatLab. </td> </tr> <tr> <td> units_description </td> <td> Description containing units of the variables. </td> </tr> <tr> <td> Bin_xdata </td> <td> Creates data binning of X and Y based on X data. </td> </tr> <tr> <td> RelativeError </td> <td> Calculate the relative error of accumulated flux between measured and simulated. </td> </tr> <tr> <td> ANN5Neurons_Retrained_Deshmukh2014 </td> <td> Trained Artificial Neural Network based on the ANN proposed by Deshmukh et al. (2014). </td> </tr> <tr> <td> ANN_Passauna_20Neurons </td> <td> Trained Artificial Neural Network with the addition of more environmental variables. </td> </tr> </tbody> </table>   Financial support The field measurements were financed by the German Federal Ministry of Education and Research (BMBF, Grant 02WGR1431A), in the framework of the research project MuDak-WRM (https://www.mudak-wrm.kit.edu). This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) – Finance Code 001. Tobias Bleninger received productivity stipend from the National Council for Scientific and Technological Development (CNPq, grant no. 312211/2020-1, call no. 09/2020). Michael Männich received productivity stipend from the National Council for Scientific and Technological Development (CNPq, grant no. 308744/2021-7, call no. 04/2021). Andreas Lorke received financial support from the German Research Foundation (DFG, grant number LO1150/16-1).

Temporal matches between monarch butterfly and milkweed population changes over the past 25,000 years

In intimate ecological interactions, the interdependency of species may result in correlated demographic histories. For species of conservation concern, understanding the long-term dynamics of such interactions may shed light on the drivers of population decline. Here we address the demographic history of the monarch butterfly, Danaus plexippus, and its dominant host plant, the common milkweed, Asclepias syriaca, using broad-scale sampling and genomic inference. Because genetic resources for milkweed have lagged behind those for monarchs, we first release a chromosome-level genome assembly and annotation for common milkweed. Next, we show that despite its enormous geographic range across eastern North America, A. syriaca is best characterized as a single, roughly panmictic population. Using Approximate Bayesian Computation via Random Forests (ABC-RF), a machine learning method for reconstructing demographic histories, we show that both monarchs and milkweed experienced population expansion during the most recent recession of North American glaciers 10,000–20,000 years ago. Our data also identify concurrent population expansions in both species during the large-scale clearing of eastern forests (~200 years ago). Finally, we find no evidence that either species experienced a reduction in effective population size over the past 75 years. Thus, the well-documented decline of monarch abundance over the past 40 years is not visible in our genomic dataset, reflecting a possible mismatch of the overwintering census population to effective population size in this species.

opencc-by-4.0Sep 2023View details →

Temporal variability of explosive activity at Tajogaite Volcano, Cumbre Vieja (Canary Islands), 2021 eruption from ground-based infrared photography and videography

Supplementary material to: Temporal variability of explosive activity at Tajogaite Volcano, Cumbre Vieja (Canary Islands), 2021 eruption from ground-based infrared photography and videography (2023).  Files are short infrared videos of explosive activity in the near-vent region of Tajogaite Volcano. Files are named by date of acquisition.

opencc-zeroSep 2023View details →

Spatial and temporal variation in toxicity and inorganic composition of hydraulic fracturing flowback and produced water

Hydraulic fracturing for oil and gas extraction produces large volumes of wastewater, termed flowback and produced water (FPW), that are highly saline and contain a variety of organic and inorganic contaminants. In the present study, FPW samples from ten hydraulically fractured wells, across two geologic formations were collected at various timepoints. Samples were analyzed to determine spatial and temporal variation in their inorganic composition. Results indicate that FPW composition varied both between formations and within a single formation, with large compositional changes occurring over short distances. Temporally, all wells showed a time-dependent increase in inorganic elements, with total dissolved solids increasing by up to 200,000 mg/L over time, primarily due to elements associated with salinity (Cl, Na, Ca, Mg, K). Toxicological analysis of a subset of the FPW samples showed median lethal concentrations (LC50) of FPW to the aquatic invertebrate Daphnia magna were highly variable, with the LC50 values ranging from 1.16% to 13.7% FPW. Acute toxicity of FPW significantly correlated with salinity, indicating salinity is a primary driver of FPW toxicity, however organic components also contributed to toxicity. This study provides insight into spatiotemporal variability of FPW composition and illustrates the difficulty in predicting aquatic risk associated with FPW.

opencc-by-4.0Sep 2023View details →

TimeTank: A Corpus of Sentences Annotated with TimeInfo for Temporal Data

Annotating temporal information in texts is a challenging and time-consuming task. It requires an understanding of natural language, as well as knowledge about the various ways in which temporal data can be expressed and structured in a text. However, the ability to access temporal semantics through computer tools is crucial for many applications that involve interpreting and understanding texts. A corpus available in this field is TimeBank (Pustejovsky et al., 2003), which was annotated using the TimeML annotation scheme (Pustejovsky et al., 2003), a scheme that does not support complex temporal expressions. We proposed a new annotation scheme for temporal information in scientific texts: TimeInfo (Yahiaoui & Atanassova, 2022) which allows for more precise and directly usable annotations. The corpus presented here, named TimeTank, consists of 1186 sentences containing a total of 1200 temporal expressions annotated according to the TimeInfo annotation scheme. These sentences are drawn from 603 scientific articles from the CORD-19 corpus (Wang et al., 2020). The sentences were identified and annotated automatically, and the quality of the annotations was manually verified. TimeTank can be employed for the evaluation or training of machine learning models focused on the detection, extraction, and annotation of temporal expressions. The corpus offers a reliable dataset labeled to serve as a foundation for supervised learning. Bibliography Pustejovsky, James, et al. "The timebank corpus." Corpus linguistics. Vol. 2003. 2003. Pustejovsky, James, et al. "TimeML: Robust specification of event and temporal expressions in text." New directions in question answering 3 (2003): 28-34. Wang, Lucy Lu, et al. "Cord-19: The covid-19 open research dataset." ArXiv (2020). Yahiaoui, Salah, and Iana Atanassova. "TimeInfo: a Semantic Annotation Framework for Temporal Information in Scientific Papers." Terminology & Ontology: Theories and applications (TOTH 2022). 2022.

opencc-zeroSep 2023View details →

Early life telomeres are influenced by environments acting at multiple temporal and spatial scales

An individual's telomere length early in life may reflect or contribute to key life history processes sensitive to environmental variation. Yet, the relative importance of genetic and environmental factors in shaping early life telomere length is not well understood as it requires samples collected from multiple generations with known developmental histories. We used a confirmed pedigree and conducted an animal model analysis of telomere lengths obtained from nestling house sparrows (Passer domesticus) sampled over a span of 22 years. We found significant additive genetic variation for early life telomere length, but it comprised a relatively small proportion (9%) of the total biological variation. Three sources of environmental variation were important: among cohorts, among breeding attempts within years and families, and among nestmates. The magnitude of variation among breeding attempts and among nestmates also differed by cohort, suggesting that interactive effects of environmental factors across time or spatial scales were important, yet we were unable to identify the specific causes of these interactions. The mean amount of precipitation during the breeding season positively predicted telomere length, but neither weather during a given breeding attempt nor date in the breeding season contributed to an offspring's telomere length. At the residual level, level of individual nestlings, offspring sex, size, and mass at 10 days of age also did not predict telomere length. Environmental effects appear especially important in shaping early life telomere length in some species, and an array of complex more focus on how environmental factors that interactions across scales may help to explain some of the variation observed among studies.

opencc-zeroSep 2023View details →

Climate change does not equally affect temporal patterns of natural selection on reproductive timing across populations in two songbird species

Climate change has led to changes in the strength of directional selection on seasonal timing. Understanding the causes and consequences of these changes is crucial to predicting the impact of climate change. But are observed patterns in one population generalisable to others, and can spatial variation in selection be explained by environmental variation among populations? We used long-term data (1955–2022) on blue and great tits co-occurring in four locations across the Netherlands to assess inter-population variation in temporal patterns of selection on laying date. To analyse selection, we combine reproduction and adult survival into a joined fitness measure. We found distinct spatial variation in temporal patterns of selection which overall acted towards earlier laying, and which was due to selection through reproduction rather than through survival. The underlying relationships between temperature, bird and caterpillar phenology were however the same across populations, and the spatial variation in selection patterns is thus caused by spatial variation in the temperatures and other habitat characteristics to which birds and caterpillars respond. This underlines that climate change is not necessarily equally affecting populations, but that we can understand this spatial variation, which enables us to predict climate change effects on selection for other populations.

opencc-zeroOct 2023View details →

Dataset for: Asymmetric response of aboveground and belowground temporal stability to nitrogen and phosphorus addition in a Tibetan alpine grassland

Anthropogenic eutrophication is known to impair the stability of aboveground net primary productivity (ANPP), but its effects on the stability of belowground (BNPP) and total (TNPP) net primary productivity remain poorly understood. Based on a nitrogen and phosphorus addition experiment in a Tibetan alpine grassland, we show that nitrogen addition had little impact on the temporal stability of ANPP, BNPP and TNPP, whereas phosphorus addition reduced the temporal stability of BNPP and TNPP, but not ANPP. Significant interactive effects of nitrogen and phosphorus addition were observed on the stability of ANPP because of the opposite phosphorus effects under ambient and enriched nitrogen conditions. We found that the stability of TNPP was primarily driven by that of BNPP rather than that of ANPP. The responses of BNPP stability cannot be predicted by those of ANPP stability, as the variations in responses of ANPP and BNPP to enriched nutrients, with ANPP increased while BNPP remained unaffected, resulted in asymmetric responses in their stability. The dynamics of grasses, the most abundant plant functional group, instead of community species diversity, largely contributed to the ANPP stability. Under the enriched nutrient condition, the synchronization of grasses reduced the grass stability, while the latter had a significant but weak negative impact on the BNPP stability. These findings challenge the prevalent view that species diversity regulates the responses of ecosystem stability to nutrient enrichment. Our findings also suggest that the ecological consequences of nutrient enrichment on ecosystem stability cannot be accurately predicted from the responses of aboveground components, and highlight the need for a better understanding of the belowground ecosystem dynamics.

opencc-by-3.0-usOct 2023View details →

Temporal Dynamics of Attitude Decisions: A Test of the Iterative Reprocessing Model using Event-related Potentials

Experimental instructions, stimulus procedures and stimuli, single trial EEG data, decoding program

opencc-zeroOct 2023View details →

Analysing spatio-temporal patterns of non-native fish in a biodiversity hotspot across decades

Aim: Analysing the spatio-temporal patterns and dynamics of non-native species is essential to understanding the mechanisms underlying successful invasions and developing effective management strategies. Yet, such analyses generally neglect the influence of receiving ecosystem types and non-native species sources (i.e. alien species, non-natives originating outside the concerned region; translocated species, nonnatives introduced to locations outside their historical range within the concerned region). Location: Yunnan, China. Methods: We analysed long-term (1950–2022) spatio-temporal patterns and potential underlying dynamics of non-native fishes in a biodiversity hotspot (Yunnan, China), paying special attention to waterbody types receiving non-native species and comparing alien and translocated species. We did this through compiling a highly comprehensive occurrence dataset of native and non-native fishes. Results: We recorded 783 native species and 94 non-native species (49 alien species and 45 translocated species), which mainly belonged to the order Cypriniformes (52 species) and were introduced via purposes for advancing aquaculture. Most frequently encountered non-native species were either intentionally introduced aquaculture species or small-bodied fish unintentionally introduced via aquaculture activities. The richness and spatial ranges of non-native fishes increased consistently since the 1950s and demonstrated a pronounced change after the 2000s, with densely populated areas and the middle to lower reaches of large rivers being more profoundly affected. The number of records of translocated species exceeded the number of records of alien species after the 2000s. Lakes and reservoirs are hotspots for both alien and translocated species introductions, and watersheds with large areas in Yunnan (e.g. the Jinsha-Yangtze and Lancang-Mekong basins) contained more non-native fish. Main Conclusions: Our study highlights the need to consider invasion sensitivities of receiving ecosystems and pay special attention to intra-regional species translocations when developing prevention and management strategies against invasions of alien species, particularly in important biodiversity hotspots around the world.

opencc-by-4.0Oct 2023View details →

Data for "Spatial and Temporal patterns of Southern Ocean Ventilation"

This contains the trajectory data used in the paper "Spatial and temporal patterns of Southern Ocean Ventilation" which has been submitted to GRL

opencc-zeroOct 2023View details →

Dispersal limitation predicts the spatial and temporal filtering of tropical bird communities in isolated forest fragments

The link between dispersal traits and patterns of community assembly remains a frontier in understanding how vertebrate communities persist in fragmented landscapes. Using experimental release trials and intensive field surveys of bird communities in fragmented forests of the Peruvian and Colombian Andes, we demonstrate that morphological traits related to movement (1) predict experimental flight performance and (2) exhibit dispersal-mediated environmental filtering at the community scale. After correcting for body size, four traits hypothesized to influence flight ability (wing length, wing pointedness, wing loading, and eye size) predicted distance flown across a hostile experimental landscape, with successful species having significantly longer pointed wings, carrying less mass per unit wing area (i.e., lower wing loading), and having smaller eyes. Species with larger eyes also displayed increased flight latency, potentially due to disability glare. At the community scale we detected a gradient of dispersal-mediated environmental filtering in fragments compared to reference forest within the same landscape, with relative differences in trait values explained by the temporal and spatial extent of patch isolation. In the Colombian landscape where fragments had been isolated for > 60 years, communities were filtered for species with long and narrow wings and small eyes, especially within the most spatially isolated fragments. We observed the opposite pattern in the more recently fragmented Peruvian landscape (15-30 years): communities within fragments tended to have shorter and more rounded wings compared to those in nearby contiguous forests, suggesting that dispersal-limited species accumulate in the initial years following patch isolation due to "restricted dispersal" and represent an extinction debt yet to be paid. Our results (1) experimentally validate the use of morphological traits as proxies for movement ability in fragmented landscapes, (2) demonstrate that visual acuity functions as a novel dimension of dispersal limitation, and (3) quantify how the spatial and temporal components of patch isolation produce a gradient in dispersal-mediated environmental filtering and extinction debt for communities inhabiting fragments.

opencc-by-4.0Oct 2023View details →

Numerical data for research paper titled "Physical mechanism for a temporal decrease of the Gutenberg-Richter b-value prior to a large earthquake"

Numerical data used to make Figures in the manuscript entitled "Physical mechanism of the temporal decrease of a Gutenberg-Richter b-value prior to a large earthquake". We provide the data used to create Figures 2 to 13 from the main text, and Figures S2, S3 and S6 from the supplementary information. We also provide Python scripts to plot them.