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Calcium-rich parent materials enhance multiple soil functions and bacterial network complexity

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ClimateNet Dataset as used in "Explaining neural networks for detection of tropical cyclones and atmospheric rivers in gridded atmospheric simulation data"

ClimateNet dataset as it was used by us for the study: "Explaining neural networks for detection of tropical cyclones and atmospheric rivers in gridded atmospheric simulation data" (https://gmd.copernicus.org/preprints/gmd-2024-60/).   For the original dataset refer to: https://portal.nersc.gov/project/ClimateNet/

Supplementary Materials for Discovery of Hub Genes and Construction of Competitive Endogenous RNA Network in Human Cytomegalovirus Infection Using Computational and Bioinformatics Tools

Table S1: List of targeted genes by 41 differentially expressed microRNAs (DEMs) agreed in Targetscan and miRDB; Table S2: Significant biological process (BP) of 144 genes associated with Human Cytomegalovirus (HCMV); Table S3: Significant cellular components (CC) of 144 genes associated with HCMV; Table S4: Enriched molecular function (MF) of 144 genes associated with HCMV; Table S5: Pathways significantly affected by 144 genes in HCMV; Figure S1: Number of interactions for each gene in protein-protein interaction (PPI) network.

Triggering Events, Opinion Leader Networks, and Framing Strategies of Climate Change on Chinese Social Media

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opencc-zeroDec 2018View details →

Data from: Seeing is believing? comparing plant-herbivore networks constructed by field co-occurrence and DNA barcoding methods for gaining insights into network structures

Plant-herbivore interaction networks provide information about community organization. Two methods are currently used to document pairwise interactions among plants and insect herbivores. One is the traditional method that collects plant-herbivore interaction data by field observation of insect occurrence on host plants. The other is the increasing application of newly developed molecular techniques based on DNA barcodes to the analysis of gut contents. The second method is more appealing because it documents realized interactions. To construct complete networks, each technique of network construction is urgent to be assessed. We addressed this question by comparing the effectiveness and reliability of the two methods in constructing plant-Lepidoptera larval network in a 50 ha subtropical forest in China. Our results showed that the accuracy of diet identification by observation method increased with the number of observed insect occurrences on food plants. In contrast, the molecular method using three plant DNA markers were able to identify food residues for 35.6% larvae and correctly resolved 77.3% plant (diet) species. Network analysis showed molecular networks had three-fold more unique host plant species but fewer links than the traditional networks had. The molecular method detected plants that were not sampled by the traditional method, e.g., bamboos, bryophytes and lianas in the diets of insect herbivores. The two networks also possessed significantly different structural properties. Our study indicates the traditional observation of co-occurrence is inadequate, while molecular method can provide higher species resolution of ecological interactions.

opencc-zeroDec 2015View details →

Data from: Replicated landscape genetic and network analyses reveal wide variation in functional connectivity for American pikas

Landscape connectivity is essential for maintaining viable populations, particularly for species restricted to fragmented habitats or naturally arrayed in metapopulations and facing rapid climate change. The importance of assessing both structural connectivity (the physical distribution of favorable habitat patches) and functional connectivity (how species move among habitat patches) for managing such species is well understood. However, the degree to which functional connectivity for a species varies among landscapes, and the resulting implications for conservation, have rarely been assessed. We used a landscape genetics approach to evaluate resistance to gene flow and, thus, to determine how landscape and climate-related variables influence gene flow for American pikas (Ochotona princeps) in eight federally managed sites in the western United States. We used those empirically-derived, individual-based landscape resistance models in conjunction with predictive occupancy models to generate patch-based network models describing functional landscape connectivity. Metareplication across landscapes enabled identification of limiting factors for dispersal that would not otherwise have been apparent. Despite the cool microclimates characteristic of pika habitat, south-facing aspects consistently represented higher resistance to movement, supporting the previous hypothesis that exposure to relatively high temperatures may limit dispersal in American pikas. We found that other barriers to dispersal included areas with a high degree of topographic relief, such as cliffs and ravines, as well as streams and distances greater than one to four kilometers depending on the site. Using the empirically-derived network models of habitat patch connectivity, we identified habitat patches that were likely disproportionately important for maintaining functional connectivity, areas in which habitat appeared fragmented, and locations that could be targeted for management actions to improve functional connectivity. We concluded that climate change, besides influencing patch occupancy as predicted by other studies, may alter landscape resistance for pikas, thereby influencing functional connectivity through multiple pathways simultaneously. Spatial autocorrelation among genotypes varied across study sites and was largest where habitat was most dispersed, suggesting that dispersal distances increased with habitat fragmentation, up to a point. This study demonstrates how landscape features linked to climate can affect functional connectivity for species with naturally fragmented distributions, and reinforces the importance of replicating studies across landscapes.

opencc-zeroDec 2013View details →

Data from: Human-induced biotic invasions and changes in plankton interaction networks

1.Pervasive and accelerating changes to ecosystems due to human activities remain major sources of uncertainty in predicting the structure and dynamics of ecological communities. Understanding which biotic interactions within natural multitrophic communities are threatened or augmented by invasions of non-native species in the context of other environmental pressures is needed for effective management. 2.We used multivariate autoregressive models with detailed time-series data from largely freshwater and brackish regions of the upper San Francisco Estuary to assess the topology, direction and strength of trophic interactions following major invasions and establishment of non-native zooplankton in the early 1990s. We simultaneously compared the effects of fish and clam predation, environmental temperature, and salinity intrusion using time-series data from > 60 monitoring locations and spanning more than three decades. 3.We found changes in the networks of biotic interactions in both regions after the major zooplankton invasions. Our results imply an increased pressure on native herbivores; intensified negative interactions between herbivores and omnivores; and stronger bottom-up influence of juvenile copepods but weaker influence of phytoplankton as a resource for higher trophic levels following the invasions. We identified salinity intrusion as a primary pressure but showed relatively stronger importance of biotic interactions for understanding the dynamics of entire communities. 4.Synthesis and applications. Our findings highlight the dynamic nature of biotic interactions and provide evidence of how simultaneous invasions of exotic species may alter interaction networks in diverse natural ecosystems over large spatial and temporal scales. Efforts to restore declining fish stocks may be in vain without fully considering the trophic dynamics that limit the flow of energy to target populations. Focusing on multitrophic interactions that may be threatened by invasions rather than a limited focus on responses of individual species or diversity is likely to yield more effective management strategies.

opencc-zeroJun 2021View details →

Early social deprivation shapes neuronal programming of the social decision-making network in a cooperatively breeding fish

The early social environment an animal experiences may have pervasive effects on its behaviour. The Social Decision-Making network (SDMN), consisting of interconnected brain nuclei from the forebrain and midbrain, is involved in the regulation of behaviours during social interactions. In species with advanced sociality such as cooperative breeders, offspring are exposed to a large number and a great diversity of social interactions every day of their early life, which may have life-long consequences on the development of several neurophysiological systems within the SDMN, although these effects are largely unknown. We studied these life-long effects in a cooperatively breeding fish, Neolamprologus pulcher, focusing on the expression in the SDMN of genes involved in the monoaminergic and stress response systems. N. pulcher fry were raised until an age of two months either with their parents, subordinate helpers and same clutch siblings (+F), or with same clutch siblings only (-F). Analysis of the expression of glucocorticoid receptor (GR), mineralcorticoid receptors (MR), corticotropin releasing factor (CRF), dopamine receptors 1 and 2, serotonin transporter (SERT) and DNA methyltransferase I (DNMT1) genes showed that early social experiences altered the neurogenomic state of the preoptic area (POA) of the hypothalamus. The dopamine receptor 1 gene was up-regulated in the POA of -F fish, compared to +F fish. -F fish also showed up-regulation of GR1 expression in the dorsal medial telencephalon (homologous to the basolateral amygdala). Our results suggest that early social environment has life-long effects on the development of several neurophysiological systems within the SDMN. --

opencc-zeroDec 2011View details →

Data from: Disentangling invasion processes in a dynamic shipping - boating network

The relative importance of multiple vectors to the initial establishment, spread, and population dynamics of invasive species remains poorly understood. This study used molecular methods to clarify the roles of commercial shipping and recreational boating in the invasion by the cosmopolitan tunicate, Botryllus schlosseri. We evaluated i) single vs. multiple introduction scenarios, ii) the relative importance of shipping and boating to primary introductions, iii) the interaction between these vectors for spread (i.e., the presence of a shipping-boating network), and iv) the role of boating in determining population similarity. Tunicates were sampled from 26 populations along the Nova Scotia, Canada, coast that were exposed to either shipping (i.e., ports), or boating (i.e., marinas) activities. A total of 874 individuals (~30 per population) from 5 ports and 21 marinas was collected and analyzed using both mitochondrial cytochrome c oxidase subunit I gene (COI) and 10 nuclear microsatellite markers. The geographical location of multiple hotspot populations indicates that multiple invasions have occurred in Nova Scotia. A loss of genetic diversity from port to marina populations suggests a stronger influence of ships than recreational boats on primary coastal introductions. Population similarity analysis reveals a clear dependence of marina populations on those that had been previously established in ports and connectivity due to a boating network better explains patterns in population similarities than does natural spread. We conclude that frequent primary introductions arise by ships and that secondary spread occurs gradually thereafter around individual ports, facilitated by recreational boating.

opencc-zeroDec 2016View details →

Data from: Sex-specific responses to territorial intrusions in a communication network: evidence from radio-tagged great tits

Signals play a key role in the ecology and evolution of animal populations, influencing processes such as sexual selection and conflict resolution. In many species, sexually selected signals have a dual function: attracting mates and repelling rivals. Yet, to what extent males and females under natural conditions differentially respond to such signals remains poorly understood, due to a lack of field studies that simultaneously track both sexes. Using a novel spatial tracking system, we tested whether or not the spatial behavior of male and female great tits (Parus major) changes in relation to the response of a territorial male neighbor to an intruder. We tracked the spatial behavior of male and female great tits (N = 44), 1 hr before and 1 hr after simulating territory intrusions, employing automatized Encounternet radio-tracking technology. We recorded the spatial and vocal response of the challenged males and quantified attraction and repulsion of neighboring males and females to the intrusion site. We additionally quantified the direct proximity network of the challenged male. The strength of a male's vocal response to an intruder induced sex-dependent movements in the neighborhood, via female attraction and male repulsion. Stronger vocal responders were older and in better body condition. The proximity networks of the male vocal responders, including the number of sex-dependent connections and average time spent with connections, did not change directly following the intrusion. The effects on neighbor movements suggest that the strength of a male's vocal response can provide relevant social information to both the males and the females in the neighborhood, resulting in both sexes adjusting their spatial behavior in contrasting ways, while the social proximity network remained stable. Moreover, our study underlines the importance of the "silent" eavesdroppers within communication networks for studying the dual functioning and evolution of sexually selected signals.

opencc-zeroDec 2015View details →

Data from: Stability and generalization in seed dispersal networks: a case study of frugivorous fish in Neotropical wetlands

When species within guilds perform similar ecological roles, functional redundancy can buffer ecosystems against species loss. Using data on the frequency of interactions between fish and fruit, we assessed whether co-occurring frugivores provide redundant seed dispersal services in three species-rich Neotropical wetlands. Our study revealed that frugivorous fishes have generalized diets; however, large-bodied fishes had greater seed dispersal breadth than small species, in some cases, providing seed dispersal services not achieved by smaller fish species. As overfishing disproportionately affects big fishes, the extirpation of these species could cause larger secondary extinctions of plant species than the loss of small specialist frugivores. To evaluate the consequences of frugivore specialization for network stability, we extracted data from 39 published seed dispersal networks of frugivorous birds, mammals and fish (our networks) across ecosystems. Our analysis of interaction frequencies revealed low frugivore specialization and lower nestedness than analyses based on binary data (presence–absence of interactions). In that case, ecosystems may be resilient to loss of any given frugivore. However, robustness to frugivore extinction declines with specialization, such that networks composed primarily of specialist frugivores are highly susceptible to the loss of generalists. In contrast with analyses of binary data, recently developed algorithms capable of modelling interaction strengths provide opportunities to enhance our understanding of complex ecological networks by accounting for heterogeneity of frugivore–fruit interactions.

opencc-zeroJun 2021View details →

Supporting Data and Code for "Managing to Climatology: Improving semi-arid agricultural risk management using crop models and a dense meteorological network"

Without reliable seasonal climate forecasts, farmers and managers in other weather-sensitive sectors might adopt practices that are optimal for recent climate conditions. To demonstrate this principle, crop simulation models driven by a dense meteorological network were used to identify climate-optimal planting dates for U.S. Southern High Plains (SHP) un-irrigated agriculture. This method converted large samples of SHP growing season weather outcomes into climate-representative cotton and sorghum yield distributions over a range of planting dates. Best planting dates were defined as those that maximized median cotton lint (April 24) and sorghum grain (July 1) yields. Those optimal yield distributions were then converted into corresponding profit distributions reflecting 2005-2019 commodity prices and fixed production costs. Both crop's profitability under variable price conditions and current SHP climate conditions were then compared based on median profits and loss probability, and through stochastic dominance analyses that assumed a slightly risk-averse producer.

opennotspecifiedJan 2014View details →

FIGURE 4 in Co-authorship networks (and other contextual factors) behind the growth of taxonomy of South American Ephemeroptera: A scientometric approach

FIGURE 4. Barplot showing the production of South American authors, including collaborative works. Production measured as number of valid species described.

opennotspecifiedJan 2014View details →

FIGURE 3 in Co-authorship networks (and other contextual factors) behind the growth of taxonomy of South American Ephemeroptera: A scientometric approach

FIGURE 3. Characteristic fraction of author production measured for different intervals. The fractions R/Wt and R/Ws represent the prevalence and representativeness of regional author production respectively. R= Number of valid species described by regional authors within the target time interval; Wt= Total number of valid species described within the target time interval: Ws= Total number of valid species described solely by regional authors. Dashed line corresponds to coefficient ς and its maximum corresponds to the period [1999, 2012]. In this period: (i) the overall production is dominated by South American authors, and (ii) the bulk of South American production is included.

opennotspecifiedJan 2014View details →

FIGURE 1 in Co-authorship networks (and other contextual factors) behind the growth of taxonomy of South American Ephemeroptera: A scientometric approach

FIGURE 1. Number of valid species described by period. Species described by foreign (F), regional (R) and mixed (M) authors are represented by different tones. Note that binned time intervals do not represent equal periods.

opencc-zeroMay 2020View details →

Data from: Recurrent circuit dynamics underlie persistent activity in the macaque frontoparietal network

During delayed oculomotor response tasks, neurons in the lateral intraparietal area (LIP) and the frontal eye fields (FEF) exhibit persistent activity that reflects the active maintenance of behaviorally relevant information. Despite many computational models of the mechanisms of persistent activity, there is a lack of circuit-level data from the primate to inform the theories. To fill this gap, we simultaneously recorded ensembles of neurons in both LIP and FEF while macaques performed a memory-guided saccade task. A population encoding model revealed strong and symmetric long-timescale recurrent excitation between LIP and FEF. Unexpectedly, LIP exhibited stronger local functional connectivity than FEF, and many neurons in LIP had longer network and intrinsic timescales. The differences in connectivity could be explained by the strength of recurrent dynamics in attractor networks. These findings reveal reciprocal multi-area circuit dynamics in the frontoparietal network during persistent activity and lay the groundwork for quantitative comparisons to theoretical models.

opencc-zeroDec 2018View details →

Data from: StomataCounter: a neural network for automatic stomata identification and counting

Stomata regulate important physiological processes in plants and are often phenotyped by researchers in diverse fields of plant biology. Currently, there are no user friendly, fully-automated methods to perform the task of identifying and counting stomata, and stomata density is generally estimated by manually counting stomata. We introduce StomataCounter, an automated stomata counting system using a deep convolutional neural network to identify stomata in a variety of different microscopic images. We use a human-in-the-loop approach to train and refine a neural network on a taxonomically diverse collection of microscopic images. Our network achieves 98.1% identification accuracy on Ginkgo SEM micrographs, and 94.2% transfer accuracy when tested on untrained species. To facilitate adoption of the method, we provide the method in a publicly available website at http://www.stomata.science/.

opennotspecifiedJun 2021View details →

FIGURE 3. Statistical parsimony haplotype network constructed from 621 in Description of two new species of Rhamphus related to R. oxyacanthae (Curculionidae, Curculioninae, Rhamphini) from Italy based on a morphological study supported by molecular data

FIGURE 3. Statistical parsimony haplotype network constructed from 621 bp of the mtCOI gene of Rhamphus bavierai n. sp. (GenBank accession number MW879286- MW879303). Circle sizes are proportional to haplotype frequency (for details see supplementary Table S1). Numbers in brackets above/beside the solid broken line represent the number of mutations connecting mitochondrial lineages.

opennotspecifiedJun 2021View details →

FIGURE 2. Statistical parsimony haplotype network constructed from 621 in Description of two new species of Rhamphus related to R. oxyacanthae (Curculionidae, Curculioninae, Rhamphini) from Italy based on a morphological study supported by molecular data

FIGURE 2. Statistical parsimony haplotype network constructed from 621 bp of the mtCOI gene of Rhamphus oxyacanthae in Italy (GenBank accession number MW879276- MW879285). Circles sizes are proportional to haplotype frequency (for details see supplementary S1).