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107 results for “interaction patterns”
STREAMS Project: Emergent landscape patterns in stream ecosystem processes resulting from groundwater/surface water interactions
This Data Set is hosted by the Luquillo LTER Program (LUQ) and owned by a LUQ's investigator. Our primary objective is to understand the linkage between surface-subsurface water interactions and ecosystem processes in neotropical lowland streams over an extended time frame (>25 yrs). Proposed research will occur at La Selva Biological Reserve in Costa Rica, which is owned and operated by the Organization for Tropical Studies In tectonically active regions of Central America, it is common for solute-rich groundwater to emerge at gradient breaks within the complex volcanic topography of mountains and foothills which intergrade with the coastal plain. These groundwaters can significantly influence solute chemistry and related ecological and ecosystem-level processes in receiving surface waters. Many solute-rich groundwaters are associated with underlying volcanic activity which has altered the chemistry of receiving streams throughout Central America. Geothermally-modified groundwaters, surfacing at the gradient break between the Central Mountain range and the coastal plain at La Selva Biological Station, have high levels of P (up to 400 mg SRP L-1) and other solutes (Ca, Cl, Mg, SO4) but are not elevated in temperature. Spatial patterns in stream solute chemistry are determined by geomorphic features of the volcanic landscape that include: upland lavas drained by P-poor streams; a gradient break (~50 m.a.s.l.), at or near where P-rich springs emerge; and lowland alluvial areas drained by streams that are both P-rich and P-poor depending on whether they receive the input of solute-rich springs. Our project is the first to determine long-term effects of nutrient enrichment in a detrital-based stream within the wet tropics. We will continue to build upon our long-term(1988-present) data set on stream solute chemistry, which is the only one that we are aware of for lowland primary rainforest of Central America. The proposed project will build on 18 years of past resear
The Effects of Plant-Microbe-Environment Interactions on Mineral Weathering Patterns in a Granular Basalt
<p>Data used in the Milici et al. <em>Geobiology </em>article "The Effects of Plant-Microbe-Environment Interactions on Mineral Weathering in Granular Basalt". The data result from a greenhouse experiment in which 14 genotypes of Alfalfa <em>(Medicago</em> sativa) were grown in an unweathered granular basaltic tephra, exposed to an early successional soil microbial community, and replicated across three different soil moisture treatments. This experiment seeks to identify the roles of vascular plants and soil microbes on mineral weathering. Please see the article for full project description. </p> <p>General File Descriptions:</p> <p>"AllPerformanceGeochem.csv" contains both the performance and geochemistry data associated with each plant grown in the experiment and is used for the majority of the analyses.</p> <p>"FullCensusTimeSeries.csv" contains the growth and survival data for the plants across the entire 3 month duration of the experiment and is used only to calculate survival rate and growth rate.</p> <p>"pottingsoilmass.csv" contains the data for alfalfa grown in potting soil and is used to compare how much the basalt limited plant growth relative to a potting soil control. </p> <p>These data are cleaned and formatted for analysis via the code in the github repository linked to this data repository. </p> <p> </p>
Fig. 2 in Hemoparasites in a wild primate: Infection patterns suggest interaction of Plasmodium and Babesia in a lemur species
Fig. 2. Age-dependence of Babesia sp. infections (grey) and Plasmodium sp. infections (black). The lines represent the predicted values according to the two different GLMMs.
Fig. 1 in Hemoparasites in a wild primate: Infection patterns suggest interaction of Plasmodium and Babesia in a lemur species
Fig. 1. Maximum likelihood tree of malaria parasite cytochrome b sequences (P. = Plasmodium). The clade formed by lemur malaria parasites is blue. The two sequences detected in this study are highlighted with grey rectangles. Bootstrap values are reported above branches when>50. The scale is in substitution per site.
Processed Hi-C contact matrices for "Three invariant Hi-C interaction patterns: applications to genome assembly"
<p>Processed Hi-C interaction matrices, saved in numpy npz format.</p> <p>Matrices were processed using Dekker lab cMapping pipeline.</p> <p>Raw sequence data was taken from:</p> <p>Hap1: Haarhuis et al 10.1016/j.cell.2017.04.013</p> <p>IMR90, H1ESC, MESC, MCORTEX: Dixon et al 10.1038/nature11082</p> <p>Worm: Crane et al 10.1038/nature14450</p> <p>Caulobacter: Le et al 10.1126/science.1242059</p> <p> </p>
Implementation of biotic interactions in niche analyses unravels the patterns underneath community composition in clownfishes
<p><span>Biotic interactions are key to understanding the ecology of species and communities. As such, integrating biotic interactions into ecological niche modelling methods has been a central topic of research for the last decade. Yet, the role of biotic interactions remains overlooked. Mutualistic systems constitute perfect study cases for analysing the effect of biotic interactions on species niches and</span><span> comm</span><span>unities' </span><span>composition. Using the clownfish-sea anemone interaction, we integrate mutualistic interactions into a niche quantification framework to analyse the effect of biotic interactions in the estimation of species niches, and competition patterns among clownfish communities. Our results show that ignoring biotic interactions can strongly affect species' ecological niche estimations. More importantly, sea anemones seem to mediate competition among clownfishes, structure communities and allow coexistence in competitive environments. These findings strongly support the importance of biotic interactions in shaping communities. Future studies could use the proposed analytical framework, which could also serve multiple conservation purposes.</span></p>
Integrating biotic interactions in niche analyses unravels patterns of community composition in clownfishes
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Global study of plant-herbivore interactions reveals similar patterns of herbivory across native and non-native plants
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Hibiscus bullseyes reveal mechanisms controlling petal pattern proportions that influence plant-pollinator interactions
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Patterns of genotype-specific interactions in an obligate host-specific insect pathogenic fungus
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Data from: Lousy grouse: comparing evolutionary patterns in Alaska galliform lice to understand host evolution and host-parasite interactions
Understanding both sides of host-parasite relationships can provide more complete insights into host and parasite biology in natural systems. For example, phylogenetic and population genetic comparisons between a group of hosts and their closely associated parasites can reveal patterns of host dispersal, interspecies interactions, and population structure that might not be evident from host data alone. These comparisons are also useful for understanding factors that drive host-parasite coevolutionary patterns (e.g., codivergence or host switching) over different periods of time. However, few studies have compared the evolutionary histories between multiple groups of parasites from the same groups of hosts at a regional geographic scale. Here, we used genomic data to compare phylogenomic and population genomic patterns of Alaska ptarmigan and grouse species (Aves: Tetraoninae) and two genera of their associated feather lice: Lagopoecus and Goniodes. We used whole-genome sequencing to obtain hundreds of genes and thousands of single nucleotide polymorphisms (SNPs) for the lice and double digest restriction associated DNA sequences to obtain SNPs from Alaska populations of two species of ptarmigan. We found that both genera of lice have some codivergence with their galliform hosts, but these relationships are primarily characterized by host switching and phylogenetic incongruence. Population structure was also uncorrelated between the hosts and lice. These patterns suggest that grouse, and ptarmigan in particular, share habitats and have likely had historical and ongoing dispersal within Alaska. However, the two genera of lice also have sufficient dissimilarities in the relationships with their hosts to suggest there are other factors, such as differences in louse dispersal ability, that shape the evolutionary patterns with their hosts.
Data from: The role of climate, water and biotic interactions in shaping biodiversity patterns in arid environments across spatial scales
Aim: Desert ecosystems, with their harsh environmental conditions, hold the key to understanding the responses of biodiversity to climate change. As desert community structure is influenced by processes acting at different spatial scales, studies combining multiple scales are essential for understanding the conservation requirements of desert biota. We investigated the role of environmental variables and biotic interactions in shaping broad and fine-scale patterns of diversity and distribution of bats in arid environments to understand how the expansion of nondesert species can affect the long-term conservation of desert biodiversity. Location: Levant, Eastern Mediterranean. Methods: We combine species distribution modelling and niche overlap statistics with a statistical model selection approach to integrate interspecific interactions into broadscale distribution models and fine-scale analysis of ecological requirements. We focus on competition between desert bats and mesic species that recently expanded their distribution into arid environment following anthropogenic land-use changes. Results: We show that both climate and water availability limit bat distributions and diversity across spatial scales. The broadscale distribution of bats was determined by proximity to water and high temperatures, although the latter did not affect the distribution of mesic species. At the fine-scale, high levels of bat activity and diversity were associated with increased water availability and warmer periods. Desert species were strongly associated with warmer and drier desert types. Range and niche overlap were high among potential competitors, but coexistence was facilitated through fine-scale spatial partitioning of water resources. Main conclusions: Adaptations to drier and warmer conditions allow desert-obligate species to prevail in more arid environments. However, this competitive advantage may disappear as anthropogenic activities encroach further into desert habitats. We conclude that reduced water availability in arid environments under future climate change projections pose a major threat to desert wildlife because it can affect survival and reproductive success and may increase competition over remaining water resources.
Data from: Latitudinal patterns of herbivore pressure in a temperate herb support the biotic interactions hypothesis
The longstanding biotic interactions hypothesis predicts that herbivore pressure declines with latitude, but the evidence is mixed. To address gaps in previous studies, we measured herbivory and defense in the same system, quantified defense with bioassays, and considered effects of leaf age. We quantified herbivory and defense of young and mature leaves along a continental gradient in eastern North America in the native herb Phytolacca americana. Herbivory in the field declined with latitude and was strongly correlated with Lepidopteran abundance. Laboratory bioassays revealed that leaf palatability was positively correlated with latitude of origin. Young leaves were more damaged than mature leaves at lower latitudes in the field, but less palatable in bioassays. Both defense and palatability displayed non-linear latitudinal patterns, suggesting potential mechanisms based on biological or climatic thresholds. In sum, observational and experimental studies find patterns consistent with high herbivore pressure and stronger plant defenses at lower latitudes.
Patterns of liana diversity and host interaction networks in selectively-logged and unlogged forests of Uppangala, Western Ghats, India
<p>Lianas shape tropical forest species composition, structure, and dynamics. Increasing climate fluctuation and anthropogenic disturbances increase liana abundance. Despite the increasing number of liana studies in India, only a few have examined the distribution and association of hosts with lianas, or liana-host interaction networks to determine their functional significance and conservational value. Therefore, our objective was to fill the knowledge gap about the diversity, abundance, and network structure of liana-host interactions in response to logging disturbance in a wet evergreen forest of Uppangala in central Western Ghats, India. We sampled lianas ≥1 cm in diameter at 1.3 m from the base and their host trees in thirty 20m x 20m plots in selectively-logged and unlogged forest management regimes. We evaluated liana-host tree interactions in logged and unlogged forests and retrieved community-level measures (nestedness, connectance, modularity, and network specialization index) and species-level indicators (species specialization index). Diversity and abundance of liana species were considerably greater in the selectively logged forest site. The logged forest site had compartmentalization, anti-nestedness, and network specialization, while unlogged forests were not showing any significant network structure. Most species of lianas and hosts were peripherals, but others were structurally important (connectors, module hubs, and network hubs) in the two forest sites. Forest management regimes had distinct structurally significant species.</p>
Social interactions generate complex selection patterns in virtual worlds
<p>Understanding the influence of social interactions on individual fitness is key to improving our predictions of phenotypic evolution. However, we often overlook the different components of selection regimes arising from interactions among organisms, including social, correlational, and indirect selection. This is due to the challenging sampling efforts required in natural populations to measure phenotypes expressed during interactions and individual fitness. Furthermore, behaviours are crucial in mediating social interactions, yet few studies have explicitly quantified these selection components on behavioural traits. In this study, we capitalize on an online multiplayer videogame as a source of extensive data recording direct social interactions among prey, where prey collaborate to escape a predator in realistic ecological settings. We estimate natural and social selection and their contribution to total selection on behavioural traits mediating competition, cooperation, and predator-prey interactions. Behaviours of other prey in a group impact an individual's survival, and thus are under social selection. Depending on whether selection pressures on behaviours are synergistic or conflicting, social interactions enhance or mitigate the strength of natural selection, although natural selection remains the main driving force. Indirect selection through correlations among traits also contributed to the total selection. Thus, failing to account for the effects of social interactions and indirect selection would lead to a misestimation of the total selection acting on traits. Dissecting the contribution of each component to the total selection differential allowed us to investigate the causal mechanisms relating behaviour to fitness and quantify the importance of the behaviours of conspecifics as agents of selection. Our study emphasizes that social interactions generate complex selective regimes even in a relatively simple ecological environment.</p>
Cross-kingdom interactions and functional patterns of active microbiota matter in governing deadwood decay
<p>Microbial community members are the primary microbial colonizers and active decomposers of deadwood. This study placed sterilized standardized beech and spruce sapwood specimens on the forest ground of 8 beech- and 8 spruce-dominated forest sites. After 370 days, specimens were assessed for mass loss, nitrogen (N) content and <sup><span>15</span></sup><span>N</span> isotopic signature, <span>hydrolytic and lignin-modifying enzyme activities. Each </span>specimen <span>was </span>incubated with bromodeoxyuridine (BrdU) to label <span>metabolically active fungal and bacterial community members, which were assessed using an amplicon sequencing. Fungal saprotrophs colonized the deadwood accompanied by a distinct bacterial community that was capable of cellulose degradation, aromatic depolymerisation, and N<sub>2</sub> fixation. The latter were governed by the genus <em>Sphingomonas</em>, which was co-present with the majority of saprotrophic fungi regardless of whether beech or spruce specimens were decayed. Moreover, the richness of the diazotrophic </span><span><em>Allorhizobium</em>-<em>Neorhizobium</em>-<em>Pararhizobium</em>-<em>Rhizobium</em></span><span> group were significantly correlated with mass loss, N content and <sup>15</sup>N isotopic signature. In contrast, presence of obligate predator <em>Bdellovibrio</em> spp. shifted bacterial community composition and were linked to decreased beech deadwood decay rates. Our study provides the first account of the composition and function of metabolically active wood-colonising bacterial and fungal communities, highlighting cross-kingdom interactions during the early and intermediate stages of wood decay.</span></p>
Meta-analysis of elevational changes in the intensity of trophic interactions: similarities and dissimilarities with latitudinal patterns
<p>The premise that the intensity of biotic interactions decreases with increasing latitudes and elevations is broadly accepted; however, whether these geographical patterns can be explained within a common theoretical framework remains unclear. Our goal was to identify the general pattern of elevational changes in trophic interactions and to explore the sources of variation among the outcomes of individual studies. Meta-analysis of 226 effect sizes calculated from 136 publications demonstrated a significant but interaction-specific decrease in the intensity of herbivory, carnivory and parasitism with increasing elevation. Nevertheless, this decrease was not significant at high latitudes and for interactions involving endothermic organisms, for herbivore outbreaks or for herbivores living within plant tissues. Herbivory similarly declined with increases in latitude and elevation, whereas carnivory showed a fivefold stronger decrease with elevation than with latitude and parasitism increased with latitude but decreased with elevation. Thus, although these gradients share a general pattern and several sources of variation in trophic interaction intensity, we discovered important dissimilarities, indicating that elevational and latitudinal changes in these interactions are partly driven by different factors. We conclude that the scope of the latitudinal biotic interaction hypothesis cannot be extended to incorporate elevational gradients.</p>
Data from: Empirically testing the influence of light regime on diel activity patterns in a marine predator reveals complex interacting factors shaping behaviour
<p>Diel cycles in marine predator diving behaviour centre around the light-mediated diel vertical migration (DVM) of prey, and are considered critical for optimizing foraging and limiting competition across global seascapes. Yet our understanding of predator diel behaviour is based primarily on examining relative depth usage between constant day/night cycles with no formal investigation of how varying light regimes interact with abiotic factors to shape diel activity. The extreme seasonal light regimes (midnight sun, polar night, day/night cycle) in the Arctic provide a unique natural experimental setting to empirically investigate the occurrence and intensity of diel behaviour in marine predators relative to changing light levels while concomitantly assessing interacting abiotic factors. Depth time series data from satellite-linked tags deployed on six belugas for up to 12 months were used to quantify diel behaviour by calculating dissimilarity in time-at-depth between periods of low and high solar altitude on each day. Generalized additive mixed effects models were used to examine the influence of hours of daylight across extreme light cycles, coupled with bathymetry and sea ice concentration; focal diel patterns were further examined relative to the thermal structure of the water column. As predicted, belugas exhibited cathemerality during the midnight sun, and initiated diel behaviour with the onset of the fall day/night cycle, with a marked increase in its intensity with the progression to equal day/night length. Occurrence of diel patterns, however, was complex; ceasing in regions with seafloor depths < 700 m, and occurring with greatest intensity when the water column was thermally homogeneous within the upper 150 m. Through empirical investigation, this study demonstrates that the onset of day/night light cycles and presumably associated prey DVM can modulate predator diel dive behaviour under certain circumstances, but highlights how the complex interaction of abiotic factors with light regime shape dynamic spatiotemporal patterns. These findings, building on a body of recent work, emphasize that the traditional view of the ubiquitous occurrence of diel behaviour tied to DVM at the base of the food web oversimplifies vertical predator-prey interactions, identifying the need for more structured investigation. </p>
Supplementary Movies – Pattern formation by bacteria-phage interactions
<p>Supplementary movies of the manuscript "Pattern formation by bacteria-phage interactions".</p>
Data from: Understanding carnivore interactions in a cold arid trans-Himalayan landscape: What drives co-existence patterns within predator guild along varying resource gradients?
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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