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PRISMA Checklist for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.
<p>PRISMA Checklist for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.</p>
Data from: Unravelling the complexities of temporal biotic homogenisation and heterogenization: Avian assemblage dynamics in Britain
<p>Biotic homogenization is a process whereby species assemblages become more similar through time. The standard way of identifying the process of biotic homogenization is to look for decreases in spatial beta-diversity. However, using a single assemblage-level metric to assess homogenization can mask important changes in the occupancy patterns of individual species. Here, we analysed changes in the spatial beta-diversity patterns (i.e., biotic heterogenization or homogenization) of British bird assemblages within 30km x 30km regions between two periods (1988-1991 and 2008-2011). We partitioned the change in spatial beta-diversity into extirpation and colonisation resultant change (i.e., change in spatial beta-diversity within each region resulting from both extirpation and colonisation). We used measures of abiotic change in combination with Bayesian modelling to disentangle the drivers of biotic heterogenization and homogenization. We detected both heterogenization and homogenization across the two time periods and three measures of diversity (taxonomic, phylogenetic, and functional). In addition, both extirpation and colonisation contributed to the observed changes, with heterogenization mainly driven by extirpation and homogenization by colonisation. These assemblage-level changes were primarily due to shifting occupancy patterns of generalist species. Compared to habitat generalists, habitat specialists had significantly (i) higher average contributions to colonisation resultant change (indicating heterogenization within a region due to colonisation) and (ii) lower average contributions to extirpation resultant change (indicating homogenization from extirpation). Generalists showed the opposite pattern. Increased extirpation resultant homogenization within regions was associated with increased urban land cover and decreased habitat diversity, precipitation, and temperature. Changes in extirpation resultant heterogenization and colonisation resultant heterogenization were associated with differences in elevation between regions and changes in temperature and land cover. Many of the 'winners' (i.e., species that increased in occupancy) were species that had benefitted from conservation action (e.g., buzzard (<em>Buteo buteo</em>)). The 'losers' (i.e., those that decreased in occupancy) consisted primarily of previously common species, such as cuckoo (<em>Cuculus canorus</em>). Our results show that focusing purely on changes in spatial beta-diversity over time may obscure important information about how changes in the occupancy patterns of individual species contribute to homogenization and heterogenization.</p>
Plant neighbors differentially alter a focal species' biotic interactions through changes to resource allocation
<p>Plant resource allocation strategies are thought to be largely a consequence of changing abiotic conditions and evolutionary history. However, biotic interactions also influence how a plant allocates resources. As a result, plants mediate indirect interactions between organisms above- and belowground through resource allocation. Neighboring plants can influence plant fitness directly through competition for resources, and indirectly by altering associated community interactions (associational effects). Given the importance of community interactions for plant success, and the known ability for plant neighbors to change these interactions, the goal of this "pandemic project" was to separate inter- and intraspecific plant associations, above- and belowground, to understand how different plant neighbors alter plant resource allocation, and if this in turn alters biotic interactions. We specifically investigated associational effects on herbivory and soil microbial community interactions. To do so, we established a common garden experiment, manipulating plant neighbors and extent of interactions (aboveground only versus above- and belowground interactions, using customized pot types), and measured changes to a focal plant and its biotic interactions over two growing seasons. We found evidence of both neighbor effects and pot type, showing that neighbor interactions affect a focal plant through both above- and belowground processes, and how the focal plant is affected depends on neighbor identity. Though neighbors did not directly alter herbivory or most soil microbial interactions, they did alter the relationship between belowground microbial communities and plant function. Resource allocation responses were reduced with time, showing the importance of extending experiments beyond a single growing season, and is an important consideration when making predictions about plant responses to changing conditions. This study contributes to a growing body of work showing how the community context affects the above- and belowground interactions of a plant through plant resource allocation strategies.</p>
StArt Protocol for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.
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Supplementary material 3 from: Iannone BV III, Potter KM, Guo Q, Jo I, Oswalt CM, Fei S (2018) Environmental harshness drives spatial heterogeneity in biotic resistance. NeoBiota 40: 87-105. https://doi.org/10.3897/neobiota.40.28558
Section-level standardised slope estimates for the 91 ecological sections from initial models of invasive richness and cover in response to four metrics of evolutionary relatedness—PSC, PSV, PD and PSE :
Supplementary material 2 from: Iannone BV III, Potter KM, Guo Q, Jo I, Oswalt CM, Fei S (2018) Environmental harshness drives spatial heterogeneity in biotic resistance. NeoBiota 40: 87-105. https://doi.org/10.3897/neobiota.40.28558
Description of differences between Northern and Southern FIA Regions in invasive plant species monitoring protocols :
Supplementary material 1 from: Iannone BV III, Potter KM, Guo Q, Jo I, Oswalt CM, Fei S (2018) Environmental harshness drives spatial heterogeneity in biotic resistance. NeoBiota 40: 87-105. https://doi.org/10.3897/neobiota.40.28558
Locations of Northern and Southern FIA Regions and of the ecological domains, provinces and sections in which study plots were located :
Fig. 4 a–c in The roles of niche divergence, dispersal, and geology on the diversification of Neotropical true frogs from the Rana palmipes species group (Amphibia, Anura, Ranidae) during the Great American Biotic Interchange
Fig. 4 a–c Predicted niche occupancies (PNO) with horizontal axes representing the occupancy profiles of predictors for species (represented by different lines), and vertical axes representing the predicted suitability (Maxent "raw probabilities"). d–f Reconstruction of niche evolution based on maximum likelihood for mean tolerances obtained
Fig. 2 in The roles of niche divergence, dispersal, and geology on the diversification of Neotropical true frogs from the Rana palmipes species group (Amphibia, Anura, Ranidae) during the Great American Biotic Interchange
Fig. 2 Best fit-model of ancestral area estimation for the Rana palmipes species group. a Geographical delimitation of the areas used to estimate ancestral areas and b ancestral areas estimated for the Rana palmipes species group (Ranidae). Arrows represent jump
Fig. 3 in The roles of niche divergence, dispersal, and geology on the diversification of Neotropical true frogs from the Rana palmipes species group (Amphibia, Anura, Ranidae) during the Great American Biotic Interchange
Fig. 3 Age-range correlation (ARC) between node age and D index. a Phylogenetic tree and nodes compared. b Correlation plot between node age and D index, each point corresponding to a specific node in the phylogenetic tree (r.2 = 0.035, P = 0.7, intercept = 0.097, slope = 0.002)
Fig. 3. Flood debris from which the sample for Appendix 1 in Coleoptera in Floods: Biotic Surveys, Fish Food, Adaptation, Reconstruction of Paleoenvironments, and Preconstruction of Neoenvironments
Fig. 3. Flood debris from which the sample for Appendix 1 was taken: Rock Creek Trail, Kensington, Maryland, USA, 21 April 2017.
Fig. 2 in Coleoptera in Floods: Biotic Surveys, Fish Food, Adaptation, Reconstruction of Paleoenvironments, and Preconstruction of Neoenvironments
Fig. 2. Jong-Seok Park and Sarah Samson collecting beetles in a temporary pond created by a flash flood in Hidalgo Co., New Mexico, USA during 2 August 2014. Insert: Beetles waiting out the flood.
Data & code from: Simulated invasion suggests rapid evolution of biotic resistance to a range-shifting competitor
<p><strong>Abstract</strong></p> <p>Variable climate-change-driven range shifts will likely create novel species interactions. Most research has focused on how these interactions may impact expansion rates and adaptation of species on the move (range-shifting invaders). However, slower-moving (resident) species could also adapt to novel competitors. Here we construct populations of eight duckweed genotypes (<em>Lemna minor</em> = resident) from various localities near and beyond the range edge of a potential range-shifting competitor, <em>S. polyrhiza</em> (invader), and invade them with one genotype of <em>S. polyrhiza</em>. Following a 14-week invasion, we observed significant rapid evolution and phenotypic plasticity in the resident. Selection favoured genotypes with faster growth and smaller root-to-frond-area ratios. These changes led to slight reductions in invasibility, indicating weakly increased biotic resistance. This suggests that range-shifting species, even at low densities, may drive evolution, plasticity, and evolution of biotic resistance in resident competitors, which could feed back to influence the range expansion of the invader.</p> <p><strong>Methods</strong></p> <p>This dataset repository contains the analysis scripts/ R markdown files and collected data from "Simulated invasion suggests rapid evolution of biotic resistance to a range-shifting competitor" by Emma Menchions and Amy Angert. The collected data includes frond counts for <em>L. minor</em> and <em>S. polyrhiza </em>in the experimental populations, images (experimental populations and sampled rafts), as well as measurements on frond area, root length, and the number of fronds per raft on duckweed rafts sampled from experimental and control populations. </p> <p><strong>Usage notes</strong></p> <p>See the README files in the repository. </p> <p> </p>
Data from: Regional climate and local-scale biotic acceptance explain native-exotic diversity relationships in Australian annual plant communities
Native and exotic species richness is expected to be negatively related at small spatial scales where individuals interact, and positive at larger spatial scales as a greater variety of habitats are sampled. However, a range of native-exotic richness relationships (NERRs) have been reported, including positive at small scales and negative at larger scales. We present a hierarchical metacommunity framework to explain how contrasting NERRs may emerge across scales and study systems, and then apply this framework to NERRs in an invaded winter annual plant system in south-west Western Australia. We analysed NERRs at increasing spatial scales from neighbourhoods (0.09 m2) to communities (225 m2) to metacommunities (>10 ha) within a multi-level structural equation model. In contrast to many previous studies, native and exotic richness were positively related at the neighbourhood scale and were not significantly associated at larger scales. Heterogeneity in soil surface properties was weakly, but positively, associated with native and exotic richness at the community-scale. Metacommunity exotic richness increased strongly with regional temperature and moisture availability, but relationships for native richness were negative and much weaker. Thus, we show that neutral NERRs can emerge at larger scales due to differential climatic filtering of native and exotic species pools.
The role of biotic interactions in determining metal hyperaccumulation in plants
<p>• Heavy metal hyperaccumulation (MH) is a rare trait found in plant species that inhabit metal contaminated soils. Two main hypotheses proposed to explain the selective advantage of MH are the elemental defense hypothesis and elemental allelopathy hypothesis. The elemental defence hypothesis suggests that MH functions as defence against herbivores while the elemental allelopathy hypothesis suggests that MH acts to inhibit the growth of neighbours. Nevertheless, these hypotheses are not likely to be mutually exclusive. Here, we present the first study to test both hypotheses simultaneously. We examined these hypotheses with the Cd hyperaccumulator Arabidopsis halleri, which inhabits both metalliferous and non-metalliferous soils, thus providing an opportunity to test the hypotheses both habitats.</p> <p>• A. halleri plants originating from several populations in both metalliferous and non-metalliferous soils were grown in a greenhouse in soils with or without cadmium (Cd), Their leaves were used in a feeding experiment with a specialist herbivore and in a set of leaf-leachate experiments that tested their effect on seed germination and seedling establishment of species co-occurring with A. halleri. Finally, a field survey in several A. halleri populations was conducted to compare herbivore load between A. halleri and neighbours from metalliferous vs. non-metalliferous soils.</p> <p>• Results of the feeding experiment and field-survey suggest that Cd accumulation in A. halleri leaves could provide it with defence against herbivores. Results of the leaf-leachate experiments reveal that Cd accumulation has no effect on seed germination of neighbouring species but inhibits seedling establishment, particularly of plant species originating from non-metalliferous soils.</p> <p>• Our results suggest that both herbivores and competing neighbours may jointly select for MH in plants. Moreover, MH could provide a selective advantage particularly in non-metalliferous soils, where neighbouring plants lack metal tolerance. These results highlight the importance of including different origins and populations of both the target species and its neighbouring plant species when studying the ecological role of metal hyperaccumulation.</p>
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.
Spatio-temporal dynamics of abiotic and biotic properties explain biodiversity-ecosystem functioning relationships
<p>There is increasing evidence that spatial and temporal dynamics of biodiversity and ecosystem functions play an essential role in biodiversity-ecosystem functioning (BEF) relationships. Despite the known importance of soil processes for forest ecosystems, belowground functions in response to tree diversity and spatio-temporal dynamics of ecological processes and conditions remain poorly described. We propose a novel conceptual framework integrating spatio-temporal dynamics in BEF relationships and hypothesized a positive tree species richness effect on soil ecosystem functions through the spatial and temporal stability of biotic and abiotic soil properties based on species complementarity and asynchrony. We tested this framework within a long-term tree diversity experiment in Central Germany by assessing soil ecosystem functions (soil microbial properties and litter decomposition) and abiotic variables (soil moisture and surface temperature) for two consecutive years in high spatial and temporal resolution. Tree species richness and identity had significant effects on soil properties (e.g., soil microbial biomass). Structural equation modeling revealed that overall soil microbial biomass was partly explained by (a) enhanced temporal stability of soil surface temperature and (b) decreased spatial stability of soil microbial biomass. Overall, spatial stability of soil microbial properties was positively correlated with their temporal stability. These results suggest that spatio-temporal dynamics are indeed crucial determinants in BEF relationships and highlight the importance of vegetation-induced microclimatic conditions for stable provisioning of soil ecosystem functions and services.</p>
Figure 1 in The effects of abiotic and biotic factors on web-decorating behaviour of an orb-weaving spider, Cyclosa octotuberculata Karsch (Araneae: Araneidae)
Figure 1. Cyclosa octotuberculata and its web decorations. (A) Close-up of female sitting at hub and facing down. (B) Spider on a web without decorations. (C) Spider at hub with a linear plant-detritus (arrows) decoration. (D) Spider at hub with a linear prey-remain (arrow) decoration. (E) Spider with a linear silk decoration. (F) Spider with a linear decoration consisting of moult (arrow), plant detritus and prey remains. (G) Spider at hub with a linear egg-sac (arrow) decoration. (H) Spider on its prey-remain-decorated web without spirals. The scale bars are 10 mm.
Figure 1 in Diversity of limno-terrestrial tardigrades of the Americas in relation to the Great American Biotic Interchange hypothesis (GABI)
Figure 1. Division of the Americas into the squares used in analysis: A, 25 X 25°; B, 10 X 10°. Gaps on the 10 X 10° map indicate lack of tardigrade data.
Figure 3 in Diversity of limno-terrestrial tardigrades of the Americas in relation to the Great American Biotic Interchange hypothesis (GABI)
Figure 3. Similarities of the faunas of North, Central and South America. Jaccard: A, 25 X 25° squares; B, 10 X 10° squares. Sorensen: C, 25 X 25° squares; D, 10 X 10° squares. Kulczynski: E, 25 X 25° squares; F, 10 X 10° squares.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.