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36 results for “nestedness”
Fig. 5 in Nestedness of stream insects in Subtropical region: importance of inter-annual temporal scale
Fig. 5. NODF nestedness of Chironomidae (Diptera) assemblages in streams of southern Brazil in the summer and winter of 2010, 2011 and 2012. (A) Each line represents a stream independent of intra- and inter-annual factor. (B, C, D) Dotted lines represent winter data and continuous lines represent summer data. In these graphs, the individual information for each stream was grouped to assess intra-annual nestedness.
Fig. 4 in Nestedness of stream insects in Subtropical region: importance of inter-annual temporal scale
Fig. 4. Boxplot of water temperature, dissolved organic carbon (DOC), dissolved oxygen (DO), dissolved total nitrogen (DTN) and precipitation in the summer and winter of 2010, 2011 and 2012 in streams of southern Brazil (only variables with significant differences for each year).
Fig. 2 in Nestedness of stream insects in Subtropical region: importance of inter-annual temporal scale
Fig. 2. Abundance and richness of Chironomidae (Diptera) in streams of southern Brazil in the summer and winter of 2010, 2011 and 2012.
Fig. 1 in Nestedness of stream insects in Subtropical region: importance of inter-annual temporal scale
Fig. 1. Location of sampling sites in southern Brazil (F, Faxinalzinho city; E, Erechim; MR, Marcelino Ramos; TA, TrÊs Arroios).
Fig. 3 in Nestedness of stream insects in Subtropical region: importance of inter-annual temporal scale
Fig. 3. Boxplot of dissolved organic carbon (DOC), dissolved oxygen (DO), dissolved total nitrogen (DTN) and precipitation in streams of southern Brazil in the summer and winter of 2010, 2011 and 2012.
APPENDIX 7 in Quantifying and interpreting nestedness of bryophytes in the Zhoushan Archipelago, China
APPENDIX 7. — The number of islands whose observed species richness of focal bryophyte category lie outside ± one standard deviation of the expected species richness based on the null model proposed by Moore & Swihart (2007).
FIG. 2 in Quantifying and interpreting nestedness of bryophytes in the Zhoushan Archipelago, China
FIG. 2. — Relationship between ranks of species of total mosses, acrocarpous mosses, and Pottiaceae in their maximally packed matrices and ranks of their spore size. Note: species were ranked from the rarest to the most common in the maximally packed matrix, namely, those with the lowest rank have the narrowest distribution range, and the spore with the lowest rank has the smallest size.
Fig. 3 in Quantitative Biogeographic Characterization Of Hungary Based On The Distribution Data Of Land Snails (Mollusca,Gastropoda): A Case Of Nestedness Of Species Ranges With Extensive Overlap Of Biotic Elements
Fig. 3. Distribution maps of four biotic elements found by PRABCLUS: (a) highland species, (b) general species, (c) localizes species distributed in the northern and (d) south–eastern parts of Hungary. The different shadings indicate the areas where>70%,>30%, and>0% of the species of an ele-
Fig. 1 in Quantitative Biogeographic Characterization Of Hungary Based On The Distribution Data Of Land Snails (Mollusca,Gastropoda): A Case Of Nestedness Of Species Ranges With Extensive Overlap Of Biotic Elements
Fig. 1. Biogeographic classification of Hungary based on distribution data of land snails according to the (a) hierarchical clustering of the (b) spatial units (ca. 50 km × 50 km). For clustering, the Sørensen–index and Ward–Orlóci fusion method was used. Shades of grey indicate main partitions of the cluster hierarchy, circled numbers 1–6 indicate lower level partitions mentioned in the text, numbers 1–49 identify spatial units (a) in the cluster foot and (b) in the map. Capital letters correspond to IndVal species groups listed in the text and in Appendix, lines associated to letters refer to
Fig. 2 in Quantitative Biogeographic Characterization Of Hungary Based On The Distribution Data Of Land Snails (Mollusca,Gastropoda): A Case Of Nestedness Of Species Ranges With Extensive Overlap Of Biotic Elements
Fig. 2. First two dimensions of the metric multidimensional scaling of the range data of the Hungarian land snail species. 1–4: biotic elements found by PRABCLUS; N: noise component.
Data from: Measuring nestedness: a comparative study of the performance of different metrics
Nullnest <p>The <code>nullnest</code> repository provides a set of programs developed for constructing a <strong>null model</strong> of bipartite networks which constraints the degree sequences -on average-, along with the measurement of the degree of <strong>nestedness</strong> of bipartite networks using a large variety of metrics allowing for the comparison of this value against the null expectation. The whole repository is documented and maintained at: <span><a href="https://github.com/cclaualc/nullnest">https://github.com/cclaualc/nullnest</a>.</span></p> <p>The package is divided into two main blocks. On the one hand, we provide a program to compute the null model, for any bipartite network introduced by the user, which keeps the original degree sequence constant on average while maximizing the entropy of the null ensemble. We also give the ready-to-use results of the null model for an important number of real networks available online. On the other hand, the package contains the programs to measure the degree of nestedness of any network, measuring as well the first two moments of its null distribution, either by using analytical expressions or by numerically sampling the null ensemble.</p> <p>For more information on the functioning, modificable options, implementation and references of this repository visit the <a href="https://github.com/cclaualc/nullnest">github link</a>. When using these programs please acknowledge the authors.</p>
Data from: Measuring nestedness: a comparative study of the performance of different metrics
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Nestedness theory suggests wetland fragments with large areas and macrophyte diversity benefit waterbirds
<p>Many artificial wetland constructions are currently underway worldwide to compensate for the degradation of natural wetland systems. Researchers face the responsibility of proposing wetland management and species protection strategies to ensure that constructed wetlands positively impact waterbird diversity. Nestedness is a commonly occurring pattern for biotas in fragmented habitats with important implications for conservation; however, only a few studies have focused on seasonal waterbird communities in current artificial wetlands. In this study, we used the nestedness theory for analyzing the annual and seasonal community structures of waterbirds in artificial wetlands at Lake Dianchi (China) to suggest artificial wetland management and waterbird conservation strategies. We carried out three waterbird surveys per month for one year to observe the annual, spring, summer, autumn, and winter waterbird assemblages in 27 lakeside artificial wetland fragments. We used the NeD program to quantify nestedness patterns of waterbirds at the annual and seasonal levels. We also determined Spearman partial correlations to examine the associations of nestedness rank and habitat variables to explore the factors underlying nestedness patterns. We found that annual and all four seasonal waterbird compositions were nested, and selective extinction and habitat nestedness were the main factors governing nestedness. Further, selective colonization was the key driver of nestedness in autumn and winter waterbirds. We suggest that the area of wetland fragments should be as large as possible and that habitat heterogeneity should be maximized to fulfill the conservation needs of different seasonal waterbirds. Furthermore, we suggest that future studies should focus on the least area criterion, and that vegetation management of artificial wetland construction should be based on the notion of sustainable development for humans and wildlife. </p>
Do functional and phylogenetic nestedness follow the same mechanisms as taxonomic nestedness? Evidence from amphibians in the largest archipelago of China
<p>1. Nested subset pattern (nestedness) has been raised to explain the distribution of species on islands and habitat fragments for over 60 years. However, previous studies on nestedness focused on species richness and composition and overlooked the role of species traits and phylogeny in generating and explaining the nestedness.</p> <p>2. To address this gap, we sampled amphibians on 37 land-bridge islands in the Zhoushan Archipelago to explore nestedness as well as the underlying causal processes through three facets of diversity, i.e. taxonomic, functional and phylogenetic diversity. The taxonomic nestedness was measured through organizing the species incidence matrix to achieve a maximum value, while the functional and phylogenetic nestedness were quantified by incorporating the similarity of species in terms of their ecological traits and phylogeny. We also obtained six island characteristics and seven species traits as predictors of nestedness.</p> <p>3. Amphibian metacommunities were significantly nested in these three facets of diversity. When relating different predictors to nestedness, island area, habitat diversity and species traits were highly correlated with taxonomic nestedness. Moreover, island area and habitat diversity significantly influenced functional and phylogenetic nestedness. Therefore, the results support the selective extinction and habitat nestedness hypotheses.</p> <p>4. Interestingly, although we did not observe significant influences of isolation on taxonomic nestedness, functional and phylogenetic diversities were significantly higher than expected when matrices were ordered by increasing distance to mainland. The result suggests that there are more functionally and phylogenetically diverse species on less-isolated islands, reflecting a selective colonization process overlooked by the traditional analysis of taxonomic nestedness.</p> <p>5. Although the three facets of nestedness and underlying processes were largely congruent, we detected the distance-related functional and phylogenetic nestedness for amphibian assemblages. Therefore, we highlight that a framework that simultaneously considers taxonomic, functional and phylogenetic nestedness contributes to a complementary understanding of nestedness processes. In addition, it also improves our ability to conserve insular biodiversity from different perspectives.</p>
FIG. 1 in Quantifying and interpreting nestedness of bryophytes in the Zhoushan Archipelago, China
FIG. 1. — Location and map of 66 islands in the Zhoushan Archipelago (Yu et al. 2019).
APPENDIX 7 in Quantifying and interpreting nestedness of bryophytes in the Zhoushan Archipelago, China
APPENDIX 7. — Continuation.
Data from: Context- and taxon-dependent small-scale taxonomic and phylogenetic nestedness of bryophytes on insular rocks in a karst natural reserve and its implication for their conservation
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Do functional and phylogenetic nestedness follow the same mechanisms as taxonomic nestedness? Evidence from amphibians in the largest archipelago of China
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Nestedness theory suggests wetland fragments with large areas and macrophyte diversity benefit waterbirds
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Data from: Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree-herbivore networks.
Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant–herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen–herbivore bipartite networks, the role of environmental variations is a dominant constraint.
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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.