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241 results for “Structural relationships”
Data from: Genetic relationships, structure and parentage simulation among the olive tree (Olea europaea L. subsp. europaea) cultivated in Southern Italy revealed by SSR markers
In this work, we assess both the morphological and genetic diversity of 68 important olive cultivars from three Southern Italian regions: Calabria, Campania and Sicily. Twenty-five phenotypic traits were evaluated and 12 simple sequence repeat (SSR) markers were analysed. All SSR primers were polymorphic and reliable. The total number of alleles per locus varied from 5 to 19 with an average number of 13.1 and a mean polymorphic information content (PIC) of 0.81. These results suggested high genetic diversity within these three olive germplasm collections. Morphological traits also showed significant variability amongst cultivars. Two cases of identity were found and ten statistically significant cases of putative parent/sibling were discovered by performing a SSR-based parentage simulation analysis with CERVUS. The Mantel test indicated low but significant correlations between the morphological data and SSR allelic frequency, origin and SSR allelic frequency, and origin and morphology. Structure software allowed inference of relationships between the three olive germplasm collections and allowed us to obtain the most consistent grouping and to identify putative admixed or exchanged cultivars. Cluster and multivariate analysis, based on morphological traits, revealed geographic grouping in agreement with UPGMA dendrogram and structure analysis using SSRs. Sicilian cultivars showed a more homogenous genetic makeup, probably due to geographical isolation, whilst Calabrian and Campanian cultivars seemed to have a less distinct genetic structure, with a greater degree of intermixing. A correlation between the presence of certain SSR alleles and fruit size was also found.
Data from: Checkerboard score-area relationships reveal spatial scales of plant community structure
Identifying the spatial scale at which particular mechanisms influence plant community assembly is crucial to understanding the mechanisms structuring communities. It has long been recognized that many elements of community structure are sensitive to area; however the majority of studies examining patterns of community structure use a single relatively small sampling area. As different assembly mechanisms likely cause patterns at different scales we investigate how plant species co-occurrence patterns change with sampling unit scale. We use the checkerboard score as an index of species segregation, and examine species C-score-sampling area patterns in two ways. First, we show via numerical simulation that the C-score-area relationship is necessarily hump shaped with respect to sample plot area. Second we examine empirical C-score-area relationships in arctic tundra, grassland, boreal forest, and tropical forest communities. The minimum sampling scale where species co-occurrence patterns were significantly different from the null model expectation was at 0.1 m2 in the tundra, 0.2 m2 in grassland, and 0.2 Ha in both the boreal and tropical forests. Species were most segregated in their co-occurrence (maximum C-score) at 0.3 m2 in the tundra (0.54 m by 0.54 m quadrats), 1.5 m2 in the grassland (1.2 by 1.2 m quadrats), 0.26 Ha in the tropical forest (71 m by 71 m quadrats), and a maximum was not reached at the largest sampling scale of 1.4 Ha in the boreal forest. The most important finding is that the dominant scales of community structure in these systems are large relative to plant body size, and hence we infer that the dominant mechanisms structuring these communities must be at similarly large scales. This provides a method for identifying the spatial scales at which communities are maximally structured; ecologists can use this information to develop hypotheses and experiments to test scale-specific mechanisms that structure communities.
Data from: Structural complexity and large-sized trees explain shifting species richness and carbon relationship across vegetation types
<p>1. It is prominently claimed that enhancing forest diversity would play a dual role of nature conservation and climate regulation. While the idea is intuitively appealing, studies show that species richness effects on aboveground carbon (AGC) are not always positive, but instead unpredictable especially across scales and complex terrestrial systems having large-diameter and tall-stature trees. Previous studies have further considered structural complexity and larger trees as determinants of AGC. Yet it remains unclear what drives differential diversity-AGC relationships across vegetation types.</p> <p>2. Here, we test whether structural complexity and large-sized trees play an influential role in explaining shifting diversity-AGC relationships across vegetation types, using a 22.3 ha sampled dataset of 124 inventory plots in woodlands, gallery forests, tree/shrub savannahs and mixed plantations in West Africa.</p> <p>3. Natural vegetation had greater species richness and structural complexity than mixed plantations, as expected. In addition, AGC was highest in gallery forests and mixed plantations, which is consistent with favorable environmental conditions in the former and high stocking densities and presence of fast-growing species in the latter. Significant interaction effects of species richness and vegetation on AGC revealed a vegetation-dependent species richness-AGC relationship: consistently, we found positive species richness-AGC relationship in both mixed plantations and woodlands, and nonsignificant patterns in gallery forests and tree/shrub savannah. Further, there was a vegetation-dependent mediation of structural complexity in linking species richness to AGC, with stronger positive structural complexity effects where species richness-AGC relationships were positive, and stronger positive large-sized trees' effect where species richness-AGC relationships were neutral.</p> <p>4. Our study provides strong evidence of vegetation-dependent species richness-AGC relationships, which operated through differential mediation by structural complexity of the species richness and large trees' effects. We conclude that even higher species richness in diversified ecosystems may not always relate positively with AGC, and that neutral pattern may arise possibly as a result of larger dominant individual trees imposing a slow stand dynamic flux and overruling species richness effects.</p>
Data from: Flow-ecology relationships are spatially structured and differ among flow regimes
1. In streams, hydrology is a predominant driver of ecological structure and function. Providing adequate flows to support aquatic life, or environmental flows, is therefore a top management priority in stream systems. 2. Flow regime classification is a widely accepted approach for establishing environmental flow guidelines. However, it is surprisingly difficult to quantify relationships between hydrology and ecology (flow-ecology relationships) while describing how these relationships vary across classified flow regimes. Developing such relationships is complicated by several sources of spatial bias, such as autocorrelation due to spatial design, flow regime classification, and other environmental or ecological sources of spatial bias. 3. We used mixed moving-average spatial stream network models to develop flow-ecology relationships across classified flow regimes and to assess spatial patterns of these relationships. We compared relationships between fish traits and life-history strategies with hydrologic metrics across flow regimes and assessed whether spatial autocorrelation influenced these relationships. 4. Trait-hydrology relationships varied between flow regimes and across all streams combined. Some relationships between traits and hydrologic metrics fit predictions based on life-history theory, while others exhibited unexpected relationships with hydrology. Spatial factors described a large proportion of variability in fish traits and different patterns of spatial autocorrelation were observed in different flow regimes. Synthesis and Applications. Further work is needed to understand why flow-ecology relationships vary across classified flow regimes and why these relationships may not fit predictions based on life-history theories. Managers determining environmental flow standards need to be aware that different hydrologic metrics are often important drivers of fish trait diversity in different flow-regimes. Flow-ecology relationships may therefore be confounded by spatial structure that is inherent in flow regime classification and much existing biological data. Complex patterns of spatial bias should be considered when managing stream systems within an environmental flows framework.
Data from: Size structuring and allometric scaling relationships in coral reef fishes
Temperate marine fish communities are often size structured, with predators consuming increasingly larger prey and feeding at higher trophic levels as they grow. Gape limitation and ontogenetic diet shifts are key mechanisms by which size structuring arises in these communities. Little is known, however, about size structuring in coral reef fishes. Here, we aimed to advance understanding of size structuring in coral reef food webs by examining the evidence for these mechanisms in two groups of reef predators. Given the diversity of feeding modes amongst coral reef fishes, we also compared gape size—body size allometric relationships across functional groups to determine if they are reliable indicators of size structuring. We used gut content analysis and quantile regressions of predator size—prey size relationships to test for evidence of gape limitation and ontogenetic niche shifts in reef piscivores (n=13 species) and benthic invertivores (n=3 species). We then estimated gape size—body size allometric scaling coefficients for 21 different species from four functional groups, including herbivores/detritivores, which are not expected to be gape-limited. We found evidence of both mechanisms for size structuring in coral reef piscivores, with maximum prey size scaling positively with predator body size, and ontogenetic diet shifts including prey type and expansion of prey size. There was, however, little evidence of size structuring in benthic invertivores. Across species and functional groups, absolute and relative gape sizes were largest in piscivores as expected, but gape size—body size scaling relationships were not indicative of size structuring. Instead, relative gape sizes and mouth morphologies may be better indicators. Our results provide evidence that coral reef piscivores are size-structured, and that gape limitation and ontogenetic niche shifts are the mechanisms from which this structure arises. Although gape allometry was not indicative of size structuring, it may have implications for ecosystem function: positively allometric gape size—body size scaling relationships in herbivores/detritivores suggests that loss of large-bodied individuals of these species will have a disproportionately negative impact on reef grazing pressure.
Data from: Population structure of mountain pine beetle symbiont Leptographium longiclavatum and the implication on the multipartite beetle-fungi relationships
Over 18 million ha of forests have been destroyed in the past decade in Canada by the mountain pine beetle (MPB) and its fungal symbionts. Understanding their population dynamics is critical to improving modeling of beetle epidemics and providing potential clues to predict population expansion. Leptographium longiclavatum and Grosmannia clavigera are fungal symbionts of MPB that aid the beetle to colonize and kill their pine hosts. We investigated the genetic structure and demographic expansion of L. longiclavatum in populations established within the historic distribution range and in the newly colonized regions. We identified three genetic clusters/populations that coincide with independent geographic locations. The genetic profiles of the recently established populations in northern British Columbia (BC) and Alberta suggest that they originated from central and southern BC. Approximate Bayesian Computation supports the scenario that this recent expansion represents an admixture of individuals originating from BC and the Rocky Mountains. Highly significant correlations were found among genetic distance matrices of L. longiclavatum, G. clavigera, and MPB. This highlights the concordance of demographic processes in these interacting organisms sharing a highly specialized niche and supports the hypothesis of long-term multipartite beetle-fungus co-evolutionary history and mutualistic relationships.
Data from: Angiosperm wood structure: global patterns in vessel anatomy and their relationship to wood density and potential conductivity
Woody stems comprise a large biological carbon fraction and determine water transport between roots and leaves; their structure and function can influence both carbon and hydrological cycles. While angiosperm wood anatomy and density determine hydraulic conductivity and mechanical strength, little is known about interrelations across many species. We compiled a global dataset comprising two anatomical traits for 3005 woody angiosperms: mean vessel lumen area ( ) and number per unit area (N). From these, we calculated vessel lumen fraction (F = N) and size/number ratio (S = /N), a new vessel composition index. We examined extent to which F and S influenced potential sapwood specific stem conductivity (KS) and wood density (D; dry mass/fresh volume). F and S varied essentially independently across angiosperms. Variation in KS was driven primarily by S, and variation in D was virtually unrelated to F and S. Tissue density outside vessel lumens (DN) must predominantly influence D. High S should confer faster Ks but incur greater freeze-thaw embolism risk. F should also affect KS, and both F and DN should influence mechanical strength, capacitance, and construction costs. Improved theory and quantification are needed to better understand ecological costs and benefits of these three distinct dimensions.
Drug scaffolds and their structural relationships
<p>A list of 779 scaffolds extracted from approved drugs is provided. For each scaffold, the number of approved drugs it represented, the number and the list of targets it was annotated with and the SMILES representation is given. In addition, pairs of drug scaffolds that formed substructure, CSK equivalence, MMP and RECAP-MMP relationships are provided in separate files. Furthermore, drug scaffold pairs that displayed distinct activity profiles and formed one or more types of structural relationships are given.</p>
Learning the structure of biomedical relationships from unstructured text (Part II)
<p>These files contain the seed sets and corresponding test sets of drug-gene pairs reflecting pharmacogenomic (PGx) and drug-target relationships that were used to evaluate EBC in the PLoS Comp Bio paper. Unfortunately, they didn't make it into the first upload for this paper. There are four zipped directories in this upload:</p> <p>data-drug-gene (PGx relationships, dense matrix)</p> <p>data-drug-target (drug-target relationships, dense matrix)</p> <p>data-drug-gene-fullmatrix (PGx relationships, sparse matrix)</p> <p>data-drug-target-fullmatrix (drug-target relationships, sparse matrix)</p>
FIGURES 2027. Crozetia larval structures. 20 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography
FIGURES 2027. Crozetia larval structures. 20. Cr. crozetensis, LM of last instar larval hypostoma. Scale bar = 0.1 mm. 21. Cr. seguyi, SEM of last instar larval hypostoma. Image foreshortened see Fig 23. Scale bar = 0.05 mm. 22. Cr. crozetensis, LM of last instar larval hypostoma and postgenal cleft. Scale bar = 0.1 mm. 23. Cr. seguyi, LM of last instar larval hypostoma and postgenal cleft. Scale bar = 0.1 mm. 24. Cr. crozetensis, LM of abdomen, last instar larvae. Scale bar = 1.0 mm. 25. Cr. seguyi, LM of abdomen, last instar larvae. Scale bar = 1.0 mm. 26. Cr. crozetensis, last instar, anal sclerites. Scale bar = 0.1 mm. 27. Cr. seguyi, last instar, anal sclerites. Scale bar = 0.1 mm.
FIGURES 19–20 in Comparison of the structure and musculature of male terminalia in the tribe Cidariini Duponchel (Lepidoptera: Geometridae: Larentiinae) once again throws into doubt a sister relationship with the Xanthorhoini
FIGURES 19–20. Pennithera firmata, male genitalia and muscles: 19. Armature (proximal part of subscaphium, distal part of muscles m2(10) on the right side, muscles m4 on the left side and ventral band of muscles m5(7) on the right side not shown). 20. Aedeagus.
FIGURES 17–18 in Comparison of the structure and musculature of male terminalia in the tribe Cidariini Duponchel (Lepidoptera: Geometridae: Larentiinae) once again throws into doubt a sister relationship with the Xanthorhoini
FIGURES 17–18. Lampropteryx suffumata, male genitalia and muscles: 17. Armature (proximal part of subscaphium, distal part of muscles m2(10) on the left side and muscles m5(7) on the right side not shown). 18. Aedeagus.
FIGURES 9–10 in Comparison of the structure and musculature of male terminalia in the tribe Cidariini Duponchel (Lepidoptera: Geometridae: Larentiinae) once again throws into doubt a sister relationship with the Xanthorhoini
FIGURES 9–10. Dysstroma citrata, male genitalia and muscles: 9. Armature (proximal part of subscaphium, proximal part of muscles m2(10) on the left side, middle part of muscles m4 on the right side and muscles m6(5) on the left side not shown). 10. Aedeagus.
FIGURES 1–2 in Comparison of the structure and musculature of male terminalia in the tribe Cidariini Duponchel (Lepidoptera: Geometridae: Larentiinae) once again throws into doubt a sister relationship with the Xanthorhoini
FIGURES 1–2. Cidaria fulvata, male genitalia and muscles: 1. Armature (subscaphium, distal part of muscles m4 on the right side and muscles m6(5) on the right side not shown). 2. Aedeagus.
FIGURES 5–6 in Comparison of the structure and musculature of male terminalia in the tribe Cidariini Duponchel (Lepidoptera: Geometridae: Larentiinae) once again throws into doubt a sister relationship with the Xanthorhoini
FIGURES 5–6. Colostygia olivata, male genitalia and muscles: 5. Armature (proximal part of subscaphium, muscles m5(7), muscles m6(5) on the right side not shown). 6. Aedeagus.
FIGURES 3–4 in Comparison of the structure and musculature of male terminalia in the tribe Cidariini Duponchel (Lepidoptera: Geometridae: Larentiinae) once again throws into doubt a sister relationship with the Xanthorhoini
FIGURES 3–4. Chloroclysta siterata, male genitalia and muscles: 3. Armature (muscles m1 on the right side, muscles m2(10) on the left side, dorsal part of muscles m3(2) on the left side, muscles m4 on the right side and muscles m6(5) on the left side not shown). 4. Aedeagus.
FIGURES 7–8 in Comparison of the structure and musculature of male terminalia in the tribe Cidariini Duponchel (Lepidoptera: Geometridae: Larentiinae) once again throws into doubt a sister relationship with the Xanthorhoini
FIGURES 7–8. Cosmorhoe ocellata, male genitalia and muscles: 7. Armature (proximal part of subscaphium, proximal part of muscles m2(10) on the right side, muscles m6(5) on the left side and middle part of muscles m4 on the right side not shown). 8. Aedeagus.
FIGURES 21–22 in Comparison of the structure and musculature of male terminalia in the tribe Cidariini Duponchel (Lepidoptera: Geometridae: Larentiinae) once again throws into doubt a sister relationship with the Xanthorhoini
FIGURES 21–22. Thera variata, male genitalia and muscles: 21. Armature (subscaphium, muscles m4 on the left side and muscles m5(7) on the right side not shown). 22. Aedeagus.
FIGURES 13–14 in Comparison of the structure and musculature of male terminalia in the tribe Cidariini Duponchel (Lepidoptera: Geometridae: Larentiinae) once again throws into doubt a sister relationship with the Xanthorhoini
FIGURES 13–14. Eulithis populata, male genitalia and muscles: 13. Armature (proximal part of subscaphium, middle part of muscles m2(10) and muscles m6(5) on the right side not shown). 14. Aedeagus.
FIGURES 11–12 in Comparison of the structure and musculature of male terminalia in the tribe Cidariini Duponchel (Lepidoptera: Geometridae: Larentiinae) once again throws into doubt a sister relationship with the Xanthorhoini
FIGURES 11–12. Ecliptopera silaceata, male genitalia and muscles: 11. Armature (muscles m2(10) not shown). 12. Aedeagus.
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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)
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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.