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R code for archaeological examples of calculating isotopic niche space and overlap using the rKIN package
<p>This R code was written to apply the tools of the rKIN package to calculate isotopic niche space and overlap for the three archaeological case studies for the manuscript Investigating Isotopic Niche Space: Using rKIN for Stable Isotope Studies in Archaeology published in the Journal of Archaeological Method and Theory. Raw data for the case studies are available in the supplemental Excel file.</p>
Fig. 2 in A closer look at the main actors of Neotropical floodplain food webs: functional classification and niche overlap of dominant benthic invertebrates in a floodplain lake of Paraná River
Fig. 2. Cluster plot depicting trophic similarity (Morisita index) among species of dominant benthic invertebrates in a floodplain lake of ParanÁ River, Argentina. Dotted line depicts the threshold similarity of 0.6.
Fig. 3 in A closer look at the main actors of Neotropical floodplain food webs: functional classification and niche overlap of dominant benthic invertebrates in a floodplain lake of Paraná River
Fig. 3. Non Metric Multidimensional scaling plot. Circles depicts taxa classified as gatherer collectors (Aulodrilus pigueti, Pristina leidyi, Dero vagus, Nais communis, Pelomus sp., Cladopelma sp., Endotribelos sp., Polypedilum sp., Chironomus sp., Parachironomus sp., Phaenopsectra sp., Americabaetis sp., Baetis sp., Campsurus violaceus, Hyalella curvispina, Crynellus sp.) [Triangles: Tanypodinae (Coelotanypus sp., Procladius sp. and Ablabesmyia (Karelia); inverted triangle: Sympetrum sp.; square: Monopelopia sp.; cross: Pomacea canaliculata].
Fig. 1 in A closer look at the main actors of Neotropical floodplain food webs: functional classification and niche overlap of dominant benthic invertebrates in a floodplain lake of Paraná River
Fig. 1. Relative importance (IRI) of food items for analyzed taxa of dominant benthic invertebrates in a floodplain lake of ParanÁ River, Argentina (parenthesis indicate sample size).
Vibroscape analysis reveals acoustic niche overlap and plastic alteration of vibratory courtship signals in ground-dwelling wolf spiders
<p>Soundscape ecology has enabled researchers to investigate natural interactions among biotic and abiotic sounds as well as their influence on local animals. To expand the scope of soundscape ecology to encompass substrate-borne vibrations (i.e. vibroscapes), we developed methods for recording and analyzing sounds produced by ground-dwelling arthropods to characterize the vibroscape of a deciduous forest floor using inexpensive contact microphone arrays followed by automated sound filtering and detection in large audio datasets. Through the collected data, we tested the hypothesis that closely related species of <em>Schizocosa</em> wolf spider partition their acoustic niche. In contrast to previous studies on acoustic niche partitioning, two closely related species - <em>S. stridulans</em> and <em>S. uetzi</em> - showed high acoustic niche overlap across space, time, and/or signal structure. Finally, we examined whether substrate-borne noise, including anthropogenic noise (e.g., airplanes) and heterospecific signals, promotes behavioral plasticity in signaling behavior to reduce the risk of signal interference. We found that all three focal <em>Schizocosa</em> species increased the dominant frequency of their vibratory courtship signals in noisier signaling environments. Also, <em>S. stridulans</em> males displayed increased vibratory signal complexity with an increased abundance of <em>S. uetzi</em>, their sister species with which they are highly overlapped in the acoustic niche.</p>
Niche overlap in rodents increases with competition but not ecological opportunity: A role of inter-individual difference
<div> <p><span>Niche variation at population level mediates niche packing (i.e., patterns of species' spread within the niche space) and species coexistence at community level. Competition and ecological opportunity (resource diversity) are two of the main mechanisms underlying niche variation. Dense niche packing could occur through increased niche partitioning or increased niche overlap.</span></p> <p><span>In this study we used stable carbon and nitrogen isotope data of 635 individual rodents from 4 species across 9 sites in the montane region of a subtropical island to test the effects of competition and ecological opportunity on population isotope niche size, inter-individual niche difference within population, and inter-specific niche overlap within community.</span></p> <p><span>We used the Bayesian Standard Ellipse Area (SEAB, the ellipse area enclosed by carbon and nitrogen isotope values of organisms on a bi-plot) to estimate population niche size and inter-specific niche overlap. Inter-individual niche difference within population was quantified as isotopic divergence and isotopic uniqueness. We used rodent abundance (the number of unique individuals captured) to measure competition and plant isotope niche size (plant SEAB) to measure ecological opportunity.</span></p> <p><span>The rodents experienced competition as evidenced by a negative relationship between population change rate and conspecific abundance. Rodent population niche size increased with ecological opportunity but not competition. The inter-individual niche difference (isotopic uniqueness) increased with competition (inter-specific competition only) but not ecological opportunity. At community level, inter-specific niche overlap (herbivore—omnivore pair only) increased with competition (the combined abundance of the pair) but not ecological opportunity.</span></p> <p><span>This study demonstrated that isotope niche variation of the rodents could be hierarchically influenced by ecological opportunity and competition, with the former setting the limit of population niche size across communities and the latter shaping inter-individual niche difference and inter-specific niche overlap within communities. Under strong intra-specific competition and limited ecological opportunity for niche expansion, individuals may choose to increase their isotopic uniqueness from conspecifics at the cost of overlapping with heterospecifics of different trophic roles within the community niche space as overall competition increases. Denser niche packing of these rodent communities might be achieved through increased niche overlap.</span></p> </div>
Figure 15 in Effects of temperature patterns on the spawining phenology and niche overlap of fish assemblages in the water bodies of the Dnipro River basin
Figure 15. The variation of the Pianka mean niche overlap index deviation from random alternative within principal components 3 and 4. Spawning start: B_bjoerkna – Blicca bjoerkna, C_gibelio – Carassius gibelio, S_erythrophthalmus – Scardinius erythrophthalmus, A_brama – Abramis brama, P_fluviatilis – Perca fluviatilis, R_rutilus – Rutilus rutilus, E_lucius – Esox lucius; regression residuals of the spawning end dependence from the start: B_delta – Blicca bjoerkna, C_delta – Carassius gibelio, S_delta – Scardinius erythrophthalmus, A_delta – Abramis brama, P_delta – Perca fluviatilis, R_delta – Rutilus rutilus, E_delta – Esox lucius.
Figure 12 in Effects of temperature patterns on the spawining phenology and niche overlap of fish assemblages in the water bodies of the Dnipro River basin
Figure 12. Spawning variance partitioning between broad-, medium-, and fine-scale temporal temperature patterns and biotope type explanatory variables. Notes: [a] – variation explained solely by broad temperature variables; [b] – variation explained solely by medium temperature variables; [c] – variation explained solely by fine temperature variables; [d] – variation explained solely by biotope type. The intersection of the ellipses corresponds to the variations explained by the respective sources together All the variance fractions shown are significant (p <0.001).
Figure 14 in Effects of temperature patterns on the spawining phenology and niche overlap of fish assemblages in the water bodies of the Dnipro River basin
Figure 14. Relative variance of the principal components (in %). Method: ANOVA Method, Type I SS, columns denote cumulative sums of variance components.
Figure 13 in Effects of temperature patterns on the spawining phenology and niche overlap of fish assemblages in the water bodies of the Dnipro River basin
Figure 13. The temporal variation of the principal components 1–5. the x-axis – years, the y-axis – the scores of the principal components 1–5.
Figure 10 in Effects of temperature patterns on the spawining phenology and niche overlap of fish assemblages in the water bodies of the Dnipro River basin
Figure 10. Distribution histograms of the Pianka mean niche overlap indexes in different types of habitats: 1 – Nikolayev system of water bodies; 2 – river Protoch system and Obukhov floodplain; 3 – the channel of the river Dnipro; 4 – water bodies of the Taromske ledge.
Figure 4 in Effects of temperature patterns on the spawining phenology and niche overlap of fish assemblages in the water bodies of the Dnipro River basin
Figure 4. Scalogram illustrating the scaling of temporally structured variation in polynomial trend residuals data. The abscissa axis – dbMEMs ordered decreasingly according to the scale of temporal patterns they represent (dbMEM 1 represents the broadest scale, dbMEM 104 the finest scale). The ordinate axis – value of R2 is the variation explained adj by individual dbMEM variables.
Figure 5. Broad-scale components RDA 1-3 in Effects of temperature patterns on the spawining phenology and niche overlap of fish assemblages in the water bodies of the Dnipro River basin
Figure 5. Broad-scale components RDA 1-3 of the annual temperature variation. Black line – the original data, colored lines – smoothed data. The abscissa axis – the number of days from 1 July of the previous year to June 31 of the next year
Data archive: Niche overlap between a cold-water coral and an associated sponge for isotopically-enriched particulate food sources
<p>Data belonging to the paper: </p> <p>Dick van Oevelen, Christina E. Mueller, Tomas Lundälv, Fleur C. van Duyl, Jasper M. de Goeij, Jack J. Middelburg<span> </span>(In press) <strong>Niche overlap between a cold-water coral and an associated sponge for isotopically-enriched particulate food sources</strong>. PLOS ONE</p>
Fig. 1 in Patterns of niche breadth and feeding overlap of the fish fauna in the seasonal Brazilian Pantanal, Cuiabá River basin
Fig. 1. Location of the sampling site in the Cuiabá River (1 and 2) and Chacororé pond (3), in the upper Pantanal region, Mato Grosso State, Brazil.
FIGURE 2 in Trophic niche size and overlap in temperate forest land snails are affected by their lifestyle and body size
FIGURE 2 Variation in SEAc of land snail species from the four studied assemblages in relation to their lifestyle (a) and body size (b). Variation in percentages of overlapping SEAc for pairwise species combinations are compared between study sites (c) and three types of lifestyle (d). Different letters refer to significant differences at p<0.0, tested by GEE (a, b) and GLM-qp (c, d). The central line of each box refers to the median value, box height to the interquartile range, whiskers to the non-outlier range (i.e., 1.5 times the interquartile range at each side), and small circles to outliers.
FIGURE 1 in Trophic niche size and overlap in temperate forest land snails are affected by their lifestyle and body size
FIGURE 1 Isotopic niches represented by Standard ellipse area corrected for small sample size (SEAc) of the land snail species collected in four study sites (A, B, C, D) at least in five individuals per site.
Vibroscape analysis reveals acoustic niche overlap and plastic alteration of vibratory courtship signals in ground-dwelling wolf spiders
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Bumble bee niche overlap along an elevation gradient: How traits can inform novel competitive pressures under climate change
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Niche expansion of capuchin monkeys to forest floor on guild-reduced islands increases interspecific spatio-temporal overlap
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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.