Find research datasets worth reusing

opencc-zeroJul 2020View details →

Data from: Specialization and niche overlap across spatial scales: revealing ecological factors shaping species richness and coexistence in Australian songbirds

1. Ecological specialization enables the partitioning of resources and thus can facilitate the coexistence of species and promote higher species richness. Specialization and niche partitioning are expected to exert a decisive influence on local spatial scales, while species richness at regional scales should be shaped mostly by historical factors and abiotic conditions. Moreover, specialization is expected to be particularly important in communities that are exceptionally species rich for their environmental conditions. Concurrently, niche overlap in these communities should be minimized to enable species coexistence. 2. We tested these hypotheses by studying specialization-richness relationship and niche overlap in assemblages of 298 species of songbirds (Passeriformes) across Australia. We used local (2-6 ha) to regional (bioregions) spatial scales, and detailed data on habitat, diet, and foraging behaviour (method, substrate, and stratum). 3. We expected the richness-specialization relationship to be particularly strong i) on local spatial scales and ii) in communities exceptionally species rich for given environmental conditions (approximated by moisture and vegetation complexity). We also expected iii) low niche overlap in assemblages with specialized species. 4. Only the third prediction was partly supported. First, while the specialization and species richness were often positively related, the strength and the direction of the relationship changed between traits and across spatial scales. The strength of the specialization-richness relationship was consistently positive only in foraging stratum, and it increased towards smaller spatial scales only in case of habitat and diet. Simultaneously, species in local communities demonstrated high overlap in habitat and diet. Second, we did not find particularly strong specialization-richness relationships in exceptionally species rich communities. Third, we found the expected negative relationship between specialization and overlap in foraging stratum and substrate (in local communities), suggesting that species partition ecological space locally in terms of where they find food. 5. Our expectations were only weakly supported. Specialization on foraging stratum was probably important in facilitating species co-existence. Conversely, although species were often specialized on habitat and diet, high overlap in these traits did not preclude their local coexistence. Overall, specialization and overlap in foraging traits were more important for species coexistence than habitat or diet.

opencc-zeroOct 2019View details →

Data from: Expanded consumer niche widths may signal an early response to spatial protection

Marine management interventions are increasingly being implemented with the explicit goal of rebuilding ocean ecosystems, but early responses may begin with alterations in ecological interactions preceding detectable changes in population-level characteristics. To establish a baseline from which to monitor the effects of spatial protection on reef fish trophic ecology and track future ecosystem-level changes, we quantified temperate reef fish densities, size, biomass, diets and isotopic signatures at nine sites nested within two fished and one five-year old marine protected area (MPA) on the northwest coast of Canada. We calculated rockfish (Sebastes spp.) community and species-specific niche breadth for fished and protected areas based on δ13C and δ15N values. We found that rockfish community niche width was greater inside the MPA relative to adjacent fished reefs due to an expanded nitrogen range, possibly reflecting early changes in trophic interactions following five years of spatial protection. Our data also demonstrated that the MPA had a positive effect on the δ15N signature of rockfish (i.e., trophic position), but the effect of rockfish length on its own was not well-supported. In addition, we found a positive interaction between rockfish length and δ15N signature, such that δ15N signatures of rockfish caught within the MPA increased more rapidly with body size than those caught in fished areas. Differences in rockfish size structure and biomass among fished and unfished areas were not clearly evident. Species of rockfish and lingcod varied in trophic and size responses, indicating that life-history traits play an important role in predicting MPA effects. These results may suggest early changes in trophic behavior of slow-growing rockfish due to predation risk by faster growing higher trophic level predators such as lingcod inside MPAs established on temperate reefs. Consequently, spatial protection may restore both the trophic and behavioral roles of previously fished consumers earlier and in measurable ways sooner than observable changes in abundance and size.

opencc-zeroDec 2017View details →

Data from: The effect of range overlap on ecological niche divergence depends on spatial scale in monkeyflowers

Patterns of niche divergence and geographical range overlap of closely related species provide insights into the evolutionary dynamics of ecological niches. When ranges overlap, shared selective pressures may preserve niche similarity along coarse‐scale macrohabitat axes (e.g., bioclimates). Alternatively, competitive interactions may drive greater divergence along local‐scale microhabitat axes (e.g., micro‐topographical features). We tested these hypotheses in 16 species pairs of western North American monkeyflowers (Erythranthe and Diplacus, formerly Mimulus) with species' niches, geographic ranges and a robust phylogeny. We found that macrohabitat niche divergence decreased with increasing range overlap, consistent with convergent selection operating at a coarse scale. No significant relationship was detected for microhabitat niches. Additionally, niche divergence was greater for young pairs along all macrohabitat niche axes, but greater for old pairs along one microhabitat axis related to vegetation cover. For a subset of species pairs with partially overlapping ranges, greater microhabitat divergence was detected in sympatry than in allopatry for at least one niche axis for three pairs, consistent with character displacement in sympatry. Thus, coarse‐ and local‐scale niche divergence show dissimilar patterns in relation to range overlap and evolutionary time, perhaps because the relative importance of convergent versus divergent selection depends on spatial scale.

opencc-zeroDec 2014View details →

Data from: Spatial and ecological population genetic structures within two island-endemic Aeonium species of different niche width

The Crassulacean genus Aeonium is a well-known example for plant species radiation on oceanic archipelagos. However, while allopatric speciation among islands is documented for this genus, the role of intra-island speciation due to population divergence by topographical isolation or ecological heterogeneity has not yet been addressed. The aim of this study was to investigate intraspecific genetic structures and to identify spatial and ecological drivers of genetic population differentiation on the island scale. We analyzed inter simple sequence repeat variation within two island-endemic Aeonium species of La Palma: one widespread generalist that covers a large variety of different habitat types (Ae. davidbramwellii) and one narrow ecological specialist (Ae. nobile), in order to assess evolutionary potentials on this island. Gene pool differentiation and genetic diversity patterns were associated with major landscape structures in both species, with phylogeographic implications. However, overall levels of genetic differentiation were low. For the generalist species, outlier loci detection and loci–environment correlation approaches indicated moderate signatures of divergent selection pressures linked to temperature and precipitation variables, while the specialist species missed such patterns. Our data point to incipient differentiation among populations, emphasizing that ecological heterogeneity and topographical structuring within the small scales of an island can foster evolutionary processes. Very likely, such processes have contributed to the radiation of Aeonium on the Canary Islands. There is also support for different evolutionary mechanisms between generalist and specialist species.

opencc-by-4.0May 2024View details →

Characterizing Spatially Continuous Variations in Tissue Microenvironment through Niche Trajectory Analysis - Dataset

Recent technological developments have made it possible to map the spatial organization of a tissue at the single-cell resolution. However, computational methods for analyzing spatially continuous variations in tissue microenvironment are still lacking. Here we present ONTraC as a strategy that constructs niche trajectories using a graph neural network-based modeling framework. Our benchmark analysis shows that ONTraC performs more favorably than existing methods for reconstructing spatial trajectories. Applications of ONTraC to public spatial transcriptomics datasets successfully recapitulated the underlying anatomical structure, and further enabled detection of tissue microenvironment-dependent changes in gene regulatory networks and cell-cell interaction activities during embryonic development. Taken together, ONTraC provides a useful and generally applicable tool for the systematic characterization of the structural and functional organization of tissue microenvironments.

opencc-by-4.0Apr 2024View details →

Learning tasks and result data for the 2024 GECCO short paper Length-niching Selection and Spatial Crossover in Variable-length Evolutionary Rule Set Learning

Learning tasks and result data for the 2024 GECCO short paper Length-niching Selection and Spatial Crossover in Variable-length Evolutionary Rule Set Learning by David Pätzel, Richard Nordsieck and Jörg Hähner.

Figure 3 in Diverging structures, perch heights, temperatures, and levels of sunlight of spatial niche dimensions ease the syntopic life of Tropidurus hispidus and Tropidurus semitaeniatus (Squamata: Tropiduridae)

Figure 3. Correlations of distance from the nearest potential shelter (cm) with (a) snout-vent length (mm) and (b) body mass (g) of Tropidurus semitaeniatus. The straight and the curved lines represent, respectively, linear and quadratic models.

Figure 1 in Diverging structures, perch heights, temperatures, and levels of sunlight of spatial niche dimensions ease the syntopic life of Tropidurus hispidus and Tropidurus semitaeniatus (Squamata: Tropiduridae)

Figure 1. Ordination by non-metric multidimensional scaling comparing proportions of leaf litter, sand, vegetation, and rock between (a) Tropidurus semitaeniatus (×) and environmental availability (∆) (stress = 0.1534), and (b) Tropidurus hispidus (○) and environmental availability (∆) (stress = 0.0877). Proximity and distance between points indicates, respectively, similarity or dissimilarity.

Figure 4 in Diverging structures, perch heights, temperatures, and levels of sunlight of spatial niche dimensions ease the syntopic life of Tropidurus hispidus and Tropidurus semitaeniatus (Squamata: Tropiduridae)

Figure 4. Differences in distances from nearest potential shelters (cm, log) among types of shelter for Tropidurus semitaeniatus. The mean distance was longer from vegetation than from rock shelters. Upwards, the horizontal lines of the boxplots represent the minimum range, first quartile, median, third quartile, and maximum range. The unit of the original measurement scale is presented for the logarithmic values of the vertical axis.

Figure 2 in Diverging structures, perch heights, temperatures, and levels of sunlight of spatial niche dimensions ease the syntopic life of Tropidurus hispidus and Tropidurus semitaeniatus (Squamata: Tropiduridae)

Figure 2. Ordination by non-metric multidimensional scaling comparing proportions of shade, filtered sunlight, and full sunlight, air temperatures and substrate temperatures between (a) Tropidurus hispidus (○) and T. semitaeniatus (×) (stress = 0.1785), (b) T. hispidus (○) and environmental availability (∆) (stress = 0.1004), and (C) T. semitaeniatus (×) and that available in the environment (∆) (stress = 0.2534). Proximity and distance between points indicates, respectively, similarity or dissimilarity.

Figure 5 in Diverging structures, perch heights, temperatures, and levels of sunlight of spatial niche dimensions ease the syntopic life of Tropidurus hispidus and Tropidurus semitaeniatus (Squamata: Tropiduridae)

Figure 5. Frequency distribution (horizontal axis; in %) of perch heights (vertical axes; in cm) used by Tropidurus hispidus and Tropidurus semitaeniatus.

opencc-by-4.0May 2024View details →

Learning tasks and result data for the 2024 IWERL@GECCO paper A Closer Look at Length-niching Selection and Spatial Crossover in Variable-length Evolutionary Rule Set Learning

Learning tasks and result data for the paper Length-niching Selection and Spatial Crossover in Variable-length Evolutionary Rule Set Learning by David Pätzel, Richard Nordsieck and Jörg Hähner, presented at the International Workshop on Evolutionary Rule-based Machine Learning taking place as part of GECCO 2024.

opencc-by-4.0Jul 2024View details →

Single Cell Spatial Transcriptomics Reveals Immunotherapy-Driven Bone Marrow Niche Remodeling in AML

Images utilized in the paper Single Cell Spatial Transcriptomics Reveals Immunotherapy-Driven Bone Marrow Niche Remodeling in AML - by  Gui, Bingham et al.

opencc-zeroDec 2017View details →

Data from: Functional traits and environmental conditions predict community isotopic niches and energy pathways across spatial scales

1. Despite ongoing research in food web ecology and functional biogeography, the links between food-web structure, functional traits and environmental conditions across spatial scales remain poorly understood. Trophic niches, defined as the amount of energy and elemental space occupied by species and food webs, may help bridge this divide. 2. Here, we ask how the functional traits of species, the environmental conditions of habitats and the spatial scale of analysis jointly determine the characteristics of trophic niches. We used isotopic niches as a proxy of trophic niches, and conducted analyses at spatial scales ranging from local food webs and metacommunities to geographically distant sites. 3. We sampled aquatic macroinvertebrates from 104 tank bromeliads distributed across five sites from Central to South America, and compiled the macroinvertebrates' functional traits and stable isotope values (δ15N and δ13C). We assessed how isotopic niches within each bromeliad were influenced by the functional trait composition of their associated invertebrates and environmental conditions (i.e., habitat size, canopy cover, and detrital concentration). We then evaluated whether the diet of dominant predators and, consequently, energy pathways within food webs, reflected functional and environmental changes among bromeliads across sites. Finally, we determined the extent to which the isotopic niches of macroinvertebrates within each bromeliad contributed to the metacommunity isotopic niches within each site, and compared these metacommunity-level niches over biogeographic scales. 4. At the bromeliad level, isotopic niches increased with the functional richness of species in the food web and the detrital concentration in the bromeliad. The diet of top predators tracked shifts in prey biomass along gradients of canopy cover and detrital concentration. Bromeliads that grew under heterogeneous canopy cover displayed less trophic redundancy and therefore combined to form larger metacommunity isotopic niches. Finally, the size of metacommunity niches depended on within-site heterogeneity in canopy cover. 5. Our results suggest that the trophic niches occupied by food webs can predictably scale from local food webs to metacommunities to biogeographic regions. This scaling process is determined by both the functional traits of species and heterogeneity in environmental conditions.

opencc-zeroDec 2017View details →

Data from: The effects of spatial scale and isoscape on consumer isotopic niche width

1. The mean and variance of ecological variables are dependent on sampling attributes such as the coverage of environmental heterogeneity (sampling extent) and spatial scale. Trophic niche width is often approximated by bulk tissue stable isotopes of C and N, i.e. the population isotopic niche. However, recent studies suggest that environmental heterogeneity (experienced by individuals) may be more important in defining the isotopic niche width than trophic variability. We hypothesised that isotopic niche width will increase monotonically with spatial scale, largely produced by environmental variation, e.g. nutrient source. 2. To refine this hypothesis, by describing the shapes of isotope scaling curves, we explored a previously published dataset describing three Chilean intertidal species representing different feeding guilds (grazing snails, suspension feeding mussel). We tested these hypotheses on a new, larger dataset describing three functionally-analogous intertidal species from Northern Ireland. We generated isotopic variance-area curves from a spatially-explicit bootstrap and investigated the scale-dependency of environment-isotope relationships, including wave exposure and sub-habitat heterogeneity. 3. Spatial scale explained 50% of the variance in population isotopic niche widths (bivariate C-N ellipse area) by simple, non-linear relationships. Finer scales (< 1 to 10 km lag) accounted for most variance. Scale dependence was strong for ẟ15N variance, of which > 40% was explained by modelling linear coefficients. A ẟ15N baseline gradient, or isoscape, dominated ẟ15N variance scaling patterns, from sheltered, terrestrially-influenced embayments to exposed, pelagic-dominated coastline. Consumer ẟ13C variance had a weaker scale-dependence, plateauing at mesoscales (> 20 km lag). 4. We show that isotopic niche width is strongly dependent on sampling spatial extent, which controls the environmental heterogeneity experienced by individual consumers. Environmental heterogeneity must be accounted for before isotopic niche width can be considered to accurately represent trophic niche width. Studies conducted at different spatial scales are likely to identify different environment-isotope relationships. 5. We recommend that spatial scale should be incorporated into sampling designs explicitly, easiest by maintaining a consistent lag distance or area within which populations are sampled. Identified isoscapes can be de-trended, where necessary.

opennotspecifiedAug 2013View details →

Figure 1 in Spatial niche variation in two sympatric species of Bokermannohyla (Anura: Hylidae) in southeastern Brazil

Figure 1. Map showing the location of the RPPN Santuário do Caraça and the three streams where we sampled microhabitat use by Bokermannohyla nanuzae and Bokermannohyla martinsi.

opencc-zeroAug 2023View details →

The relationships of plant species occupancy to niches and traits vary with spatial scale

Aim: Support for different underlying mechanisms of species occupancy is inconsistent, yet this could be related to spatial scale. Since abiotic filtering typically acts at broader scales than biotic interactions, we hypothesise that occupancy could be more driven by species' abiotic niche (i.e., tolerance and preference of abiotic conditions) at broad scales, whereas species' traits affecting competitive ability could be more important at fine scales. Here we test these hypotheses by assessing relationships of occupancy to niche and trait metrics across spatial scales. Location: Four study areas located north of Arctic Circle. Taxon: Vascular plants. Methods: We derived occupancy for 106 species at four spatial scales (Micro-scale with plot size of 0.04 m 2 and extent of 2 km, Local-scale with plot size of 4 m 2 and extent of 40 km, Regional-scale with plot size of 4 ha and extent of 800 km, and Polar-scale with plot size of 4 km 2 and extent of 5200 km). We then assessed using generalized additive models whether the relationships between occupancy and species' niche breadth, niche marginality, intraspecific trait variability (ITV) and trait distinctiveness vary across the scales. Results: At the finer scales, ITV (especially of specific leaf area) had the highest contribution with positive relationship in explaining occupancy. At the broader scales, occupancy was better explained by niche metrics. Especially at the broadest scale, the occupancy had a positive relationship with species' climatic tolerance. Main conclusions: Abiotic filtering, especially related to macro-climate, drives species occupancy at broader spatial scales while biotic interactions are relatively more important at local scales. This scale-dependency of factors behind species occupancy should be accounted for when, for example, planning conservation of rare species, forecasting invasions, or anticipating the effects of changing climate on biota at local versus global scales.