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21 results for “realized niche”
Telemetry data from: Realized thermal niche approach eliminates temperature bias in 3 bioenergetic model estimates
<h4>Raw data for Ivanova et al paper in Ecology and Evolution</h4><p>Datafile is an .rds file.</p>
Data from: Trees have overlapping potential niches that extend beyond their realized niches
<p>Tree species appear to prefer distinct climatic conditions, but the true nature of these preferences is obscured by species interactions and dispersal, which limit species' ranges. We quantified realized and potential thermal niches of 188 North American tree species to conduct the first continental-scale test of the architecture of niches. We found strong and consistent evidence that species occurring at thermal extremes occupy less than three-quarters of their potential niches and species' thermal niches overlap at a mean annual temperature of approximately 12 °C. These results clarify the breadth of thermal tolerances of temperate tree species and support the centrifugal organization of thermal niches. Accounting for the non-realized components of ecological niches will advance theory and prediction in global change ecology.</p>
Dataset for the manuscript: "Three-dimensional species distribution modeling reveals the realized spatial niche for coral recruitment on contemporary Caribbean reefs"
<p>Whether the three-dimensional (3D) structure of habitats influences and partition recruitment niches of corals is unknown. We developed a new method that combined Species Distribution Modeling and Structure from Motion to characterize and map the three-dimensional recruitment niches of two ecosystem engineers on Caribbean coral reefs, scleractinian corals and octocorals. </p> <p>In this repository, we include 48 3D models of small areas of the reef (i.e., within ~ 0.25 m<sup>2</sup> quadrats) reconstructed with Structure-from-Motion, as well as the geospatial data used to characterize and map the realized recruitment niche for scleractinian corals and octocorals on Caribbean coral reefs. We conducted the study at two shallow, fringing reefs off the south shore of St. John, US Virgin Islands, named Grootpan and Europa Bays (18° 18.360’N, 64° 43.140’W, and 18° 19.016’N, 64° 43.798’W, respectively). Within each 0.25 m<sup>2</sup> quadrat, we counted and marked all recruits (octocorals ≤ 5 cm height, and scleractinians ≤ 4 cm wide).</p> <p><em>DATASET DESCRIPTIONS:</em></p> <ul> <li><strong>"Quadname_data.zip":</strong> In each of this folders we included all the data calculated within a quadrat: <ul> <li>ASCII files (.txt).</li> <li>The annotated dense point cloud (.las) for each quadrat.</li> <li>The quadrat 3D model texture (.jpg).</li> <li>The quadrat 3D polygon mesh (.ply).</li> <li>The quadrat 2.5D Digital Elevation Model (i.e., DEM; .tif).</li> <li>Shape files with recruits local coordinates within each quadrat (.dbf, .prj, .shp, .shx).</li> </ul> </li> <li><strong>"datawide.rds": </strong>This is the file needed to run the analyses performed in Martínez-Quintana et al., 2023. This file is obtained after processing all the raw data calculated within each quadrat. All code associated with the workflow used to obtain the datawide.rds file and run the analyses performed in Martínez-Quintana et al., 2023 is available at <a href="https://github.com/AdamWilsonLab/meshSDM">github.com/AdamWilsonLab/meshSDM</a>.</li> </ul> <p><strong>IMPORTANT NOTES: </strong></p> <ul> <li>Quadrat names starting with the letters “eu” indicate the data were collected at Europa Bay, whereas those starting with the letters “ec” indicate that data were collected at Grootpan Bay (commonly named East Cabritte).</li> <li>Each ASCII file (quadname_ASCII_subsampled_X.txt) contains the slope and roughness of the quadrat calculated on the point cloud at 5, 10, 20, and 100 mm scales, and the smooth point cloud used to calculate the topographic exposure index (TEI) described in Martínez-Quintana et al., 2023. Calculations were performed and ASCII files were created with CloudCompare.</li> <li>Each dense point cloud, mesh, texture, and DEM were calculated with Agisoft Metashape.</li> <li>Agisoft Metashape allows the user to classify and annotate groups of points in the dense point cloud. However, the list of classes provided by the software corresponds to the standard list used for terrestrial LiDAR data; these classes cannot be renamed within the software. Thus, for the present study, we coded the automatic semantic classifications available in Metashape as follows: <ul> <li>Ground = Calcareous rock.</li> <li>Building = Igneous rock.</li> <li>High noise = Sand.</li> <li>Low vegetation = Adult Scleractinian corals.</li> <li>Medium vegetation = Adult Octocoral base.</li> <li>High vegetation = Sponge.</li> <li>Water = Octocoral recruit (named also ocr).</li> <li>Road Surface = Scleractinian recruit (named also scr).</li> <li>Unclassified = created points but never classified (excluded from the analyses).</li> <li>Low Point = noise (unreliable points).</li> <li>Transmission tower and Rail = Points outside the quadrat and excluded from the analysis.</li> </ul> </li> </ul>
Data from: Trees have overlapping potential niches that extend beyond their realized niches
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Data from: Ecological stasis in Spinicaudata (Crustacea, Branchiopoda)? Early Cretaceous clam shrimp of the Yixian Formation of north‐east China occupied a broader realized ecological niche than extant members of the group
The palaeoecology of Spinicaudata, the dominant group of benthic invertebrates in many pre-Cenozoic freshwater environments, remains poorly understood. In analogy with extant taxa, it has been oversimplified and often reduced to shallow, temporary environments characterised by few trophic levels, implying ecological stasis from the Devonian to the Recent. We excavated 43 horizons of the Lower Cretaceous Yixian Formation (Anjiagou and Hengdaozi beds) to evaluate whether spinicaudatan ecology can be simplified to such an extent. Sedimentological evidence suggests general perennial conditions during the excavated lake interval. Based on 33,226 specimen counts, we identified three arthropod-dominated macrobenthic associations and two assemblages. Response curves indicate that the spinicaudatan Eosestheria middendorfii was exceptionally tolerant to environmental gradients, followed, in decreasing order, by mayfly larvae, water boatmen and oligochaetes. Also, many spinicaudatan-yielding layers represent death after reproductive senescence rather than mass-mortality events. Spinicaudatan size varies significantly according to faunal association. A forward stepwise regression model suggests that growth responded to population density and diversity: lower densities and higher diversities triggered fast growth, and vice versa. The proposed strong density effect on carapace size has been corroborated by rearing experiments: As for E. middendorfii, natural log regression provided the best fit for the two extant species Eulimnadia texana and Eocyzicus argillaquus. Hence, Eosestheria middendorfii was a tolerant and morphologically variable species adapted to perennial waters and the frequent presence of higher trophic levels. Although there are rare records of extant taxa co-occurring with fish, the described Early Cretaceous environment is commonly not realized by extant Spinicaudata.
Data from: Realized trophic niche driven by apparent competition: an example with marsupials
According to apparent competition theory, the co-occurrence of two species that share the same predators appears to affect each other's population growth and abundance. However, due to habitat loss and over-hunting, top predators are being made rare worldwide. Considering that apparent competitors share similar resources, we would expect the absence of top predators to reflect in changes on prey realized trophic niches. To test our hypothesis, we developed a model to predict the abundance ratio of apparent competitor species based on changes in their realized trophic niches. We tested our model against field data on the Neotropical marsupials Didelphis aurita and Metachirus nudicaudatus. Our results revealed that D. aurita and M. nudicaudatus are two species under apparent competition and their realized trophic niche and diet overlap change according to the presence of top predators. The model was able to predict the actual relative abundances of D. aurita and M. nudicaudatus in the three empirical studies analyzed. Our study presents quantitative support to the apparent competition theory; however, the model's applications to other groups still need to be verified. Additionally, our study shows that the lack of top predators has consequences on the realized trophic niche of their prey, and therefore, we reinforce that conservation plans need to focus on the effects of top predator loss on ecosystems.
Data from: Realized niche and microhabitat selection of the eastern green lizard (Lacerta viridis) at the core and periphery of its distribution range
The available range of habitats and suitable abiotic conditions like temperature and radiation tend to be narrower towards the periphery of the distribution range of species. Peripheral populations of generalist species could then be more specialized and have a smaller and differentiated realized niche (habitat niche in our study) compared to populations at the core. Likewise, patterns of microhabitat selection can differ between periphery and core. In our study we compared niche size and microhabitat selection among core (Bulgaria) and northern peripheral (Germany, Czech Republic) populations of Lacerta viridis and estimated niche differentiation among regions. We collected data on vegetation structure and abiotic parameters at the microhabitat scale in each region. In order to compare niche size among regions and estimate niche differentiation we built multidimensional niche hypervolumes. We applied generalized linear mixed models and model averaging, accounting for spatial autocorrelation when necessary, to analyze microhabitat differences among regions and microhabitat selection in each region. Peripheral populations were more specialized, having a smaller niche than core ones, and their niche differed from that in the core (Sørensen overlap in all comparisons < 0.3). Microhabitats at the periphery had lower radiation and soil compaction and less structured vegetation. Microhabitat selection at the core depended solely on abiotic parameters, while at the periphery it was defined by only vegetation structure (Czech Republic) or a combination of both, vegetation structure and abiotic factors (Germany). Thus, peripheral populations seem to compensate for overall harsher climatic conditions by responding to different parameters of the microhabitat compared to core populations. We suggest specific conservation measures for L. virids in each studied region and point out the general implications of a higher specialization degree of peripheral populations in relation to climate change and habitat fragmentation.
Data from: Fundamental and realized feeding niche breadths of sexual and asexual stick insects
The factors contributing to the maintenance of sex over asexuality in natural populations remain unclear. Ecological divergences between sexual and asexual lineages could help to maintain reproductive polymorphisms, at least transiently, but the consequences of asexuality for the evolution of ecological niches are unknown. Here, we investigated how niche breadths change in transitions from sexual reproduction to asexuality. We used host plant ranges as a proxy to compare the realized feeding niche breadths of five independently derived asexual Timema stick insects' species and their sexual relatives at both the species and population levels. Asexual species had a systematically narrower realized niche than sexual species, though this pattern was not apparent at the population level. To investigate how the narrower realized niches of asexual species arise, we performed feeding experiments to estimate fundamental niche breadths but found no systematic differences between reproductive modes. The narrow realized niches found in asexual species are therefore likely a consequence of biotic interactions such as predation or competition, that constrain realized niche size in asexuals more strongly than in sexuals.
Figure 1 in Distribution of the meadow lizard in Europe and its realized ecological niche model
Figure 1. Distribution map of the meadow lizard (Darevskia praticola) in south-eastern Europe given on an MGRS UTM 10 × 10 km grid scale. A small overview map shows the study region and the two separate parts of the meadow lizard distribution – separate geographic units and evolutionary lineages of the species (modified from Agasyan et al. 2009). Letters on the distribution map refer to the names of larger (100 × 100 km) MGRS squares. Occurrence records were compiled from a large literature survey and our own data (see Supplemental material 1) and classified on the map according to the time frame of the findings.
Figure 2 in Distribution of the meadow lizard in Europe and its realized ecological niche model
Figure 2. Habitat suitability maps for the meadow lizard (Darevskia praticola) in south-eastern Europe given separately for the low resolution (a) and the high resolution ecological niche model (b). Training points used for fitting the ecological niche models are represented with white dots, while the discarded occurrences are shown as '×' signs and placed for the overall visual representation of the model accuracy.
Figure 3 in Distribution of the meadow lizard in Europe and its realized ecological niche model
Figure 3. Examples showing details from the forest cover (Vegetation Continuous Fields layer) and the Maxent's habitat suitability map for the meadow lizard (Darevskia praticola). The maps show two localities: (a) a part of a fragmented forest area in southern Romania where the species occurs, and (b) an area near the Danube River along the border between Serbia and Romania, which is one of the places of greater habitat suitability for this species. The maps also show the difference between the low (upper images) and high (lower images) resolution of both the VCF layer and the habitat suitability.
Data from: Realized niche and microhabitat selection of the eastern green lizard (Lacerta viridis) at the core and periphery of its distribution range
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Data from: Vertical biogeography and realized niche traits of living coccolithophore community in the eastern Indian Ocean
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Data from: Realized trophic niche driven by apparent competition: an example with marsupials
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Data from: Fundamental and realized feeding niche breadths of sexual and asexual stick insects
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Data from: Ecological stasis in Spinicaudata (Crustacea, Branchiopoda)? Early Cretaceous clam shrimp of the Yixian Formation of north‐east China occupied a broader realized ecological niche than extant members of the group
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Supporting data to: Evolution of realized Eltonian niches across Rajidae species
<p><span><span><span><span><span><span><span><span><span><span><span>The notion that closely related species resemble each other in ecological niche space (<i>i.e.</i>, phylogenetic dependence) has been a longstanding, contentious paradigm in evolutionary biology, the incidence of which is important for predicting the ecosystem-level effects of species loss. Despite being examined across a multitude of terrestrial taxa, many aspects of niche conservatism have yet to be explored in marine species, especially for characteristics related to resource use and trophic behavior (Eltonian niche characteristics, ENCs). We combined ENCs derived from stable isotope ratios at assemblage- and species-levels with phylogenetic comparative methods to test the hypotheses that benthic marine fishes: 1) will exhibit similar assemblage-wide ENCs regardless of geographic location, and 2) will display phylogenetically dependent ENCs at the species-level. We used a 12-species sub-set of the monophyletic group <i>Rajidae</i> sampled from three independent assemblages (Central California, Gulf of Alaska, and Northwest Atlantic), which span two ocean basins. Assemblage-level ENCs implied low trophic diversity and high evenness, suggesting that <i>Rajidae </i>assemblages may exhibit a well-defined trophic role, a trend consistent regardless of geographic location. At the species-level we found evidence for phylogenetic dependence of ENCs relating to trophic diversity (<i>i.e.,</i> isotopic niche width [SEAc]). Whether individuals can be considered functional equivalents across assemblages is hard to ascertain because we did not detect a significant phylogenetic signal for ENCs relating to trophic function (<i>e.g.,</i> trophic position). Thus, additional, complimentary approaches are required to further examine the phylogenetic dependence of species functionality. Our approach illustrates the potential of stable isotope derived niche characteristics to provide insight on macroecological processes occurring across evolutionary time, which could help predict how assemblages may respond to the effects of species loss. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Separation of realized ecological niche axes among sympatric tilefishes provides insight into potential drivers of co‐occurrence in the NW Atlantic
<p class="Default">Golden and Blueline Tilefish (<i>Lopholatilus chamaeleonticeps</i> and <i>Caulolatilus microps</i>) are keystone taxa in northwest (NW) Atlantic continental shelf‐edge environments due to their biotic (trophic‐mediated) and abiotic (ecosystem engineering) functional roles combined with high‐value fisheries. Despite this importance, the ecological niche dynamics (i.e., those relating to trophic behavior and food‐web interactions) of these sympatric species are poorly understood, knowledge of which may be consequential for maintaining both ecosystem function and fishery sustainability. We used stable isotope ratios of carbon (δ<sup>13</sup>C) and nitrogen (δ<sup>15</sup>N) to build realized ecological niche hypervolumes to serve as proxies for diet and production use patterns of <i>L</i>. <i>chamaeleonticeps</i> and <i>C. microps</i>. We hypothesized that: (a) species exhibit ontogenetic shifts in diet and use of production sources; (b) species acquire energy from spatially distinct resource pools that reflect a sedentary life‐history and differential use of the continental shelf‐edge; and (c) species exhibit differentiation in one or more measured niche axes. We found evidence for ontogenetic shifts in diet (δ<sup>15</sup>N) but not production source (δ<sup>13</sup>C) in both species, suggesting a subtle expansion of measured ecological niche axes. Spatial interpolation of stable isotope ratios showed distinct latitudinal gradients; for example, individuals were <sup>13</sup>C enriched in northern and <sup>15</sup>N enriched in southern regions, supporting the assertion that tilefish species acquire energy from regional resource pools. High isotopic overlap was observed among species (≥82%); however, when hypervolumes included depth and region of capture, overlap among species substantially decreased to overlap estimates of 15%–77%. This suggests that spatial segregation could alleviate potential competition for resources among tilefish species inhabiting continental shelf‐edge environments. Importantly, our results question the consensus interpretation of isotopic overlap estimates as representative of direct competition among species for shared resources or habitats, instead of identifying habitat segregation as a possible mechanism for the coexistence of tilefish species in the NW Atlantic.</p>
Supporting data to: Evolution of realized Eltonian niches across Rajidae species
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Data from: Separation of realized ecological niche axes among sympatric tilefishes provides insight into potential drivers of co‐occurrence in the NW Atlantic
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