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opencc-zeroNov 2019View details →

Assessing the Ecological Impacts of Biomass Harvesting along a Disturbance Severity Gradient

Disturbance is a central driver of forest development and ecosystem processes with variable effects within and across ecosystems. Despite the high levels of variation in disturbance severity often observed in forests following natural and anthropogenic disturbance, studies quantifying disturbance impacts often rely on categorical classifications, thus limiting opportunities to examine potential gradients in ecosystem response to a given disturbance or management regime. Given the potential increases in disturbance severity associated with global change, as well as shifts in management regimes related to procurement of biofuel feedstocks, there is an increasing need to quantitatively describe disturbance severity and associated responses of forest development, soil processes, and structural conditions. This study took advantage of two replicated large-scale studies of forest biomass harvesting in Populus tremuloides and Pinus bansksiana forests, respectively, to develop and test the utility of a continuous, quantitative disturbance severity index (DSI) for describing post-harvest response of plant communities and nutrient pools to different levels of biomass removal and legacy retention (i.e., live trees and coarse woody material). There was a high-degree of variability in DSI within categorical treatments associated with different levels of legacy retention and regression models using DSI as a predictor explained a portion of the variation (>50%) for many of the ecosystem- and community-level responses to biomass harvesting examined. Nutrient losses associated with biomass harvesting were positively related to disturbance severity, particularly in P. tremuloides forests, with post-harvest nutrient availability generally declining along the gradient of impacts. Consistent with expectations from ecological theory, species richness and diversity of woody plant communities were greatest at intermediate disturbance severities and regeneration densities of dominant trees species were most abundant at highest levels of disturbance. Although categorical benchmarks will continue to be the primary way through which management guidelines are conveyed to practitioners, evaluation of their effectiveness at sustaining ecosystem functioning should be through continuous analyses, such as the DSI approach used in this study, to allow for the more precise identification of thresholds that ensure a range of desirable outcomes exist across managed landscapes.

opencc-zeroDec 2016View details →

Data from: Quantifying the effects of ecological constraints on trait expression using novel trait-gradient analysis parameters

1. Complex processes related to biotic and abiotic forces can impose limitations to assembly and composition of plant communities. Quantifying the effects of these constraints on plant functional traits across environmental gradients, and among communities, remains challenging. We define ecological constraint (Ci) as the combined, limiting effect of biotic interactions and environmental filtering on trait expression (i.e., the mean value and range of functional traits). 2. Here we propose a set of novel parameters to quantify this constraint by extending the trait-gradient analysis (TGA) methodology. The key parameter is ecological constraint, which is dimensionless and can be measured at various scales, e.g., on population and community levels. It facilitates comparing the effects of ecological constraints on trait expressions across environmental gradients, as well as within and among communities. 3. We illustrate the implementation of the proposed parameters using the bark thickness of 14 woody species along an aridity gradient on granite outcrops in southwestern Australia. We found a positive correlation between increasing environmental stress and strength of ecological constraint on bark thickness expression. Also, plants from more stressful habitats (shrublands on shallow soils and in sun-exposed locations) displayed higher ecological constraint for bark thickness than plants in more benign habitats (woodlands on deep soils and in sheltered locations). 4. The relative ease of calculation and dimensionless nature of Ci allow it to be readily implemented at various scales and make it widely applicable. It therefore has the potential to advance the mechanistic understanding of the ecological processes shaping trait expression. Some future applications of the new parameters could be investigating the patterns of ecological constraints i) among communities from different regions, ii) on different traits across similar environmental gradients, and iii) for the same trait across different gradient-types.

opencc-zeroDec 2010View details →

Data from: Testing alternative hypotheses for evolutionary diversification in an African songbird: rainforest refugia versus ecological gradients

Geographic isolation in rainforest refugia and local adaptation to ecological gradients may both be important drivers of evolutionary diversification. However, their relative importance and the underlying mechanisms of these processes remain poorly understood because few empirical studies address both putative processes in a single system. A key question is to what extent is divergence in signals that are important in mate and species recognition driven by isolation in rainforest refugia or by divergent selection across ecological gradients? We studied the little greenbul, Andropadus virens, an African songbird, in Cameroon and Uganda, to determine whether refugial isolation or ecological gradients better explain existing song variation. We then tested whether song variation attributable to refugial or ecological divergence was biologically meaningful using reciprocal playback experiments to territorial males. We found that much of the existing song variation can be explained by both geographic isolation and ecological gradients, but that divergence across the gradient, and not geographic isolation, affects male response levels. These data suggest that ecologically divergent traits, independent of historical isolation during glacial cycles, can promote reproductive isolation. Our study provides further support for the importance of ecology in explaining patterns of evolutionary diversification in ecologically diverse regions of the planet.

opencc-zeroDec 2015View details →

Data from: Extremophile Poeciliidae: multivariate insights into the complexity of speciation along replicated ecological gradients

Background: Replicate population pairs that diverge in response to similar selective regimes allow for an investigation of (a) whether phenotypic traits diverge in a similar and predictable fashion, (b) whether there is gradual variation in phenotypic divergence reflecting variation in the strength of natural selection among populations, (c) whether the extent of this divergence is correlated between multiple character suites (i.e., concerted evolution), and (d) whether gradual variation in phenotypic divergence predicts the degree of reproductive isolation, pointing towards a role for adaptation as a driver of (ecological) speciation. Here, we use poeciliid fishes of the genera Gambusia and Poecilia that have repeatedly evolved extremophile lineages able to tolerate high and sustained levels of toxic hydrogen sulfide (H2S) to answer these questions. Results: We investigated evolutionary divergence in response to H2S in Gambusia spp. (and to a lesser extent Poecilia spp.) using a multivariate approach considering the interplay of life history, body shape, and population genetics (nuclear miscrosatellites to infer population genetic differentiation as a proxy for reproductive isolation). We uncovered both shared and unique patterns of evolution: most extremophile Gambusia predictably evolved larger heads and offspring size, matching a priori predictions for adaptation to sulfidic waters, while variation in adult life histories was idiosyncratic. When investigating patterns for both genera (Gambusia and Poecilia), we found that divergence in offspring-related life histories and body shape were positively correlated across populations, but evidence for individual-level associations between the two character suites was limited, suggesting that genetic linkage, developmental interdependencies, or pleiotropic effects do not explain patterns of concerted evolution. We further found that phenotypic divergence was positively correlated with both environmental H2S-concentration and neutral genetic differentiation (a proxy for gene flow). Conclusions: Our results suggest that higher toxicity exerts stronger selection, and that divergent selection appears to constrain gene flow, supporting a scenario of ecological speciation. Nonetheless, progress toward ecological speciation was variable, partially reflecting variation in the strength of divergent selection, highlighting the complexity of selective regimes even in natural systems that are seemingly governed by a single, strong selective agent.

opencc-zeroOct 2019View details →

Ecological limits as the driver of bird species richness patterns along the east Himalayan elevational gradient

Variation in species richness across environmental gradients results from a combination of historical non-equilibrium processes (time, speciation, extinction) and present-day differences in environmental carrying capacities (i.e., ecological limits, affected by species interactions and the abundance and diversity of resources). In a study of bird richness along the sub-tropical east Himalayan elevational gradient, we test the prediction that species richness patterns are consistent with ecological limits using data on morphology, phylogeny, elevational distribution, and arthropod resources. Species richness peaks at mid-elevations. Occupied morphological volume is roughly constant from low to mid-elevations, implying more species are packed into the same space at mid-elevations compared with low elevations. However, variance in beak length, and differences in beak length between close relatives decline with elevation, a consequence of the addition of many small insectivores at mid-elevations. These patterns are predicted from resource distributions: arthropod size diversity declines from low to mid elevations, largely because many more small insects are present at mid-elevations. Weak correlations of species mean morphological traits with elevation also match predictions based on resources and habitats. Elevational transects in the tropical Andes, New Guinea and Tanzania similarly show declines in mean arthropod size and mean beak length, and in these cases likely contribute to declining numbers of insectivorous bird species richness along these gradients. The results imply conditions for ecological limits are met, although historical non-equilibrium processes are likely to also contribute to the pattern of species richness.

opencc-zeroMay 2019View details →

Data from: Ecological gradients drive insect wing loss and speciation: the role of the alpine treeline

Alpine ecosystems are frequently characterised by an abundance of wing-reduced insect species, but the drivers of this biodiversity remain poorly understood. Insect wing reduction in these environments has variously been attributed to altitude, temperature, isolation, habitat stability, or decreased habitat size. We used fine-scale ecotypic and genomic analyses, along with broad-scale distributional analyses of ecotypes, to unravel the ecological drivers of wing reduction in the wing-dimorphic stonefly Zelandoperla fenestrata complex. Altitudinal transects within populations revealed dramatic wing reduction over very fine spatial scales, tightly linked to the alpine treeline. Broad biogeographic analyses confirm that the treeline has a much stronger effect on these ecotype distributions than altitude per se. Molecular analyses revealed parallel genomic divergence between vestigial-winged (high altitude) and full-winged (low altitude) ecotypes across distinct streams. These data thus highlight the role of the alpine treeline as a key driver of rapid speciation, providing a new model for ecological diversification along exposure gradients

opencc-zeroDec 2015View details →

Data from: Genetic signatures of ecological diversity along an urbanization gradient

Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.

Figure 8 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Figure 8. Vegetation predictors of the pimpline community across traps (n = 30). (a) Epiphyte density against log richness; (b) herb ground cover against the log of inverse Simpson's Index of Diversity;

Figure 7 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Figure 7. Pimplinae community composition, as measured by the first axis of a Non-Metric Multidimensional Scaling analysis (NMDS1, see Figure 6) across sampling sites (n = 15), against the first Principal Component (PC1) of the habitat variables at those sites (see Table 4). The line is the linear regression (±95% CI in gray). The figure demonstrates that pimpline community composition is very strongly associated with differences in habitat characteristics across sites.

Figure 6 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Figure 6. An ordination using Non-metric Multidimensional Scaling (NMDS) of the pimpline community at the site level. Black numbers and points indicate the 15 sampling sites, going from the bottom of the mountain (1) to the top (15). Species are in gray, small lettering.

Figure 4 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Figure 4. Pimplinae wasp community metrics against elevation (altitude) across 30 traps. (a) Abundance; (b) Log10 Species Richness; (c) Log10 Simpson's Index (1/D); and (d) Shannon Index. Lines are the equations of the polynomial linear model in Table 2 with the lowest AICc, ±95%CI; (a,b): cubic models (c,d): quadratic models.

Figure 2 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Figure 2. Some of the Pimplinae wasp species sampled (all are females). (a) Dolichomitus megalourus (scale bar 4 mm), 10 individuals sampled; (b) Neotheronia charli (scale bar 1 mm), 24 individuals sampled; (c) Neotheronia sp. 6 (scale bar 1 mm), 26 individuals sampled; (d) Pimpla caerulea (scale bar 1 mm), 447 individuals sampled; (e) Polysphincta organensis (scale bar 2 mm), 19 individuals sampled; and (f) Polysphincta teresa (scale bar 2 mm), 8 individuals sampled.

Figure 3 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Figure 3. Species richness of pimplines against sampling intensity. (a) Estimates of total species richness against number of traps sampled (filled circles: observed data; open circles: bootstrap; diamonds: first-order jackknife; triangles: Chao; squares: second-order jackknife); (b) site-level rarefaction (±SD); (c) trap-level rarefaction (±SD); (d) mean individual-level rarefaction for the whole data (top line) and altitudinally-zoned subsets (from top to bottom, 332–549 m, 703–887 m, 952–1071 m, 110–150 m, and 1236–1482 m, which are superimposed, 1649–1812 m and 1935–2169 m), points are literature-based data covering the same span of sampling intensities for comparison from [45]. Note the log scale on the y-axis.

Figure 1 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Figure 1. (a) Location of the Serra dos Órgãos National Park (gray shaded area), a protected tropical Atlantic Rain Forest in the State of Rio de Janeiro, southeast Brazil. (b) Map of the 15 study sites and their respective altitudes along the elevational gradient in the Park, where four different phytophysiognomies are observed: (c) lower montane forest (up to 500 m), which presents a 20 m high canopy but normally no other well-defined forest layers; (d) montane forest (500 m to 1500 m), with its clear stratification into arboreal, shrub, and herb layers, and large emergent trees reaching 40 m covered with abundant lianas and epiphytes; (e) high montane forest (1500 m to 2000 m) with smaller trees of up to 10 m covered with mosses and epiphytes, and great diversity of shrubs; and (f) high-altitude grassland, also known as campos de altitude (above 2000 m), dominated by herbal vegetation growing around rocks and scattered shrubs.

Figure 5. Pimplinae wasp community metrics against mean monthly temperature across 15 in Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Figure 5. Pimplinae wasp community metrics against mean monthly temperature across 15 sites. (a) Abundance; (b) Log10 Species Richness; (c) Log10 Simpson's Index (1/D); and (d) Shannon Index. Lines are the equations of the model in Table 3 ± 95%CI. (a) cubic model; (b,d) quadratic models; and (c): linear model.

opencc-zeroDec 2021View details →

Data from: Ecological drivers of avian community assembly along a tropical elevation gradient

Community assembly theory hypothesizes that two main niche-based processes act to shape composition and organization of biological assemblages: abiotic filtering and biological interactions. Here, we conducted repeated surveys of bird abundance along an undisturbed elevational gradient in the tropical Andes to investigate (1) signals of deterministic processes driving community assembly and (2) potential mechanisms by which these forces operate (temperature, habitat complexity, fruit and insect availability), while correcting for imperfect detection and modeling species abundances with N-mixture models. We observed strong signals of abiotic filtering driving functionally and phylogenetically clustered assemblages towards higher elevations, and a weaker signal of limiting similarity resulting in few overdispersed assemblages at lower elevations. Whereas the decay in species richness with increasing elevation was explained by temperature, trait and phylogenetic dispersion were explained by both temperature and vegetation structure, implying that an interplay of abiotic and biotic mechanisms determines abundance-based community structure in our montane assemblages. Interestingly, trait and phylogenetic dispersion consistently decreased until ~3000 m but increased above this elevation, highlighting a potential role of competition in resource-scarce habitats. Combined, our findings suggest abiotic filters are still the main process shaping montane biotas across elevations, whereas resource availability might act locally upon assemblages further modifying them. Our study challenges recent studies in tropical mountains that suggest that biotic filters are a stronger force than abiotic filters in shaping tropical montane assemblages, and exemplifies how accounting for imperfect detection might overcome potential biases in detecting environmental filtering signals in community assembly studies.

opencc-by-4.0May 2022View details →

Data for the journal article: 'Ecology of testate amoebae along an environmental gradient from bogs to calcareous fens in East-Central Europe: development of transfer functions for palaeoenvironmental reconstructions'

DATA DESCRIPTION: This repository provides training sets and R scripts for the development of three transfer function models that allow reconstructions of Holocene hydrochemical or hydrological (hydroclimatic) conditions from testate amoeba assemblages preserved in mires of East-Central Europe. Specifically, the repository contains (i) the full dataset and an R script for the development of the final MLRC model for inferring past water-mineral richness (expressed as pH) in various types of mires; (ii) the minerotrophic subset and an R script for the development of the final WAPLS com1 model for the reconstructions of past water-mineral richness (expressed as pH) in calcareous and rich fens; and (iii) the ombrotrophic subset and an R script for the development of the final PLS com2 model for inferring past depth to water table (DWT) in bogs and poor fens. Additionally, the repository includes the original versions of the full, minerotrophic and ombrotrophic training sets (i.e., the versions before removing outlier samples and rare taxa due to transfer function optimisation), and the compiled dataset, from which the three above-mentioned training sets were generated. For details, see <a href="https://doi.org/10.1016/j.palaeo.2022.111145">&Scaron;ímová et al. (2022)</a>. ARTICLE ABSTRACT: Testate amoebae play an important role in biomonitoring and the understanding of peatland (palaeo)ecology. However, their application has been mainly limited to Sphagnum-dominated peatlands, especially ombrotrophic bogs. To facilitate wider use of these microorganisms, we explored their ecology along a gradient from mineral-poor acidic bogs to mineral-rich calcareous fens with tufa formation using a new calibration dataset of over 250 samples from East-Central Europe. Specifically, we examined environmental controls on testate amoebae along the complete gradient and separately in the minerotrophic (pH >5.5) and ombrotrophic (pH <5) parts. Based on these findings, we developed and statistically evaluated transfer function models for the dominant factors controlling the community composition of these protists. Multivariate statistical analysis showed that groundwater pH was the main driver of species composition in the full and minerotrophic datasets. In contrast, testate amoeba communities in the ombrotrophic dataset were primarily structured by depth to water table (DWT). Under leave-one-out cross-validation (LOO), the best-performing model for DWT gave a prediction error (RMSEP) of 5.43 cm. The most robust models for groundwater mineral richness yielded RMSEPLOO of 0.45 and 0.27 pH units, for the full and the minerotrophic dataset respectively. This is the first study to present a complete set of testate amoeba-based transfer functions that allow reconstructions of Holocene hydrochemical and hydrological (hydroclimatic) variability in different mire types within one region. The new models open up the possibility for testate amoebae to become a valuable tool in palaeoecological research, although further work is needed to fully assess their performance and usefulness in practice.

opencc-zeroDec 2018View details →

Data from: Multiple facets of stream macroinvertebrate alpha diversity are driven by different ecological factors across an extensive altitudinal gradient

Environmental filtering and spatial structuring are important ecological processes for the generation and maintenance of biodiversity. However, the relative importance of these ecological drivers for multiple facets of diversity is still poorly understood in highland streams. Here, we examined the responses of three facets of stream macroinvertebrate alpha diversity to local environmental, landscape-climate and spatial factors in a near-pristine highland riverine ecosystem. Taxonomic (species richness, Shannon diversity and evenness), functional (functional richness, evenness, divergence and Rao's Quadratic entropy) and a proxy of phylogenetic alpha diversity (taxonomic distinctness and variation in taxonomic distinctness) were calculated for macroinvertebrate assemblages in 55 stream sites. Then Pearson correlation coefficient was used to explore congruence of indices within and across the three diversity facets. Finally, multiple linear regression models and variation partitioning were employed to identify the relative importance of different ecological drivers of biodiversity. We found most correlations between the diversity indices within the same facet, and between functional richness and species richness were relatively strong. The two phylogenetic diversity indices were quite independent from taxonomic diversity but correlated with functional diversity indices to some extent. Taxonomic and functional diversity were more strongly determined by environmental variables, while phylogenetic diversity was better explained by spatial factors. In terms of environmental variables, habitat-scale variables describing habitat complexity and water physical features played the primary role in determining the diversity patterns of all three facets, whereas landscape factors appeared less influential. Our findings indicated that both environmental and spatial factors are important ecological drivers for biodiversity patterns of macroinvertebrates in Tibetan streams, although their relative importance was contingent on different facets of diversity. Such findings verified the complementary roles of taxonomic, functional and phylogenetic diversity, and highlighted the importance of comprehensively considering multiple ecological drivers for different facets of diversity in biodiversity assessment.

opencc-zeroDec 2014View details →

Data from: Small-mammal isotope ecology tracks climate and vegetation gradients across western North America

Stable carbon, nitrogen, hydrogen and oxygen isotopes have been used to infer aspects of species ecology and environment in both modern ecosystems and the fossil record. Compared to large mammals, stable isotopic studies of small-mammal ecology are limited; however, high species and ecological diversity within small mammals presents several advantages for quantifying resource use and organism–environment interactions using stable isotopes over various spatial and temporal scales. We analyzed the isotopic composition of hair from two heteromyid rodent species, Dipodomys ordii and Perognathus parvus, from localities across western North America in order to characterize dietary variation in relation to vegetation and climatic gradients. Significant correlations between the carbon isotopic composition (δ13C) of these species and several climatic variables imply that seasonal temperature and precipitation control the composition and distribution of dietary resources (grass seeds). Our results also suggest a moisture influence on the nitrogen isotopic composition (δ15N) of heteromyid diets. Population- and species-level variation in δ13C and δ15N values record fine-scale habitat heterogeneity and significant differences in resource use between species. Using classification and regression-tree techniques, we modeled the geographic variation in heteromyid δ13Cdiet values based on 10 climatic variables and generated an isotope landscape model ('isoscape'). The isoscape predictions for δ13Cdiet differ from expectations based on observed C4 distributions and instead indicate that D. ordii and P. parvus record seasonally abundant grass resources, with additional model deviations potentially attributed to geographic variation in dietary selection. The oxygen and hydrogen isotopic composition of D. ordii is enriched relative to local meteoric water and suggests that individuals rely on highly evaporated water sources, such as seed moisture. Based on the climatic influences on vegetation and diet documented in this study, the isotopic composition of small mammals has high potential for recording ecological responses to environmental changes over short and long time scales.