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opencc-zeroMay 2022View details →

Niche overlap in rodents increases with competition but not ecological opportunity: A role of inter-individual difference

<div> 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. 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. 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. 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. 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. </div>

Fig. 2 in Ecological niche difference associated with varied ethanol tolerance between Drosophila suzukii and Drosophila melanogaster (Diptera: Drosophilidae)

Fig. 2. Mortality of Drosophila melanogaster (A) and Drosophila suzukii (B) adults exposed to varying concentrations of ethanol.

Fig. 4 in Ecological niche difference associated with varied ethanol tolerance between Drosophila suzukii and Drosophila melanogaster (Diptera: Drosophilidae)

Fig. 4. ADH and ALDH activity levels of Drosophila melanogaster and Drosophila suzukii exposed to ethanol. (A) ADH activity in Drosophila melanogaster; (B) ALDH activity in Drosophila melanogaster; (C) ADH activity in Drosophila suzukii; (D) ALDH activity in Drosophila suzukii. Different letters in each figure (A, B, C, D) indicate a significant difference between adults and larvae (One-way ANOVA: α = 0.05).

Fig. 3 in Ecological niche difference associated with varied ethanol tolerance between Drosophila suzukii and Drosophila melanogaster (Diptera: Drosophilidae)

Fig. 3. Mortality of Drosophila melanogaster and Drosophila suzukii larvae exposed to varying concentrations of ethanol.

Fig. 1 in Ecological niche difference associated with varied ethanol tolerance between Drosophila suzukii and Drosophila melanogaster (Diptera: Drosophilidae)

Fig. 1. Ethanol (A) and acetaldehyde (B) contents of grapes infested by Drosophila melanogaster and Drosophila suzukii.

opencc-zeroDec 2018View details →

Data from: Difference in reproductive mode rather than ploidy explains niche differentiation in sympatric sexual and apomictic populations of Potentilla puberula

Apomicts tend to have larger geographical distributional ranges and to occur in ecologically more extreme environments than their sexual progenitors. However, the expression of apomixis is typically linked to polyploidy. Thus, it is a priori not clear whether intrinsic effects related to the change in the reproductive mode or rather in the ploidy drive ecological differentiation. We used sympatric sexual and apomictic populations of Potentilla puberula to test for ecological differentiation. To distinguish the effects of reproductive mode and ploidy on the ecology of cytotypes, we compared the niches (i) of sexuals (tetraploids) and autopolyploid apomicts (penta-, hepta- and octoploids) and (ii) of the three apomictic cytotypes. We based comparisons on a ploidy screen of 238 populations along a latitudinal transect through the Eastern European Alps and associated bioclimatic, soil and topographic data. Sexual tetraploids preferred primary habitats at drier, steeper, more south-oriented slopes, while apomicts mostly occurred in human-made habitats with higher water availability. Contrariwise, we found no or only marginal ecological differentiation among the apomictic higher ploids. Based on the pronounced ecological differences found between sexuals and apomicts, in addition to the lack of niche differentiation among cytotypes of the same reproductive mode, we conclude that reproductive mode rather than ploidy is the main driver of the observed differences. Moreover, we compared our system with others from the literature, to stress the importance of identifying alternative confounding effects (such as hybrid origin). Finally, we underline the relevance of studying ecological parthenogenesis in sympatry, to minimise the effects of differential migration abilities

opencc-zeroSep 2021View details →

Data from: Traits mediate niches and co-occurrences of forest beetles in ways that differ among bioclimatic regions

Aim To investigate the role of traits in beetle community assembly and test for consistency in these effects among several bioclimatic regions. We asked (1) whether traits predicted species' responses to environmental gradients (i.e., their niches), (2) whether these same traits could predict co-occurrence patterns, and (3) how consistent were niches and the role of traits among study regions. Location Boreal forests in Norway and Finland, temperate forests in Germany. Methods We complied capture records of 468 wood-living beetle species from the three regions, along with nine morphological and ecological traits. Eight climatic and forest covariates were also collected. We used Bayesian hierarchical joint species distribution models to estimate the influence of traits and phylogeny on species' niches. We also tested for correlations between species associations and trait similarity. Finally, we compared species niches and the effects of traits among study regions. Results Traits explained some of the variability in species' niches, but their effects differed among study regions. However, substantial phylogenetic signal in species niches implies that unmeasured but phylogenetically structured traits have a stronger effect. Degree of trait similarity was correlated with species associations but depended idiosyncratically on the trait and region. Species niches were much more consistent – widespread taxa often responded similarly to an environmental gradient among regions. Main conclusions The inconsistent effects of traits among regions limits their current use in understanding beetle community assembly. Phylogenetic signal in niches, however, implies that better predictive traits can eventually be identified. Consistency of species niches among regions means niches may remain relatively stable under future climate and land use changes; this lends credibility to predictive distribution models based on future climate projections but may imply that species' scope for short-term adaptation is limited.

opencc-zeroNov 2022View details →

Different measures of niche and fitness differences tell different tales

In Modern Coexistence Theory, species coexistence can either arise via strong niche differences or weak fitness differences. Having a common currency for interpreting these mechanisms is essential for synthesizing knowledge across different studies and systems. However, several methods for quantifying niche and fitness differences exist, with little guidance on how and why these methods differ. Here, we first organize the available methods into three groups and review their differences from a conceptual point of view.Next, we apply four methods to quantify niche and fitness differences to one simulated and one empirical data set. We show that these methods do not only differ quantitatively, but affect how we interpret coexistence. Specifically, the different methods disagree on how resource supply rates (simulated data) or plant traits (empirical data) affect niche and fitness differences. We argue for a better theoretical understanding of what connects and sets apart different methods and more precise empirical measurements to foster appropriate method selection in coexistence theory.

opencc-by-4.0Apr 2022View details →

Not the same: phylogenetic relationships and ecological niche comparisons between two different forms of Aglaoctenus lagotis from Argentina and Uruguay

We extracted genomic DNA from three species of Aglaoctenus: A. lagotis, and A. castaneus from Uruguay and Argentina. From those we obtained three mitochondrial markers including the 5’ half of cytochrome c oxidase subunit I (cox1), the 3’ half of the 16S rRNA ribosomal subunit plus the complete tRNA-Leu plus 5’ half of the NADH dehydrogenase subunit I (16S+L1+nad1), and a partial fragment of the small ribosomal unit (12S). Additionally, we sequenced the nuclear intron of the gene encoding translation initiation factor 5A (tif5A). The sequences of the 12S, 16S+L1+nad1 and tif5A gene fragments were aligned using the online version of MAFFT v7 using the Q-ins-i algorithm. The alignment of the partial fragment of cox1 sequences was trivial since no insertions/deletions (indels) were observed. The alleles in heterozygous individuals for the tif5A intron were separated using the PHASE algorithm, as implemented in DnaSP v6. 12.03. With this data we inferred gene trees with Maximum Likelihood, Bayesian and statistical parsimony analyses. We perform molecular species delimitation analyses conducted with STACEY, and the species tree and divergence times were co-estimated with *BEAST. Additionally, we build a haplotype network of the nuclear intron tif5A, the concatenated mitochondrial genes cox1+12S+16S+L1+nad1, and a partial fragment of cox1 gene were estimated using statistical parsimony in TCS and implemented in PopART v1.7.

publicNov 2022View details →

Different measures of niche and fitness differences tell different tales

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publicJan 2020View details →

Data from: Difference in reproductive mode rather than ploidy explains niche differentiation in sympatric sexual and apomictic populations of Potentilla puberula

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publicMar 2022View details →

Data from: Traits mediate niches and co-occurrences of forest beetles in ways that differ among bioclimatic regions

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publicJun 2022View details →

Niche overlap in rodents increases with competition but not ecological opportunity: A role of inter-individual difference

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opencc-zeroMar 2024View details →

Niche and neutral-based processes differ in importance for common and rare species in a metacommunity of anurans in subtropical grasslands

Most species-rich communities consist of a limited number of common species and many rare species. This widespread ecological pattern can arise due to the predominance of either niche-based or neutral-based processes in community structuring. We tested two hypotheses related to this pattern for an anuran metacommunity composed of 35 species distributed in 187 ponds in the South Brazilian grasslands: (1) for common species, niche processes should prevail over neutral ones because common species evolved under a wider range of ecological filters than rare species; (2) for rare species, neutral processes should prevail because rare species are more prone to ecological drift and dispersion limitation. We found that the densities of both common (i.e., the 25% higher density ones) and rare (i.e., the 75% lower density ones) species depended mostly on pond structure and land use, indicating a similar response to niche-based processes in both groups of species. The importance of pond descriptors and type of land use, however, differed between the two groups, confirming that common and rare species represent ecologically distinct groups within the metacommunity. In addition, neutral processes—related to dispersion limitation or not—influenced both species groups, but the spatial filters selected explained a smaller portion of the variation in species densities compared to environmental descriptors. Our findings showcase the prevalence of niche processes in structuring communities of common and rare species of anurans in subtropical grasslands and indicate the variables of pond structure and land use that are relevant to guide conservation practices for the metacommunity of anurans in the South Brazilian grasslands.

zenodo36/100

Data from: Higher-order species interactions cause time-dependent niche and fitness differences: experimental evidence in plant-feeding arthropods

trajectories.csv (the raw data) id: replicate identifier variant: co-existence status ("competition" or "monoculture") day: day of experiment species: mite species ("CRM" or "WCM") n: population density   model.R The R script with the GAMM fitted to the trajectory data (the GAMM model is saved as model.RData); also produces simulations from this model (saved as sim.csv).   model.RData The GAMM for growth rates.   sim.csv (simulations from the GAMM) day: day of experiment spec_var: combination of co-existence status ("competition" or "monoculture") and species ("CRM" or "WCM") X1:X1000: population densities simulated from the fitted GAMM (on the log scale)   NFD_over_time_monte_carlo_gam.py Python script to compute niche and fitness differences. Takes sim.csv (densities over time for different instantiations) and model.RData (stores the GAMM from R for the growth rates) as input and generates the file Data_NFD_monte_carlo_multi_c.csv which stores the niche and fitness differences computed for these communities.   figures.R The R script that produces Figures 2-4.   plot_biotic_model.py Python code to generate the figures S3 and S4 showing the simulations of a biotic resource competition model.    plot_abiotic_model.py Python code to generate the figures S1 and S2 showing simulations of an abiotic resource competition model.

opencc-by-4.0Nov 2023View details →

opencc-zeroFeb 2022View details →

Genetic data and niche differences suggest that disjunct populations of Diglossa brunneiventris are not sister lineages

Disjunct distributions within a species are of great interest in systematics and biogeography. This separation can function as a barrier to gene flow when the distance among populations exceeds the dispersal capacity of individuals, and depending on the duration of the barrier, it may eventually lead to speciation. Here we describe patterns of geographic differentiation of two disjunct populations of Diglossa brunneiventris separated by approximately 1000 km along the Andes. Diglossa brunneiventris vuilleumieri is isolated in northern Colombia, while Diglossa brunneiventris brunneiventris has a seemingly continuous distribution across Peru, Bolivia, and Chile. We sequenced mitochondrial and nuclear DNA of the two Diglossa brunneiventris subspecies to evaluate whether they form a monophyletic clade, while including the other three species within the carbonaria complex (D. gloriosa, D. humeralis and D. carbonaria). We also constructed ecological niche models for each Diglossa brunneiventris subspecies to compare their climatic niches. We found that when using all available molecular data, the two D. brunneiventris subspecies are not sister lineages. In fact, each subspecies is more closely related to other species in the carbonaria complex. Our niche modeling analyses showed that the subspecies are occupying almost entirely different climatic niches. An additional, and not expected result was that the carbonaria complex might encompass more cryptic species than previously considered. We suggest reevaluating the taxonomic status of these brunneiventris populations, especially the northern subspecies, given its highly restricted range and potential threatened status.

opencc-zeroAug 2022View details →

The generality of cryptic dietary niche differences in diverse large-herbivore assemblages

Ecological niche differences are necessary for stable species coexistence but are often difficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth-forms but are agnostic towards food-plant species identity. Empirical support for these models is variable, suggesting that additional mechanisms of resource partitioning may be important in sustaining large-herbivore diversity in African savannas. We used DNA metabarcoding to conduct a taxonomically explicit analysis of large-herbivore diets across southeastern Africa, analyzing ~4,000 fecal samples of 30 species from 10 sites in 7 countries over 6 years. We detected 893 food-plant taxa from 124 families, but just two families—grasses and legumes—accounted for the majority of herbivore diets. Nonetheless, herbivore species almost invariably partitioned food-plant taxa; diet composition differed significantly in 97% of pairwise comparisons between sympatric species, and dissimilarity was pronounced even between the strictest grazers (grass eaters), strictest browsers (non-grass eaters), and closest relatives at each site. Niche differentiation was weakest in an ecosystem recovering from catastrophic defaunation, indicating that food-plant partitioning is driven by species interactions, and stronger at low rainfall, as expected if interspecific competition is a predominant driver. Diets differed more between browsers than grazers, which predictably shaped community organization: grazer-dominated trophic networks had higher nestedness and lower modularity. That dietary differentiation is structured along taxonomic lines complements prior work on how herbivores partition plant parts and patches and suggests that common mechanisms govern herbivore coexistence and community assembly in savannas.

zenodo36/100

Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies

Supplementary Tree 1.nex Nymphalidae backbone tree inferred with RAxML and time-calibrated using BEAST, with mean posterior node ages and 95% credibility intervals summarized. More information can be found in Chazot et al. (2021). Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies. Nature Communications.   Supplementary Tree 2.nex Maximum clade credibility tree of all Nymphalidae included in "Chazot et al. (2021). Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies. Nature Communications.", with mean posterior node ages and 95% credibility intervals estimated from the posterior distribution of 1000 grafted trees (1000 subclades posterior trees combined with 1000 backbone posterior trees).  More information can be found in Chazot et al. (2021). Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies. Nature Communications.

opencc-by-4.0Dec 2020View details →