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opencc-zeroMar 2024View details →

Habitat selection and refuge-use by a color polymorphic salamander reveal behavioral niche differences

Color polymorphic species provide an excellent opportunity to investigate the ecology and evolution of intraspecific niche differences. The red-backed salamander, Plethodon cinereus, is a fully terrestrial lungless salamander with two common color forms, striped and unstriped. Previous research suggests the morphs may be differentially adapted to surface and subsurface microhabitats, with the unstriped morph being more fossorial. This hypothesis predicts that the unstriped morph should be more sensitive to the risks of surface activity (e.g., thermal stress, dehydration, predation), and therefore be more selective than striped morphs when choosing soil surface microhabitats. To test this hypothesis, we experimentally manipulated leaf litter mass in small forest patches (~0.45m2). Leaf litter addition reduced soil temperatures, buffered against changes in air temperature, and likely provided physical protection from predators. Over three years, we found that unstriped adults responded positively to leaf litter addition, but striped adults did not. In addition, unstriped morphs spent significantly more time in protective refuges (opaque, moistened tubes) than striped morphs in laboratory assays. Taken together, the field and laboratory results support the hypothesis that the unstriped morph is more sensitive to the risks of surface activity, and therefore is more likely to be fossorial. This difference in microhabitat use, combined with spatiotemporal variation in leaf litter accumulation on the forest floor, may play an important role in the maintenance of the polymorphism.

opencc-zeroDec 2022View details →

Worldclim 2.1 versus Worldclim 1.4: climatic niche and grid resolution affect between-version mismatches in habitat suitability models predictions across Europe

The influence of climate on the distribution of taxa has been extensively investigated in the last two decades through Habitat Suitability Models (HSMs). In this context, the Worldclim database represents an invaluable data source as it provides worldwide climate surfaces for both historical and future time horizons. Thousands of HSMs-based papers have been published taking advantage of Worldclim 1.4, the first online version of this repository. In 2017, Worldclim 2.1 was released. Here, we evaluated spatially explicit prediction mismatch at continental scale, focusing on Europe, between HSMs fitted using climate surfaces from the two Worldclim versions (between-version differences). To this aim, we simulated occurrence probability and presence-absence across Europe of four virtual species (VS) with differing climate-occurrence relationships. For each VS, we fitted HSMs upon uncorrelated bioclimatic variables derived from each Worldclim version at three grid resolutions. For each factor combination, HSMs attaining sufficient discrimination performance on spatially independent test data were projected across Europe under current conditions and various future scenarios, and importance scores of the single variables were computed. HSMs failed in accurately retrieving the simulated climate-occurrence relationships for the climate-tolerant VS and the one occurring under a narrow combination of climatic conditions. Under current climate, noticeable between-version prediction mismatch emerged across most of Europe for these two VSs, whose simulated suitability mainly depended upon diurnal or yearly variability in temperature; differently, between-version differences were more clustered toward areas showing extreme values, like mountainous massifs or southern regions, for VSs responding to average temperature and precipitation trends. Under future climate, the chosen emission scenarios and Global Climate Models did not evidently influence between-version prediction discrepancies, while grid resolution synergistically interacted with VSs' niche characteristics in determining extent of such differences. Our findings could help in re-evaluating previous biodiversity-related works relying on geographical predictions from Worldclim-based HSMs.

Figure 4 in First ecological assessment of the endangered Lichtenfelder's Tiger Gecko (Goniurosaurus lichtenfelderi) from northern Vietnam: micro-habitat and macro-climatic niche comparisons between island and mainland populations

Figure 4. (A) Substrate types between island and mainland populations of Goniurosaurus lichtenfelderi; (B) Number of observed individuals at positions (in or out) in different time intervals; (C) Elevations resided by island and mainland populations; (D) Distances from the observed animal to the near stream shore among four study areas.

Figure 3 in First ecological assessment of the endangered Lichtenfelder's Tiger Gecko (Goniurosaurus lichtenfelderi) from northern Vietnam: micro-habitat and macro-climatic niche comparisons between island and mainland populations

Figure 3. Micro-habitat characteristics of Goniurosaurus lichtenfelderi (A) Substrate temperature; (B) Canopy coverage; (C) Height above the ground in relation to the Snout-Vent Length (From low to high levels mentioned the frequency of captured animals); (D) Stream section type; (E) Surface substrate condition; (F) Activity status.

Figure 6 in First ecological assessment of the endangered Lichtenfelder's Tiger Gecko (Goniurosaurus lichtenfelderi) from northern Vietnam: micro-habitat and macro-climatic niche comparisons between island and mainland populations

Figure 6. Comparisons of macro-climatic niches of Goniurosaurus lichtenfelderi between island and mainland populations. (A) Climate niche space of the mainland population; (B) Climate niche space of the mainland population along the first two axes of the PCA-env (The solid (100%) and dashed contour (50%) lines illustrate the available macro-climate space); (C) The contribution of 19 climatic variables for loading PCA-env axes and the percentage of inertia explained by axes one and two.

Figure 5 in First ecological assessment of the endangered Lichtenfelder's Tiger Gecko (Goniurosaurus lichtenfelderi) from northern Vietnam: micro-habitat and macro-climatic niche comparisons between island and mainland populations

Figure 5. (A) Scatterplot of all variable groups for the first (Dim1) and second (Dim2) axes in the Multiple factor analysis (MFA) (green triangles as inactive groups, red triangles as active groups or variables); (B) Scatterplot of all qualitative variables in the Multiple correspondence analysis (MCA); (C) The first four important variables of the Dim1; and (D) The Dim2; (E) Scatter diagram illustrating the micro-habitat niche space of island and mainland populations.

Figure 1 in First ecological assessment of the endangered Lichtenfelder's Tiger Gecko (Goniurosaurus lichtenfelderi) from northern Vietnam: micro-habitat and macro-climatic niche comparisons between island and mainland populations

Figure 1. Records of Goniurosaurus lichtenfelderi (orange circles – surveyed locations; blue green circles – other recorded occurrences); (1): Bai Tu Long National Park, Quang Ninh Province (2): Chi Linh District, Hai Duong Province, (3): Yen Tu Mountain, Quang Ninh Province, (4): Tay Yen Tu Nature Reserve, Bac Giang Province. The background depicts elevation in northern Vietnam and southern China (from dark blue to red indicating higher elevation).

Figure 2 in First ecological assessment of the endangered Lichtenfelder's Tiger Gecko (Goniurosaurus lichtenfelderi) from northern Vietnam: micro-habitat and macro-climatic niche comparisons between island and mainland populations

Figure 2. (A) Natural micro-habitat of Goniurosaurus lichtenfelderi; (B) An adult male resting on a moss-rock substrate.

opencc-zeroJun 2021View details →

Habitat alteration facilitates the dominance of invasive species through disrupting niche partitioning in floodplain wetlands

Aim: Exotic species invasion often leads to declines in local and regional biodiversity, particularly in freshwater ecosystems. This biodiversity loss is generally facilitated by human activities such as land cover change and hydrological alternation. Recent advances in stable isotope analysis (SIA) have been highlighted in many studies addressing fundamental issues in invasion ecology, especially in quantifying competition for resources between native and exotic species. However, how anthropogenic disturbance influences trophic relationships among invasive and native species remains poorly understood. Location: Middle-lower Yangtze River region, China Methods: To investigate the effects of human disturbance on interspecific trophic interactions, this study compared isotopic niche space and overlap of the introduced red swamp crayfish (Procambarus clarkii) and the native oriental river shrimp (Macrobrachium nipponense) and freshwater snail (Bellamya aeruginosa) in natural and modified wetlands. Results: Based on carbon and nitrogen SIA, we found ubiquitous niche shifts in macroinvertebrates with increased competition, which might lead to significant niche contraction in modified habitats at both community and population scales. Moreover, the isotopic niche width of the exotic crayfish was twice as larger as that of natives at both habitats, suggesting that the exotic P. clarkii had great competitive superiority over the native species. However, the effects of habitat modification on niche overlap were inconsistent. While the niche overlap between crayfish and shrimp was significantly higher in modified habitats than in natural open waters, niche overlap between crayfish and the snail was significantly reduced. Main conclusions: Collectively, our findings highlight that the competitive outcomes of interspecific trophic interactions can be dependent on the prey availability and diversity, which embraces both the classic optimal foraging theory and competition theory to understand how environmental change, such as habitat alternation, affects the biological invasion processes.

opencc-by-4.0Aug 2021View details →

Supplementary Table S1 for manuscript Two new species of Russula subsection Amoeninae described from dry dipterocarp forest in Thailand suggest niche speciali-zation to this habitat type

Specimens and GenBank accession number of DNA sequences used in the phylogenetic analyses. The newly generated sequences in this study are presented in boldface. The A is indicated for angiocarpic specimens.

opencc-zeroAug 2021View details →

Data and Code for: Isotopic Niche Size of Coregonus artedi (sensu lato) Increases in the Presence of Mysis diluviana, Expanded Habitat Use and Phenotypic Diversity

Post-glacial colonization of lakes in Algonquin Park, Ontario, Canada resulted in food webs with cisco (Coregonus artedi sensu lato) and either Mysis diluviana or Chaoborus spp. as the dominant diel migrator. Mysis as prey, its diel movements and benthic occupancy, are hypothesized to be key elements of ecological opportunity for cisco diversity in the Laurentian Great Lakes. If correct, the hypothesis strongly implies that lakes with Mysis would have greater trophic niche size and drive greater adaptive radiation of cisco forms relative to lakes without Mysis. The dichotomy in diel migrator in Algonquin Park lakes was an opportunity to assess the isotopic niche size of cisco (δ15N and δ13C) and determine if niche size expands with Mysis presence. We found the presence of Mysis is necessary to expand isotopic niche size in our study lakes. The use of habitats not typically associated with the ancestral form of cisco (e.g., benthic habitats) and phenotypic diversity (blackfin and cisco) also continue to expand niche size in Mysis-based food webs. Partial ecological speciation based on a large niche space appears to be present in one lake (Cauchon Lake) where use of alternative habitats is the only real difference in cisco. The presence of blackfin expands niche space in Cedar and Radiant Lakes. This was not matched in Hogan Lake where niche space was relatively smaller with similar forms. Possible reasons for this discrepancy may be related to the asymmetric basin of Hogan Lake and whether the two forms overlap during cool and cold-water periods of the annual temperature cycle. By comparing trophic niche size among lakes with and without Mysis we conclude that Mysis provides a key ecological opportunity for cisco diversity in our study lakes and likely more widely.

opennotspecifiedJan 2023View details →

FIG. 1 in Habitat Usage, Dietary Niche Overlap, and Potential Partitioning between the Endangered Spotted Turtle (Clemmys guttata) and Other Turtle Species

FIG. 1. The path analysis shows the relationship between habitat parameters associated with PC1 (which was strongly positively loaded with salinity, depth, dissolved O2, canopy cover, and pH) and three turtle species: Chrysemys picta, Kinosternon subrubrum, and Clemmys guttata on the Atlantic Coastal Plain. The solid and dashed lines represent direct and indirect effects, respectively, and black lines indicate positive effects while gray lines indicate negative effects. The numbers associated with each line represent the direction and magnitude of each effect, with the strength of the interaction increasing as the values approach 1.

opennotspecifiedJan 2023View details →

FIG. 2 in Habitat Usage, Dietary Niche Overlap, and Potential Partitioning between the Endangered Spotted Turtle (Clemmys guttata) and Other Turtle Species

FIG. 2. Biplots of d15N and d13C for four turtle species at all sites with ellipses around each species (filled squares/solid black line ¼ Kinosternon subrubrum, filled triangles/solid gray line ¼ Chrysemys picta, open circles/gray dashed line¼ Chelydra serpentina, filled diamonds/ lack dashed line ¼ Clemmys guttata). There is a large overlap in isotopic compositions for all species, resulting in no significant differences in isotopic niche space between species (see text).

opennotspecifiedJan 2023View details →

FIG. 3 in Habitat Usage, Dietary Niche Overlap, and Potential Partitioning between the Endangered Spotted Turtle (Clemmys guttata) and Other Turtle Species

FIG. 3. Bivariate SIBER (Stable Isotope Bayesian Ellipses in R) plots of ellipses estimating isotopic niche based on the d13C and d15N compositions with all species, excluding C. serpentina. The black circles represent the mode, while the three ellipses from the center outwards show where 50%, 75%, and 95% of the data lie, respectively. The numbers indicate the site numbers, while the letter codes indicate species names (MUDT ¼ Kinosternon subrubrum, PATU ¼ Chrysemys picta, SPTU ¼ Clemmys guttata). Together, these bivariate data of the isotopic compositions create ellipses which represent the relative sizes of the isotopic niche of each turtle species at all of our sites on the Atlantic Coastal Plain. Despite the lack of any significant differences in isotopic niche, these ellipses allow us to see some degree of niche overlap among C. guttata at all sites.

opencc-zeroMay 2023View details →

Data for: Habitat functionality: integrating environmental and geographic space in niche modelling for conservation planning

Niche modelling is typically used to assess the effects of anthropogenic land use and climate change on species distributions and to inform spatial conservation planning. These models focus on the suitability of local biotic and abiotic conditions for a species in environmental space (E-space). Although movements also affect species occurrence, efforts to formally integrate geographic space (G-space) into niche modelling have been hindered by the lack of comprehensive theoretical frameworks. We propose the 'functional habitat' framework to define areas that are simultaneously of high-quality in E-space and functionally connected to other suitable habitat in G-space. Originating in metapopulation ecology, approaches have been developed to assess the amount of suitable connected habitat, based on the proximity between pairs of locations. Using network theory, which operates in topological space (T-space, defined by a network), we extended these metapopulation approaches to integrate movement constraints in G-space with niche modelling in E-space. We demonstrate the functional habitat framework using empirical data (GPS-tracking and population monitoring) throughout the European wild mountain reindeer (Rangifer t. tarandus) distribution range. We show that functional habitat outperforms traditional suitability in explaining the species' distribution. This approach integrates effects from habitat loss and fragmentation for spatial conservation planning and avoids overemphasizing small, inaccessible areas with locally suitable habitat. The functional habitat framework formally integrates biotic, abiotic, and movement constraints in niche modeling using network theory, thus opening a wide range of applications in spatial conservation planning.