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At least 19 recordsLinked to original sources
PubMed2025

Climatic data sources and limitations of ecological niche models impact the estimations of historical ranges and niche overlaps in distantly related Korean salamanders.

BACKGROUND: Ecological niche models (ENMs) and analyses of niche overlap/divergence have become popular methods in ecology and evolutionary biology. These analyses rely on environmental data available from several databases. However, the influence of data sources on these analyses is rarely tested. Here, we test the impact of climatic data choice on the prediction of current and Plio-Pleistocene suitable habitats for two distantly related, but broadly sympatric, salamanders endemic to the Korean Peninsula. We ran MaxEnt separately on WorldClim and CHELSA climate data. We then hindcasted ENMs to five time periods of the Plio-Pleistocene, bracketing the estimated intraspecific divergence times for these species. We then quantified the differences in predictions between WorldClim- and CHELSA-based models. Also, given the sympatry and similar habitat requirements of the two species, we tested for niche overlaps using niche identity and background tests and tested the sensitivity of the results to climatic data choice. RESULTS: The ENMs successfully predicted contemporary suitable habitats for the two species. However, the predictions were highly sensitive to climatic data choice as well as variable combinations. The hindcasted ENMs produced contrasting predictions depending on the choice of climatic dataset and failed to predict suitable habitats for some Pleistocene time periods regardless of the climatic data choice. The niche analyses were also sensitive to climatic data choice, with results suggesting either niche overlaps or divergence depending on the climatic dataset used for the analyses. CONCLUSIONS: Our study highlights the influence of climatic data choice on the outcomes of ENMs and niche analyses. Our results also underscore the limitations of macroclimate-based ENMs, especially when the species is likely buffered from macroclimatic changes by microhabitat. We argue for the need for additional ecological, ecophysiological, and population genomic studies to better understand the range formation of these enigmatic species.

Animals↗
PubMed2026

Quantifying niche overlap and transgression in allopolyploid hybrids: Case study of Sorbus subgenus Aria.

BACKGROUND AND AIMS: Apomixis, the formation of seeds without recombination, facilitates adaptation and persistence under environmental change. By preserving hybrid genotypes over long time periods, apomixis may conserve adaptive trait combinations from parental niche margins. We tested whether apomictic entities occupy intermediate, marginal, or transgressive niche space relative to their parents and whether differentiation is associated with ploidy. METHODS: We studied polyploid Sorbus subgenus Aria in the Franconian Jura (Germany), comprising two progenitors Sorbus aria and S. collina, seven triploid entities, and a pool of genetically heterogenous individuals (single genotypes). Genetic structure was assessed using MIG-seq. Overall niche differentiation between parental taxa and hybrids was evaluated using Sørensen similarity of two-dimensional hypervolumes derived from principal component analysis (PCA) axes. Niche shifts were further analyzed using hypervolumes based on the three strongest PCA variables. Across 762 occurrences, observations ranged from 11 to 453 individuals per entity. KEY RESULTS: Environmental niche space was transgressive in three, significantly allocated towards the margins of parental niche space in one, while remaining intermediate in the other entities. Niche transgression occurred towards milder temperatures and drier conditions. Genetic analyses confirmed morphologically defined entities, although one morphotype was polyphyletic. Tetraploid S. collina significantly occupied warmer and wetter environments compared to other cytotypes. Triploids differed from S. aria along microtopographic gradients represented by the second PCA axis. CONCLUSIONS: Apomictic Sorbus entities show diverse strategies in niche occupation and can occupy environmental niche space at and beyond the limits of their parental taxa. Apomicts may conserve evolutionary adaptations at the edges of parental niche space that may otherwise be lost from, or fail to emerge in, the parental gene pool. Over long timescales these trait combinations may re-enter the parental gene pool through introgression, thereby reintroducing adaptations critical for survival under changing conditions.

Aria↗
PubMed1994

Niche restriction in parasites: proximate and ultimate causes.

Hutchinson's (1957) definition of an ecological niche as a multidimensional hypervolume determined by a number of physical and biotic variables is adopted. The number of niche dimensions is very great, but as a working hypothesis it is assumed that a few are sufficient to characterize the niche of a parasite species to a high degree of accuracy. They are host species, microhabitat(s), macrohabitat(s), geographical range, sex and age of host, season, food and hyperparasites. Methods to measure niche width, in particular specificity indices, are discussed, and some examples of niche restriction are described. Proximate and ultimate causes of niche restriction are discussed, mainly using marine parasites as examples. Among proximate causes of one niche dimension, host specificity, are ecological factors restricting exposure to infection to certain host species; host-specific chemical factors that induce hatching, direct infective stages to a host and bring about settlement of a parasite; factors that lead to mortality in or on the wrong host; morphological adaptations that guarantee survival in or on the 'correct' host; and availability of suitable hosts. Many factors are likely to be responsible for microhabitat specificity, but have been little studied, except for some physiological and morphological adaptations to particular microhabitats. Macrohabitats and geographical range may be determined by the distribution of intermediate hosts and certain food items, and by a variety of chemical and physical factors. Hosts of different sexes may differ in feeding habits and the composition of the skin, and thus acquire parasites differentially. Hosts of different age may be differentially infected due to accumulation of parasites with age, loss of parasites due to developing resistance (or immunity), and different size and feeding habits. Among ultimate causes of niche restriction and segregation are avoidance of competition, predation and hyperparasites; facilitation of mating; reinforcement of reproductive barriers; and adaptations to environmental complexity. Few studies permit a decision on which factor or factors are responsible in particular cases. Interspecific competition may play a greater role in helminth communities of some host groups than of others, but it seems that, overall, its role has been exaggerated at least for marine parasites. Some 'classical' examples of microhabitat segregation explained by interspecific competition can also be explained by reinforcement of reproductive barriers. There is evidence for the importance of facilitation of mating in microhabitat restriction, and the availability of many vacant niches indicates that competition, overall, is not of great importance.

Animals↗
PubMed2026

Cooperation and the evolution of bacterial niche breadth.

Bacteria exhibit varying niche breadths, with generalists thriving in diverse environments and specialists confined to specific habitats. Although genes for cooperative traits have been suggested to influence niche breadth evolution, their precise role remains unclear. We used a combination of phylogeny-based comparative methods to test causal hypotheses about the directionality of the relationship between genes for cooperation and bacterial niche breadth evolution across 25,785 species. Our results revealed 1) a positive correlation between the proportion of genes for cooperation and niche breadth; 2) genes for cooperation influenced niche breadth evolution, with a decreased proportion of such genes promoting niche contraction as the predominant evolutionary direction; and 3) genes for cooperation experience more frequent gain and loss within species rather than across species. These findings suggest a role of bacterial cooperation in influencing niche breadth evolution and maintaining the ecological versatility of bacteria. While our results are consistent with a simple relationship under the hypotheses tested, more complex causal scenarios are possible, including the role of factors that influence both cooperation and niche breadth.

Phylogeny↗
PubMed1989

Computer-aided three-dimensional reconstruction and measurement of the round window niche.

The goal of this study was to clarify the three-dimensional shape of the round window niche and to measure this structure three-dimensionally using the computer-aided reconstruction method we developed. The equipment used in this study included a personal computer (NEC 98-XA), a high-resolution 14-inch color CRT, a digitizer (Hitachi HDG-1111), and a printer. We studied five normal temporal bones obtained from five individuals with negative otologic histories, who had been 5 months and 14, 15, 18, and 59 years old at death. In each case the round window niche was located posteroinferior to the round window. The round window niches had wide openings to the middle ear cavity that became narrower near the aperture; thus, the round window niche seemed to be shaped like a pouch. The maximal diameter of the round window niche was 2.98 +/- 0.23 mm. The shortest distance between the aperture of the round window niche and the margin of the round window was 0.66 +/- 0.16 mm. The volume of the round window niche, on average, was 4.65 +/- 0.67 mm3. The volume of the round window niche was found to be correlated with the area of the round window.

Adolescent↗
PubMed1990

Cholesteatoma in the oval window niche.

The histopathological changes in the oval window niche into which a cholesteatoma is spreading are described in 14 temporal bones. Extension of the matrix into the niche was found commonly. In some cases the matrix passed from the facial canal to the promontory but failed to reach the niche. The perimatrix of the cholesteatoma was composed of inflamed and vascularized granulation tissue or fibrocystic tissue. A matrix covering the walls of the niche and the footplate of the stapes or the oval window was rarely found. It was surrounded by a thin layer of non-inflamed fibrous or fibrocystic tissue which covered the niche. Bone destruction of the superstructures of the stapes was observed in 12 of the 14 cases examined. The footplate of the stapes was partially or totally destroyed in 4 cases. Bone destruction of the tympanic portion of the facial canal adjacent to the oval window niche was present in all cases. Our present studies further suggest that surgical removal of a cholesteatoma from the niche may be difficult, even when done very carefully.

Cholesteatoma↗
PubMed1994

The developmental niche: a theoretical framework for analyzing the household production of health.

Recent efforts to promote child survival and development internationally have focused new attention on the importance of the household as a mediator of both environmental risks and programmatic interventions to promote better health. In this paper, we introduce a theoretical framework, the 'developmental niche,' derived from studies of children's behavior and development in different cultural contexts, as a tool for analyzing the household production of health. The developmental niche is conceptualized in terms of three basic components: (1) the physical and social settings of the child's everyday life; (2) culturally regulated customs of child care and child rearing; and (3) the psychology of the caretakers. The relevance of each of these components to the household production of health is illustrated through examples from research in several cultures, including Malaysia, Kenya, Bangladesh, India, and the U.S. Further discussion centers on three corollaries of the developmental niche framework that point to the interactive relationships among the three components, between the niche and the larger environment, and between the niche and the child (or any individual seen from a developmental perspective). It is suggested that this approach is useful for identifying and collecting relevant information on household-level factors that affect health outcomes, and thus for organizing more effective interventions. At a theoretical level, the developmental niche framework also facilitates understanding processes of mutual adaptation between the individual and the environment as they are filtered through the constraints of household settings, customs and caretaker psychologies.

Child↗
PubMed1974

Niche overlap and diffuse competition.

Current theory predicts a distinct upper limit on the permissible degree of niche overlap; moreover, theory suggests that maximal tolerable overlap should be relatively insensitive to environmental variability. Data presented here demonstrate that, within the lizard subset of natural desert communities, niche overlap decreases both with increasing environmental variability and with increasing numbers of lizard species. The latter two factors are themselves positively correlated. A partial correlation analysis is interpreted as indicating that the extent of tolerable niche overlap does not necessarily decrease due to environmental variability, but rather that overlap is probably more closely related to the number of potential interspecific competitors in a community, or what has been termed "diffuse competition." This result lends support to the "niche overlap hypothesis," which asserts that maximal tolerable overlap should vary inversely with the intensity of competition. Moreover, this empirical discovery indicates that niche overlap theory could be profitably expanded to incorporate the number of competing species. Although the average amount of overlap between pairs of species decreases with the intensity of diffuse competition, the overall degree of competitive inhibition tolerated by individuals comprising an average species could nevertheless remain relatively constant, provided that extensive niche overlap with a few competitors is roughly equivalent to lower average overlap with a greater number of competitors.

Animals↗
PubMed1977

Therapeutic testing by acetazolamide in the differentiation of a benign from a malignant niche.

Recognising the inhibitory activity of acetazolamide upon acid gastric secretion and its favorable effects in the treatment of gastric ulcer which we have described (see reference) - we applied the therapeutical testing by acetazolamide in the differentiation of benign from malignant niches of the stomach. Acetazolamide was administered orally at doses of 25-30 mg per kilogram body weight in a long term trial, together with 3 gr sodium bicarbonate, 1 gr potassium bicarbonate, 1.5 gr magnesium oxide per day and an increased quantity of liquids, to 741 patients with radiologically demonstrated ulcer craters. The fundamental criterion was the size of the niche as established by radiologic examination. In all gastric ulcers the size of the niche was considerably reduced after 7-9 days of treatment with acetazolamide; the niche disappeared in 2-3 weeks. This favorable result was obtained without diet and rest. In 38 cases in which there was no significant radiologic change of the niche after 7-9 days of treatment with acetazolamide - the malignancy of the niche was confirmed. The simplicity and the effectiveness of this rapid therapeutic test, makes it useful in the differentiation of benign from a malignant ulcer craters.

Acetazolamide↗
PubMed2026

Aging of hair follicle stem cells and their niche: mechanisms and regenerative therapeutic strategies.

Hair follicles (HFs) are vital skin appendages that perform fundamental functions including protection, thermoregulation, and sensation. Orchestrated by hair follicle stem cells (HFSCs), HFs undergo cyclic regeneration throughout the lifespan. However, during chronological aging, this mini-organ experiences progressive physiological decline, clinically characterized by a marked reduction in hair density and hair graying due to pigmentation dysfunction. This aging process involves HFSC exhaustion accompanied by diminished regenerative potential and differentiation capacity, leading to degenerative changes in the bulge architecture. Concurrently, the niche supporting HFSC homeostasis undergoes multi-dimensional and systemic degradation. This niche deterioration disrupts the delicate balance between HFSC quiescence and activation, further impeding hair regeneration. In this review, we delineate the dynamic anatomical changes throughout the hair growth cycle and describe the alterations of HFSCs during aging. We specifically focus on the mechanisms underlying the multi-dimensional degradation of the HFSC niche at tissue, cellular, and molecular levels. Furthermore, we discuss various therapeutic strategies aimed at ameliorating HF aging, offering potential insights for future clinical translation in hair regeneration. Finally, we propose that integrating spatiotemporal high-resolution technologies with genomic data to further decipher the spatiotemporal behaviors of aging HFSCs and niche cells will facilitate the establishment of a robust mechanistic framework for HFSC and niche aging.

Hair Follicle↗
PubMed1982

Competition theory, evolution, and the concept of an ecological niche.

This article examines some of the main tenets of competition theory in light of the theory of evolution and the concept of an ecological niche. The principle of competitive exclusion and the related assumption that communities exist at competitive equilibrium - fundamental parts of many competition theories and models - may be violated if non-equilibrium conditions exist in natural communities or are incorporated into competition models. Furthermore, these two basic tenets of competition theory are not compatible with the theory of evolution. Variation in ecologically significant environmental factors and non-equilibrium in population numbers should occur in most natural communities, and such changes have important effects on community relations, niche overlap, and the evolution of ecosystems. Ecologists should view competition as a process occurring within a complex dynamic system, and should be wary of theoretical positions built upon simple laboratory experiments or simplistic mathematical models. In considering the relationship between niche overlap and competition, niche overlap should not be taken as a sufficient condition for competition; many factors may prevent or diminish competition between population with similar resource utilization patterns. The typically opposing forces of intraspecific and interspecific competition need to be simultaneously considered, for it is the balance between them that in large part determines niche boundaries.

Animals↗
PubMed2026

Spatial Transcriptomics Identifies Characteristic Immunological Niches in Atopic Dermatitis.

BACKGROUND: Atopic dermatitis (AD) is primarily driven by a Type 2 immune response, with T helper (TH2) cells producing IL-4 and IL-13, thereby promoting inflammation, itch, and a compromised skin barrier. Yet, the spatial organization of pathogenic immune cells and their interactions with stromal and epithelial compartments in human AD skin remain incompletely understood. METHODS: We performed 10× Genomics Visium spatial transcriptomics on FFPE skin biopsies from patients with AD (n = 6), psoriasis (n = 2), and healthy controls (n = 5). Data were integrated with AD single-cell RNA sequencing (scRNA-seq) datasets and complemented by imaging mass cytometry (IMC) and multiplex immunofluorescence (IF) to validate the spatial localization of immune cells. Cell-cell communication analysis revealed putative signaling interactions within immune niches. RESULTS: Spatial clustering resolved tissue compartments and demonstrated transcriptional dysregulation in keratinocytes in AD and psoriasis. AD lesions showed a conserved spatial organization of immune aggregates within the superficial dermis. Integration of scRNA-seq signatures revealed spatially organized co-localization of T cells and mature migratory dendritic cells (mmDCs). We developed a ring-based neighborhood analysis to characterize the cellular organization of the immune-stromal niches, revealing T cell-enriched regions surrounded by inflammatory fibroblasts and activated keratinocytes. Intercellular communication analysis further identified putative signaling within mmDC-T cell niches that may promote pathogenic T cell recruitment and activation. Application of tertiary lymphoid structure (TLS) signatures indicated the presence of TLS-like regions. IMC and IF validated the close spatial proximity between activated TH2 cells and mmDCs. CONCLUSION: AD lesions contain spatially organized TLS-like immune niches at the dermal-epidermal junction, characterized by the close association of T cells and mmDCs and coordinated interactions with surrounding stromal and epithelial compartments. These mmDC-T cell niches may represent potential targets for future therapeutic strategies aimed at disrupting persistent local inflammatory pathways and improving long-term disease control.

atopic dermatitis↗
PubMed2026

Uncovering Immune Niches in Health and Disease Using Spatial Transcriptomics.

Spatial transcriptomics allows for the investigation of complex cellular ecosystems directly in their native tissues and enables the dissection of immune niches as spatially organized and functionally diverse microenvironments across homeostatic, inflammatory, and malignant settings. In this review, we examine how spatial transcriptomics tools have been applied to interrogate the cellular and molecular architecture of immune niches, including the emerging studies of B and T cell clonal niches. We focus on immune niches in intestinal and tumor tissues due to their importance to both health and pathology, discuss pressing immunological questions these technologies may help to address, and highlight future developments in the field.

Humans↗
PubMed2025

Environmental Stresses Constrain Soil Microbial Community Functions by Regulating Deterministic Assembly and Niche Width.

Increasing evidence indicates that the loss of soil microbial α-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial α-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal α- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal α-diversity declined under high environmental stress across three soil layers (0-20 cm, 20-40 cm and 40-60 cm). Metagenomic-based analyses showed that the diversity of functional genes decreased along the stress gradients. High stress enhanced the abundance of genes associated with broad functional categories (e.g., glycolysis/gluconeogenesis, TCA cycle, DNA replication/repair and cell growth/death) but reduced the abundance of genes linked to specialised functional categories (e.g., C, N, S and methane metabolism). Phylogenetic null models and niche analyses indicated that stochastic assembly processes predominated in high-diversity communities, in which bacterial and fungal taxa had a narrow ecological niche. However, in low-diversity communities, deterministic assembly processes were dominant, and taxa had wide niches, correlating with the reduction in gene abundance observed for broad and specialised functional categories. Given the essential role of the microbiome in regulating ecosystem functions, our findings suggest that low-diversity-induced deterministic community assembly processes and a wide niche under high environmental stress may regulate microbial functions. These findings emphasise the ecological mechanisms through which microbial biodiversity regulates terrestrial ecosystem functioning.

Soil Microbiology↗
PubMed1976

Herniation of the singular nerve into the round window niche.

We report two cases of herniation of the singular nerve into the round window niche and one case of bony dehiscence without herniation between the round window niche and the posterior canal ampulla. It is believed that the middle ear and the inner ear are completely separate. However, in the temporal bone of a 10- to 15-week-old human fetus, a communication between the round window niche and the posterior canal ampulla is observed. Later, the mesenchymal tissue in the communication is replaced by cartilage from near the posterior canal ampulla. If the communication does not fill with cartilage, ossification is not able to begin behind the posterior canal crista. When there is bony dehiscence behind the crista, the singular nerve fibers are easily pressed out by ossified endosteal bone and herniated into the round window niche.

Ear↗