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Results for “Spatial niche”

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PubMed2005

Spatial self-organization in a cyclic resource-species model.

Biological communities are remarkable in their ability to form cooperative ensembles that lead to coexistence through various types of niche partitioning, usually intimately tied to spatial structure. This is especially true in microbial settings where differential expression and regulation of genes allows members of a given species to alter their lifestyle so as to fill a functional role within the community. The resulting species interactions can involve feedback, as in the case of some bacterial consortia that participate in the cooperative degradation of a given resource in a succession of steps and in such a way that certain "later" species provide catalytic support for the primary degrader. We seek to capture the essential features of such spatially extended biological systems by introducing a lattice-based stochastic spatial model (interacting particle system) with cyclic local dynamics. Here, a given site progresses through a sequence of resource and species states in a prescribed order. Furthermore, this succession of states (at a site) is assumed to form a cyclic pattern due to a natural feedback mechanism. We explore conditions under which all the species are able to coexist and consider the extent to which this coexistence requires the development of spatio-temporal patterns, including spiral waves. This self-organization, if it occurs, results when synchronization of the dynamics at the microscopic level leads to macroscopic patterns. These patterns result in consumer-driven resource fluctuations that generate a form of spatio-temporal niche partitioning. As with most models of this complexity, we employ a mixture of mathematical analysis and simulations to develop an understanding of the resulting dynamics.

Adaptation, Biological↗

PubMed2004

[Principle of "multiple ecological niche of one-species (variety)" and its application in high yield cotton cultivation].

The multiple ecological niche of one-species (variety) (MENOS) population is formed by one species (variety), but the ecological units have different temporal, spatial, nutritional, temperature, or water ecological niche. The formation of MENOS population is characterized by its specific object, one species (variety), multiple layer canopy, human being's active adjustment, specific niche breadth, and overlap and separation of ecological units. This paper analyzed the characteristics of the super high yield cotton population with dual ecological niche of one-species (variety) (DENOS). As for the yield components, MENOS has the characteristics of high yield canopy and different yield plants.

Adaptation, Biological↗

PubMed1993

The niche of the gill parasite Dactylogyrus banghami (Monogenea: Dactylogyridae) on Notropis stramineus (Pisces: Cyprinidae).

Distribution of the monogenean Dactylogyrus banghami on the gills of the fish Notropis stramineus (Cyprinidae) was described by calculation of mean relative positions and Levins' niche breadths on the linear spatial resource gradients gill filament length and gill arch length. Thirty fish with 276 worms were examined; only 1 of the fish had an additional gill parasite species (Trichodina sp). Worms were more broadly and evenly distributed across the length of the gill arch than they were on the filament (breadths of 0.91 and 0.67, respectively). Mean worm positions were near the center of both resources: 54% of the distance from the arch cartilage on the filament, and 54% from the ventral end of the arch itself. The results are considered consistent with predictions about the niche structures of species in unsaturated noninteractive specialist communities.

Animals↗

PubMed2006

Speciation dynamics in the Australo-Papuan Meliphaga honeyeaters.

The Australo-Papuan Meliphaga honeyeaters have diversified over a wide range of habitats and elevational zones and are one of the few regionally known cryptic avian radiations. Using a combined 1580 bp of mitochondrial and nuclear DNA we investigate the species limits, systematic affinities and biogeographic history of Meliphaga. We also investigate the role of spatial sorting mechanisms, including altitudinal replacement and niche partitioning, as mechanisms underlying the adaptive radiation of this group. Phylogenetic analysis indicates that the genus Meliphaga comprises at least 16 species, three more than recognized in current classifications. The genus divides into two clades; the species-poor lewinii group, and the larger analoga group that has diversified into a wider range of vertical, vegetational and elevational niches. The basal division of each clade into an Australian and New Guinean assemblage was likely induced by the formation of the Arafura Sea during the early Pliocene ( approximately 4 MYA) with a single reinvasion of Australia by the open forest species M. gracilis during the early Pleistocene (1.2-1.5 MYA) via intermittent land bridges or island hopping. Most recent sister species were found to replace each other geographically within the same ecological and elevational zone conforming to the classical allopatric mode of speciation. In contrast, M. orientalis (650-1950 m) and M. analoga (0-1100 m) were found to replace each other altitudinally across ecological zones providing empirical support for altitudinal speciation as a mechanism of diversification in a montane avifauna. We find no evidence of sympatric speciation (co-existing sister lineages) and suggest that spatial segregation within the habitat (niche partitioning) is primarily a mechanism enabling more divergent species to coexist.

Animals↗

PubMed2026

Beyond species trees: pervasive gene flow limits phylogenomic resolution in the diversification of Juniperus from the Qinghai-Tibet Plateau.

Understanding how lineages diversify despite persistent ancestral polymorphism and recurrent gene flow remains a central challenge in evolutionary biology. Juniperus distributed across the Qinghai-Tibet Plateau provide an ideal system for addressing this question because repeated geological uplift and climatic oscillations have likely promoted cycles of lineage divergence, range shifts, and secondary contact. Here, we combined approximately 1.08 million genome-wide SNPs from 164 individuals representing thirteen Juniperus lineages with phylogenomic datasets comprising 3,381 nuclear single-copy genes and nearly complete plastomes. We detected extensive phylogenomic discordance and cytonuclear incongruence across genomic datasets. Topology weighting, coalescent simulations, quartet-based tests, and analyses of gene flow and reticulation collectively support the interpretation that these patterns were shaped by the combined effects of prolonged incomplete lineage sorting and gene flow during lineage diversification. Ecological niche analyses further provide a spatial and climatic context in which environmentally similar lineages may have had greater opportunities for secondary contact during historical range shifts. Collectively, our results reveal that the evolutionary history of Qinghai-Tibet Plateau Juniperus is characterized by reticulate diversification rather than strictly bifurcating evolution, and demonstrate how genome-wide discordance can provide biological insights into the evolutionary processes underlying lineage diversification.

Gene Flow↗

PubMed1992

Structure of the pinworm (Oxyurida: Nematoda) guild in the hindgut of the American cockroach, Periplaneta americana.

The pinworm (Oxyurida: Nematoda) guild in a laboratory colony of Periplaneta americana was investigated to answer the following questions. (1) Is guild structure stable with time? (2) Is there evidence of interaction among the species? (3) Is there evidence for niche diversification with respect to spatial distribution or developmental stage of host? Four species were found: Thelastoma periplaneticola, Thelastoma bulhoesi, Hammerschmidtiella diesingi and Leidynema appendiculatum; females of the first two could not be distinguished and they were lumped and referred to as Thelastoma sp.; 328 mid-instar hosts were dissected between September 1987 and February 1990, and the number of adult females of each pinworm species was recorded to investigate changes in guild structure through time. Seventy-five percent of hosts had Thelastoma sp., 62% had H. diesingi and 40% had L. appendiculatum; mean intensities were 6.5 (Thelastoma), 2.9 (H. diesingi) and 1.9 (L. appendiculatum). Relative numbers were stable with time and intensities of the species were similar whether they occurred alone in the host or in conjunction with other species. Thelastoma sp. and L. appendiculatum occurred together less often than expected and their numbers in individual hosts were negatively correlated. Both species occurred alone more often than expected. Surprisingly, H. diesingi and L. appendiculatum occurred together more often than expected. Intestines of 44 roaches were frozen in liquid nitrogen and divided into 5 equal sections to study longitudinal distributions of the species in the gut. Most L. appendiculatum and H. diesingi were found in the first, whereas most Thelastoma sp. occurred in the second segment. However, Thelastoma sp. dominated all segments of the gut. Worms were counted in 192 hosts belonging to 4 categories (early instar, late instar, adult male and adult female). Single species infections were more common in early instar hosts but there was no evidence that different species preferred different host stages. Modal distributions in male L. appendiculatum and T. bulhoesi suggest that these species may exhibit intraspecific interference competition similar to that observed in other pinworms. Such effects may be more important than interspecific effects in maintaining guild stability.

Animals↗

PubMed2006

Spatial organization of embryonic stem cell responsiveness to autocrine gp130 ligands reveals an autoregulatory stem cell niche.

Highly ordered aggregates of cells, or niches, regulate stem cell fate. Specific tissue location need not be an obligatory requirement for a stem cell niche, particularly during embryogenesis, where cells exist in a dynamic environment. We investigated autoregulatory fixed-location-independent processes controlling cell fate by analyzing the spatial organization of embryonic stem cells (ESCs) using quantitative single-cell immunocytochemistry and a computational approach involving Delaunay triangulation. ESC colonies demonstrated radial organization of phosphorylated signal transducer and activator of transcription 3, Nanog, and Oct4 (among others) in the presence and absence of exogenous leukemia inhibitory factor (LIF). Endogenous self-renewal signaling resulted from autocrine non-LIF gp130 ligands, which buffered cells against differentiation upon exogenous LIF deprivation. Together with a radial organization of differential responsiveness to gp130 ligands within colonies, autocrine signaling produced a radial organization of self-renewal, generating a fixed-location-independent autoregulatory niche. These findings reveal fundamental properties of niches and elucidate mechanisms colonies of cells use to transition between fates during morphogenesis.

Animals↗

PubMed2025

Spatial mutual nearest neighbors for spatial transcriptomics data.

MOTIVATION: Mutual nearest neighbors (MNN) is a widely used computational tool to perform batch correction for single-cell RNA-sequencing data. However, in applications such as spatial transcriptomics, it fails to take into account the 2D spatial information. RESULTS: Here, we present spatialMNN, an algorithm that integrates multiple spatial transcriptomic samples and identifies spatial domains. Our approach begins by building a k-nearest neighbors (kNN) graph based on the spatial coordinates, prunes noisy edges, and identifies niches to act as anchor points for each sample. Next, we construct a MNN graph across the samples to identify similar niches. Finally, the spatialMNN graph can be partitioned using existing algorithms, such as the Louvain algorithm to predict spatial domains across the tissue samples. We demonstrate the performance of spatialMNN using large datasets, including one with N = 31 10x Genomics Visium samples. We also evaluate the computing performance of spatialMNN to other popular spatial clustering methods. AVAILABILITY AND IMPLEMENTATION: Our software package is available on GitHub (https://github.com/Pixel-Dream/spatialMNN). The code is available on Zenodo (https://doi.org/10.5281/zenodo.15073963).

Algorithms↗

PubMed1996

Fitness patterns and phenotypic plasticity in a spatially heterogeneous environment.

We analyse patterns of the means and variances of genotypic fitnesses across different niches in a randomly mating haploid population. The population inhabits a spatially heterogeneous environment where it is subject to mutation and weak multilocus additive selection, with different election coefficients in different niches. Approximate analytical expressions are derived for the stationary mean and variance of genotypic fitnesses among the niches in terms of environmental and genetic parameters. As a special case, we analyse an environment described by a variable t, distributed among the niches with mean t(star) and variance D(star) and quadratic decrease in correlation between environments as a function of the difference in values of t. If the niches have the same qualities, the mean and variance of genotypic fitnesses evolve to be quadratic functions of t that achieve their maximum and minimum, respectively, at t(star). With unequal niche qualities, these are non-polynomial functions that attain their extrema at different, usually intermediate values of t, although the coefficient of variation of the genotypic fitnesses still attains its minimum near t(star). The functions involve the total mutation rate, the combination of the loci to genotypic fitnesses, and the frequency and quality distributions of the niches. Thus, for this relatively simple model the norms of reaction may be calculated in terms of the detailed properties of the environmental heterogeneity, and the genetic system.

Biological Evolution↗

PubMed1996

Of mice and mazes: similarities between mice and rats on dry land but not water mazes.

Mice are impaired relative to rats in place and matching-to-place learning when tests are given in a swimming pool. The rat advantage may stem from a superior spatial ability or from adaptation to a niche that has prepared them for competency in the water. In the present study, mice (C57BL/6) were compared with rats (Long-Evans) in a number of dry-land spatial tasks given on a radial arm maze and in a place task given in a swimming pool. The performance of the mice matched that of the rats in all dry-land tasks, but was inferior to that of the rats in the swimming pool. The results provide further evidence for a species difference in swimming-pool performance but do not support the idea that there are necessary differences in spatial abilities between mice and rats. It is suggested that, if optimal place learning is required for neurobehavioral studies of mice, such performance is more likely to be obtained in dry-land tasks than in swimming-pool tasks. Nevertheless, the species differences warrant further study because they could provide important insights into species differences is spatial learning more generally.

Animals↗

PubMed1999

Spatial and reversal learning in congeneric lizards with different foraging strategies.

Environmental demands that require intensive search for mates, food and nest sites are correlated with efficient spatial memory in many mammalian and avian species. This convergence of evidence has led to the view that spatial memory, and the neurological structures associated with it, have been selected in niches that require memory for the location of goal objects. Whether such evolutionary demands are also correlated with nonspatial abilities that require flexible use of associations similar to those required for spatial memory has not been well studied. In addition, correlations between niche types and the use of spatial or nonspatial memory have not been investigated in nonmammalian, nonavian taxa. In this study, we investigated the relationship between foraging strategies and performance on two tasks, one spatial and the other nonspatial, in congeneric lizard species: Acanthodactylus boskianus, an active forager that collects clumped sedentary prey, Acanthodactylus scutellatus, a sit-and-wait predator that collects distributed mobile prey. The two species did not differ in their performance of a spatial memory task, but A. boskianus, the active forager, performed better on the reversal of a visual discrimination, a nonspatial task. These findings question the generality of the spatial adaptation model for vertebrates. We present the pliancy hypothesis, which we developed to account for these results. Copyright 1999 The Association for the Study of Animal Behaviour.

Journal Article↗

PubMed2004

Optimal photosynthetic characteristics of individual plants in vegetation stands and implications for species coexistence.

AIMS: This paper reviews the way optimization theory has been used in canopy models to analyse the adaptive significance of photosynthesis-related plant characteristics and their consequences for the structure and species composition of vegetation stands. SCOPE: In most studies simple optimization has been used with trait values optimal when they lead to maximum whole-stand photosynthesis. This approach is subject to the condition that the optimum for one individual is independent of the characteristics of its neighbours. This seems unlikely in vegetation stands where neighbour plants strongly influence each other's light climate. Not surprisingly, there are consistent deviations between predicted plant traits and real values: plants tend to be taller, distribute nitrogen more evenly among their leaves and produce more leaf area which is projected more horizontally than predicted by models. CONCLUSIONS: By applying game theory to individual plant-based canopy models, other studies have shown that optimal vegetation stands with maximum whole-stand photosynthesis are not evolutionarily stable. They can be successfully invaded by mutants that are taller, project their leaves more horizontally or that produce greater than optimal leaf areas. While these individual-based models can successfully predict the canopy structure of vegetation stands, they are invariably determined at unique optimal trait values. They do not allow for the co-existence of more than one species with different characteristics. Canopy models can contribute to our understanding of species coexistence through (a) simultaneous analysis of the various traits that determine light capture and photosynthesis and the trade-offs between them, and (b) consideration of trade-offs associated with specialization to different positions in the niche space defined by temporal and spatial heterogeneity of resources.

Adaptation, Physiological↗

PubMed2006

Does disturbance and restoration of alpine grassland soils affect the genetic structure and diversity of bacterial and N2-fixing populations?

Responses of bacterial communities to disturbance and restoration processes were investigated on alpine grassland soil. Bulk soil, rhizosphere soil and two soil separates, i.e. sand-size (2000-200 microm) and silt-size (50-2 microm) were sampled from undisturbed grassland soil to soil under restoration for 1 month, 1 year, 4 years and 13 years after disturbance. Automated ribosomal intergenic spacer analysis (ARISA) and restriction fragment length polymorphism (RFLP) of nifH gene pools were used to assay genetic structure of the bacterial communities and N2-fixing guild. According to the distribution of ARISA band length in bacterial phyla, the dominance of ARISA bands below 400 bp showed that Gram-positive bacteria would be predominant in the studied grassland soil when not disturbed. Disturbance affected the genetic structure of bacterial community and of N2-fixing guild in relation to their location within the selected habitats. Shifts in IGS and nifH profiles of bulk soil metagenome were larger than those observed from sand-size- and silt-size-fractions, accounting for 40-50% of the variance in the profiles. Restoration of the genetic structure of telluric bacteria community and N2-fixing populations was found to be influenced by the spatial heterogeneity of the soil and niche diversification. Particular bacterial genetic structure within distinct habitats were evidenced and must be defined as subdivisions of the meta-community of bulk soil. Scale of soil microbial diversity/stability relationships is discussed with special attention to disconnected bacterial habitat compared with whole soil with multiple niches.

Bacteria↗

PubMedDate not supplied

[Ecological niches of ectoparasites].

On mammals and birds communities of ectoparasites are present, which can include scores of ticks, mites and insects species. The parasitizing of arthropods terrestrial vertebrates appeared as far back a the Cretaceous period, and after 70-100 mil. years of the coevolution ectoparasites have assimilated all food resources and localities of the hosts' bodies. To the present only spatial and (to the less extent) trophic niches of parasitic insects, ticks and mites are studied completely enough. The main results these investigations are discussed in the present paper. A high abundance of the communities is reached because of their partition into the number of ecological niches. Host is complex of ecological niches for many ectoparasites species. These niches reiterate in the populations of a species closely related species of hosts and repeat from generation to generation. The each part of host (niche) being assimilated be certain parasite species is available potentially for other species. The partition of host into ecological niches is clearer than the structure of ecosystems including free-living organisms. A real extent of the ecological niches occupation by different species of ticks, mites and insects is considerably lower than a potential maximum. The degree of ecological niches saturation depends on the history of the coevolution of parasites community components, previous colonization be new ectoparasite species and many other ecological factors affecting host-parasite system. The use of the ecological niche conception in parasitology is proved to be rather promising. Ectoparasites communities because of their species diversity, different types of feeding and a number of habitats on host represent convenient models and study of them can contribute significantly to the developmeht of the general conception of ecological niche.

Animals↗

PubMed2026

Integrative transcriptomic, spatial and functional-genomic analysis identifies a UFMylation-related vascular-stromal program and prioritizes WWTR1 in glioblastoma.

Glioblastoma (GBM) contains spatially organized stress-adaptive and vascular niches. Because transcript abundance does not measure UFM1 conjugation, we asked whether a UFMylation-related transcriptional axis identifies a reproducible tissue program and alters candidate prioritization. In 518 unique primary TCGA-GBM tumors profiled on the Affymetrix HT Human Genome U133A array, weighted gene co-expression network analysis of 8,000 variable genes yielded 12 modules. The 278-gene green module ranked first across nine prespecified traits (mean |r|=0.637). Direct overlap comprised 1/3 measurable UFMylation-core, 5/19 ER-stress/UPR, and 2/15 proteostasis genes; after excluding overlapping genes, correlations with the green eigengene remained significant (r = 0.373, 0.831, 0.639, and 0.699 for UFMylation-core, ER-stress/UPR, proteostasis, and composite scores, respectively). The green score was associated with overall survival per standard-deviation increase (HR 1.17, 95% CI 1.07-1.28), although clinical adjustment attenuated the estimate. In a 10-sample single-cell dataset, sample-level scores were higher in pericytes and endothelial cells than in malignant cells. Donor-aware IvyGAP analysis supported regional organization, whereas one Visium section showed stronger concordance with ER-stress/UPR and mesenchymal scores than with the UFMylation-core score. CellChat indicated pathway-selective rather than global remodeling of inferred vascular communication. Layer ablation moved WWTR1 from rank 48 using WGCNA alone to rank 4 overall and rank 1 among non-common-essential genes after cross-platform integration. These findings define an ER-stress/mesenchymal-weighted, UFMylation-related vascular-stromal transcriptional association and nominate WWTR1 for experimental testing.

Humans↗

PubMed2026

Identification of cryosensitive niches and a targetable FOS/AP‑1 program in the human ovarian cortex by single‑cell and spatial transcriptomics.

BACKGROUND: The ovary is a vital and dynamic reproductive organ. Ovarian tissue cryopreservation (OTC) plays a vital role in preserving female fertility. However, the cellular subtypes most susceptible to cryoinjury and the molecular mechanisms underlying cryopreservation-associated damage remain poorly understood. This study aimed to identify cell populations vulnerable to freezing-thawing and to elucidate the key transcriptomic alterations and signaling pathways associated with ovarian cryoinjury at the single-cell and spatial levels. METHODS: Ovarian cortical tissues from patients undergoing three gender reassignment surgery (GRS) were divided into fresh and vitrification-rapid warming groups. Following collagenase IV digestion, 10x Genomics single-cell RNA-seq was used for dissociated ovarian cell suspensions (27,185 fresh and 25,480 frozen-thawed cells). Eight major cell clusters were identified. Additionally, 110 oocytes (66 fresh, 44 vitrification-rapid warming) were isolated and analyzed using the Smart-seq2 platform. Spatial transcriptomics was performed via BGI Stereo-seq. Molecular validation was performed via β-galactosidase staining, immunofluorescence, and qRT-PCR. RESULTS: Cryopreservation significantly altered the activity of pathways related to focal adhesion, oxidative stress, and apoptosis, particularly in stromal and perivascular cells. The number of FOS-positive perivascular cells was notably increased after vitrification-rapid warming, whereas the number of PTGDS-positive stromal cells decreased. Oocyte analysis revealed that cryopreservation primarily disrupted pathways involved in the cell cycle and meiosis, although the damage was not irreversible, supporting the relative safety of long-term cryostorage. Spatial transcriptomics and functional validation further confirmed the rapid and robust activation of the FOS/AP-1 pathway after vitrification-rapid warming, particularly in perivascular and granulosa cells. Treatment with T-5224 (a FOS/AP-1 inhibitor) significantly rescued the morphology and function of cultured frozen-thawed ovaries. CONCLUSIONS: Stromal and perivascular cells are the main cell types that are sensitive to ovarian cryopreservation. The FOS/AP-1 pathway is markedly activated after, suggesting the exacerbation of metabolic impairment. In oocytes within the ovarian cortex, the cell cycle and meiosis-related physiological processes were the primary processes affected.

Female↗

PubMed2005

Beta1 integrins and neural stem cells: making sense of the extracellular environment.

Neural Stem Cells (NSC) are present in the developing and adult CNS. In both the embryonic and adult neurogenic regions, beta1 integrins may act as sensors for the changing extracellular matrix. Here we highlight the integrative functions that beta1 integrins may play in the "niche" by regulating NSC growth factor responsiveness in a timely and spatially controlled manner. beta1 integrins may provide NSC with the capacity to react to a dynamic "niche", and to respond adequately by either remaining as stem cells or by differentiating and migrating away to shape the developing cortex.

Animals↗

PubMed2006

Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale.

Consideration of the scale at which communities are defined both taxonomically and spatially can reconcile apparently contradictory results on the extent to which plants show phylogenetic niche conservatism. In plant communities in north central Florida, we collected species abundances in 55 0.1-ha plots in several state parks. When communities were defined narrowly to include a single phylogenetic lineage, such as Quercus, Pinus, or Ilex, neighbors tended to be less related than expected (phylogenetic overdispersion) or there was no pattern. If the same communities were defined more broadly, such as when all seed plants were included, neighbors tended to be more related than expected (phylogenetic clustering). These results provide evidence that species interactions among close relatives influence community structure, but they also show that niche conservatism is increasingly evident as communities are defined to include greater phylogenetic diversity. We also found that, as the spatial scale is increased to encompass greater environmental heterogeneity, niche conservatism emerges as the dominant pattern. We then examined patterns of trait evolution in relation to trait similarity within communities for 11 functional traits for a single phylogenetic lineage (Quercus) and for all woody plants. Among the oaks, convergent evolution of traits important for environmental filtering contributes to the observed pattern of phylogenetic overdispersion. At the broader taxonomic scale, traits tend to be conserved, giving rise to phylogenetic clustering. The shift from overdispersion to clustering can be explained by the increasing conservatism of traits at broader phylogenetic scales.

Biological Evolution↗