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PubMed2004

Use of spatial, visual, and olfactory information during foraging in wild nocturnal and diurnal anthropoids: A field experiment comparing Aotus, Callicebus, and Saguinus.

Early in their evolution, the ancestors of anthropoid primates radiated from a nocturnal to a diurnal niche. Foraging during the night differs from foraging during the day in terms of the availability of light and color cues, and in the movement of odor molecules through the canopy. In this study, we compared the ability of nocturnal and diurnal New World monkeys to use perceptual cues (i.e., the sight or smell of food) and spatial information (place predictability) in within-patch foraging decisions. An experimental field study was conducted on wild groups of night monkeys (Aotus nigriceps), tamarins (Saguinus imperator imperator and S. fuscicollis weddelli), and titi monkeys (Callicebus cupreus) at the Zoobotanical Park/UFAC, Rio Branco, Brazil. Our research design included the construction of feeding stations located in the home range of the study groups. Each feeding station consisted of eight visually identical feeding platforms located in a circular arrangement. In all test settings, two platforms at each feeding station contained a food reward (banana), and the remaining six platforms contained a sham reward (yellow plastic or inaccessible banana). In the night-monkey experiments, each feeding platform was illuminated by a 40-W red bulb to aid the researcher in observing their behavior. When the location of reward sites was predictable over time, individuals in all four species successfully relocated food rewards based solely on spatial information. Each species was also successful in using visual information to distinguish real from sham food rewards. However, only night monkeys and one group of emperor tamarins used olfactory information alone to locate food rewards. Overall, the species' performances did not clearly differentiate Aotus from diurnal New World primates in these experiments.

Animals↗

PubMed2026

Spatial profiling of the spleen in mouse and human myelofibrosis reveals complement-driven immune-stromal interactions as a therapeutic target.

Splenomegaly is a defining feature of myelofibrosis, yet the contribution of splenic mesenchymal stroma to disease progression remains unclear. We combined spatial and single-nucleus transcriptomics of patient spleens with spatial and single-cell transcriptomics, as well as imaging analyses, of murine spleens to map extramedullary hematopoiesis niches. Activated red pulp reticular cells localize near hematopoietic stem and progenitor cells, and early disease is characterized by marginal zone disruption with lymphoid depletion preceding stromal remodeling. Trajectory analyses reveal a shift in reticular cells from hematopoiesis-supportive to inflammatory and pro-fibrotic states, driven by macrophage- and megakaryocyte-derived signals that activate complement and induce tumor necrosis factor α (TNF-α), transforming growth factor β (TGF-β), extracellular matrix, and Thbs1 programs. Non-hematopoietic complement component C3 deficiency or pharmacological C3 inhibition suppresses these pathways, restores splenic architecture, and reduces splenomegaly and bone marrow fibrosis. These findings identify complement-dependent stromal reprogramming as a mechanism governing hematopoietic niches and as a targetable axis in myelofibrosis.

Animals↗

PubMed2005

Spatial epidemiology and natural population structure of Campylobacter jejuni colonizing a farmland ecosystem.

Recent progress in determining the population structure of Campylobacter jejuni, and discerning associations between genotypes and specific niches, has emphasized the shortfall in our understanding of the ecology and epidemiology of this bacterium. We examined the natural structure of the C. jejuni community associated with cattle farmland in the UK by structured spatiotemporal sampling of habitats, including livestock and wild animal faeces, environmental water and soil, over a 10-week period within a 100 km2 area. A total of 172 isolates were characterized using multilocus sequence typing into 65 sequence types (STs). Isolates from cattle faeces were significantly over-represented in the ST-61 complex, whereas isolates from wildlife faeces and water were more likely to belong to the ST-45 complex and a number of unusual STs, many of which were first encountered during this study. Sampling within a narrow spatiotemporal window permitted the application of novel statistical methods exploring the relationship between the genetic relatedness and spatial separation of isolates. This approach showed that isolates from the same sampling squares and squares separated by <1.0 km were genetically more similar than isolates separated by greater distances. Our study demonstrates the potential of multilocus sequence typing combined with spatial modelling in exploring natural transmission pathways for C. jejuni.

Agriculture↗

PubMed2002

Adaptive divergence in experimental populations of Pseudomonas fluorescens. I. Genetic and phenotypic bases of wrinkly spreader fitness.

A central feature of all adaptive radiations is morphological divergence, but the phenotypic innovations that are responsible are rarely known. When selected in a spatially structured environment, populations of the bacterium Pseudomonas fluorescens rapidly diverge. Among the divergent morphs is a mutant type termed "wrinkly spreader" (WS) that colonizes a new niche through the formation of self-supporting biofilms. Loci contributing to the primary phenotypic innovation were sought by screening a WS transposon library for niche-defective (WS(-)) mutants. Detailed analysis of one group of mutants revealed an operon of 10 genes encoding enzymes necessary to produce a cellulose-like polymer (CLP). WS genotypes overproduce CLP and overproduction of the polymer is necessary for the distinctive morphology of WS colonies; it is also required for biofilm formation and to maximize fitness in spatially structured microcosms, but overproduction of CLP alone is not sufficient to cause WS. A working model predicts that modification of cell cycle control of CLP production is an important determinant of the phenotypic innovation. Analysis of >30 kb of DNA encoding traits required for expression of the WS phenotype, including a regulatory locus, has not revealed the mutational causes, indicating a complex genotype-phenotype map.

Adaptation, Physiological↗

PubMed2026

DPAS-Graph: adaptive spatial-feature relation learning for spatial RNA-to-protein prediction and virtual protein profiling.

Paired spatial multi-omics provides a supervised basis for learning RNA-protein correspondence in situ, but predicting protein abundance from spatial transcriptomic data alone remains challenging across tissue contexts and protein panels. Here, we present DPAS-Graph, an adaptive relation-learning framework for spatial RNA-to-protein prediction. Rather than directly merging spatial proximity and transcriptomic similarity as fixed graph priors, DPAS-Graph represents them as two relation channels on a shared edge support and updates their contributions during representation learning for protein prediction. Its Niche-Coupled Field Encoder combines layer-wise edge-relation modeling, intra-branch relation refinement, and cross-branch residual correction to learn spot representations for protein abundance prediction. In a leave-one-dataset-out benchmark across seven paired spatial multi-omics datasets, DPAS-Graph achieved lower aggregate prediction errors and improved spot-level agreement of protein expression profiles, with gains mainly reflected in error-based metrics and PCC-Spot. Spatial autocorrelation and protein-derived domain agreement analyses were further used to characterize the spatial behavior of the predicted protein maps. When applied to external RNA-only spatial sections, DPAS-Graph generated qualitatively interpretable marker-level virtual protein maps, illustrating its use as a complementary tool for protein-level interpretation of transcriptomics-only spatial data.

RNA↗

PubMedDate not supplied

[The dynamics of the spatial organization of communities of small mammals (exemplified by rodents of the trans-Altai Gobi of Mongolia)].

Between-year variation of rodent population densities was studied in the central part of trans-Altai Gobi, Mongolia, in summers of a nine year period. Variation in spatial structure of the desert rodent community in 1982-84 and in 1992 was examined by the use of discriminant function analysis. Although population densities, breadth and positions of niches of many species tended to vary independently, the positive conjunct variation was found for the most ecologically distinctive species. This can be explained by limitations of the climate. Although a guild structure of the community was pronounced each year, there were significant between year shifts in niche breadth and niche centres along certain axes of ecological space. Within year nearest neighbours in niche overlap (high seasonal overlap) differed in between year variation in abundance. It is supposed that interspecific competition could contribute to development of community structure.

Animals↗

PubMed2004

Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia.

Bacterioplankton community diversity was investigated in the subtropical Brisbane River-Moreton Bay estuary, Australia (27 degrees 25 minutes S, 153 degrees 5 minutes E). Bacterial communities were studied using automated rRNA intergenic spacer analysis (ARISA), which amplifies 16S-23S ribosomal DNA internally transcribed spacer regions from mixed-community DNA and detects the separated products on a fragment analyzer. Samples were collected from eight sites throughout the estuary and east to the East Australian Current (Coral Sea). Bacterioplankton communities had the highest operational taxonomic unit (OTU) richness, as measured by ARISA at eastern bay stations (S [total richness] = 84 to 85 OTU) and the lowest richness in the Coral Sea (S = 39 to 59 OTU). Richness correlated positively with bacterial abundance; however, there were no strong correlations between diversity and salinity, NO(3)(-) and PO(4)(3-) concentrations, or chlorophyll a concentration. Bacterioplankton communities at the riverine stations were different from communities in the bay or Coral Sea. The main differences in OTU richness between stations were in taxa that each represented 0.1% (the detection limit) to 0.5% of the total amplified DNA, i.e., the "tail" of the distribution. We found that some bacterioplankton taxa are specific to distinct environments while others have a ubiquitous distribution from river to sea. Bacterioplankton richness and diversity patterns in the estuary are potentially a consequence of greater niche availability, mixing of local and adjacent environment communities, or intermediate disturbance. Furthermore, these results contrast with previous reports of spatially homogeneous bacterioplankton communities in other coastal waters.

Animals↗

PubMed2001

Local abundance and regional distribution of tree species of forest fragments in Brazil: a test of models.

Patterns of local abundance and regional distribution of tree species were analyzed on three spatial scales and compared with those predicted by Hanski's 1982 original core-satellite model, Brown's 1984 niche-based model, and Tokeshi's 1992 model. Data were collected in seven forest fragments dispersed over approximately 7200 km2, remnants of a former continuous forest in the south of Mato Grosso do Sul state, southwestern Brazil. Fifty-six east-west-oriented 10 m yen 150 m plots were randomly demarcated in those fragments from 1994 to 1996. In each plot all trees having DBH > or = 0.15 m were recorded and measured. The smallest scale was that of the fragments themselves and the greatest was that of the entire region. No evidence was found of the bimodality predicted by Hanski's 1982 model on any scale. On all scales, an unimodal pattern was found whose mode was on the left side (satellite mode) of the distribution. This pattern was in best agreement with the predictions of Tokeshi's 1992 model.

Brazil↗

PubMed1986

Spatial resolution of the Galago.

The spatial vision of two adult galagos (Galago crassicaudatus) was assessed using a two choice discrimination task to determine their contrast sensitivity. Both contrast sensitivity functions exhibited low and high spatial frequency attenuation with the peak sensitivity at 1%. For one animal, the peak occurred at 0.5 c/deg and the extrapolated cutoff frequency was 2.6 c/deg; for the other, the peak was 1 c/deg and the cutoff was 4.3 c/deg. For this animal, grating acuity was also tested and, depending upon definition of threshold, yielded threshold estimates from 4.8 to 6.0 c/deg. The data supports the conclusion that the spatial vision of the galago and the cat is quite similar, a congruence that presumably reflects their adaptation to a nocturnal niche, rather than their divergent phylogenetic origins.

Animals↗

PubMed2004

Spatial and temporal distribution of two diazotrophic bacteria in the Chesapeake Bay.

The aim of this study was to initiate autecological studies on uncultivated natural populations of diazotrophic bacteria by examining the distribution of specific diazotrophs in the Chesapeake Bay. By use of quantitative PCR, the abundance of two nifH sequences (907h22 and 912h4) was quantified in water samples collected along a transect from the head to the mouth of the Chesapeake Bay during cruises in April and October 2001 and 2002. Standard curves for the quantitative PCR assays demonstrated that the relationship between gene copies and cycle threshold was linear and highly reproducible from 1 to 10(7) gene copies. The maximum number of 907h22 gene copies detected was approximately 140 ml(-1) and the maximum number of 912h4 gene copies detected was approximately 340 ml(-1). Sequence 912h4 was most abundant at the mouth of the Chesapeake Bay, and in general, its abundance increased with increasing salinity, with the highest abundances observed in April 2002. Overall, the 907h22 phylotype was most abundant at the mid-bay station. Additionally, 907h22 was most abundant in the April samples from the mid-bay and mouth of the Chesapeake Bay. Despite the fact that the Chesapeake Bay is rarely nitrogen limited, our results show that individual nitrogen-fixing bacteria have distinct nonrandom spatial and seasonal distributions in the Chesapeake Bay and are either distributed by specific physical processes or adapted to different environmental niches.

Bacteria↗

PubMed2001

Evidence for stem-cell niches in the tracheal epithelium.

It is generally important to elucidate airway epithelial cell lineages and to identify multipotent progenitors as targets for gene therapy. Stem (S) cells are typically present in specialized compartments spatially proximal to their differentiated progeny, but an equivalent paradigm has not been demonstrated in the airway. We discovered a distinct population of cells displaying high levels of keratin expression in murine tracheal submucosal gland ducts, and tested the hypothesis that bromodeoxyuridine (BrdU) label-retaining cells (LRCs), thought to represent the S-cells, were present in this compartment. Mice received weekly epithelial damage by intratracheal detergent or SO(2) inhalation for 4 wk and received intraperitoneal injections of BrdU every 48 h during the injury and repair period. At 3 and 6 d after injury, BrdU-positive epithelial cells were noted along the entire tracheal length in both basal and lumenal cell positions. At later time points (20 and 95 d) LRCs were localized to gland ducts in the upper trachea and to systematically arrayed foci in the lower trachea, typically near the cartilage-intercartilage junction. LRCs were not pulmonary neuroendocrine cells. Heterotopic tracheal grafts after surface epithelial removal demonstrated reconstitution of a surface-like epithelium from gland remnants. These results suggest that airway epithelial S cells are localized to specific niches.

Animals↗

PubMed1998

Adaptive radiation in a heterogeneous environment.

Successive adaptive radiations have played a pivotal role in the evolution of biological diversity. The effects of adaptive radiation are often seen, but the underlying causes are difficult to disentangle and remain unclear. Here we examine directly the role of ecological opportunity and competition in driving genetic diversification. We use the common aerobic bacterium Pseudomonas fluorescens, which evolves rapidly under novel environmental conditions to generate a large repertoire of mutants. When provided with ecological opportunity (afforded by spatial structure), identical populations diversify morphologically, but when ecological opportunity is restricted there is no such divergence. In spatially structured environments, the evolution of variant morphs follows a predictable sequence and we show that competition among the newly evolved niche-specialists maintains this variation. These results demonstrate that the elementary processes of mutation and selection alone are sufficient to promote rapid proliferation of new designs and support the theory that trade-offs in competitive ability drive adaptive radiation.

Adaptation, Physiological↗

PubMed2026

Species Distribution Models Support Distinct and Non-Random Climatic Constraints on Globally Distributed Generalist Fungi.

Fungi play essential roles in ecosystems as pathogens, mutualists, and ubiquitous decomposers. However, like many important microbes, the spatial distribution of species and natural populations remains poorly understood compared to plants and animals. Many fungi are described as global generalists because they occur across wide geographic areas, but it remains unclear how and if these species are constrained by climate or geographic barriers. In this study, we used Species Distribution Models to infer the global climatic suitability of three common and globally distributed fungi: Aspergillus flavus, Penicillium chrysogenum and Aspergillus fumigatus. Models were constructed using global occurrence data from the Global Biodiversity Information Facility and were trained with Bioclimatic variables from the WorldClim dataset. All species' models showed high prediction fit, with predicted occurrence concentrated in the temperate and subtropical regions and broadly structured patterns. Each species showed distinct predicted distributions, but they displayed considerable spatial overlap on a global scale. Together, these results demonstrate that even apparently globally occurring and generalist fungal species occupy climatically structured niches. This study highlights the utility of SDMs and it provides a framework for future studies integrating ecological, genomics and evolutionary perspectives among the difficult to assess geographically widespread and common fungi.

comparative biogeography↗

PubMed1999

Community structure of digenean parasites of sparid and labrid fishes of the Mediterranean sea: a new approach.

The aim of this work was to study the structure of the parasite communities of Digeneans of 2 families of Teleost fishes (Sparidae and Labridae) of the Mediterranean sea. We tried to quantify the importance of both the microhabitat requirements of the parasite species and the effect of host biological factors on the parasite communities. We applied, for the first time in parasite community studies, the Canonical Correspondence Analysis (CCA) to analyse (i) the spatial distribution of parasite species within the digestive tract of the hosts; (ii) the host's biological factors (such as diet, host length, gregariousness and abundance) that may influence this spatial distribution of parasite species. Our results showed that potential microhabitats were vacant in the 2 host families studied revealing a lack of niche saturation because either there was little inter- and/or intraspecific competition or there were enough available space and resources within the host. Our results also indicated that the position of the parasite in the digestive tract is much more important than host biological factors for the structure of parasite community. Finally, we highlight the potential use of the CCA method for controlling for phylogenetic constraints in multi-species analyses.

Animals↗

PubMed2000

Persistence of selected Spartina alterniflora rhizoplane diazotrophs exposed to natural and manipulated environmental variability.

Rhizoplane-rhizosphere nitrogen-fixing microorganisms (diazotrophs) are thought to provide a major source of biologically available nitrogen in salt marshes dominated by Spartina alterniflora. Compositional and functional stability has been demonstrated for this important functional group; however, the quantitative responses of specific diazotroph populations to environmental variability have not been assessed. Changes in the relative abundances of selected rhizoplane diazotrophs in response to long-term fertilization were monitored quantitatively by reverse sample genome probing. Fertilization stimulated Spartina, with plant height nearly tripling after 1 year. Fertilization also resulted in significant changes in interstitial porewater parameters. Diazotrophic activity (acetylene reduction assay) was sensitive to the fertilization treatments and was inhibited in some plots on several sampling dates. However, inhibition was never consistent across all of the replicates within a treatment and activity always recovered. The rhizoplane diazotrophs were quite responsive to environmental variability and to experimental treatments, but none were displaced by either environmental variability or experimental treatments. All strains were detected consistently throughout this study, and extensive spatial heterogeneity in the distribution patterns of these organisms was observed. The physiological traits that differentiate the diazotroph populations presumably support competitiveness and niche specialization, resulting in the observed resilience of the diazotroph populations in the rhizosphere.

Acetylene↗

PubMed2006

Potential effects of climate change on ecosystem and tree species distribution in British Columbia.

A new ecosystem-based climate envelope modeling approach was applied to assess potential climate change impacts on forest communities and tree species. Four orthogonal canonical discriminant functions were used to describe the realized climate space for British Columbia's ecosystems and to model portions of the realized niche space for tree species under current and predicted future climates. This conceptually simple model is capable of predicting species ranges at high spatial resolutions far beyond the study area, including outlying populations and southern range limits for many species. We analyzed how the realized climate space of current ecosystems changes in extent, elevation, and spatial distribution under climate change scenarios and evaluated the implications for potential tree species habitat. Tree species with their northern range limit in British Columbia gain potential habitat at a pace of at least 100 km per decade, common hardwoods appear to be generally unaffected by climate change, and some of the most important conifer species in British Columbia are expected to lose a large portion of their suitable habitat. The extent of spatial redistribution of realized climate space for ecosystems is considerable, with currently important sub-boreal and montane climate regions rapidly disappearing. Local predictions of changes to tree species frequencies were generated as a basis for systematic surveys of biological response to climate change.

British Columbia↗

PubMed2006

Temporal differentiation and spatial coexistence of sexual and facultative asexual lineages of an aphid species at mating sites.

Cases of coexisting sexual and asexual relatives are puzzling, as evolutionary theory predicts that competition for the same ecological niches should lead to the exclusion of one or the other population. In the cyclically parthenogenetic aphid, Rhopalosiphum padi, sexual and facultative asexual lineages are admixed in space at the time of sexual reproduction. We investigated how the interaction of reproductive mode and environment can lead to temporal niche differentiation. We demonstrated theoretically that differential sensitivity of sexual and facultatively asexual aphids to an environmental parameter (mating host suitability) shapes the two strategies: whereas the sexual lineages switch earlier to the production of sexual forms, the facultative asexual lineages delay and spread out their investment in sexual reproduction. This predicted pattern of niche specialization is in agreement with the temporal structure revealed in natura by demographic and genetic data. We propose that partial loss of sex by one pool of aphids and subsequent reduction in gene flow between lineages may favour temporal specialization through disruptive selection.

Animals↗

PubMed2003

Membrane-bound stem cell factor is a key regulator in the initial lodgment of stem cells within the endosteal marrow region.

OBJECTIVE: The transmembrane isoform of stem cell factor (tm-SCF) has been implicated in the adhesion of hemopoietic stem cells to the extracellular matrix within the bone marrow microenvironment in vitro. In addition, in vivo SCF has been shown to play a role in cell mobilization and migration. The aim of this study was to determine if SCF is an integral component of the hemopoietic "niche" of the bone marrow in situ. MATERIALS AND METHODS: To analyze the role of tm-SCF in cell lodgment, purified populations of primitive progenitors and hemopoietic stem cells (HSC) were transplanted into a hemopoietic microenvironment devoid of tm-SCF, and the spatial distribution of engrafted cells was analyzed. In addition, populations of HSC were isolated using non-neutralizing and neutralizing antibodies to the SCF receptor c-kit, and their spatial distribution was analyzed post-transplant. RESULTS: The data demonstrated a significant impairment in the lodgment of transplanted cells within the endosteal marrow region in mice lacking tm-SCF, with a reduction of almost 30% by 15 hours post-transplant. The role of tm-SCF was confirmed by analyzing the spatial distribution of HSC isolated using a neutralizing antibody to c-kit. CONCLUSION: The data demonstrate that although tm-SCF does not appear to play a role in the homing of transplanted cells to the bone marrow, it is critical in the lodgment and detainment of HSC within their hemopoietic "niche."

Animals↗