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 complexdynamic 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 populations 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.     

Novel fungi from an ancient niche: lachnoid and chalara-like fungi on ferns

A survey was conducted in Brazil to collect fungi on ferns. Based on morphology and inferred phylogeny from DNA sequences of two loci, namely the internal transcribed spacer (ITS) regions and the large subunit nuclear ribosomal RNA gene (LSU), several species belonging to chalara-like genera and lachnoid fungi were recognized. Eighteen fungal isolates, collected from five host species, representing 10 different localities were studied. Three novel genera (Lachnopsis, Scolecolachnum and Zymochalara), and six novel species (Bloxamia cyatheicola, Lachnopsis catarinensis, Lachnopsis dicksoniae, Scolecolachnum pteridii, Zymochalara lygodii and Zymochalara cyatheae) are introduced. Furthermore, two new combinations (Erioscyphella euterpes and Erioscyphella lushanensis) are proposed. Two novel taxa (Lachnopsis catarinensis and Lachnopsis dicksoniae) may be included in the list of potentially endangered fungal species in Brazil, if proven to be restricted to their tree-fern host, Dicksonia sellowiana, which is included in the official list of endangered plant species in Brazil.     

Learning the ecological niche

A cornerstone of ecological theory is the ecological niche. Yet little is known about how individuals come to adopt it: whether it is innate or learned. Here, we report a cross-fostering experiment in the wild where we transferred eggs of blue tits, Cyanistes caeruleus, to nests of great tits, Parus major, and vice versa, to quantify the consequences of being reared in a different social context, but in an environment otherwise natural to the birds. We show that early learning causes a shift in the feeding niche in the direction of the foster species and that this shift lasts for life (foraging conservatism). Both species changed their feeding niches, but the change was greater in the great tit with its less specialized feeding behaviour. The study shows that cultural transmission through early learning is fundamental to the realization of ecological niches, and suggests a mechanism to explain learned habitat preference and sympatric speciation in animals.     

Soil microedges provide an ecological niche for Desmodium canadense

Plant Ecology - Within a plant community, variation among species in their abilities to exploit different types of soil patches can promote increased species diversity. However, it also has been...     

ModEco: an integrated software package for ecological niche modeling

ModEco is a software package for ecological niche modeling. It integrates a range of niche modeling methods within a geographical information system. ModEco provides a user friendly platform that enables users to explore, analyze, and model species distribution data with relative ease. ModEco has several unique features: 1) it deals with different types of ecological observation data, such as presence and absence data, presence‐only data, and abundance data; 2) it provides a range of models when dealing with presence‐only data, such as presence‐only models, pseudo‐absence models, background vs presence data models, and ensemble models; and 3) it includes relatively comprehensive tools for data visualization, feature selection, and accuracy assessment.     

Bryophytes and ecological niche theory

Classical niche theory, particularly in terms of competitive exclusion, does not appear to apply as well to bryophytes as to other organisms. Bryophyte communities, as well as those of other plants and of animals, can be thought of in terms of individual species each utilizing particular portions of various resource or habitat continua. Quantitative studies carried out since 1981, particularly those involving niche breadth and overlap, are reviewed. Special attention is given to niche diversification in Sphagnum , Splachnaceae, bryophyte communities in streams, and to ephemeral bryophyte communities. Some bryophyte communities appear to have equilibrium characteristics and to contain species with relatively narrow niche breadths and with no or only partial niche overlap. In many habitats, however, bryophyte communites have non-equilibrium characteristics and diversification of species in microhabitats is opportunistic. Do any bryophyte communities persist long enough for complete saturation by species which have realized niches determined by competitive interactions? Recent studies indicate that this is the case for at least some Sphagnum communities, but that it is the exception not the rule for bryophytes.     

Reconstructing ancient ecological conditions from insect remains; some problems and an experimental approach

• 1 Analysis of insect ‘death assemblages’ from ancient natural and anthropogenic deposits can provide valuable information about conditions in the past but the theoretical basis of such investigations is weak, especially with respect to the quantification of habitats on archaeological sites.
• 2 Evidence is presented for the existence of a transported component, termed ‘background fauna’, in death assemblages, as well as the remains of insects derived from the immediate surroundings.
• 3 The background component is derived principally from airborne insects and from bird droppings and may seriously detract from the accuracy of reconstructions of past ecological conditions. Factors affecting its relative importance are discussed.
• 4 As well as including species from distant habitats, the background fauna may be biased in favour of species from temporary habitats.
• 5 Some solutions to the problems presented by the background fauna are discussed. A high proportion of a species or ecological group will usually be evidence that its habitat existed near to the deposit enclosing the fauna, although there may be exceptions.
• 6 The structure of the background rain of insects has probably altered with changes in town and countryside brought about by man. Attempts to recognize background fauna in ancient assemblages must take account of this.
• 7 Many ancient assemblages, especially if small, will give no useful ecological information.

     

Microbial diversity in ikaite tufa columns: an alkaline,cold ecological niche in Greenland

Ikaite tufa columns from the Ikka Fjord in south-western Greenland constitute a natural, stable environment at low temperature and with a pH ranging from neutral at the exterior to very alkaline (pH 10.4) at the interior of the column. Phylogenetic analysis of culturable organisms revealed ten different isolates representing three of the major bacterial divisions. Nine of the isolates showed 94-99% similarity to known sequences, whereas one isolate displayed a low degree of similarity (less than 90%) to a Cyclobacterium species. Seven of the isolates were shown to be cold active alkaliphiles, whereas three isolates showed optimal growth at neutral pH. Phylogenetic analysis of DNA isolated directly from the ikaite material demonstrated the presence of a microbial flora more diverse than the culturable isolates. Whereas approximately half of the phylotypes showed 90-99% similarity to known meso- or thermophilic alkaliphiles, the rest of the sequences displayed less than 90% similarity when compared to known 16S rRNA gene sequences in databases. Thus, in the present paper, we demonstrate that ikaite columns that host a specialized macroscopic flora and fauna also contain a unique, cold active, alkaliphilic microflora.     

Using ecological niche modelling to evaluate niche stability in deep time

Aim To investigate relative niche stability in species responses to various types of environmental pressure (biotic and abiotic) on geological time‐scales using the fossil record. Location The case study focuses on Late Ordovician articulate brachiopods of the Cincinnati Arch in eastern North America. Methods Species niches were modelled for a suite of fossil brachiopod species based on five environmental variables inferred from sedimentary parameters using GARP and Maxent . Niche stability was assessed by comparison of (1) the degree of overlap of species distribution models developed for a time‐slice and those generated by projecting niche models of the previous time‐slice onto environmental layers of a second time‐slice using GARP and Maxent , (2) Schoener’s D statistic, and (3) the similarity of the contribution of each environmental parameter within Maxent niche models between adjacent time‐slices. Results Late Ordovician brachiopod species conserved their niches with high fidelity during intervals of gradual environmental change but responded to inter‐basinal species invasions through niche evolution. Both native and invasive species exhibited similar levels of niche evolution in the invasion and post‐invasion intervals. Niche evolution was related mostly to decreased variance within the former ecological niche parameters rather than to shifts to new ecospace. Main conclusions Although the species examined exhibited morphological stasis during the study interval, high levels of niche conservatism were observed only during intervals of gradual environmental change. Rapid environmental change, notably inter‐basinal species invasions, resulted in high levels of niche evolution among the focal taxa. Both native and invasive species responded with similar levels of niche evolution during the invasion interval and subsequent environmental reorganization. The assumption of complete niche conservatism frequently employed in ecological niche modelling (ENM) analyses to forecast or hindcast species geographical distributions is more likely to be accurate for climate change studies than for invasive species analyses over geological time‐scales.     

Species pools in cultural landscapes – niche construction,ecological opportunity and niche shifts

This paper discusses the ecology of species that were favoured by the development of the cultural landscape in central and NW Europe beginning in the Neolithic and the Bronze Age, with a focus on mechanisms behind species responses to this landscape transformation. A fraction of species may have maintained their realized niches from the pre‐ agricultural landscape and utilized similar niches created by the landscape transformation. However, I suggest that many species responded by altering their niche relationships, and a conceptual model is proposed for this response, based on niche construction, ecological opportunity and niche shifts. Human‐mediated niche construction, associated with clearing of forests and creation of pastures and fields promoted niche shifts towards open habitats, and species exploited the ecological opportunity provided by these created environments. This process was initially purely ecological, i.e. the new habitats must have been included in the original fundamental niche of the species. Two other features of human‐mediated niche construction, increased interconnectivity and increased spatial stability of open habitats, resulted in species accumulating in the habitats of the constructed landscape. As a consequence, selection processes were initiated favouring traits promoting fitness in the constructed landscape. This process implied a feed‐back to niche shifts, but now also including evolutionary changes in fundamental niches. I briefly discuss whether this model can be applied also to present‐day anthropogenic impact on landscapes. A general conclusion is that ecological and evolutionary changes in species niches should be more explicitly considered in modeling and predictions of species response to present‐day landscape and land‐use changes.     

Enemy-free space: a new name for an ancient ecological concept

While the importance of enemy-free space in structuring animal communities well merits the attention recently given to it, the concept is far more ancient than has been suggested. Far from Charles Darwin being the first to argue this, as recently claimed, it has long been known that major aspects of species' lifestyles are moulded by the impact of natural enemies. Examples from the literature spanning a period of more than two millenia, some of them far more specific than Darwin's comment, are cited.     

Novel ecological niche of Cetobacterium somerae, an anaerobic bacterium in the intestinal tracts of freshwater fish

AIMS: This study was conducted to clarify the taxonomic status of Bacteroides type A strains with high vitamin B(12)-producing ability that is widely distributed in the intestinal tracts of freshwater fish. METHODS AND RESULTS: Seventeen strains of Bacteroides type A isolated from five fish species were all rod-shaped and gram-negative. The strains were positive for esculin hydrolysis, nitrate reduction, resistance to bile, acid phosphatase, and negative for the production of catalase and urease and the susceptibility to vancomycin. The G+C content of DNA from the 17 strains was 29 x 1-31 x 9 mol%, and 16S rDNA sequence analysis revealed a close phylogenetic relationship between Bacteroides type A strains and Cetobacterium somerae sharing 99 x 7-100% sequence similarity. In addition, strains were capable of producing vitamin B(12) at a rate of 1 x 82-13 x 98 ng ml(-1) in 48 h. CONCLUSION: Phenotypic and phylogenetic characteristics indicated that all isolates previously classified as Bacteroides type A strains belong to C. someare. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provided the important finding of novel niche of vancomycin-resistant bacteria such as C. somerae in the intestinal tract of freshwater fish.     

Analyzing niche stability and biogeography of Late Ordovician brachiopod species using ecological niche modeling

Gauging the potential impacts of environmental change on the geographic distributions of species is a central area of modern biogeographic analysis, often involving complex models of species–environment interactions. The geographic distribution of fossil species can also provide a framework to test the impact of environmental change on biogeography and ecological niches of species, yet few paleontological analyses have attacked this question in deep time. Herein we present a quantitative biogeographic analysis to examine the stability of ecological niches and geographic ranges of rhynchonelliform brachiopods during an interval of sea level change preserved in Upper Ordovician strata of the Cincinnati Arch.The intensive sampling, excellent preservation, and numerous prior paleoecological and sedimentological analyses within the tri-state region of Kentucky, Indiana, and Ohio provide a robust framework for detailed paleobiogeographic study. Quantitative biogeographic modeling methods incorporating GIS (Geographic Information Systems) are utilized in order to spatially analyze the geographic ranges of brachiopod species of the Corryville and Mt. Auburn Formations of the C3 (uppermost Maysvillian) depositional sequence.This study employs the ecological niche modeling program GARP (Genetic Algorithm using Rule-set Prediction) to predict the geographic distribution of eight brachiopod species during three time slices within the C3 sequence. This method estimates a species’ geographic range by modeling the ecological niche of the species based on a set of known species occurrence data coupled with environmental data inferred from sedimentologic proxies. Once environmental tolerances for a species are modeled; the species is predicted to occur wherever its preferred set of environmental conditions occurs within the study region.Distributional patterns were reconstructed for three time slices during the C3 sequence. Recovered range predictions were quantitatively analyzed for evidence of temporal range changes. Results indicate that average species range within the study area decreased and species tracked their preferred niche with high fidelity during the transition from the early to middle portions of the C3 depositional sequence, an interval of rapid relative sea level change. However, during the transition from the middle to late portions of the sequence, gradual shallowing within the basin and development of discontinuous habitat patches correlates with niche evolution of five of the eight species modeled. The average area a species occupied within the basin increased during this interval, but there is a mixed response including both increases and decreases in range size within the study group. In general, the species that exhibit niche evolution increased their geographic range size while those that continue to track their niche with high fidelity experience a decrease in geographic range size. During the latter half of the C3 sequence, previously continuous habitats become fragmented, thereby isolating individual populations and providing a mechanism for niche evolution. The rate of sea level change and the corresponding fragmentation of previously continuous habitats into isolated patches appear to be the primary controls on both mean geographic range size and relative degree of niche evolution.     

Predicting the spread of an invasive plant: combining experiments and ecological niche model

Rapid evolutionary adjustments to novel environments may contribute to the successful spread of invasive species, and can lead to niche shifts making range dynamics unpredictable. These effects might be intensified by artificial selection in the course of breeding efforts, since many successful plant invaders were deliberately introduced and cultivated as ornamentals. We hypothesized that the invasion success of Buddleja davidii, the ornamental butterfly bush, is facilitated by local adaptation to minimum temperatures and thus, exhibits unpredictable range dynamics. To assess the potential effects of adaptive evolution and artificial selection on the spread of B. davidii, we combined a common garden experiment investigating local adaptation to frost, with ecological niche modelling of the species’ native and invasive ranges. We expected that populations naturalized in sub‐continental climate are less susceptible to frost than populations from oceanic climate, and that the invasive range does not match predictions based on climatic data from the native range. Indeed, we revealed significant variation among invasive B. davidii populations in frost resistance. However, frost hardiness was not related to geographic location or climatic variables of the populations’ home site, suggesting that invasive B. davidii populations are not locally adapted to minimum temperatures. This is in line with results of our ecological niche model that did not detect a niche shift between the species’ native range in China, and its invasive range in Europe and North America. Furthermore, our niche model showed that the potential invasive range of B. davidii is still not completely occupied. Together with the frost resistance data obtained in our experiment, the results indicate that climatic conditions are currently not limiting the further spread of the species in Europe and North America.     

A reference business process for ecological niche modelling

Ecological niche modelling combines species occurrence points with environmental raster layers in order to obtain models for describing the probabilistic distribution of species. The process to generate an ecological niche model is complex. It requires dealing with a large amount of data, use of different software packages for data conversion, for model generation and for different types of processing and analyses, among other functionalities. A software platform that integrates all requirements under a single and seamless interface would be very helpful for users. Furthermore, since biodiversity modelling is constantly evolving, new requirements are constantly being added in terms of functions, algorithms and data formats. This evolution must be accompanied by any software intended to be used in this area. In this scenario, a Service-Oriented Architecture (SOA) is an appropriate choice for designing such systems. According to SOA best practices and methodologies, the design of a reference business process must be performed prior to the architecture definition. The purpose is to understand the complexities of the process (business process in this context refers to the ecological niche modelling problem) and to design an architecture able to offer a comprehensive solution, called a reference architecture, that can be further detailed when implementing specific systems. This paper presents a reference business process for ecological niche modelling, as part of a major work focused on the definition of a reference architecture based on SOA concepts that will be used to evolve the openModeller software package for species modelling. The basic steps that are performed while developing a model are described, highlighting important aspects, based on the knowledge of modelling experts. In order to illustrate the steps defined for the process, an experiment was developed, modelling the distribution of Ouratea spectabilis (Mart.) Engl. (Ochnaceae) using openModeller. As a consequence of the knowledge gained with this work, many desirable improvements on the modelling software packages have been identified and are presented. Also, a discussion on the potential for large-scale experimentation in ecological niche modelling is provided, highlighting opportunities for research. The results obtained are very important for those involved in the development of modelling tools and systems, for requirement analysis and to provide insight on new features and trends for this category of systems. They can also be very helpful for beginners in modelling research, who can use the process and the experiment example as a guide to this complex activity.     

Influence of a road on a population in an ecological niche facing climate change

Journal of Mathematical Biology - We introduce a model designed to account for the influence of a line with fast diffusion–such as a road or another transport network–on the dynamics of...     

Syntrophic growth on formate: a new microbial niche in anoxic environments

Anaerobic syntrophic associations of fermentative bacteria and methanogenic archaea operate at the thermodynamic limits of life. The interspecies transfer of electrons from formate or hydrogen as a substrate for the methanogens is key. Contrary requirements of syntrophs and methanogens for growth-sustaining product and substrate concentrations keep the formate and hydrogen concentrations low and within a narrow range. Since formate is a direct substrate for methanogens, a niche for microorganisms that grow by the conversion of formate to hydrogen plus bicarbonate--or vice versa--may seem unlikely. Here we report experimental evidence for growth on formate by syntrophic communities of (i) Moorella sp. strain AMP in coculture with a thermophilic hydrogen-consuming Methanothermobacter species and of (ii) Desulfovibrio sp. strain G11 in coculture with a mesophilic hydrogen consumer, Methanobrevibacter arboriphilus AZ. In pure culture, neither Moorella sp. strain AMP, nor Desulfovibrio sp. strain G11, nor the methanogens grow on formate alone. These results imply the existence of a previously unrecognized microbial niche in anoxic environments.